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2019 |
Kumar, Thirumal D; Niazullah, Umer M; Tasneem, S; Judith, E; Susmita, B; Doss, George Priya C; Selvarajan, E; Zayed, H A computational method to characterize the missense mutations in the catalytic domain of GAA protein causing Pompe disease Journal Article Journal of Cellular Biochemistry, 120 (3), pp. 3491-3505, 2019. @article{ThirumalKumar20193491, title = {A computational method to characterize the missense mutations in the catalytic domain of GAA protein causing Pompe disease}, author = {D Thirumal Kumar and M Umer Niazullah and S Tasneem and E Judith and B Susmita and C George Priya Doss and E Selvarajan and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054333356&doi=10.1002%2fjcb.27624&partnerID=40&md5=8651aac694717492b4fbafba14ac02a8}, doi = {10.1002/jcb.27624}, year = {2019}, date = {2019-01-01}, journal = {Journal of Cellular Biochemistry}, volume = {120}, number = {3}, pages = {3491-3505}, publisher = {Wiley-Liss Inc.}, abstract = {Pompe disease is an autosomal recessive lysosomal storage disease caused by acid α-glucosidase (GAA) deficiency, resulting in intralysosomal accumulation of glycogen, including cardiac, skeletal, and smooth muscle cells. The GAA gene is located on chromosome 17 (17q25.3), the GAA protein consists of 952 amino acids; of which 378 amino acids (347-726) falls within the catalytic domain of the protein and comprises of active sites (518 and 521) and binding sites (404, 600, 616, and 674). In this study, we used several computational tools to classify the missense mutations in the catalytic domain of GAA for their pathogenicity and stability. Eight missense mutations (R437C, G478R, N573H, Y575S, G605D, V642D, L705P, and L712P) were predicted to be pathogenic and destabilizing to the protein structure. These mutations were further subjected to phenotyping analysis using SNPeffect 4.0 to predict the chaperone binding sites and structural stability of the protein. The mutations R437C and G478R were found to compromise the chaperone-binding activity with GAA. Molecular docking analysis revealed that the G478R mutation to be more significant and hinders binding to the DNJ (Miglustat) compared with the R437C. Further molecular dynamic analysis for the two mutations demonstrated that the G478R mutation was acquired higher deviation, fluctuation, and lower compactness with decreased intramolecular hydrogen bonds compared to the mutant R437C. These data are expected to serve as a platform for drug design against Pompe disease and will serve as an ultimate tool for variant classification and interpretations. © 2018 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Pompe disease is an autosomal recessive lysosomal storage disease caused by acid α-glucosidase (GAA) deficiency, resulting in intralysosomal accumulation of glycogen, including cardiac, skeletal, and smooth muscle cells. The GAA gene is located on chromosome 17 (17q25.3), the GAA protein consists of 952 amino acids; of which 378 amino acids (347-726) falls within the catalytic domain of the protein and comprises of active sites (518 and 521) and binding sites (404, 600, 616, and 674). In this study, we used several computational tools to classify the missense mutations in the catalytic domain of GAA for their pathogenicity and stability. Eight missense mutations (R437C, G478R, N573H, Y575S, G605D, V642D, L705P, and L712P) were predicted to be pathogenic and destabilizing to the protein structure. These mutations were further subjected to phenotyping analysis using SNPeffect 4.0 to predict the chaperone binding sites and structural stability of the protein. The mutations R437C and G478R were found to compromise the chaperone-binding activity with GAA. Molecular docking analysis revealed that the G478R mutation to be more significant and hinders binding to the DNJ (Miglustat) compared with the R437C. Further molecular dynamic analysis for the two mutations demonstrated that the G478R mutation was acquired higher deviation, fluctuation, and lower compactness with decreased intramolecular hydrogen bonds compared to the mutant R437C. These data are expected to serve as a platform for drug design against Pompe disease and will serve as an ultimate tool for variant classification and interpretations. © 2018 Wiley Periodicals, Inc. |
Kumar, Thirumal D; Mendonca, E; Christy, Priyadharshini J; Doss, George Priya C; Zayed, H A computational model to predict the structural and functional consequences of missense mutations in O6-methylguanine DNA methyltransferase Book Chapter Academic Press Inc., 2019. @inbook{ThirumalKumar2019b, title = {A computational model to predict the structural and functional consequences of missense mutations in O6-methylguanine DNA methyltransferase}, author = {D Thirumal Kumar and E Mendonca and J Priyadharshini Christy and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059518718&doi=10.1016%2fbs.apcsb.2018.11.006&partnerID=40&md5=4731d1d768b8b2a4c5a39e81ab0241ce}, doi = {10.1016/bs.apcsb.2018.11.006}, year = {2019}, date = {2019-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, publisher = {Academic Press Inc.}, abstract = {DNA repair mechanism is a process through which the cell repairs its damaged DNA. Although there are several mechanisms involved in the DNA repair mechanisms, the direct reversal method is the simplest and does not require a reference template, in which the guanine bases are often methylated, and the methyl guanine methyl transferase protein (MGMT) reverses them. The mutations occurring in the MGMT protein might result in dysfunction of such DNA repair mechanism. In this study, we attempted to evaluate the impact of six missense mutations (Y114E, Y114A, R128G, R128A, R128K, and C145A) at three active-site positions (Y114, C145, and R128) as this might hinder the DNA binding to the protein. These six mutations were subjected to pathogenicity, stability, and conservation analysis using online servers such as PredictSNP, iStable, and ConSurf, respectively. From the predictions, all the six mutations were almost predicted to be significant. Considering true positives, true negatives, false positives, and false negatives, three mutations (Y114E, R128G, and C145A) showed “loss of DNA repair activity,” and were analyzed further using molecular dynamics simulations (MDS) using GROMACS for 50 ns. MDS run showed that the C145A mutant demonstrated higher structural deviation, decreased compactness, and the binding patterns. The Y114E mutant showed almost a null effect from the structural analysis. Finally, the R128G mutant showed structural variations in between the C145A and Y114E mutations of MGMT protein. We believe that the observed findings in this computational approach might further pave a way of providing better treatment measures by understanding the DNA repair mechanisms. © 2019 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } DNA repair mechanism is a process through which the cell repairs its damaged DNA. Although there are several mechanisms involved in the DNA repair mechanisms, the direct reversal method is the simplest and does not require a reference template, in which the guanine bases are often methylated, and the methyl guanine methyl transferase protein (MGMT) reverses them. The mutations occurring in the MGMT protein might result in dysfunction of such DNA repair mechanism. In this study, we attempted to evaluate the impact of six missense mutations (Y114E, Y114A, R128G, R128A, R128K, and C145A) at three active-site positions (Y114, C145, and R128) as this might hinder the DNA binding to the protein. These six mutations were subjected to pathogenicity, stability, and conservation analysis using online servers such as PredictSNP, iStable, and ConSurf, respectively. From the predictions, all the six mutations were almost predicted to be significant. Considering true positives, true negatives, false positives, and false negatives, three mutations (Y114E, R128G, and C145A) showed “loss of DNA repair activity,” and were analyzed further using molecular dynamics simulations (MDS) using GROMACS for 50 ns. MDS run showed that the C145A mutant demonstrated higher structural deviation, decreased compactness, and the binding patterns. The Y114E mutant showed almost a null effect from the structural analysis. Finally, the R128G mutant showed structural variations in between the C145A and Y114E mutations of MGMT protein. We believe that the observed findings in this computational approach might further pave a way of providing better treatment measures by understanding the DNA repair mechanisms. © 2019 Elsevier Inc. |
Kumar, Thirumal D; Iyer, S; Christy, J P; Siva, R; Tayubi, I A; Doss, George Priya C; Zayed, H A comparative computational approach toward pharmacological chaperones (NN-DNJ and ambroxol) on N370S and L444P mutations causing Gaucher's disease Book Chapter 114 , pp. 315-339, Academic Press Inc., 2019. @inbook{ThirumalKumar2019315, title = {A comparative computational approach toward pharmacological chaperones (NN-DNJ and ambroxol) on N370S and L444P mutations causing Gaucher's disease}, author = {D Thirumal Kumar and S Iyer and J P Christy and R Siva and I A Tayubi and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057382710&doi=10.1016%2fbs.apcsb.2018.10.002&partnerID=40&md5=8885e8b7ca8ec73c938e79aee7c8b49d}, doi = {10.1016/bs.apcsb.2018.10.002}, year = {2019}, date = {2019-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {114}, pages = {315-339}, publisher = {Academic Press Inc.}, abstract = {Gaucher's disease (GD) is the most commonly known lysosomal disorder that occurs due to mutations in the β-glucocerebrosidase (GBA) protein. Our previous findings (Thirumal Kumar, Eldous, Mahgoub, George Priya Doss, Zayed, 2018) and other reports concluded that the mutations N370S and L444P are the most significant mutations that could cause disruptions in protein stability and structure. These disruptions lead to protein misfolding and result in a diseased condition. Enzyme Replacement Therapy (ERT) and Pharmacological chaperone therapy (PCT) are currently used to treat GD caused by mutations in the GBA protein. The extreme disparity in cost between ERT and chaperone therapy, shifted the attention toward chaperone therapy. The most common chaperones in the market and trial phases to treat GD are Isofagomine, Miglustat, Eliglustat, NN-DNJ, and Ambroxol. In the era of personalized medicine, it is often necessary to understand the drug likeliness of each chaperone. In this context, the present study utilized molecular docking analysis to understand the interaction behavior of the chaperone toward the native and the two mutants N370S and L444P. The molecular dynamics simulation analyses performed on chaperones (NN-DNJ and Ambroxol) interaction showed that the chaperone NN-DNJ possesses better affinity toward the protein with N370S mutation whereas chaperone Ambroxol showed better activity against both the significant mutations (N370S and L444P). This study is expected to serve as a platform for drug repurposing. © 2019 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Gaucher's disease (GD) is the most commonly known lysosomal disorder that occurs due to mutations in the β-glucocerebrosidase (GBA) protein. Our previous findings (Thirumal Kumar, Eldous, Mahgoub, George Priya Doss, Zayed, 2018) and other reports concluded that the mutations N370S and L444P are the most significant mutations that could cause disruptions in protein stability and structure. These disruptions lead to protein misfolding and result in a diseased condition. Enzyme Replacement Therapy (ERT) and Pharmacological chaperone therapy (PCT) are currently used to treat GD caused by mutations in the GBA protein. The extreme disparity in cost between ERT and chaperone therapy, shifted the attention toward chaperone therapy. The most common chaperones in the market and trial phases to treat GD are Isofagomine, Miglustat, Eliglustat, NN-DNJ, and Ambroxol. In the era of personalized medicine, it is often necessary to understand the drug likeliness of each chaperone. In this context, the present study utilized molecular docking analysis to understand the interaction behavior of the chaperone toward the native and the two mutants N370S and L444P. The molecular dynamics simulation analyses performed on chaperones (NN-DNJ and Ambroxol) interaction showed that the chaperone NN-DNJ possesses better affinity toward the protein with N370S mutation whereas chaperone Ambroxol showed better activity against both the significant mutations (N370S and L444P). This study is expected to serve as a platform for drug repurposing. © 2019 Elsevier Inc. |
Kumar, Thirumal D; Susmita, B; Judith, E; Christy, Priyadharshini J; Doss, George Priya C; Zayed, H Elucidating the role of interacting residues of the MSH2-MSH6 complex in DNA repair mechanism: A computational approach Book Chapter Academic Press Inc., 2019. @inbook{ThirumalKumar2019d, title = {Elucidating the role of interacting residues of the MSH2-MSH6 complex in DNA repair mechanism: A computational approach}, author = {D Thirumal Kumar and B Susmita and E Judith and J Priyadharshini Christy and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059517782&doi=10.1016%2fbs.apcsb.2018.11.005&partnerID=40&md5=061126a1cac8a265ced9527a8d467d20}, doi = {10.1016/bs.apcsb.2018.11.005}, year = {2019}, date = {2019-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, publisher = {Academic Press Inc.}, abstract = {The DNA repair system is crucial to repair the error resulting in DNA replication. MSH2-MSH6 protein complex plays a significant role in maintaining the mismatch repair mechanism. Mutations in the interface between the two proteins compromise their function in the repair process. The present study aims to understand the impact of missense mutations in the interacting sites of the MSH2-MSH6 protein complex. MSH6 is unstable due to the disordered N-terminal domain. This is stabilized by the MSH2 hetero-dimerization. We used pathogenicity and stability predictors to identify the missense mutations that could be more pathogenic with the destabilizing property. The mutations W764C of MSH2, and L1201F and G1316E of MSH6 were predicted to be highly deleterious and destabilizing by all the in silico predictors. The dynamic motion of the native and mutant (W764C) MSH2-MSH6 protein complexes was further investigated using Molecular Dynamics Simulations of the GROMACS package. The Root Mean Square Deviation (RMSD), Radius of Gyration (Rg), and change in a number of intramolecular hydrogen bonds (H-bonds) were analyzed using the embedded packages of GROMACS. From the simulation studies, we observed higher deviation, lower protein compactness, and a decrease in the number of intramolecular hydrogen bonds in the mutant W764C MSH2-MSH6 protein complex. The observed results from the computational methods suggest the involvement of higher structural impact on the MSH2-MSH6 protein complex upon W764C mutation could affect the DNA repair mechanism. © 2019 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } The DNA repair system is crucial to repair the error resulting in DNA replication. MSH2-MSH6 protein complex plays a significant role in maintaining the mismatch repair mechanism. Mutations in the interface between the two proteins compromise their function in the repair process. The present study aims to understand the impact of missense mutations in the interacting sites of the MSH2-MSH6 protein complex. MSH6 is unstable due to the disordered N-terminal domain. This is stabilized by the MSH2 hetero-dimerization. We used pathogenicity and stability predictors to identify the missense mutations that could be more pathogenic with the destabilizing property. The mutations W764C of MSH2, and L1201F and G1316E of MSH6 were predicted to be highly deleterious and destabilizing by all the in silico predictors. The dynamic motion of the native and mutant (W764C) MSH2-MSH6 protein complexes was further investigated using Molecular Dynamics Simulations of the GROMACS package. The Root Mean Square Deviation (RMSD), Radius of Gyration (Rg), and change in a number of intramolecular hydrogen bonds (H-bonds) were analyzed using the embedded packages of GROMACS. From the simulation studies, we observed higher deviation, lower protein compactness, and a decrease in the number of intramolecular hydrogen bonds in the mutant W764C MSH2-MSH6 protein complex. The observed results from the computational methods suggest the involvement of higher structural impact on the MSH2-MSH6 protein complex upon W764C mutation could affect the DNA repair mechanism. © 2019 Elsevier Inc. |
Kumar, Thirumal D; Judith, E; Christy, Priyadharshini J; Siva, R; Tayubi, I A; Chakraborty, C; Doss, George Priya C; Zayed, H Computational and modeling approaches to understand the impact of the Fabry's disease causing mutation (D92Y) on the interaction with pharmacological chaperone 1-deoxygalactonojirimycin (DGJ) Book Chapter 114 , pp. 341-407, Academic Press Inc., 2019. @inbook{ThirumalKumar2019341, title = {Computational and modeling approaches to understand the impact of the Fabry's disease causing mutation (D92Y) on the interaction with pharmacological chaperone 1-deoxygalactonojirimycin (DGJ)}, author = {D Thirumal Kumar and E Judith and J Priyadharshini Christy and R Siva and I A Tayubi and C Chakraborty and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058569755&doi=10.1016%2fbs.apcsb.2018.10.009&partnerID=40&md5=20e2d504ca583d5fd6ab09dbcf22f6d0}, doi = {10.1016/bs.apcsb.2018.10.009}, year = {2019}, date = {2019-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {114}, pages = {341-407}, publisher = {Academic Press Inc.}, abstract = {Fabry's disease (FD) is the second most commonly occurring lysosomal storage disorders (LSDs). The mutations in α-galactosidase A (GLA) protein were widely found to be causative for the Fabry's disease. These mutations result in alternate splicing methods that affect the stability and function of the protein. The mutations near the active site of the protein results in protein misfolding. In this study, we have retrieved the missense mutation data from the three public databases (NCBI, UniProt, and HGMD). We used multiple in silico tools to predict the pathogenicity and stability of these mutations. Mutations in the active sites (D92Y, C142Y, D170V, and D266N) of the protein were screened for the phenotyping analysis using SNPeffect 4.0. Mutant D92Y was predicted to increase the amyloid propensity as well as severely reduce the protein stability and the remaining mutations showed no significant results by SNPeffect 4.0. Protein dynamics simulations (PDS) were performed to understand the behavior of the proteins due to the mutations. The simulation results showed that the D92Y mutant was more severe (higher deviation, loss of intramolecular hydrogen bonds, and lower compactness) than the other protein mutants (C142Y, D170V, and D266N). Further, the action of pharmacological chaperone 1-deoxygalactonojirimycin (DGJ) over the severe mutation was studied using the molecular docking analysis. Chaperone DGJ, an iminosugar plays a convincing role in repairing the misfolded protein and helps the protein to achieve its normal function. From the molecular docking analysis, we observed that both the native protein and protein with D92Y mutation followed similar interaction patterns. Further, the docked complexes (native-DGJ and mutant-DGJ) were subjected to PDS analysis. From the simulation analysis, we observed that DGJ had shown the better effect on the protein with the D92Y mutation. This elucidates that DGJ can still be used as a promising chaperone to treat the FD caused by mutations of GLA protein. © 2019 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Fabry's disease (FD) is the second most commonly occurring lysosomal storage disorders (LSDs). The mutations in α-galactosidase A (GLA) protein were widely found to be causative for the Fabry's disease. These mutations result in alternate splicing methods that affect the stability and function of the protein. The mutations near the active site of the protein results in protein misfolding. In this study, we have retrieved the missense mutation data from the three public databases (NCBI, UniProt, and HGMD). We used multiple in silico tools to predict the pathogenicity and stability of these mutations. Mutations in the active sites (D92Y, C142Y, D170V, and D266N) of the protein were screened for the phenotyping analysis using SNPeffect 4.0. Mutant D92Y was predicted to increase the amyloid propensity as well as severely reduce the protein stability and the remaining mutations showed no significant results by SNPeffect 4.0. Protein dynamics simulations (PDS) were performed to understand the behavior of the proteins due to the mutations. The simulation results showed that the D92Y mutant was more severe (higher deviation, loss of intramolecular hydrogen bonds, and lower compactness) than the other protein mutants (C142Y, D170V, and D266N). Further, the action of pharmacological chaperone 1-deoxygalactonojirimycin (DGJ) over the severe mutation was studied using the molecular docking analysis. Chaperone DGJ, an iminosugar plays a convincing role in repairing the misfolded protein and helps the protein to achieve its normal function. From the molecular docking analysis, we observed that both the native protein and protein with D92Y mutation followed similar interaction patterns. Further, the docked complexes (native-DGJ and mutant-DGJ) were subjected to PDS analysis. From the simulation analysis, we observed that DGJ had shown the better effect on the protein with the D92Y mutation. This elucidates that DGJ can still be used as a promising chaperone to treat the FD caused by mutations of GLA protein. © 2019 Elsevier Inc. |
2018 |
Kumar, Thirumal D; Eldous, H G; Mahgoub, Z A; Doss, George Priya C; Zayed, H Computational modelling approaches as a potential platform to understand the molecular genetics association between Parkinson’s and Gaucher diseases Journal Article Metabolic Brain Disease, 33 (6), pp. 1835-1847, 2018. @article{ThirumalKumar20181835, title = {Computational modelling approaches as a potential platform to understand the molecular genetics association between Parkinson’s and Gaucher diseases}, author = {D Thirumal Kumar and H G Eldous and Z A Mahgoub and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049602193&doi=10.1007%2fs11011-018-0286-3&partnerID=40&md5=490aa3e7f6ebc4466aea070f4f8b9aad}, doi = {10.1007/s11011-018-0286-3}, year = {2018}, date = {2018-01-01}, journal = {Metabolic Brain Disease}, volume = {33}, number = {6}, pages = {1835-1847}, publisher = {Springer New York LLC}, abstract = {Gaucher’s disease (GD) is a genetic disorder in which glucocerebroside accumulates in cells and specific organs. It is broadly classified into type I, type II and type III. Patients with GD are at high risk of Parkinson’s disease (PD), and the clinical and pathological presentation of GD patients with PD is almost identical to idiopathic PD. Several experimental models like cell culture, animal models, and transgenic mice models were used to understand the molecular mechanism behind GD and PD association; however, such mechanism remains unclear. In this context, based on literature reports, we identified the most common mutations K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H, in the Glucosylceramidase (GBA) protein that are known to cause GD1, and represent a risk of developing PD. However, to date, no computational analyses have designed to elucidate the potential functional role of GD mutations with increased risk of PD. The present computational pipeline allows us to understand the structural and functional significance of these GBA mutations with PD. Based on the published data, the most common and severe mutations were E326K, N370S, and L444P, which further selected for our computational analysis. PredictSNP and iStable servers predicted L444P mutant to be the most deleterious and responsible for the protein destabilization, followed by the N370S mutation. Further, we used the structural analysis and molecular dynamics approach to compare the most frequent deleterious mutations (N370S and L444P) with the mild mutation E326K. The structural analysis demonstrated that the location of E326K and N370S in the alpha helix region of the protein whereas the mutant L444P was in the starting region of the beta sheet, which might explain the predicted pathogenicity level and destabilization effect of the L444P mutant. Finally, Molecular Dynamics (MD) at 50 ns showed the highest deviation and fluctuation pattern in the L444P mutant compared to the two mutants E326K and N370S and the native protein. This was consistent with more loss of intramolecular hydrogen bonds and less compaction of the radius of gyration in the L444P mutant. The proposed study is anticipated to serve as a potential platform to understand the mechanism of the association between GD and PD, and might facilitate the process of drug discovery against both GD and PD. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gaucher’s disease (GD) is a genetic disorder in which glucocerebroside accumulates in cells and specific organs. It is broadly classified into type I, type II and type III. Patients with GD are at high risk of Parkinson’s disease (PD), and the clinical and pathological presentation of GD patients with PD is almost identical to idiopathic PD. Several experimental models like cell culture, animal models, and transgenic mice models were used to understand the molecular mechanism behind GD and PD association; however, such mechanism remains unclear. In this context, based on literature reports, we identified the most common mutations K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H, in the Glucosylceramidase (GBA) protein that are known to cause GD1, and represent a risk of developing PD. However, to date, no computational analyses have designed to elucidate the potential functional role of GD mutations with increased risk of PD. The present computational pipeline allows us to understand the structural and functional significance of these GBA mutations with PD. Based on the published data, the most common and severe mutations were E326K, N370S, and L444P, which further selected for our computational analysis. PredictSNP and iStable servers predicted L444P mutant to be the most deleterious and responsible for the protein destabilization, followed by the N370S mutation. Further, we used the structural analysis and molecular dynamics approach to compare the most frequent deleterious mutations (N370S and L444P) with the mild mutation E326K. The structural analysis demonstrated that the location of E326K and N370S in the alpha helix region of the protein whereas the mutant L444P was in the starting region of the beta sheet, which might explain the predicted pathogenicity level and destabilization effect of the L444P mutant. Finally, Molecular Dynamics (MD) at 50 ns showed the highest deviation and fluctuation pattern in the L444P mutant compared to the two mutants E326K and N370S and the native protein. This was consistent with more loss of intramolecular hydrogen bonds and less compaction of the radius of gyration in the L444P mutant. The proposed study is anticipated to serve as a potential platform to understand the mechanism of the association between GD and PD, and might facilitate the process of drug discovery against both GD and PD. © 2018, Springer Science+Business Media, LLC, part of Springer Nature. |
Unissa, A N; C, Doss G P; Kumar, T; Sukumar, S; Lakshmi, A R; Hanna, L E Significance of catalase-peroxidase (KatG) mutations in mediating isoniazid resistance in clinical strains of Mycobacterium tuberculosis Journal Article Journal of Global Antimicrobial Resistance, 15 , pp. 111-120, 2018. @article{Unissa2018111, title = {Significance of catalase-peroxidase (KatG) mutations in mediating isoniazid resistance in clinical strains of Mycobacterium tuberculosis}, author = {A N Unissa and G P Doss C and T Kumar and S Sukumar and A R Lakshmi and L E Hanna}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054441286&doi=10.1016%2fj.jgar.2018.07.001&partnerID=40&md5=d3518af59afdc9d47c1a9310cfcd967e}, doi = {10.1016/j.jgar.2018.07.001}, year = {2018}, date = {2018-01-01}, journal = {Journal of Global Antimicrobial Resistance}, volume = {15}, pages = {111-120}, publisher = {Elsevier Ltd}, abstract = {Objectives: Isoniazid (INH) is still the most important first-line antitubercular drug. INH resistance is regarded as a major impediment to the tuberculosis (TB) control programme and contributes to the emergence of multidrug-resistant strains. Mutation at position 315 in the katG gene, encoding the catalase-peroxidase (KatG) enzyme, is the major cause of INH resistance in Mycobacterium tuberculosis. Therefore, investigation of the molecular mechanisms of INH resistance is the need of the hour. Methods: To understand the clinical importance of KatG mutants (MTs) leading to INH resistance, in this study five MTs (S315T, S315I, S315R, S315N and S315G) were modelled, docked and interacted with INH in dynamic state. Results: The binding affinity based on docking was found to be higher for MTs than for wild-type (WT) isolates, except for MT-S315R, indicating rigid binding of INH with MT proteins compared with the flexible binding seen in the WT. Analysis of molecular dynamics (MD) experiments suggested that fluctuations and deviations were higher at the INH binding residues for MTs than for the WT. Reduction in the hydrogen bond network after MD in all KatG enzymes implies an increase in the flexibility and stability of protein structures. Superimposition of MTs upon the WT structure showed a significant deviation that varies for the different MTs. Conclusions: It can be inferred that the five KatG MTs affect enzyme activity in different ways, which could be attributed to conformational changes in MT KatG that result in altered binding affinity to INH and eventually to INH resistance. © 2018 International Society for Chemotherapy of Infection and Cancer}, keywords = {}, pubstate = {published}, tppubtype = {article} } Objectives: Isoniazid (INH) is still the most important first-line antitubercular drug. INH resistance is regarded as a major impediment to the tuberculosis (TB) control programme and contributes to the emergence of multidrug-resistant strains. Mutation at position 315 in the katG gene, encoding the catalase-peroxidase (KatG) enzyme, is the major cause of INH resistance in Mycobacterium tuberculosis. Therefore, investigation of the molecular mechanisms of INH resistance is the need of the hour. Methods: To understand the clinical importance of KatG mutants (MTs) leading to INH resistance, in this study five MTs (S315T, S315I, S315R, S315N and S315G) were modelled, docked and interacted with INH in dynamic state. Results: The binding affinity based on docking was found to be higher for MTs than for wild-type (WT) isolates, except for MT-S315R, indicating rigid binding of INH with MT proteins compared with the flexible binding seen in the WT. Analysis of molecular dynamics (MD) experiments suggested that fluctuations and deviations were higher at the INH binding residues for MTs than for the WT. Reduction in the hydrogen bond network after MD in all KatG enzymes implies an increase in the flexibility and stability of protein structures. Superimposition of MTs upon the WT structure showed a significant deviation that varies for the different MTs. Conclusions: It can be inferred that the five KatG MTs affect enzyme activity in different ways, which could be attributed to conformational changes in MT KatG that result in altered binding affinity to INH and eventually to INH resistance. © 2018 International Society for Chemotherapy of Infection and Cancer |
Sneha, P; Zenith, T U; Habib, Abu U S; Evangeline, J; Kumar, Thirumal D; Doss, George Priya C; Siva, R; Zayed, H Impact of missense mutations in survival motor neuron protein (SMN1) leading to Spinal Muscular Atrophy (SMA): A computational approach Journal Article Metabolic Brain Disease, 33 (6), pp. 1823-1834, 2018. @article{Sneha20181823, title = {Impact of missense mutations in survival motor neuron protein (SMN1) leading to Spinal Muscular Atrophy (SMA): A computational approach}, author = {P Sneha and T U Zenith and U S Abu Habib and J Evangeline and D Thirumal Kumar and C George Priya Doss and R Siva and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049831111&doi=10.1007%2fs11011-018-0285-4&partnerID=40&md5=1e9fda2d60a1a84e42fb687a5d18b021}, doi = {10.1007/s11011-018-0285-4}, year = {2018}, date = {2018-01-01}, journal = {Metabolic Brain Disease}, volume = {33}, number = {6}, pages = {1823-1834}, publisher = {Springer New York LLC}, abstract = {Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by the mutations in survival motor neuron 1 gene (SMN1). The molecular pathology of missense mutations in SMN1 is not thoroughly investigated so far. Therefore, we collected all missense mutations in the SMN1 protein, using all possible search terms, from three databases (PubMed, PMC and Google Scholar). All missense mutations were subjected to in silico pathogenicity, conservation, and stability analysis tools. We used statistical analysis as a QC measure for validating the specificity and accuracy of these tools. PolyPhen-2 demonstrated the highest specificity and accuracy. While PolyPhen-1 showed the highest sensitivity; overall, PolyPhen2 showed better measures in comparison to other in silico tools. Three mutations (D44V, Y272C, and Y277C) were identified as the most pathogenic and destabilizing. Further, we compared the physiochemical properties of the native and the mutant amino acids and observed loss of H-bonds and aromatic stacking upon the cysteine to tyrosine substitution, which led to the loss of aromatic rings and may reduce protein stability. The three mutations were further subjected to Molecular Dynamics Simulation (MDS) analysis using GROMACS to understand the structural changes. The Y272C and Y277C mutants exhibited maximum deviation pattern from the native protein as compared to D44V mutant. Further MDS analysis predicted changes in the stability that may have been contributed due to the loss of hydrogen bonds as observed in intramolecular hydrogen bond analysis and physiochemical analysis. A loss of function/structural impact was found to be severe in the case of Y272C and Y277C mutants in comparison to D44V mutation. Correlating the results from in silico predictions, physiochemical analysis, and MDS, we were able to observe a loss of stability in all the three mutants. This combinatorial approach could serve as a platform for variant interpretation and drug design for spinal muscular dystrophy resulting from missense mutations. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by the mutations in survival motor neuron 1 gene (SMN1). The molecular pathology of missense mutations in SMN1 is not thoroughly investigated so far. Therefore, we collected all missense mutations in the SMN1 protein, using all possible search terms, from three databases (PubMed, PMC and Google Scholar). All missense mutations were subjected to in silico pathogenicity, conservation, and stability analysis tools. We used statistical analysis as a QC measure for validating the specificity and accuracy of these tools. PolyPhen-2 demonstrated the highest specificity and accuracy. While PolyPhen-1 showed the highest sensitivity; overall, PolyPhen2 showed better measures in comparison to other in silico tools. Three mutations (D44V, Y272C, and Y277C) were identified as the most pathogenic and destabilizing. Further, we compared the physiochemical properties of the native and the mutant amino acids and observed loss of H-bonds and aromatic stacking upon the cysteine to tyrosine substitution, which led to the loss of aromatic rings and may reduce protein stability. The three mutations were further subjected to Molecular Dynamics Simulation (MDS) analysis using GROMACS to understand the structural changes. The Y272C and Y277C mutants exhibited maximum deviation pattern from the native protein as compared to D44V mutant. Further MDS analysis predicted changes in the stability that may have been contributed due to the loss of hydrogen bonds as observed in intramolecular hydrogen bond analysis and physiochemical analysis. A loss of function/structural impact was found to be severe in the case of Y272C and Y277C mutants in comparison to D44V mutation. Correlating the results from in silico predictions, physiochemical analysis, and MDS, we were able to observe a loss of stability in all the three mutants. This combinatorial approach could serve as a platform for variant interpretation and drug design for spinal muscular dystrophy resulting from missense mutations. © 2018, Springer Science+Business Media, LLC, part of Springer Nature. |
Kumar, Thirumal D; Emerald, Jerushah L; Doss, George Priya C; Sneha, P; Siva, R; Jebaraj, Charles Emmanuel W; Zayed, H Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2 Journal Article Metabolic Brain Disease, 33 (5), pp. 1699-1710, 2018. @article{ThirumalKumar20181699, title = {Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2}, author = {D Thirumal Kumar and L Jerushah Emerald and C George Priya Doss and P Sneha and R Siva and W Charles Emmanuel Jebaraj and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049629060&doi=10.1007%2fs11011-018-0278-3&partnerID=40&md5=74c5f15e2e39f6d7527ab2ca31abd5e3}, doi = {10.1007/s11011-018-0278-3}, year = {2018}, date = {2018-01-01}, journal = {Metabolic Brain Disease}, volume = {33}, number = {5}, pages = {1699-1710}, publisher = {Springer New York LLC}, abstract = {The 2-hydroxyglutaric aciduria (2-HGA) is a rare neurometabolic disorder that leads to the development of brain damage. It is classified into three categories: D-2-HGA, L-2-HGA, and combined D,L-2-HGA. The D-2-HGA includes two subtypes: type I and type II caused by the mutations in D2HGDH and IDH2 proteins, respectively. In this study, we studied six mutations, four in the D2HGDH (I147S, D375Y, N439D, and V444A) and two in the IDH2 proteins (R140G, R140Q). We performed in silico analysis to investigate the pathogenicity and stability changes of the mutant proteins using pathogenicity (PANTHER, PhD-SNP, SIFT, SNAP, and META-SNP) and stability (i-Mutant, MUpro, and iStable) predictors. All the mutations of both D2HGDH and IDH2 proteins were predicted as disease causing except V444A, which was predicted as neutral by SIFT. All the mutants were also predicted to be destabilizing the protein except the mutants D375Y and N439D. DSSP plugin of the PyMOL and Molecular Dynamics Simulations (MDS) were used to study the structural changes in the mutant proteins. In the case of D2HGDH protein, the mutations I147S and V444A that are positioned in the beta sheet region exhibited higher Root Mean Square Deviation (RMSD), decrease in compactness and number of intramolecular hydrogen bonds compared to the mutations N439D and D375Y that are positioned in the turn and loop region, respectively. While the mutants R140Q and R140QG that are positioned in the alpha helix region of the protein. MDS results revealed the mutation R140Q to be more destabilizing (higher RMSD values, decrease in compactness and number of intramolecular hydrogen bonds) compared to the mutation R140G of the IDH2 protein. This study is expected to serve as a platform for drug development against 2-HGA and pave the way for more accurate variant assessment and classification for patients with genetic diseases. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The 2-hydroxyglutaric aciduria (2-HGA) is a rare neurometabolic disorder that leads to the development of brain damage. It is classified into three categories: D-2-HGA, L-2-HGA, and combined D,L-2-HGA. The D-2-HGA includes two subtypes: type I and type II caused by the mutations in D2HGDH and IDH2 proteins, respectively. In this study, we studied six mutations, four in the D2HGDH (I147S, D375Y, N439D, and V444A) and two in the IDH2 proteins (R140G, R140Q). We performed in silico analysis to investigate the pathogenicity and stability changes of the mutant proteins using pathogenicity (PANTHER, PhD-SNP, SIFT, SNAP, and META-SNP) and stability (i-Mutant, MUpro, and iStable) predictors. All the mutations of both D2HGDH and IDH2 proteins were predicted as disease causing except V444A, which was predicted as neutral by SIFT. All the mutants were also predicted to be destabilizing the protein except the mutants D375Y and N439D. DSSP plugin of the PyMOL and Molecular Dynamics Simulations (MDS) were used to study the structural changes in the mutant proteins. In the case of D2HGDH protein, the mutations I147S and V444A that are positioned in the beta sheet region exhibited higher Root Mean Square Deviation (RMSD), decrease in compactness and number of intramolecular hydrogen bonds compared to the mutations N439D and D375Y that are positioned in the turn and loop region, respectively. While the mutants R140Q and R140QG that are positioned in the alpha helix region of the protein. MDS results revealed the mutation R140Q to be more destabilizing (higher RMSD values, decrease in compactness and number of intramolecular hydrogen bonds) compared to the mutation R140G of the IDH2 protein. This study is expected to serve as a platform for drug development against 2-HGA and pave the way for more accurate variant assessment and classification for patients with genetic diseases. © 2018, Springer Science+Business Media, LLC, part of Springer Nature. |
Sneha, P; Ebrahimi, E A; Ghazala, S A; Kumar, Thirumal D; Siva, R; C, Priya Doss G; Zayed, H Structural analysis of missense mutations in galactokinase 1 (GALK1) leading to galactosemia type-2 Journal Article Journal of Cellular Biochemistry, 119 (9), pp. 7585-7598, 2018. @article{Sneha20187585, title = {Structural analysis of missense mutations in galactokinase 1 (GALK1) leading to galactosemia type-2}, author = {P Sneha and E A Ebrahimi and S A Ghazala and D Thirumal Kumar and R Siva and G Priya Doss C and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053257744&doi=10.1002%2fjcb.27097&partnerID=40&md5=7ec108a8b4907aa7c360ad71a9bc054f}, doi = {10.1002/jcb.27097}, year = {2018}, date = {2018-01-01}, journal = {Journal of Cellular Biochemistry}, volume = {119}, number = {9}, pages = {7585-7598}, publisher = {Wiley-Liss Inc.}, abstract = {Galactosemia type 2 is an autosomal recessive disorder characterized by the deficiency of galactokinase (GALK) enzyme due to missense mutations in GALK1 gene, which is associated with various manifestations such as hyper galactosemia and formation of cataracts. GALK enzyme catalyzes the adenosine triphosphate (ATP)–dependent phosphorylation of α-d-galactose to galactose-1-phosphate. We searched 4 different literature databases (Google Scholar, PubMed, PubMed Central, and Science Direct) and 3 gene-variant databases (Online Mendelian Inheritance in Man, Human Gene Mutation Database, and UniProt) to collect all the reported missense mutations associated with GALK deficiency. Our search strategy yielded 32 missense mutations. We used several computational tools (pathogenicity and stability, biophysical characterization, and physiochemical analyses) to prioritize the most significant mutations for further analyses. On the basis of the pathogenicity and stability predictions, 3 mutations (P28T, A198V, and L139P) were chosen to be tested further for physicochemical characterization, molecular docking, and simulation analyses. Molecular docking analysis revealed a decrease in interaction between the protein and ATP in all the 3 mutations, and molecular dynamic simulations of 50 ns showed a loss of stability and compactness in the mutant proteins. As the next step, comparative physicochemical changes of the native and the mutant proteins were carried out using essential dynamics. Overall, P28T and A198V were predicted to alter the structure and function of GALK protein when compared to the mutant L139P. This study demonstrates the power of computational analysis in variant classification and interpretation and provides a platform for developing targeted therapeutics. © 2018 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Galactosemia type 2 is an autosomal recessive disorder characterized by the deficiency of galactokinase (GALK) enzyme due to missense mutations in GALK1 gene, which is associated with various manifestations such as hyper galactosemia and formation of cataracts. GALK enzyme catalyzes the adenosine triphosphate (ATP)–dependent phosphorylation of α-d-galactose to galactose-1-phosphate. We searched 4 different literature databases (Google Scholar, PubMed, PubMed Central, and Science Direct) and 3 gene-variant databases (Online Mendelian Inheritance in Man, Human Gene Mutation Database, and UniProt) to collect all the reported missense mutations associated with GALK deficiency. Our search strategy yielded 32 missense mutations. We used several computational tools (pathogenicity and stability, biophysical characterization, and physiochemical analyses) to prioritize the most significant mutations for further analyses. On the basis of the pathogenicity and stability predictions, 3 mutations (P28T, A198V, and L139P) were chosen to be tested further for physicochemical characterization, molecular docking, and simulation analyses. Molecular docking analysis revealed a decrease in interaction between the protein and ATP in all the 3 mutations, and molecular dynamic simulations of 50 ns showed a loss of stability and compactness in the mutant proteins. As the next step, comparative physicochemical changes of the native and the mutant proteins were carried out using essential dynamics. Overall, P28T and A198V were predicted to alter the structure and function of GALK protein when compared to the mutant L139P. This study demonstrates the power of computational analysis in variant classification and interpretation and provides a platform for developing targeted therapeutics. © 2018 Wiley Periodicals, Inc. |
Hemachandran, H; Jain, F; Mohan, S; D, Kumar T; C., Priya Doss G; Ramamoorthy, S Glandular hair constituents of Mallotus philippinensis Muell. fruit act as tyrosinase inhibitors: Insights from enzyme kinetics and simulation study Journal Article International Journal of Biological Macromolecules, 107 , pp. 1675-1682, 2018. @article{Hemachandran20181675, title = {Glandular hair constituents of Mallotus philippinensis Muell. fruit act as tyrosinase inhibitors: Insights from enzyme kinetics and simulation study}, author = {H Hemachandran and F Jain and S Mohan and T Kumar D and G Priya Doss C. and S Ramamoorthy}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033441363&doi=10.1016%2fj.ijbiomac.2017.10.036&partnerID=40&md5=c2db1b1a151675d834dcbd9b2c78eb7a}, doi = {10.1016/j.ijbiomac.2017.10.036}, year = {2018}, date = {2018-01-01}, journal = {International Journal of Biological Macromolecules}, volume = {107}, pages = {1675-1682}, publisher = {Elsevier B.V.}, abstract = {The glandular hair extracts from the fruit rind of Mallotus philippinensis Muell. is employed to treat various skin infections, however the anti-tyrosinase activity remains unknown. Hence the present study inspected on the anti-melanogenic activity of M. philippinensis constituents. Lineweaver Burk plot revealed mixed inhibition for Rottlerin; non-competitive type of inhibition for mallotophilippen A and B respectively. Thermodynamic studies resulted in static quenching forming ground state complex with higher binding constant temperature dependently. Fluorescence and circular dichroism study implicated conformational change in secondary and tertiary structure of tyrosinase. Molecular docking suggests rottlerin has high binding affinity to the active site pocket of tyrosinase. Simulation study further proved that the compactness of inhibitor with tyrosinase by hydrogen bonding influenced the stability of the enzyme. Depigmentation efficacy is further proved in Aspergillus niger spores. Thus our findings delineate that rottlerin could be utilized as a depigmentation agent in food pharmaceutical and agricultural industries. © 2017 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The glandular hair extracts from the fruit rind of Mallotus philippinensis Muell. is employed to treat various skin infections, however the anti-tyrosinase activity remains unknown. Hence the present study inspected on the anti-melanogenic activity of M. philippinensis constituents. Lineweaver Burk plot revealed mixed inhibition for Rottlerin; non-competitive type of inhibition for mallotophilippen A and B respectively. Thermodynamic studies resulted in static quenching forming ground state complex with higher binding constant temperature dependently. Fluorescence and circular dichroism study implicated conformational change in secondary and tertiary structure of tyrosinase. Molecular docking suggests rottlerin has high binding affinity to the active site pocket of tyrosinase. Simulation study further proved that the compactness of inhibitor with tyrosinase by hydrogen bonding influenced the stability of the enzyme. Depigmentation efficacy is further proved in Aspergillus niger spores. Thus our findings delineate that rottlerin could be utilized as a depigmentation agent in food pharmaceutical and agricultural industries. © 2017 Elsevier B.V. |
Kumar, Thirumal D; Sneha, P; Uppin, J; Usha, S; Doss, George Priya C Investigating the Influence of Hotspot Mutations in Protein–Protein Interaction of IDH1 Homodimer Protein: A Computational Approach Book Chapter 111 , pp. 243-261, Academic Press Inc., 2018. @inbook{ThirumalKumar2018243, title = {Investigating the Influence of Hotspot Mutations in Protein–Protein Interaction of IDH1 Homodimer Protein: A Computational Approach}, author = {D Thirumal Kumar and P Sneha and J Uppin and S Usha and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031326778&doi=10.1016%2fbs.apcsb.2017.08.002&partnerID=40&md5=fe37284538b18df951326cf95fb221f0}, doi = {10.1016/bs.apcsb.2017.08.002}, year = {2018}, date = {2018-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {111}, pages = {243-261}, publisher = {Academic Press Inc.}, abstract = {Protein–protein interaction (PPI) helps in maintaining the cellular homeostasis. In particular, the homodimeric proteins play a crucial role as cell regulators. Studying the critical functions of each PPI on the living system is very challenging. The mutations in the PPIs have given birth to various diseases including many types of cancers and it has soon become the target for drug discovery. The mutations in IDH1, an asymmetric homodimer in the cytoplasm, leads to various diseases including gliomas. In this study, we have used extensive computational approaches to identify the impact of missense mutations (R132C, R132G, R132H, R132L, R132S, and V178I) occurring in the interacting region of the IDH1 homodimer. By in silico pathogenicity analysis, all the mutations occurring at the positions 132 and 178 were found to be pathogenic and neutral respectively. Furthermore, the mutants R132C and R132G were found to be responsible for increasing the stability, whereas the mutants R132H, R132L, and R132S were found to be responsible for the decrease in stability by stability analysis. R132H, R132L, and R132S mutants exhibited higher destabilization when compared to the structures of R132C and R132G mutants by molecular docking and molecular dynamics analysis. © 2018 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Protein–protein interaction (PPI) helps in maintaining the cellular homeostasis. In particular, the homodimeric proteins play a crucial role as cell regulators. Studying the critical functions of each PPI on the living system is very challenging. The mutations in the PPIs have given birth to various diseases including many types of cancers and it has soon become the target for drug discovery. The mutations in IDH1, an asymmetric homodimer in the cytoplasm, leads to various diseases including gliomas. In this study, we have used extensive computational approaches to identify the impact of missense mutations (R132C, R132G, R132H, R132L, R132S, and V178I) occurring in the interacting region of the IDH1 homodimer. By in silico pathogenicity analysis, all the mutations occurring at the positions 132 and 178 were found to be pathogenic and neutral respectively. Furthermore, the mutants R132C and R132G were found to be responsible for increasing the stability, whereas the mutants R132H, R132L, and R132S were found to be responsible for the decrease in stability by stability analysis. R132H, R132L, and R132S mutants exhibited higher destabilization when compared to the structures of R132C and R132G mutants by molecular docking and molecular dynamics analysis. © 2018 Elsevier Inc. |
Sneha, P; Kumar, Thirumal D; Lijo, J; Megha, M; Siva, R; Doss, George Priya C Probing the Protein–Protein Interaction Network of Proteins Causing Maturity Onset Diabetes of the Young Book Chapter 110 , pp. 167-202, Academic Press Inc., 2018. @inbook{Sneha2018167, title = {Probing the Protein–Protein Interaction Network of Proteins Causing Maturity Onset Diabetes of the Young}, author = {P Sneha and D Thirumal Kumar and J Lijo and M Megha and R Siva and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030837718&doi=10.1016%2fbs.apcsb.2017.07.004&partnerID=40&md5=0299d94822637efbe502a4e347df7712}, doi = {10.1016/bs.apcsb.2017.07.004}, year = {2018}, date = {2018-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {110}, pages = {167-202}, publisher = {Academic Press Inc.}, abstract = {Protein–protein interactions (PPIs) play vital roles in various cellular pathways. Most of the proteins perform their responsibilities by interacting with an enormous number of proteins. Understanding these interactions of the proteins and their interacting partners has shed light toward the field of drug discovery. Also, PPIs enable us to understand the functions of a protein by understanding their interacting partners. Consequently, in the current study, PPI network of the proteins causing MODY (Maturity Onset Diabetes of the Young) was drawn, and their correlation in causing a disease condition was marked. MODY is a monogenic type of diabetes caused by autosomal dominant inheritance. Extensive research on transcription factor and their corresponding genetic pathways have been studied over the last three decades, yet, very little is understood about the molecular modalities of highly dynamic interactions between transcription factors, genomic DNA, and the protein partners. The current study also reveals the interacting patterns of the various transcription factors. Consequently, in the current work, we have devised a PPI analysis to understand the plausible pathway through which the protein leads to a deformity in glucose uptake. © 2018 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Protein–protein interactions (PPIs) play vital roles in various cellular pathways. Most of the proteins perform their responsibilities by interacting with an enormous number of proteins. Understanding these interactions of the proteins and their interacting partners has shed light toward the field of drug discovery. Also, PPIs enable us to understand the functions of a protein by understanding their interacting partners. Consequently, in the current study, PPI network of the proteins causing MODY (Maturity Onset Diabetes of the Young) was drawn, and their correlation in causing a disease condition was marked. MODY is a monogenic type of diabetes caused by autosomal dominant inheritance. Extensive research on transcription factor and their corresponding genetic pathways have been studied over the last three decades, yet, very little is understood about the molecular modalities of highly dynamic interactions between transcription factors, genomic DNA, and the protein partners. The current study also reveals the interacting patterns of the various transcription factors. Consequently, in the current work, we have devised a PPI analysis to understand the plausible pathway through which the protein leads to a deformity in glucose uptake. © 2018 Elsevier Inc. |
Xu, Q; Wu, N; Cui, L; Lin, M; Kumar, Thirumal D; Doss, George Priya C; Wu, Z; Shen, J; Song, X; Qiu, G Comparative analysis of the two extremes of FLNB-mutated autosomal dominant disease spectrum: From clinical phenotypes to cellular and molecular findings Journal Article American Journal of Translational Research, 10 (5), pp. 1400-1412, 2018. @article{Xu20181400, title = {Comparative analysis of the two extremes of FLNB-mutated autosomal dominant disease spectrum: From clinical phenotypes to cellular and molecular findings}, author = {Q Xu and N Wu and L Cui and M Lin and D Thirumal Kumar and C George Priya Doss and Z Wu and J Shen and X Song and G Qiu}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047661907&partnerID=40&md5=f72906321051db1d83c3167fae870922}, year = {2018}, date = {2018-01-01}, journal = {American Journal of Translational Research}, volume = {10}, number = {5}, pages = {1400-1412}, publisher = {E-Century Publishing Corporation}, abstract = {Non-randomly distributed missense mutations of Filamin B (FLNB) can lead to a spectrum of autosomal dominant-inherited skeletal malformations caused by bone hypoplasia, including Larsen syndrome (LS), atelosteogenesi-I (AO-I), atelosteogenesi-I (AO-III) and boomerang dysplasia (BD). Among this spectrum of diseases, LS causes a milder hypoplasia of the skeletal system, compared to BD’s much more severe symptoms. Previous studies revealed limited molecular mechanisms of FLNB-related diseases but most of them were carried out with HEK293 cells from the kidney which could not reproduce FLNB’s specificity to skeletal tissues. Instead, we elected to use ATDC5, a chondrogenic stem cell line widely used to study endochondral osteogenesis. In this study, we established FLNB-transfected ATDC5 cell model. We reported a pedigree of LS with mutation of FLNBG1586R and reviewed a case of BD with mutation of FLNBL171R. Using the ATDC5 cell model above, we compared cellular and molecular phenotypes of BD-associated FLNBL171R and LS-associated FLNBG1586R. We found that while both phenotypes had an increased expression of Runx2, FLNBL171R-expressing ATDC5 cells presented globular aggregation of FLNB protein and increased cellular apoptosis rate while FLNBG1586R-expressing ATDC5 cells presented evenly distributed FLNB protein and decreased cellular migration. These findings support our explanation for the cause of differences in clinical phenotypes between LS and BD. Our study makes a comparative analysis of two extremes of the FLNB-mutated autosomal dominant spectrum, relating known clinical phenotypes to our new cellular and molecular findings. These results indicated next steps for future research on the role of FLNB in the physiological process of endochondral osteogenesis. © 2018, E-Century Publishing Corporation. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Non-randomly distributed missense mutations of Filamin B (FLNB) can lead to a spectrum of autosomal dominant-inherited skeletal malformations caused by bone hypoplasia, including Larsen syndrome (LS), atelosteogenesi-I (AO-I), atelosteogenesi-I (AO-III) and boomerang dysplasia (BD). Among this spectrum of diseases, LS causes a milder hypoplasia of the skeletal system, compared to BD’s much more severe symptoms. Previous studies revealed limited molecular mechanisms of FLNB-related diseases but most of them were carried out with HEK293 cells from the kidney which could not reproduce FLNB’s specificity to skeletal tissues. Instead, we elected to use ATDC5, a chondrogenic stem cell line widely used to study endochondral osteogenesis. In this study, we established FLNB-transfected ATDC5 cell model. We reported a pedigree of LS with mutation of FLNBG1586R and reviewed a case of BD with mutation of FLNBL171R. Using the ATDC5 cell model above, we compared cellular and molecular phenotypes of BD-associated FLNBL171R and LS-associated FLNBG1586R. We found that while both phenotypes had an increased expression of Runx2, FLNBL171R-expressing ATDC5 cells presented globular aggregation of FLNB protein and increased cellular apoptosis rate while FLNBG1586R-expressing ATDC5 cells presented evenly distributed FLNB protein and decreased cellular migration. These findings support our explanation for the cause of differences in clinical phenotypes between LS and BD. Our study makes a comparative analysis of two extremes of the FLNB-mutated autosomal dominant spectrum, relating known clinical phenotypes to our new cellular and molecular findings. These results indicated next steps for future research on the role of FLNB in the physiological process of endochondral osteogenesis. © 2018, E-Century Publishing Corporation. All rights reserved. |
Pragsam, A K; Kumar, D T; Doss, C G P; Iyadurai, R; Satyendra, S; Rodrigues, C; Joshi, S; Roy, I; Chaudhuri, B N; Chitnis, D S; Tapan, D; Veeraraghavan, B In silico and in vitro activity of ceftolozane/tazobactam against pseudomonas aeruginosa collected across Indian hospitals Journal Article Indian Journal of Medical Microbiology, 36 (1), pp. 127-130, 2018. @article{Pragsam2018127, title = {In silico and in vitro activity of ceftolozane/tazobactam against pseudomonas aeruginosa collected across Indian hospitals}, author = {A K Pragsam and D T Kumar and C G P Doss and R Iyadurai and S Satyendra and C Rodrigues and S Joshi and I Roy and B N Chaudhuri and D S Chitnis and D Tapan and B Veeraraghavan}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046738164&doi=10.4103%2fijmm.IJMM_17_349&partnerID=40&md5=82dc74af3ab34d558e76c586de05b8e4}, doi = {10.4103/ijmm.IJMM_17_349}, year = {2018}, date = {2018-01-01}, journal = {Indian Journal of Medical Microbiology}, volume = {36}, number = {1}, pages = {127-130}, publisher = {Wolters Kluwer Medknow Publications}, abstract = {Ceftolozane/tazobactam is a novel antimicrobial agent with activity against Pseudomonas aeruginosa and other common Gram-negative pathogens. In this study, we determined the antimicrobial susceptibility for a total of 149 clinical isolates of P. aeruginosa for the most commonly used antimicrobials including the new agent ceftolozane/tazobactam (C/T). Broth microdilution was performed to determine the minimum inhibitory concentration against various antimicrobials including C/T. Among the β-lactam/β-lactamase inhibitor, overall susceptibility was 67%, 55% and 51% for C/T, Piperacillin/Tazobactam (P/T) and Cefoperazone/Sulbactam, respectively. The variations in the susceptibility rates were noted among the three different β-lactam/β-lactamase inhibitors. Interestingly, 33% susceptibility was noted for C/T against isolates that were resistant to P/T, indicating the higher activity of C/T. This finding suggests about 33% of the P/T-resistant isolates can still be treated effectively with C/T. C/T could be a better alternative for the treatment of ESBL-producing organism, and thereby usage of higher antimicrobials can be minimised. © 2018 Indian Journal of Medical Microbiology | Published by Wolters Kluwer -Medknow.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ceftolozane/tazobactam is a novel antimicrobial agent with activity against Pseudomonas aeruginosa and other common Gram-negative pathogens. In this study, we determined the antimicrobial susceptibility for a total of 149 clinical isolates of P. aeruginosa for the most commonly used antimicrobials including the new agent ceftolozane/tazobactam (C/T). Broth microdilution was performed to determine the minimum inhibitory concentration against various antimicrobials including C/T. Among the β-lactam/β-lactamase inhibitor, overall susceptibility was 67%, 55% and 51% for C/T, Piperacillin/Tazobactam (P/T) and Cefoperazone/Sulbactam, respectively. The variations in the susceptibility rates were noted among the three different β-lactam/β-lactamase inhibitors. Interestingly, 33% susceptibility was noted for C/T against isolates that were resistant to P/T, indicating the higher activity of C/T. This finding suggests about 33% of the P/T-resistant isolates can still be treated effectively with C/T. C/T could be a better alternative for the treatment of ESBL-producing organism, and thereby usage of higher antimicrobials can be minimised. © 2018 Indian Journal of Medical Microbiology | Published by Wolters Kluwer -Medknow. |
2017 |
Unissa, A N; C., Doss G P; Kumar, T; Swathi, S; Lakshmi, A R; Hanna, L E Analysis of interactions of clinical mutants of catalase-peroxidase (KatG) responsible for isoniazid resistance in Mycobacterium tuberculosis with derivatives of isoniazid Journal Article Journal of Global Antimicrobial Resistance, 11 , pp. 57-67, 2017. @article{Unissa201757, title = {Analysis of interactions of clinical mutants of catalase-peroxidase (KatG) responsible for isoniazid resistance in Mycobacterium tuberculosis with derivatives of isoniazid}, author = {A N Unissa and G P Doss C. and T Kumar and S Swathi and A R Lakshmi and L E Hanna}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030671257&doi=10.1016%2fj.jgar.2017.06.014&partnerID=40&md5=8a034a5f5a11d778c19b3fd83347c580}, doi = {10.1016/j.jgar.2017.06.014}, year = {2017}, date = {2017-01-01}, journal = {Journal of Global Antimicrobial Resistance}, volume = {11}, pages = {57-67}, publisher = {Elsevier Ltd}, abstract = {Objectives Isoniazid (INH) resistance is a major contributor to the emergence of multidrug resistance in Mycobacterium tuberculosis (MTB), hampering the success of tuberculosis treatment. This study aimed to identify good leads based on INH derivatives against INH-resistant MTB strains. Mutations at codon 315 in the katG gene encoding catalase-peroxidase (KatG) are the major cause of INH resistance in MTB. The most prevalent substitution is S315T; other substitutions include S315I, S315R, S315N and S315G. Methods In this study, all five naturally occurring mutants (S315T, S315I, S315R, S315N and S315G) of KatG were docked and simulated with 50 INH derivatives in comparison with the wild-type (WT) KatG. Results The docking results suggested that compounds C30, C45 and C50 gave the highest scores when bound to the mutants of KatG. Of note, C50 produced a high score with the WT as well as with three mutants (S315T, S315I and S315R). Simulation studies indicated that C50 exhibited minimal deviation and fluctuation between WT and three mutants compared with C30 and C45, which displayed significant changes with WT and the S315N and S315G mutants, respectively. Conclusions C50 can be considered as a better lead for INH-resistant strains. These models demonstrate the binding interaction of all naturally occurring KatG mutants of MTB at position 315 with derivatives of INH. This information will be helpful for lead compound-based identification of derivatives that may be used against INH-resistant MTB strains and may provide a useful structural framework for designing new antitubercular agents that can circumvent INH resistance. © 2017 International Society for Chemotherapy of Infection and Cancer}, keywords = {}, pubstate = {published}, tppubtype = {article} } Objectives Isoniazid (INH) resistance is a major contributor to the emergence of multidrug resistance in Mycobacterium tuberculosis (MTB), hampering the success of tuberculosis treatment. This study aimed to identify good leads based on INH derivatives against INH-resistant MTB strains. Mutations at codon 315 in the katG gene encoding catalase-peroxidase (KatG) are the major cause of INH resistance in MTB. The most prevalent substitution is S315T; other substitutions include S315I, S315R, S315N and S315G. Methods In this study, all five naturally occurring mutants (S315T, S315I, S315R, S315N and S315G) of KatG were docked and simulated with 50 INH derivatives in comparison with the wild-type (WT) KatG. Results The docking results suggested that compounds C30, C45 and C50 gave the highest scores when bound to the mutants of KatG. Of note, C50 produced a high score with the WT as well as with three mutants (S315T, S315I and S315R). Simulation studies indicated that C50 exhibited minimal deviation and fluctuation between WT and three mutants compared with C30 and C45, which displayed significant changes with WT and the S315N and S315G mutants, respectively. Conclusions C50 can be considered as a better lead for INH-resistant strains. These models demonstrate the binding interaction of all naturally occurring KatG mutants of MTB at position 315 with derivatives of INH. This information will be helpful for lead compound-based identification of derivatives that may be used against INH-resistant MTB strains and may provide a useful structural framework for designing new antitubercular agents that can circumvent INH resistance. © 2017 International Society for Chemotherapy of Infection and Cancer |
Kumar, Thirumal D; Lavanya, P; Doss, George Priya C; Tayubi, I A; Kumar, Naveen D R; Yesurajan, Francis I; Siva, R; Balaji, V A Molecular Docking and Dynamics Approach to Screen Potent Inhibitors Against Fosfomycin Resistant Enzyme in Clinical Klebsiella pneumoniae Journal Article Journal of Cellular Biochemistry, 118 (11), pp. 4088-4094, 2017. @article{ThirumalKumar20174088, title = {A Molecular Docking and Dynamics Approach to Screen Potent Inhibitors Against Fosfomycin Resistant Enzyme in Clinical Klebsiella pneumoniae}, author = {D Thirumal Kumar and P Lavanya and C George Priya Doss and I A Tayubi and D R Naveen Kumar and I Francis Yesurajan and R Siva and V Balaji}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029591226&doi=10.1002%2fjcb.26064&partnerID=40&md5=9318e4d07059712d111d69ce57d11213}, doi = {10.1002/jcb.26064}, year = {2017}, date = {2017-01-01}, journal = {Journal of Cellular Biochemistry}, volume = {118}, number = {11}, pages = {4088-4094}, publisher = {Wiley-Liss Inc.}, abstract = {Klebsiella pneumoniae, BA6753 was cultured from a patient in the Clinical Microbiology Laboratory of Christian Medical College. K. pneumoniae, BA6753 has a multidrug resistance plasmid encoding novel FosA variant-7, fosfomycin resistance enzyme. Minimal side effects and a wide range of bactericidal activity of fosfomycin have resulted in its expanded clinical use that prompts the rise of fosfomycin-resistant strains. At present, there are no effective inhibitors available to conflict the FosA-medicated fosfomycin resistance. To develop effective FosA inhibitors, it is crucial to understand the structural and dynamic properties of resistance enzymes. Hence, the present study focuses on the identification of potent inhibitors that can effectively bind to the fosfomycin resistance enzyme, thus predispose the target to inactivate by the second antibiotic. Initially, a series of active compounds were screened against the resistant enzyme, and the binding affinities were confirmed using docking simulation analysis. For efficient activity, the binding affinity of the resistance enzyme ought to be high with the inhibitor than the fosfomycin drug. Consequently, the enzyme-ligand complex which showed higher binding affinity than the fosfomycin was employed for subsequent analysis. The stability of the top scoring enzyme-ligand complex was further validated using molecular dynamics simulation studies. On the whole, we presume that the compound 19583672 demonstrates a higher binding affinity for the resistance enzyme comparing to other compounds and fosfomycin. We believe that further enhancement of the lead compound can serve as a potential inhibitor against resistance enzyme in drug discovery process. J. Cell. Biochem. 118: 4088–4094, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Klebsiella pneumoniae, BA6753 was cultured from a patient in the Clinical Microbiology Laboratory of Christian Medical College. K. pneumoniae, BA6753 has a multidrug resistance plasmid encoding novel FosA variant-7, fosfomycin resistance enzyme. Minimal side effects and a wide range of bactericidal activity of fosfomycin have resulted in its expanded clinical use that prompts the rise of fosfomycin-resistant strains. At present, there are no effective inhibitors available to conflict the FosA-medicated fosfomycin resistance. To develop effective FosA inhibitors, it is crucial to understand the structural and dynamic properties of resistance enzymes. Hence, the present study focuses on the identification of potent inhibitors that can effectively bind to the fosfomycin resistance enzyme, thus predispose the target to inactivate by the second antibiotic. Initially, a series of active compounds were screened against the resistant enzyme, and the binding affinities were confirmed using docking simulation analysis. For efficient activity, the binding affinity of the resistance enzyme ought to be high with the inhibitor than the fosfomycin drug. Consequently, the enzyme-ligand complex which showed higher binding affinity than the fosfomycin was employed for subsequent analysis. The stability of the top scoring enzyme-ligand complex was further validated using molecular dynamics simulation studies. On the whole, we presume that the compound 19583672 demonstrates a higher binding affinity for the resistance enzyme comparing to other compounds and fosfomycin. We believe that further enhancement of the lead compound can serve as a potential inhibitor against resistance enzyme in drug discovery process. J. Cell. Biochem. 118: 4088–4094, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc. |
Sekar, G; Tripathi, A; Kumar, D T; Doss, C G P; Mukherjee, A; Chandrasekaran, N Characterizing the binding interaction between titanium (IV) oxide nanoparticles and human serum albumin: Spectroscopic and molecular docking methods Journal Article Journal of Bionanoscience, 11 (5), pp. 376-383, 2017. @article{Sekar2017376, title = {Characterizing the binding interaction between titanium (IV) oxide nanoparticles and human serum albumin: Spectroscopic and molecular docking methods}, author = {G Sekar and A Tripathi and D T Kumar and C G P Doss and A Mukherjee and N Chandrasekaran}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028776169&doi=10.1166%2fjbns.2017.1466&partnerID=40&md5=558b49f09e1ff09c9bdc6002274c1d6e}, doi = {10.1166/jbns.2017.1466}, year = {2017}, date = {2017-01-01}, journal = {Journal of Bionanoscience}, volume = {11}, number = {5}, pages = {376-383}, publisher = {American Scientific Publishers}, abstract = {Herein, we have reported the binding interaction between Human Serum Albumin and the titanium dioxide nanoparticles in vitro. Characterization of the nanoparticles physicochemical and morphological properties was done with X-ray Diffraction, Fourier Transform Infra Red, Raman spectroscopic and microscopic methods. XRD and FT-Raman studies have confirmed the anatase phase of the nanoparticles. Surface active functional groups have been identified from FTIR studies. SEMEDAX has figured out the spherical shape of the particles with their metallic constituents. Hyperchromic effect observed against the absorbance and the quenching behavior of the nanoparticles on the intrinsic fluorescence of the HSA has confirmed the complex formation to exist via static mechanism. Circular Dichroism studies have dictated the loss in the secondary structures. Docking studies showed the binding mode of TNPs-HSA complex system. Copyright © 2017 American Scientific Publishers All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Herein, we have reported the binding interaction between Human Serum Albumin and the titanium dioxide nanoparticles in vitro. Characterization of the nanoparticles physicochemical and morphological properties was done with X-ray Diffraction, Fourier Transform Infra Red, Raman spectroscopic and microscopic methods. XRD and FT-Raman studies have confirmed the anatase phase of the nanoparticles. Surface active functional groups have been identified from FTIR studies. SEMEDAX has figured out the spherical shape of the particles with their metallic constituents. Hyperchromic effect observed against the absorbance and the quenching behavior of the nanoparticles on the intrinsic fluorescence of the HSA has confirmed the complex formation to exist via static mechanism. Circular Dichroism studies have dictated the loss in the secondary structures. Docking studies showed the binding mode of TNPs-HSA complex system. Copyright © 2017 American Scientific Publishers All rights reserved. |
Kumar, Thirumal D; Doss, George Priya C Role of E542 and E545 missense mutations of PIK3CA in breast cancer: a comparative computational approach Journal Article Journal of Biomolecular Structure and Dynamics, 35 (12), pp. 2745-2757, 2017. @article{ThirumalKumar20172745, title = {Role of E542 and E545 missense mutations of PIK3CA in breast cancer: a comparative computational approach}, author = {D Thirumal Kumar and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84988953461&doi=10.1080%2f07391102.2016.1231082&partnerID=40&md5=9121bbc2f8a7fdca4ae6cd2754d87062}, doi = {10.1080/07391102.2016.1231082}, year = {2017}, date = {2017-01-01}, journal = {Journal of Biomolecular Structure and Dynamics}, volume = {35}, number = {12}, pages = {2745-2757}, publisher = {Taylor and Francis Ltd.}, abstract = {Recent statistics describe breast cancer as the leading cause of death among women across the world with varied causes and reasons. Lifestyle, diet, genetic and environmental factors introduce their generous contributions towards breast cancer, among which genetic factors have lately become one of the most important aspects in understanding the mechanism. Although various genes have already been reported in causing breast cancer, PIK3CA stands second on the list. Mutations observed in this gene have the ability to trigger the different activities of the cell, thereby bypassing the regular cellular cycle. Among the mutations in PIK3CA, three hotspot mutations were commonly reported, one in the catalytic domain (position HIS1047) and other two in the helical domain (position GLU542 and GLU545). In the helical domain of PIK3CA, the lysine substitution at 542–545 positions was significantly studied in causing breast cancer. To compare the deleterious effect of these mutations, in silico prediction tools along with molecular dynamics simulations and molecular docking approach was initiated to analyse the change in binding landscape upon mutation. In this comparative analysis, we report that the mere existence of mutant E545K can trigger the function of the protein but may not be as harmful as H1047R. Among the two mutations E542K and E545K, the latter shows the most deleterious effect that correlates with the previous reported experimental studies. We assume the results observed in this combinatorial computational study might further pave a better way for providing better treatment procedures. © 2016 Informa UK Limited, trading as Taylor & Francis Group.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent statistics describe breast cancer as the leading cause of death among women across the world with varied causes and reasons. Lifestyle, diet, genetic and environmental factors introduce their generous contributions towards breast cancer, among which genetic factors have lately become one of the most important aspects in understanding the mechanism. Although various genes have already been reported in causing breast cancer, PIK3CA stands second on the list. Mutations observed in this gene have the ability to trigger the different activities of the cell, thereby bypassing the regular cellular cycle. Among the mutations in PIK3CA, three hotspot mutations were commonly reported, one in the catalytic domain (position HIS1047) and other two in the helical domain (position GLU542 and GLU545). In the helical domain of PIK3CA, the lysine substitution at 542–545 positions was significantly studied in causing breast cancer. To compare the deleterious effect of these mutations, in silico prediction tools along with molecular dynamics simulations and molecular docking approach was initiated to analyse the change in binding landscape upon mutation. In this comparative analysis, we report that the mere existence of mutant E545K can trigger the function of the protein but may not be as harmful as H1047R. Among the two mutations E542K and E545K, the latter shows the most deleterious effect that correlates with the previous reported experimental studies. We assume the results observed in this combinatorial computational study might further pave a better way for providing better treatment procedures. © 2016 Informa UK Limited, trading as Taylor & Francis Group. |
Sekar, G; Haldar, M; Kumar, Thirumal D; Doss, George Priya C; Mukherjee, A; Chandrasekaran, N Exploring the interaction between iron oxide nanoparticles (IONPs) and Human serum albumin (HSA): Spectroscopic and docking studies Journal Article Journal of Molecular Liquids, 241 , pp. 793-800, 2017. @article{Sekar2017793, title = {Exploring the interaction between iron oxide nanoparticles (IONPs) and Human serum albumin (HSA): Spectroscopic and docking studies}, author = {G Sekar and M Haldar and D Thirumal Kumar and C George Priya Doss and A Mukherjee and N Chandrasekaran}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021219396&doi=10.1016%2fj.molliq.2017.06.093&partnerID=40&md5=736a6ff5971e6821e1b5f810fedb3251}, doi = {10.1016/j.molliq.2017.06.093}, year = {2017}, date = {2017-01-01}, journal = {Journal of Molecular Liquids}, volume = {241}, pages = {793-800}, publisher = {Elsevier B.V.}, abstract = {The combination of the spectroscopic and molecular modeling methods was utilized to understand the iron (III) oxide nanoparticles (IONPs) interaction with Human serum albumin (HSA). Initial characterization of the IONPs using FTIR and FT-Raman techniques showed the bands corresponding to the Fe–O bonds at the low frequency region. Also, the XRD diffraction planes obtained confirms the magnetite phase of IONPs with the spinel structure. SEM-EDAX analysis showed the spherical morphology of the IONPs with weight percentage of iron metal constituents. Fluorescence and UV–Visible spectra of the HSA-IONPs complex dictated the quenching mechanism as static. Synchronous spectra found more affinity of IONPs against the Trp residues of HSA. 3D scan spectra added additional insight into the conformational changes of HSA on interaction with IONPs. CD spectra showed both the changes in the alpha helical contents and the Trp absorbance of the polypeptide backbone. Molecular docking result coherence with the spectroscopic findings in confirming the binding interaction between HSA and IONPs and showed the nearby amino acid residues including tyrosine. © 2016 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The combination of the spectroscopic and molecular modeling methods was utilized to understand the iron (III) oxide nanoparticles (IONPs) interaction with Human serum albumin (HSA). Initial characterization of the IONPs using FTIR and FT-Raman techniques showed the bands corresponding to the Fe–O bonds at the low frequency region. Also, the XRD diffraction planes obtained confirms the magnetite phase of IONPs with the spinel structure. SEM-EDAX analysis showed the spherical morphology of the IONPs with weight percentage of iron metal constituents. Fluorescence and UV–Visible spectra of the HSA-IONPs complex dictated the quenching mechanism as static. Synchronous spectra found more affinity of IONPs against the Trp residues of HSA. 3D scan spectra added additional insight into the conformational changes of HSA on interaction with IONPs. CD spectra showed both the changes in the alpha helical contents and the Trp absorbance of the polypeptide backbone. Molecular docking result coherence with the spectroscopic findings in confirming the binding interaction between HSA and IONPs and showed the nearby amino acid residues including tyrosine. © 2016 Elsevier B.V. |
Bakthavatchalam, Y D; Kumar, D T; Tayubi, I A; Shankar, B A; Babu, P; Munusamy, E; Thukkaram, B; Ravi, R; Doss, C G P; Veeraraghavan, B In vitro efficacy and in silico analysis of cefixime–ofloxacin combination for Salmonella Typhi from bloodstream infection Journal Article Journal of Applied Microbiology, 123 (3), pp. 615-624, 2017. @article{Bakthavatchalam2017615, title = {In vitro efficacy and in silico analysis of cefixime–ofloxacin combination for Salmonella Typhi from bloodstream infection}, author = {Y D Bakthavatchalam and D T Kumar and I A Tayubi and B A Shankar and P Babu and E Munusamy and B Thukkaram and R Ravi and C G P Doss and B Veeraraghavan}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027497556&doi=10.1111%2fjam.13522&partnerID=40&md5=72c49cfcd93ec4bfaf54f8f0c478d02b}, doi = {10.1111/jam.13522}, year = {2017}, date = {2017-01-01}, journal = {Journal of Applied Microbiology}, volume = {123}, number = {3}, pages = {615-624}, publisher = {Blackwell Publishing Ltd}, abstract = {Aims: Recently, the cefixime–ofloxacin combination is approved by Drug Controller General of India to treat typhoid fever. We sought to evaluate the antimicrobial activity of cefixime–ofloxacin combination against Salmonella Typhi. Methods and Results: A total of 283 nonduplicate S. Typhi isolates collected during 2012–2014 were included in this study. Minimum inhibitory concentration (MIC) of cefixime and ofloxacin was determined by using broth microdilution method. Combinational testing was performed by using checkerboard assay. In checkerboard assay, synergistic activity was seen in 11% of isolates, while the majority of the isolate showed indifference and none of them showed antagonism. An in silico strategy, an alternative to the animal model, was carried out to understand drug interaction and toxicity. Molecular docking results elucidated that cefixime and ofloxacin are capable of inhibiting the cell wall synthesis and DNA replication, respectively. Computational ADMET analysis showed no toxicity and no drug–drug interaction between cefixime and ofloxacin. Conclusion: Cefixime–ofloxacin combination could be effective against moderately susceptible fluoroquinolone S. Typhi but not fluoroquinolone-resistant isolates. Significance and Impact of the Study: Cefixime–ofloxacin combination with no drug–drug interaction and nontoxic predicted through computational analysis did not show antagonism against S. Typhi in in vitro. Although this study showed no adverse effects with the cefixime–ofloxacin combination, further studies on pharmacokinetic and pharmacodynamic (PK-PD) parameters of cefixime and ofloxacin combination are warranted. © 2017 The Society for Applied Microbiology}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aims: Recently, the cefixime–ofloxacin combination is approved by Drug Controller General of India to treat typhoid fever. We sought to evaluate the antimicrobial activity of cefixime–ofloxacin combination against Salmonella Typhi. Methods and Results: A total of 283 nonduplicate S. Typhi isolates collected during 2012–2014 were included in this study. Minimum inhibitory concentration (MIC) of cefixime and ofloxacin was determined by using broth microdilution method. Combinational testing was performed by using checkerboard assay. In checkerboard assay, synergistic activity was seen in 11% of isolates, while the majority of the isolate showed indifference and none of them showed antagonism. An in silico strategy, an alternative to the animal model, was carried out to understand drug interaction and toxicity. Molecular docking results elucidated that cefixime and ofloxacin are capable of inhibiting the cell wall synthesis and DNA replication, respectively. Computational ADMET analysis showed no toxicity and no drug–drug interaction between cefixime and ofloxacin. Conclusion: Cefixime–ofloxacin combination could be effective against moderately susceptible fluoroquinolone S. Typhi but not fluoroquinolone-resistant isolates. Significance and Impact of the Study: Cefixime–ofloxacin combination with no drug–drug interaction and nontoxic predicted through computational analysis did not show antagonism against S. Typhi in in vitro. Although this study showed no adverse effects with the cefixime–ofloxacin combination, further studies on pharmacokinetic and pharmacodynamic (PK-PD) parameters of cefixime and ofloxacin combination are warranted. © 2017 The Society for Applied Microbiology |
Zaki, O K; Doss, George Priya C; Ali, S A; Murad, G G; Elashi, S A; Ebnou, M S A; Kumar, Thirumal D; Khalifa, O; Gamal, R; Abd, El H S A; Nasr, B N; Zayed, H Genotype-phenotype correlation in patients with isovaleric acidaemia: Comparative structural modelling and computational analysis of novel variants Journal Article Human Molecular Genetics, 26 (16), pp. 3105-3115, 2017. @article{Zaki20173105, title = {Genotype-phenotype correlation in patients with isovaleric acidaemia: Comparative structural modelling and computational analysis of novel variants}, author = {O K Zaki and C George Priya Doss and S A Ali and G G Murad and S A Elashi and M S A Ebnou and D Thirumal Kumar and O Khalifa and R Gamal and H S A El Abd and B N Nasr and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027698606&doi=10.1093%2fhmg%2fddx195&partnerID=40&md5=f143daa4560ba7fd5b8f2164091f7140}, doi = {10.1093/hmg/ddx195}, year = {2017}, date = {2017-01-01}, journal = {Human Molecular Genetics}, volume = {26}, number = {16}, pages = {3105-3115}, publisher = {Oxford University Press}, abstract = {Isovaleric acidaemia (IVA) is an autosomal recessive inborn error of leucine metabolism. It is caused by a deficiency in the mitochondrial isovaleryl-CoA dehydrogenase (IVD) enzyme. In this study, we investigated eight patients with IVA. The patients' diagnoses were confirmed by urinary organic acid analysis and the blood C5-Carnitine value. A molecular genetic analysis of the IVD gene revealed nine different variants: five were missense variants (c.1193G > A; p. R398Q, c.1207T > A; p. Y403N, c.872C > T; p. A291V, c.749G > C; p. G250A, c.1136T > C; p.I379T), one was a frameshift variant (c.ins386 T; p. Y129fs), one was a splicing variant (c.465+2T > C), one was a polymorphism (c.732C > T; p. D244D), and one was an intronic benign variant (c.287+14T > C). Interestingly, all variants were in homozygous form, and four variants were novel (p. Y403N, p. Y129fs, p. A291V, p. G250A) and absent from 200 normal chromosomes. We performed protein modelling and dynamics analyses, pathogenicity and stability analyses, and a physiochemical properties analysis of the five missense variants (p.Y403N, R398Q, p.A291V, p.G250A, and p.I379T). Variants p.I379T and p.R398Q were found to be the most deleterious and destabilizing compared to variants p.A291V and p.Y403N. However, the four variants were predicted to be severe by the protein dynamic and in silico analysis, which was consistent with the patients' clinical phenotypes. The p.G250A variant was computationally predicted as mild, which was consistent with the severity of the clinical phenotype. This study reveals a potentially meaningful genotype-phenotype correlation for our patient cohort and highlights the development and use of this computational analysis for future assessments of genetic variants in the clinic. © The Author 2017. Published by Oxford University Press. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Isovaleric acidaemia (IVA) is an autosomal recessive inborn error of leucine metabolism. It is caused by a deficiency in the mitochondrial isovaleryl-CoA dehydrogenase (IVD) enzyme. In this study, we investigated eight patients with IVA. The patients' diagnoses were confirmed by urinary organic acid analysis and the blood C5-Carnitine value. A molecular genetic analysis of the IVD gene revealed nine different variants: five were missense variants (c.1193G > A; p. R398Q, c.1207T > A; p. Y403N, c.872C > T; p. A291V, c.749G > C; p. G250A, c.1136T > C; p.I379T), one was a frameshift variant (c.ins386 T; p. Y129fs), one was a splicing variant (c.465+2T > C), one was a polymorphism (c.732C > T; p. D244D), and one was an intronic benign variant (c.287+14T > C). Interestingly, all variants were in homozygous form, and four variants were novel (p. Y403N, p. Y129fs, p. A291V, p. G250A) and absent from 200 normal chromosomes. We performed protein modelling and dynamics analyses, pathogenicity and stability analyses, and a physiochemical properties analysis of the five missense variants (p.Y403N, R398Q, p.A291V, p.G250A, and p.I379T). Variants p.I379T and p.R398Q were found to be the most deleterious and destabilizing compared to variants p.A291V and p.Y403N. However, the four variants were predicted to be severe by the protein dynamic and in silico analysis, which was consistent with the patients' clinical phenotypes. The p.G250A variant was computationally predicted as mild, which was consistent with the severity of the clinical phenotype. This study reveals a potentially meaningful genotype-phenotype correlation for our patient cohort and highlights the development and use of this computational analysis for future assessments of genetic variants in the clinic. © The Author 2017. Published by Oxford University Press. All rights reserved. |
Hemachandran, H; Anantharaman, A; Mohan, S; Mohan, G; Kumar, D T; Dey, D; Kumar, D; Dey, P; Choudhury, A; Doss, George Priya C; Ramamoorthy, S Unraveling the inhibition mechanism of cyanidin-3-sophoroside on polyphenol oxidase and its effect on enzymatic browning of apples Journal Article Food Chemistry, 227 , pp. 102-110, 2017. @article{Hemachandran2017102, title = {Unraveling the inhibition mechanism of cyanidin-3-sophoroside on polyphenol oxidase and its effect on enzymatic browning of apples}, author = {H Hemachandran and A Anantharaman and S Mohan and G Mohan and D T Kumar and D Dey and D Kumar and P Dey and A Choudhury and C George Priya Doss and S Ramamoorthy}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009986225&doi=10.1016%2fj.foodchem.2017.01.041&partnerID=40&md5=fc683f1685b6fe3e6f65d88b515ba355}, doi = {10.1016/j.foodchem.2017.01.041}, year = {2017}, date = {2017-01-01}, journal = {Food Chemistry}, volume = {227}, pages = {102-110}, publisher = {Elsevier Ltd}, abstract = {The hunt for anti-browning agents in the food and agricultural industries aims to minimize nutritional loss and prolong post harvest storage. In the present study, the effect of cyanidin-3-sophoroside (CS) from Garcinia mangostana rind, on polyphenol oxidase (PPO) activity was investigated. The non-competitive inhibition mode of CS was determined by Lineweaver Burk plot. CS forms a ground-state complex by quenching the intrinsic fluorescence of PPO. The static quenching was temperature-dependent with an activation energy of 4.654 ± 0.1091 kJ mol−1 to withstand the disruption of amino acid residues of the enzyme binding site. The enzyme conformational change was validated by 3D fluorescence and CD spectrum. Docking (binding energy −8.124 kcal/mol) and simulation studies confirmed the binding pattern and stability. CS decreased PPO activity and browning index of fresh cut apples and prolonged the shelf life. Thus, CS appears to be a promising anti-browning agent to control enzymatic browning. © 2017 Elsevier Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } The hunt for anti-browning agents in the food and agricultural industries aims to minimize nutritional loss and prolong post harvest storage. In the present study, the effect of cyanidin-3-sophoroside (CS) from Garcinia mangostana rind, on polyphenol oxidase (PPO) activity was investigated. The non-competitive inhibition mode of CS was determined by Lineweaver Burk plot. CS forms a ground-state complex by quenching the intrinsic fluorescence of PPO. The static quenching was temperature-dependent with an activation energy of 4.654 ± 0.1091 kJ mol−1 to withstand the disruption of amino acid residues of the enzyme binding site. The enzyme conformational change was validated by 3D fluorescence and CD spectrum. Docking (binding energy −8.124 kcal/mol) and simulation studies confirmed the binding pattern and stability. CS decreased PPO activity and browning index of fresh cut apples and prolonged the shelf life. Thus, CS appears to be a promising anti-browning agent to control enzymatic browning. © 2017 Elsevier Ltd |
Sneha, P; Thirumal, Kumar D; Tanwar, H; Siva, R; Doss, George Priya C; Zayed, H Structural Analysis of G1691S Variant in the Human Filamin B Gene Responsible for Larsen Syndrome: A Comparative Computational Approach Journal Article Journal of Cellular Biochemistry, 118 (7), pp. 1900-1910, 2017. @article{Sneha20171900, title = {Structural Analysis of G1691S Variant in the Human Filamin B Gene Responsible for Larsen Syndrome: A Comparative Computational Approach}, author = {P Sneha and D Kumar Thirumal and H Tanwar and R Siva and C George Priya Doss and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85017354863&doi=10.1002%2fjcb.25920&partnerID=40&md5=f329f0f5820124e82717392b9dbfdb44}, doi = {10.1002/jcb.25920}, year = {2017}, date = {2017-01-01}, journal = {Journal of Cellular Biochemistry}, volume = {118}, number = {7}, pages = {1900-1910}, publisher = {Wiley-Liss Inc.}, abstract = {Larsen syndrome (LRS) is a rare genetic disease associated with variable manifestations including skeletal malformations, dislocations of the large joints, and notable changes in facial and limb features. Genetic variants in the Filamin B (FLNB) gene are associated with the development of LRS. We searched two literature databases (OMIM and PubMed) and three gene variant databases (HGMD, UniProt, & dbSNP) to capture all the possible variants associated with LRS phenotype, which may have an impact on the FLNB function. Our search yielded 77 variants that might impact the FLNB protein function in patients with LRS. We performed rigorous computational analysis such as conservational, biochemical, pathogenicity, and structural computational analyses to understand the deleterious effect of the G1691S variant. Further, the structural changes of the G1691S variant was compared with a null variant (G1691A) and the native protein through a molecular dynamic simulation study of 50 ns. We found that the variant G1691S was highly deleterious and destabilize the protein when compared to the native and variant G1691A. This might be due to the physicochemical changes in the variant G1691S when compared to the native and variant G1691A. The destabilization was further supported by transformation of bend to coil in variant G1691S whereas bend was retained in native and variant G1691A through molecular dynamics analysis. Our study shed light on the importance of computational methods to understand the molecular nature of genetic variants and structural insights on the function of the FLNB protein. J. Cell. Biochem. 118: 1900–1910, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Larsen syndrome (LRS) is a rare genetic disease associated with variable manifestations including skeletal malformations, dislocations of the large joints, and notable changes in facial and limb features. Genetic variants in the Filamin B (FLNB) gene are associated with the development of LRS. We searched two literature databases (OMIM and PubMed) and three gene variant databases (HGMD, UniProt, & dbSNP) to capture all the possible variants associated with LRS phenotype, which may have an impact on the FLNB function. Our search yielded 77 variants that might impact the FLNB protein function in patients with LRS. We performed rigorous computational analysis such as conservational, biochemical, pathogenicity, and structural computational analyses to understand the deleterious effect of the G1691S variant. Further, the structural changes of the G1691S variant was compared with a null variant (G1691A) and the native protein through a molecular dynamic simulation study of 50 ns. We found that the variant G1691S was highly deleterious and destabilize the protein when compared to the native and variant G1691A. This might be due to the physicochemical changes in the variant G1691S when compared to the native and variant G1691A. The destabilization was further supported by transformation of bend to coil in variant G1691S whereas bend was retained in native and variant G1691A through molecular dynamics analysis. Our study shed light on the importance of computational methods to understand the molecular nature of genetic variants and structural insights on the function of the FLNB protein. J. Cell. Biochem. 118: 1900–1910, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc. |
Kumar, Thirumal D; Doss, George Priya C; Sneha, P; Tayubi, I A; Siva, R; Chakraborty, C; Magesh, R Influence of V54M mutation in giant muscle protein titin: a computational screening and molecular dynamics approach Journal Article Journal of Biomolecular Structure and Dynamics, 35 (5), pp. 917-928, 2017. @article{ThirumalKumar2017917, title = {Influence of V54M mutation in giant muscle protein titin: a computational screening and molecular dynamics approach}, author = {D Thirumal Kumar and C George Priya Doss and P Sneha and I A Tayubi and R Siva and C Chakraborty and R Magesh}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976291704&doi=10.1080%2f07391102.2016.1166456&partnerID=40&md5=afaf004daa840aadf3ec06f9e24d8db8}, doi = {10.1080/07391102.2016.1166456}, year = {2017}, date = {2017-01-01}, journal = {Journal of Biomolecular Structure and Dynamics}, volume = {35}, number = {5}, pages = {917-928}, publisher = {Taylor and Francis Ltd.}, abstract = {Recent genetic studies have revealed the impact of mutations in associated genes for cardiac sarcomere components leading to dilated cardiomyopathy (DCM). The cardiac sarcomere is composed of thick and thin filaments and a giant muscle protein known as titin or connectin. Titin interacts with T-cap/telethonin in the Z-line region and plays a vital role in regulating sarcomere assembly. Initially, we screened all the variants associated with giant protein titin and analyzed their impact with the aid of pathogenicity and stability prediction methods. V54M mutation found in the hydrophobic core region of the protein associated with abnormal clinical phenotype leads to DCM was selected for further analysis. To address this issue, we mapped the deleterious mutant V54M, modeled the mutant protein complex, and deciphered the impact of mutation on binding with its partner telethonin in the titin crystal structure of PDB ID: 1YA5 with the aid of docking analysis. Furthermore, two run molecular dynamics simulation was initiated to understand the mechanistic action of V54M mutation in altering the protein structure, dynamics, and stability. According to the results obtained from the repeated 50 ns trajectory files, the overall effect of V54M mutation was destabilizing and transition of bend to coil in the secondary structure was observed. Furthermore, MMPBSA elucidated that V54M found in the Z-line region of titin decreases the binding affinity of titin to Z-line proteins T-cap/telethonin thereby hindering the protein–protein interaction. © 2016 Informa UK Limited, trading as Taylor & Francis Group.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent genetic studies have revealed the impact of mutations in associated genes for cardiac sarcomere components leading to dilated cardiomyopathy (DCM). The cardiac sarcomere is composed of thick and thin filaments and a giant muscle protein known as titin or connectin. Titin interacts with T-cap/telethonin in the Z-line region and plays a vital role in regulating sarcomere assembly. Initially, we screened all the variants associated with giant protein titin and analyzed their impact with the aid of pathogenicity and stability prediction methods. V54M mutation found in the hydrophobic core region of the protein associated with abnormal clinical phenotype leads to DCM was selected for further analysis. To address this issue, we mapped the deleterious mutant V54M, modeled the mutant protein complex, and deciphered the impact of mutation on binding with its partner telethonin in the titin crystal structure of PDB ID: 1YA5 with the aid of docking analysis. Furthermore, two run molecular dynamics simulation was initiated to understand the mechanistic action of V54M mutation in altering the protein structure, dynamics, and stability. According to the results obtained from the repeated 50 ns trajectory files, the overall effect of V54M mutation was destabilizing and transition of bend to coil in the secondary structure was observed. Furthermore, MMPBSA elucidated that V54M found in the Z-line region of titin decreases the binding affinity of titin to Z-line proteins T-cap/telethonin thereby hindering the protein–protein interaction. © 2016 Informa UK Limited, trading as Taylor & Francis Group. |
Sneha, P; Thirumal, K D; George, P D C; Siva, R; Zayed, H Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach Journal Article PLoS ONE, 12 (4), 2017. @article{Sneha2017b, title = {Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach}, author = {P Sneha and K D Thirumal and P D C George and R Siva and H Zayed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85017462181&doi=10.1371%2fjournal.pone.0174953&partnerID=40&md5=9d7180e856d9a4c68afd48de17f6550e}, doi = {10.1371/journal.pone.0174953}, year = {2017}, date = {2017-01-01}, journal = {PLoS ONE}, volume = {12}, number = {4}, publisher = {Public Library of Science}, abstract = {Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism. First, the pathogenicity and stability of the mutations were analyzed to determine whether they alter protein structure and function. Second, the sequence conservation and DNA-binding sites of the mutant positions were assessed; as HNF1A protein is a transcription factor. Finally, the biochemical properties of the biological system were validated using molecular dynamic simulations in Gromacs 4.6.3 package. Two arginine residues (131 and 203) in the HNF1A protein are highly conserved residues and contribute to the function of the protein. Furthermore, the R131W, R131Q, and R203C mutations were predicted to be highly deleterious by in silico tools and showed lower binding affinity with DNA when compared to the native protein using the molecular docking analysis. Triplicate runs of molecular dynamic (MD) simulations (50ns) revealed smaller changes in patterns of deviation, fluctuation, and compactness, in complexes containing the R131Q and R131W mutations, compared to complexes containing the R203C mutant complex. We observed reduction in the number of intermolecular hydrogen bonds, compactness, and electrostatic potential, as well as the loss of salt bridges, in the R203C mutant complex. Substitution of arginine with cysteine at position 203 decreases the affinity of the protein for DNA, thereby destabilizing the protein. Based on our current findings, the MD approach is an important tool for elucidating the impact and affinity of mutations in DNA-protein interactions and understanding their function. © 2017 P. et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism. First, the pathogenicity and stability of the mutations were analyzed to determine whether they alter protein structure and function. Second, the sequence conservation and DNA-binding sites of the mutant positions were assessed; as HNF1A protein is a transcription factor. Finally, the biochemical properties of the biological system were validated using molecular dynamic simulations in Gromacs 4.6.3 package. Two arginine residues (131 and 203) in the HNF1A protein are highly conserved residues and contribute to the function of the protein. Furthermore, the R131W, R131Q, and R203C mutations were predicted to be highly deleterious by in silico tools and showed lower binding affinity with DNA when compared to the native protein using the molecular docking analysis. Triplicate runs of molecular dynamic (MD) simulations (50ns) revealed smaller changes in patterns of deviation, fluctuation, and compactness, in complexes containing the R131Q and R131W mutations, compared to complexes containing the R203C mutant complex. We observed reduction in the number of intermolecular hydrogen bonds, compactness, and electrostatic potential, as well as the loss of salt bridges, in the R203C mutant complex. Substitution of arginine with cysteine at position 203 decreases the affinity of the protein for DNA, thereby destabilizing the protein. Based on our current findings, the MD approach is an important tool for elucidating the impact and affinity of mutations in DNA-protein interactions and understanding their function. © 2017 P. et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
Benny, B; Doss, George Priya C; Kumar, Thirumal D; Devi, Asha S Assessing reproductive toxicity and antioxidant enzymes on beta asarone induced male Wistar albino rats: In vivo and computational analysis Journal Article Life Sciences, 173 , pp. 150-160, 2017. @article{Benny2017150, title = {Assessing reproductive toxicity and antioxidant enzymes on beta asarone induced male Wistar albino rats: In vivo and computational analysis}, author = {B Benny and C George Priya Doss and D Thirumal Kumar and S Asha Devi}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85013807539&doi=10.1016%2fj.lfs.2016.08.021&partnerID=40&md5=51e26338ea67ee62e8fd8e104be68273}, doi = {10.1016/j.lfs.2016.08.021}, year = {2017}, date = {2017-01-01}, journal = {Life Sciences}, volume = {173}, pages = {150-160}, publisher = {Elsevier Inc.}, abstract = {Aim Beta asarone is the major constituent of oil obtained from Acorus calamus, the Indian traditional medicine plant. Several studies have shown that beta asarone causes liver and cardiac damages but the reproductive toxicity is not well understood. The present study was initiated to investigate whether beta asarone has the potential to cause reproductive toxicity by inducing oxidative stress in the testis of male Wistar albino rats. Materials and methods For this study, the animals were divided into six groups: Group I was treated with saline (normal saline), Group II with DMSO (vehicle control) and Group III with cisplatin (10 mg/kg b.wt.). Group IV, V and VI animals were administrated at three dose levels of beta asarone 12.5, 25 and 50 mg/kg b.wt. The treatment was carried out for 14 days and animals were sacrificed on 29th day and processed for sperm analysis, hormone assay, histopathological, and antioxidant enzymatic assays. We also used molecular docking studies to predict the binding nature of beta asarone with luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR). Key findings Beta asarone administered at a dose of 50 mg/kg b.wt. was responsible for inducing certain noticeable degenerative changes in histopathological analysis of the tissue. This was supported by altered sperm morphology and hormonal variations when compared to the control groups. Antioxidant enzyme levels were also found to be decreased. This was further validated by molecular docking studies. Significance The present study provides evidence that beta asarone administered at a dose of 50 mg/kg b.wt. is capable enough in bringing about moderate amount of degenerative changes in rat testis and altered antioxidant status. Therefore provides a suitable evidence to prove that beta asarone causes reproductive toxicity. © 2016 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aim Beta asarone is the major constituent of oil obtained from Acorus calamus, the Indian traditional medicine plant. Several studies have shown that beta asarone causes liver and cardiac damages but the reproductive toxicity is not well understood. The present study was initiated to investigate whether beta asarone has the potential to cause reproductive toxicity by inducing oxidative stress in the testis of male Wistar albino rats. Materials and methods For this study, the animals were divided into six groups: Group I was treated with saline (normal saline), Group II with DMSO (vehicle control) and Group III with cisplatin (10 mg/kg b.wt.). Group IV, V and VI animals were administrated at three dose levels of beta asarone 12.5, 25 and 50 mg/kg b.wt. The treatment was carried out for 14 days and animals were sacrificed on 29th day and processed for sperm analysis, hormone assay, histopathological, and antioxidant enzymatic assays. We also used molecular docking studies to predict the binding nature of beta asarone with luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR). Key findings Beta asarone administered at a dose of 50 mg/kg b.wt. was responsible for inducing certain noticeable degenerative changes in histopathological analysis of the tissue. This was supported by altered sperm morphology and hormonal variations when compared to the control groups. Antioxidant enzyme levels were also found to be decreased. This was further validated by molecular docking studies. Significance The present study provides evidence that beta asarone administered at a dose of 50 mg/kg b.wt. is capable enough in bringing about moderate amount of degenerative changes in rat testis and altered antioxidant status. Therefore provides a suitable evidence to prove that beta asarone causes reproductive toxicity. © 2016 Elsevier Inc. |
Sneha, P; Kumar, Thirumal D; Saini, S; Kajal, K; Magesh, R; Siva, R; Doss, George Priya C Analyzing the Effect of V66M Mutation in BDNF in Causing Mood Disorders: A Computational Approach Book Chapter 108 , pp. 85-103, Academic Press Inc., 2017. @inbook{Sneha201785, title = {Analyzing the Effect of V66M Mutation in BDNF in Causing Mood Disorders: A Computational Approach}, author = {P Sneha and D Thirumal Kumar and S Saini and K Kajal and R Magesh and R Siva and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014633745&doi=10.1016%2fbs.apcsb.2017.01.006&partnerID=40&md5=37c6706ebb8e43af1f5dfaed666fb8de}, doi = {10.1016/bs.apcsb.2017.01.006}, year = {2017}, date = {2017-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {108}, pages = {85-103}, publisher = {Academic Press Inc.}, abstract = {Mental disorders or mood disorders are prevalent globally irrespective of region, race, and ethnic groups. Of the types of mood disorders, major depressive disorder (MDD) and bipolar disorder (BPD) are the most prevalent forms of psychiatric condition. A number of preclinical studies emphasize the essential role of brain-derived neurotrophic factor (BDNF) in the pathophysiology of mood disorders. Additionally, BDNF is the most common growth factor in the central nervous system along with their essential role during the neural development and the synaptic elasticity. A malfunctioning of this protein is associated with many types of mood disorders. The variant methionine replaces valine at 66th position is strongly related to BPD, and an individual with a homozygous condition of this allele is at a greater risk of developing MDD. There are very sparse reports suggesting the structural changes of the protein occurring upon the mutation. Consequently, in this study, we applied a computational pipeline to understand the effects caused by the mutation on the protein's structure and function. With the use of in silico tools and computational macroscopic methods, we identified a decrease in the alpha-helix nature, and an overall increase in the random coils that could have probably resulted in deformation of the protein. © 2017 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Mental disorders or mood disorders are prevalent globally irrespective of region, race, and ethnic groups. Of the types of mood disorders, major depressive disorder (MDD) and bipolar disorder (BPD) are the most prevalent forms of psychiatric condition. A number of preclinical studies emphasize the essential role of brain-derived neurotrophic factor (BDNF) in the pathophysiology of mood disorders. Additionally, BDNF is the most common growth factor in the central nervous system along with their essential role during the neural development and the synaptic elasticity. A malfunctioning of this protein is associated with many types of mood disorders. The variant methionine replaces valine at 66th position is strongly related to BPD, and an individual with a homozygous condition of this allele is at a greater risk of developing MDD. There are very sparse reports suggesting the structural changes of the protein occurring upon the mutation. Consequently, in this study, we applied a computational pipeline to understand the effects caused by the mutation on the protein's structure and function. With the use of in silico tools and computational macroscopic methods, we identified a decrease in the alpha-helix nature, and an overall increase in the random coils that could have probably resulted in deformation of the protein. © 2017 Elsevier Inc. |
Tanwar, H; Sneha, P; Kumar, Thirumal D; Siva, R; Walter, C E J; Doss, George Priya C A Computational Approach to Identify the Biophysical and Structural Aspects of Methylenetetrahydrofolate Reductase (MTHFR) Mutations (A222V, E429A, and R594Q) Leading to Schizophrenia Book Chapter 108 , pp. 105-125, Academic Press Inc., 2017. @inbook{Tanwar2017105, title = {A Computational Approach to Identify the Biophysical and Structural Aspects of Methylenetetrahydrofolate Reductase (MTHFR) Mutations (A222V, E429A, and R594Q) Leading to Schizophrenia}, author = {H Tanwar and P Sneha and D Thirumal Kumar and R Siva and C E J Walter and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016078536&doi=10.1016%2fbs.apcsb.2017.01.007&partnerID=40&md5=7356b97c7330a4b19de696a55d4acac7}, doi = {10.1016/bs.apcsb.2017.01.007}, year = {2017}, date = {2017-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {108}, pages = {105-125}, publisher = {Academic Press Inc.}, abstract = {The association between depression and methylenetetrahydrofolate reductase (MTHFR) has been continually demonstrated in clinical studies, yet there are sparse resources available to build a relationship between the mutations associated with MTHFR and depression. The common mutations found to be associated with schizophrenia and MTHFR are A222V, E429A, and R594Q. Although abundant research on structural and functional effects caused by A222V mutation is available, very less amount of studies have been done on the other two mutants (E429A and R594Q). Hence in this study, a comparative analysis was carried out between the most common A222V mutation, a prevalent E429A mutation, and a less prevalent and less deleterious R594Q mutation. To predict structural rearrangements upon mutation, we proposed a computational pipeline using in silico prediction tools, molecular docking, and molecular dynamics simulation analysis. Since the association of flavin adenine dinucleotide (FAD) is important for the functioning of the protein, binding analysis between protein and the coenzyme was performed. This would enable us to understand the interference level of each mutation over FAD-binding activity. Consequently, we found that two mutations (A222V and E429A) showed lesser binding activity and structural deviations when compared to the native molecule and mutant R594Q. Comparatively, higher structural changes were observed with A222V mutant complex in comparison to other mutant complexes. Computational studies like this could render better insights into the structural changes in the protein and their relationship with the disease condition. © 2017 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } The association between depression and methylenetetrahydrofolate reductase (MTHFR) has been continually demonstrated in clinical studies, yet there are sparse resources available to build a relationship between the mutations associated with MTHFR and depression. The common mutations found to be associated with schizophrenia and MTHFR are A222V, E429A, and R594Q. Although abundant research on structural and functional effects caused by A222V mutation is available, very less amount of studies have been done on the other two mutants (E429A and R594Q). Hence in this study, a comparative analysis was carried out between the most common A222V mutation, a prevalent E429A mutation, and a less prevalent and less deleterious R594Q mutation. To predict structural rearrangements upon mutation, we proposed a computational pipeline using in silico prediction tools, molecular docking, and molecular dynamics simulation analysis. Since the association of flavin adenine dinucleotide (FAD) is important for the functioning of the protein, binding analysis between protein and the coenzyme was performed. This would enable us to understand the interference level of each mutation over FAD-binding activity. Consequently, we found that two mutations (A222V and E429A) showed lesser binding activity and structural deviations when compared to the native molecule and mutant R594Q. Comparatively, higher structural changes were observed with A222V mutant complex in comparison to other mutant complexes. Computational studies like this could render better insights into the structural changes in the protein and their relationship with the disease condition. © 2017 Elsevier Inc. |
2016 |
Nagasundaram, N; Doss, G P C; Chakraborty, C; Karthick, V; Kumar, D T; Balaji, V; Siva, R; Lu, A; Ge, Z; Zhu, H Mechanism of artemisinin resistance for malaria PfATP6 L263 mutations and discovering potential antimalarials: An integrated computational approach Journal Article Scientific Reports, 6 , 2016. @article{Nagasundaram2016, title = {Mechanism of artemisinin resistance for malaria PfATP6 L263 mutations and discovering potential antimalarials: An integrated computational approach}, author = {N Nagasundaram and G P C Doss and C Chakraborty and V Karthick and D T Kumar and V Balaji and R Siva and A Lu and Z Ge and H Zhu}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84982737930&doi=10.1038%2fsrep30106&partnerID=40&md5=a61af38e76af1466e108311df15d0194}, doi = {10.1038/srep30106}, year = {2016}, date = {2016-01-01}, journal = {Scientific Reports}, volume = {6}, publisher = {Nature Publishing Group}, abstract = {Artemisinin resistance in Plasmodium falciparum threatens global efforts in the elimination or eradication of malaria. Several studies have associated mutations in the PfATP6 gene in conjunction with artemisinin resistance, but the underlying molecular mechanism of the resistance remains unexplored. Associated mutations act as a biomarker to measure the artemisinin efficacy. In the proposed work, we have analyzed the binding affinity and efficacy between PfATP6 and artemisinin in the presence of L263D, L263E and L263K mutations. Furthermore, we performed virtual screening to identify potential compounds to inhibit the PfATP6 mutant proteins. In this study, we observed that artemisinin binding affinity with PfATP6 gets affected by L263D, L263E and L263K mutations. This in silico elucidation of artemisinin resistance enhanced the identification of novel compounds (CID: 10595058 and 10625452) which showed good binding affinity and efficacy with L263D, L263E and L263K mutant proteins in molecular docking and molecular dynamics simulations studies. Owing to the high propensity of the parasite to drug resistance the need for new antimalarial drugs will persist until the malarial parasites are eventually eradicated. The two compounds identified in this study can be tested in in vitro and in vivo experiments as possible candidates for the designing of new potential antimalarial drugs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Artemisinin resistance in Plasmodium falciparum threatens global efforts in the elimination or eradication of malaria. Several studies have associated mutations in the PfATP6 gene in conjunction with artemisinin resistance, but the underlying molecular mechanism of the resistance remains unexplored. Associated mutations act as a biomarker to measure the artemisinin efficacy. In the proposed work, we have analyzed the binding affinity and efficacy between PfATP6 and artemisinin in the presence of L263D, L263E and L263K mutations. Furthermore, we performed virtual screening to identify potential compounds to inhibit the PfATP6 mutant proteins. In this study, we observed that artemisinin binding affinity with PfATP6 gets affected by L263D, L263E and L263K mutations. This in silico elucidation of artemisinin resistance enhanced the identification of novel compounds (CID: 10595058 and 10625452) which showed good binding affinity and efficacy with L263D, L263E and L263K mutant proteins in molecular docking and molecular dynamics simulations studies. Owing to the high propensity of the parasite to drug resistance the need for new antimalarial drugs will persist until the malarial parasites are eventually eradicated. The two compounds identified in this study can be tested in in vitro and in vivo experiments as possible candidates for the designing of new potential antimalarial drugs. |
Naine, S J; Devi, C S; Mohanasrinivasan, V; Doss, C G P; Kumar, D T Binding and molecular dynamic studies of sesquiterpenes (2R-acetoxymethyl-1,3,3-trimethyl-4t-(3-methyl-2-buten-1-yl)-1t-cyclohexanol) derived from marine Streptomyces sp. VITJS8 as potential anticancer agent Journal Article Applied Microbiology and Biotechnology, 100 (6), pp. 2869-2882, 2016. @article{Naine20162869, title = {Binding and molecular dynamic studies of sesquiterpenes (2R-acetoxymethyl-1,3,3-trimethyl-4t-(3-methyl-2-buten-1-yl)-1t-cyclohexanol) derived from marine Streptomyces sp. VITJS8 as potential anticancer agent}, author = {S J Naine and C S Devi and V Mohanasrinivasan and C G P Doss and D T Kumar}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959114315&doi=10.1007%2fs00253-015-7156-2&partnerID=40&md5=6a7b277134aa724bbc2f6c6c9e94dddd}, doi = {10.1007/s00253-015-7156-2}, year = {2016}, date = {2016-01-01}, journal = {Applied Microbiology and Biotechnology}, volume = {100}, number = {6}, pages = {2869-2882}, publisher = {Springer Verlag}, abstract = {The main aim of the current study is to explore the bioactive potential of Streptomyces sp. VITJS8 isolated from the marine saltern. The cultural, biochemical, and morphological studies were performed to acquire the characteristic features of the potent isolate VITJS8. The 16Sr DNA sequencing was performed to investigate the phylogenetic relationship between the Streptomyces genera. The structure of the compound was elucidated by gas chromatography-mass spectrometry (GC-MS), infra-red (IR), and ultra-violet (UV) spectroscopic data analysis. The GC-MS showed the retention time at 22.39 with a single peak indicating the purity of the active compound, and the molecular formula was established as C14H9ONCl2 based on the peak at m/z 277 [M]+. Furthermore, separated by high-performance liquid chromatography (HPLC), their retention time (tr) 2.761 was observed with the absorption maxima at 310 nm. The active compound showed effective inhibitory potential against four clinical pathogens at 500 μg/mL. The antioxidant activity was found effective at the IC50 value of 500 μg/mL with 90 % inhibition. The 3-(4,5-dimethylthiazol-2-yl)-2,5-ditetrazolium bromide (MTT) assay revealed the cytotoxicity against HepG2 cells at IC50 of 250 μg/mL. The progression of apoptosis was evidenced by morphological changes by nuclear staining. The DNA fragmentation pattern was observed at 250 μg/mL concentration. Based on flow cytometric analysis, it was evident that the compound was effective in inhibiting the sub-G0/G1 phase of cell cycle. The in vitro findings were also supported by the binding mode molecular docking studies. The active compound revealed minimum binding energy of −7.84 and showed good affinity towards the active region of topoisomerase-2α that could be considered as a suitable inhibitor. Lastly, we performed 30 ns molecular dynamic simulation analysis using GROMACS to aid in better designing of anticancer drugs. Simulation result of root mean square deviation (RMSD) analysis showed that protein-ligand complex reaches equilibration state around 10 ns that illustrates the docked complex is stable. We propose the possible mechanism of sesquiterpenes to play a significant role in antitumor cascade. Hence, our studies open up a new facet for a potent drug as an anticancer agent. © 2015, Springer-Verlag Berlin Heidelberg.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The main aim of the current study is to explore the bioactive potential of Streptomyces sp. VITJS8 isolated from the marine saltern. The cultural, biochemical, and morphological studies were performed to acquire the characteristic features of the potent isolate VITJS8. The 16Sr DNA sequencing was performed to investigate the phylogenetic relationship between the Streptomyces genera. The structure of the compound was elucidated by gas chromatography-mass spectrometry (GC-MS), infra-red (IR), and ultra-violet (UV) spectroscopic data analysis. The GC-MS showed the retention time at 22.39 with a single peak indicating the purity of the active compound, and the molecular formula was established as C14H9ONCl2 based on the peak at m/z 277 [M]+. Furthermore, separated by high-performance liquid chromatography (HPLC), their retention time (tr) 2.761 was observed with the absorption maxima at 310 nm. The active compound showed effective inhibitory potential against four clinical pathogens at 500 μg/mL. The antioxidant activity was found effective at the IC50 value of 500 μg/mL with 90 % inhibition. The 3-(4,5-dimethylthiazol-2-yl)-2,5-ditetrazolium bromide (MTT) assay revealed the cytotoxicity against HepG2 cells at IC50 of 250 μg/mL. The progression of apoptosis was evidenced by morphological changes by nuclear staining. The DNA fragmentation pattern was observed at 250 μg/mL concentration. Based on flow cytometric analysis, it was evident that the compound was effective in inhibiting the sub-G0/G1 phase of cell cycle. The in vitro findings were also supported by the binding mode molecular docking studies. The active compound revealed minimum binding energy of −7.84 and showed good affinity towards the active region of topoisomerase-2α that could be considered as a suitable inhibitor. Lastly, we performed 30 ns molecular dynamic simulation analysis using GROMACS to aid in better designing of anticancer drugs. Simulation result of root mean square deviation (RMSD) analysis showed that protein-ligand complex reaches equilibration state around 10 ns that illustrates the docked complex is stable. We propose the possible mechanism of sesquiterpenes to play a significant role in antitumor cascade. Hence, our studies open up a new facet for a potent drug as an anticancer agent. © 2015, Springer-Verlag Berlin Heidelberg. |
Sudhakar, N; Doss, George Priya C; Kumar, D; Chakraborty, C; Anand, K; Suresh, M Deciphering the impact of somatic mutations in exon 20 and exon 9 of PIK3CA gene in breast tumors among Indian women through molecular dynamics approach Journal Article Journal of Biomolecular Structure and Dynamics, 34 (1), pp. 29-41, 2016. @article{Sudhakar201629, title = {Deciphering the impact of somatic mutations in exon 20 and exon 9 of PIK3CA gene in breast tumors among Indian women through molecular dynamics approach}, author = {N Sudhakar and C George Priya Doss and D Kumar and C Chakraborty and K Anand and M Suresh}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84954368506&doi=10.1080%2f07391102.2015.1007483&partnerID=40&md5=5078a023acba763c69ad1701ce1432fd}, doi = {10.1080/07391102.2015.1007483}, year = {2016}, date = {2016-01-01}, journal = {Journal of Biomolecular Structure and Dynamics}, volume = {34}, number = {1}, pages = {29-41}, publisher = {Taylor and Francis Ltd.}, abstract = {We examined 25 breast tumor samples for somatic mutations in exon 20 and exon 9 of PIK3CA gene in South Indian population. Genomic DNA was isolated and amplified for PIK3CA gene, followed by direct sequencing of purified polymerase chain reaction products. We identified PI3K3CA mutations in 5 of 25 (20%), including four of the mutations in p.H1047R and one in p.H1047L. Nucleotide base substitution A to G (c.3140A > G) and A to T (c.3140A > T) results in p.H1047R and p.H1047L mutation in exon 20 of PIK3CA gene. We did not observe any mutation in exon 9 of PIK3CA gene. Furthermore, we investigated the effect of mutations on protein structure and function by the combination of sequence and structure-based in silico prediction methods. This determined the underlying relationship between the mutation and its phenotypic effects. Next step, we complemented by molecular dynamics simulation analysis (30 ns) of native and mutant structures that measured the effect of mutation on protein structure. The obtained results support that the application of computational methods helps predict the biological significance of mutations. © 2015 Taylor and Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We examined 25 breast tumor samples for somatic mutations in exon 20 and exon 9 of PIK3CA gene in South Indian population. Genomic DNA was isolated and amplified for PIK3CA gene, followed by direct sequencing of purified polymerase chain reaction products. We identified PI3K3CA mutations in 5 of 25 (20%), including four of the mutations in p.H1047R and one in p.H1047L. Nucleotide base substitution A to G (c.3140A > G) and A to T (c.3140A > T) results in p.H1047R and p.H1047L mutation in exon 20 of PIK3CA gene. We did not observe any mutation in exon 9 of PIK3CA gene. Furthermore, we investigated the effect of mutations on protein structure and function by the combination of sequence and structure-based in silico prediction methods. This determined the underlying relationship between the mutation and its phenotypic effects. Next step, we complemented by molecular dynamics simulation analysis (30 ns) of native and mutant structures that measured the effect of mutation on protein structure. The obtained results support that the application of computational methods helps predict the biological significance of mutations. © 2015 Taylor and Francis. |
Kumar, Thirumal D; Doss, George Priya C Investigating the inhibitory effect of Wortmannin in the hotspot mutation at codon 1047 of PIK3CA kinase domain: A molecular docking and molecular dynamics approach Book Chapter 102 , pp. 267-297, Academic Press Inc., 2016. @inbook{ThirumalKumar2016267, title = {Investigating the inhibitory effect of Wortmannin in the hotspot mutation at codon 1047 of PIK3CA kinase domain: A molecular docking and molecular dynamics approach}, author = {D Thirumal Kumar and C George Priya Doss}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84958766455&doi=10.1016%2fbs.apcsb.2015.09.008&partnerID=40&md5=227b8f059ad65ca16df56bd91e307015}, doi = {10.1016/bs.apcsb.2015.09.008}, year = {2016}, date = {2016-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {102}, pages = {267-297}, publisher = {Academic Press Inc.}, abstract = {Oncogenic mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) are the most frequently reported in association with various forms of cancer. Several studies have reported the significance of hotspot mutations in a catalytic subunit of PIK3CA in association with breast cancer. Mutations are frequently observed in the highly conserved region of the kinase domain (797-1068 amino acids) of PIK3CA are activating or gain-of-function mutations. Mutation in codon 1047 occurs in the C-terminal region of the kinase domain with histidine (H) replaced by arginine (R), lysine (L), and tyrosine (Y). Pathogenicity and protein stability predictors PhD-SNP, Align GVGD, HANSA, iStable, and MUpro classified H1047R as highly deleterious when compared to H1047L and H1047Y. To explore the inhibitory activity of Wortmannin toward PIK3CA, the three-dimensional structure of the mutant protein was determined using homology modeling followed by molecular docking and molecular dynamics analysis. Docking studies were performed for the three mutants and native with Wortmannin to measure the differences in their binding pattern. Comparative docking study revealed that H1047R-Wortmannin complex has a higher number of hydrogen bonds as well as the best binding affinity next to the native protein. Furthermore, 100 ns molecular dynamics simulation was initiated with the docked complexes to understand the various changes induced by the mutation. Though Wortmannin was found to nullify the effect of H1047R over the protein, further studies are required for designing a better compound. As SNPs are major genetic variations observed in disease condition, personalized medicine would provide enhanced drug therapy. © 2016 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Oncogenic mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) are the most frequently reported in association with various forms of cancer. Several studies have reported the significance of hotspot mutations in a catalytic subunit of PIK3CA in association with breast cancer. Mutations are frequently observed in the highly conserved region of the kinase domain (797-1068 amino acids) of PIK3CA are activating or gain-of-function mutations. Mutation in codon 1047 occurs in the C-terminal region of the kinase domain with histidine (H) replaced by arginine (R), lysine (L), and tyrosine (Y). Pathogenicity and protein stability predictors PhD-SNP, Align GVGD, HANSA, iStable, and MUpro classified H1047R as highly deleterious when compared to H1047L and H1047Y. To explore the inhibitory activity of Wortmannin toward PIK3CA, the three-dimensional structure of the mutant protein was determined using homology modeling followed by molecular docking and molecular dynamics analysis. Docking studies were performed for the three mutants and native with Wortmannin to measure the differences in their binding pattern. Comparative docking study revealed that H1047R-Wortmannin complex has a higher number of hydrogen bonds as well as the best binding affinity next to the native protein. Furthermore, 100 ns molecular dynamics simulation was initiated with the docked complexes to understand the various changes induced by the mutation. Though Wortmannin was found to nullify the effect of H1047R over the protein, further studies are required for designing a better compound. As SNPs are major genetic variations observed in disease condition, personalized medicine would provide enhanced drug therapy. © 2016 Elsevier Inc. All rights reserved. |
Hridya, H; Amrita, A; Mohan, S; Gopalakrishnan, M; Kumar, D; Doss, G P; Siva, R Functionality study of santalin as tyrosinase inhibitor: A potential depigmentation agent Journal Article International Journal of Biological Macromolecules, 86 , pp. 383-389, 2016. @article{Hridya2016383, title = {Functionality study of santalin as tyrosinase inhibitor: A potential depigmentation agent}, author = {H Hridya and A Amrita and S Mohan and M Gopalakrishnan and D Kumar and G P Doss and R Siva}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956679755&doi=10.1016%2fj.ijbiomac.2016.01.098&partnerID=40&md5=285d58baba42a6ba0e73ba28c6b988ce}, doi = {10.1016/j.ijbiomac.2016.01.098}, year = {2016}, date = {2016-01-01}, journal = {International Journal of Biological Macromolecules}, volume = {86}, pages = {383-389}, publisher = {Elsevier B.V.}, abstract = {Excessive melanin production leads to hyperpigmentation disorders which results in distressing aesthetic values. Though there are some synthetic depigmentation agents available it has been reported to possess cytotoxic and mutagenic effects. Hence there is a need for the development of safe and non toxic natural tyrosinase inhibitors. Here we report the role of santalin, the chief constituent of Pterocarpus santalinus in inhibition of tyrosinase and melanin synthesis. Santalin inhibited tyrosinase activity dose dependently. Inhibitory kinetic studies revealed mixed type of inhibition with reversible mechanism. Santalin was found to interact with the fluorophore amino acid residue of tyrosinase. Analysis of circular dichroism spectra showed the binding of santalin to tyrosinase which induced the loss of secondary helical structure. Molecular docking result suggested that santalin interact with the catalytic core of tyrosinase through strong hydrogen and hydrophobic bonding. The results of in vitro studies showed santalin inhibited melanogenesis through down regulation of MITF, tyrosinase, TRP-1 and TRP-2 without any cytotoxic effects towards B16F0 melanoma cells. Therefore, our results suggested that santalin possesses anti-tyrosinase activity, which could be utilized as a safe depigmentation agent in the cosmetic field for the treatment of hyperpigmentation disorder. © 2016 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Excessive melanin production leads to hyperpigmentation disorders which results in distressing aesthetic values. Though there are some synthetic depigmentation agents available it has been reported to possess cytotoxic and mutagenic effects. Hence there is a need for the development of safe and non toxic natural tyrosinase inhibitors. Here we report the role of santalin, the chief constituent of Pterocarpus santalinus in inhibition of tyrosinase and melanin synthesis. Santalin inhibited tyrosinase activity dose dependently. Inhibitory kinetic studies revealed mixed type of inhibition with reversible mechanism. Santalin was found to interact with the fluorophore amino acid residue of tyrosinase. Analysis of circular dichroism spectra showed the binding of santalin to tyrosinase which induced the loss of secondary helical structure. Molecular docking result suggested that santalin interact with the catalytic core of tyrosinase through strong hydrogen and hydrophobic bonding. The results of in vitro studies showed santalin inhibited melanogenesis through down regulation of MITF, tyrosinase, TRP-1 and TRP-2 without any cytotoxic effects towards B16F0 melanoma cells. Therefore, our results suggested that santalin possesses anti-tyrosinase activity, which could be utilized as a safe depigmentation agent in the cosmetic field for the treatment of hyperpigmentation disorder. © 2016 Elsevier B.V. |
Anantharaman, A; Hemachandran, H; Mohan, S; Ayyathan, Manikoth D; Kumar, D T; Doss, George Priya C; Siva, R Induction of apoptosis by apocarotenoids in B16 melanoma cells through ROS-mediated mitochondrial-dependent pathway Journal Article Journal of Functional Foods, 20 , pp. 346-357, 2016. @article{Anantharaman2016346, title = {Induction of apoptosis by apocarotenoids in B16 melanoma cells through ROS-mediated mitochondrial-dependent pathway}, author = {A Anantharaman and H Hemachandran and S Mohan and D Manikoth Ayyathan and D T Kumar and C George Priya Doss and R Siva}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84953426145&doi=10.1016%2fj.jff.2015.11.019&partnerID=40&md5=fa72aa68c72afcaffc92ade3cf64185d}, doi = {10.1016/j.jff.2015.11.019}, year = {2016}, date = {2016-01-01}, journal = {Journal of Functional Foods}, volume = {20}, pages = {346-357}, publisher = {Elsevier Ltd}, abstract = {Bixin and norbixin are natural food colourants synthesised from Bixa orellana L seeds. This study explores the mechanism of apocarotenoids (bixin and norbixin) on the aggressive B16 murine melanoma as an anti-cancer agent. The apocarotenoids inhibited the cell viability of B16 melanoma in a time- and concentration-dependent manner. Apocarotenoids markedly induced cell morphology change, nuclear condensation, DNA fragmentation, and mitochondrial dysfunction through the depletion of glutathione activity, and also induced reactive oxygen species (ROS) generation. Furthermore, apocarotenoids effectively enhanced sub-G1 population and also activated caspase 9 and caspase 3 activities. It decreased and increased the gene expression of the microphthalmia-associated transcription factor, anti-apoptotic Bcl-2 and pro-apoptotic Bax, respectively. Furthermore, molecular docking studies revealed that apocarotenoids inhibited anti-apoptotic protein (Bcl-2 and Bcl-XL) through hydrophobic interaction. These findings suggest that bixin and norbixin act as a promising chemotherapeutic agent against melanoma by inducing apoptosis through mitochondrial-associated death pathway. © 2015 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bixin and norbixin are natural food colourants synthesised from Bixa orellana L seeds. This study explores the mechanism of apocarotenoids (bixin and norbixin) on the aggressive B16 murine melanoma as an anti-cancer agent. The apocarotenoids inhibited the cell viability of B16 melanoma in a time- and concentration-dependent manner. Apocarotenoids markedly induced cell morphology change, nuclear condensation, DNA fragmentation, and mitochondrial dysfunction through the depletion of glutathione activity, and also induced reactive oxygen species (ROS) generation. Furthermore, apocarotenoids effectively enhanced sub-G1 population and also activated caspase 9 and caspase 3 activities. It decreased and increased the gene expression of the microphthalmia-associated transcription factor, anti-apoptotic Bcl-2 and pro-apoptotic Bax, respectively. Furthermore, molecular docking studies revealed that apocarotenoids inhibited anti-apoptotic protein (Bcl-2 and Bcl-XL) through hydrophobic interaction. These findings suggest that bixin and norbixin act as a promising chemotherapeutic agent against melanoma by inducing apoptosis through mitochondrial-associated death pathway. © 2015 Elsevier Ltd. |
Sujitha, S P; Kumar, D T; Doss, C G P; Aavula, K; Ramesh, R; Lakshmanan, S; Gunasekaran, S; Anilkumar, G DNA repair gene (XRCC1) polymorphism (Arg399Gln) associated with schizophrenia in South Indian Population: A genotypic and molecular dynamics study Journal Article PLoS ONE, 11 (1), 2016. @article{Sujitha2016, title = {DNA repair gene (XRCC1) polymorphism (Arg399Gln) associated with schizophrenia in South Indian Population: A genotypic and molecular dynamics study}, author = {S P Sujitha and D T Kumar and C G P Doss and K Aavula and R Ramesh and S Lakshmanan and S Gunasekaran and G Anilkumar}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959018749&doi=10.1371%2fjournal.pone.0147348&partnerID=40&md5=18709f735b274c78fe757095758610a0}, doi = {10.1371/journal.pone.0147348}, year = {2016}, date = {2016-01-01}, journal = {PLoS ONE}, volume = {11}, number = {1}, publisher = {Public Library of Science}, abstract = {This paper depicts the first report from an Indian population on the association between the variant Arg399Gln of XRCC1 locus in the DNA repair system and schizophrenia, the debilitating disease that affects 1% of the world population. Genotypic analysis of a total of 523 subjects (260 patients and 263 controls) revealed an overwhelming presence of Gln399Gln in the case subjects against the controls (P < 0.0068), indicating significant level of association of this nsSNP with schizophrenia; the Gln399 allele frequency was also perceptibly more in cases than in controls (p < 0.003; OR = 1.448). The results of the genotypic studies were further validated using pathogenicity and stability prediction analysis employing computational tools [I-Mutant Suite, iStable, PolyPhen2, SNAP, and PROVEAN], with a view toassess the magnitude of deleteriousness of the mutation. The pathogenicity analysis reveals that the nsSNP could be deleterious inasmuch as it could affect the functionality of the gene, and interfere with protein function. Molecular dynamics simulation of 60ns was performed using GROMACS to analyse structural change due to a mutation (Arg399Gln) that was never examined before. RMSD, RMSF, hydrogen bonds, radius of gyration and SASA analysis showedthe existence of asignificant difference between the native and the mutant protein. The present study gives astrong indication that the XRCC1 locus deserves serious attention, as it could be a potential candidatecontributing to the etio-pathogenesis of the disease. © 2016 Sujitha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper depicts the first report from an Indian population on the association between the variant Arg399Gln of XRCC1 locus in the DNA repair system and schizophrenia, the debilitating disease that affects 1% of the world population. Genotypic analysis of a total of 523 subjects (260 patients and 263 controls) revealed an overwhelming presence of Gln399Gln in the case subjects against the controls (P < 0.0068), indicating significant level of association of this nsSNP with schizophrenia; the Gln399 allele frequency was also perceptibly more in cases than in controls (p < 0.003; OR = 1.448). The results of the genotypic studies were further validated using pathogenicity and stability prediction analysis employing computational tools [I-Mutant Suite, iStable, PolyPhen2, SNAP, and PROVEAN], with a view toassess the magnitude of deleteriousness of the mutation. The pathogenicity analysis reveals that the nsSNP could be deleterious inasmuch as it could affect the functionality of the gene, and interfere with protein function. Molecular dynamics simulation of 60ns was performed using GROMACS to analyse structural change due to a mutation (Arg399Gln) that was never examined before. RMSD, RMSF, hydrogen bonds, radius of gyration and SASA analysis showedthe existence of asignificant difference between the native and the mutant protein. The present study gives astrong indication that the XRCC1 locus deserves serious attention, as it could be a potential candidatecontributing to the etio-pathogenesis of the disease. © 2016 Sujitha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
2015 |
Ali, S K; Doss, C G P; Kumar, D T; Zhu, H CoagVDb: A comprehensive database for coagulation factors and their associated SAPs Journal Article Biological Research, 48 , 2015. @article{Ali2015, title = {CoagVDb: A comprehensive database for coagulation factors and their associated SAPs}, author = {S K Ali and C G P Doss and D T Kumar and H Zhu}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941342109&doi=10.1186%2fs40659-015-0028-5&partnerID=40&md5=91484f6bebbe04cb9a30223e0f980690}, doi = {10.1186/s40659-015-0028-5}, year = {2015}, date = {2015-01-01}, journal = {Biological Research}, volume = {48}, publisher = {Society of Biology of Chile}, abstract = {The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure–function relationship and disease genotype–phenotype correlation. © 2015 Ali et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure–function relationship and disease genotype–phenotype correlation. © 2015 Ali et al. |
2014 |
Doss, George Priya C; Chakraborty, C; Narayan, V; Kumar, D Computational approaches and resources in single amino acid substitutions analysis toward clinical research Book Chapter 94 , pp. 365-423, Academic Press Inc., 2014. @inbook{GeorgePriyaDoss2014365, title = {Computational approaches and resources in single amino acid substitutions analysis toward clinical research}, author = {C George Priya Doss and C Chakraborty and V Narayan and D Kumar}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896290562&doi=10.1016%2fB978-0-12-800168-4.00010-X&partnerID=40&md5=4db24b9c1d181ac663667e022363bc76}, doi = {10.1016/B978-0-12-800168-4.00010-X}, year = {2014}, date = {2014-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {94}, pages = {365-423}, publisher = {Academic Press Inc.}, abstract = {Single amino acid substitutions (SAPs) belong to a class of SNPs in the coding region, which alter the protein function during the translation process. Storage of more information regarding SAPs in public databases will soon become a major hurdle in characterizing the functional SAPs. In such a demanding era, biology has to rely on bioinformatics, which can work its way through to solve the problems at hand by cutting huge amount of time and resources that are otherwise wasted. Here, we describe an overview of the existing repositories of variant databases and computational methods in predicting the effects of functional SAPs on protein stability, structure, function, drug response, and protein dynamics. This chapter will inspire many biologists with a greater promise in identifying the functional SAPs at the structural level, thereby understanding the molecular effects that are critical for personalized medicine diagnosis, prognosis, and treatment for diseases. © 2014 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Single amino acid substitutions (SAPs) belong to a class of SNPs in the coding region, which alter the protein function during the translation process. Storage of more information regarding SAPs in public databases will soon become a major hurdle in characterizing the functional SAPs. In such a demanding era, biology has to rely on bioinformatics, which can work its way through to solve the problems at hand by cutting huge amount of time and resources that are otherwise wasted. Here, we describe an overview of the existing repositories of variant databases and computational methods in predicting the effects of functional SAPs on protein stability, structure, function, drug response, and protein dynamics. This chapter will inspire many biologists with a greater promise in identifying the functional SAPs at the structural level, thereby understanding the molecular effects that are critical for personalized medicine diagnosis, prognosis, and treatment for diseases. © 2014 Elsevier Inc. |
Doss, George Priya C; Chakraborty, C; Abishek, Monford Paul N; Kumar, D; Narayanan, V Application of evolutionary based in silico methods to predict the impact of single amino acid substitutions in vitelliform macular dystrophy Book Chapter 94 , pp. 177-267, Academic Press Inc., 2014. @inbook{GeorgePriyaDoss2014177, title = {Application of evolutionary based in silico methods to predict the impact of single amino acid substitutions in vitelliform macular dystrophy}, author = {C George Priya Doss and C Chakraborty and N Monford Paul Abishek and D Kumar and V Narayanan}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896258307&doi=10.1016%2fB978-0-12-800168-4.00006-8&partnerID=40&md5=6d7e00c9cc15fe6eb79dc17f8cea9386}, doi = {10.1016/B978-0-12-800168-4.00006-8}, year = {2014}, date = {2014-01-01}, journal = {Advances in Protein Chemistry and Structural Biology}, volume = {94}, pages = {177-267}, publisher = {Academic Press Inc.}, abstract = {Recent developments in high-throughput discovery and genotyping have generated a tremendous amount of information about the existence of single amino acid polymorphisms (SAPs). Detailed understanding of the SAPs that affect protein structure and function can provide us valuable insight into disease genotype-phenotype correlations. Functional variants of biological importance are likely to be missed in large-scale analysis. Over the past decade, numerous efforts are underway in understanding and characterizing the potential consequences of variants in assessing the risk associated with vitelliform macular dystrophy (VMD). Yet, in spite of this success, we conducted a first SAP analysis via evolutionary-based in silico pipeline to unravel functional SAPs from a pool, containing both functional and neutral ones. Furthermore, based on the prediction scores, a ranking system was developed to prioritize the functional SAPs in order to minimize the number of SAPs screened for further genotyping. © 2014 Elsevier Inc.}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } Recent developments in high-throughput discovery and genotyping have generated a tremendous amount of information about the existence of single amino acid polymorphisms (SAPs). Detailed understanding of the SAPs that affect protein structure and function can provide us valuable insight into disease genotype-phenotype correlations. Functional variants of biological importance are likely to be missed in large-scale analysis. Over the past decade, numerous efforts are underway in understanding and characterizing the potential consequences of variants in assessing the risk associated with vitelliform macular dystrophy (VMD). Yet, in spite of this success, we conducted a first SAP analysis via evolutionary-based in silico pipeline to unravel functional SAPs from a pool, containing both functional and neutral ones. Furthermore, based on the prediction scores, a ranking system was developed to prioritize the functional SAPs in order to minimize the number of SAPs screened for further genotyping. © 2014 Elsevier Inc. |
