Potential target identification for breast cancer and screening of small molecule inhibitors: A bioinformatics approach

References

• Agarwal, S., Verma, E., Kumar, V., Lall, N., Sau, S., Iyer, A. K., & Kashaw, S. K. (2018). An integrated computational approach of molecular dynamics simulations, receptor binding studies and pharmacophore mapping analysis in search of potent inhibitors against tuberculosis. Journal of Molecular Graphics and Modelling, 83, 17–32. DOI:. doi:10.1016/j.jmgm.2018.04.019
   PubMed Web of Science ®Google Scholar
• Alanis-Lobato, G., Andrade-Navarro, M. A., & Schaefer, M. H. (2017). HIPPIE v2. 0: Enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Research, 45(D1), D408–D414. doi:10.1093/nar/gkw985
   PubMed Web of Science ®Google Scholar
• Allen, M. P. (2004). Introduction to molecular dynamics simulation. Computational Soft Matter: From Synthetic Polymers to Proteins, 23, 1–28.
   Google Scholar
• Bosshard, H. R., Marti, D. N., & Jelesarov, I. (2004). Protein stabilization by salt bridges: Concepts, experimental approaches and clarification of some misunderstandings. Journal of Molecular Recognition, 17(1), 1–16. doi:10.1002/jmr.657
   PubMed Web of Science ®Google Scholar
• Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., & Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, 68(6), 394–424. doi:10.3322/caac.21492
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. doi:10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Dahm, G. M., Gubin, M. M., Magee, J. D., Techasintana, P., Calaluce, R., & Atasoy, U. (2012). Method for the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts using RIP-Chip. Journal of Visualized Experiments: JoVE, (67), 1–6. doi:10.1038/nprot.2006.47
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N-log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. DOI:. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• DeSantis, C. E., Ma, J., Goding Sauer, A., Newman, L. A., & Jemal, A. (2017). Breast cancer statistics, 2017, racial disparity in mortality by state. CA: A Cancer Journal for Clinicians, 67, 439–448. doi:10.3322/caac.21412
   PubMed Web of Science ®Google Scholar
• Gao, Y., Wang, H., Wang, J., & Cheng, M. (2019). In silico studies on p21-activated kinase 4 inhibitors: Comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations, and MM-GBSA calculation. Journal of Biomolecular Structure and Dynamics, 1–15. DOI:. doi:10.1080/07391102.2019.1673823
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. doi:10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gu, X., Wang, Y., Wang, M., Wang, J., & Li, N. (2019). Computational investigation of imidazopyridine analogs as Protein kinase B (Akt1) allosteric inhibitors by using 3D-QSAR, molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 1–20. doi:10.1080/07391102.2019.1705185
   Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. DOI:. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• John, A., Sivashanmugam, M., Umashankar, V., & Natarajan, S. K. (2017). Virtual screening, molecular dynamics, and binding free energy calculations on human carbonic anhydrase IX catalytic domain for deciphering potential leads. Journal of Biomolecular Structure and Dynamics, 35(10), 2155–2168. DOI:. doi:10.1080/07391102.2016.1207565
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. DOI:. doi:10.1063/1.445869
   Web of Science ®Google Scholar
• Kapetanovic, I. M. (2008). Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chemico-Biological Interactions, 171(2), 165–176. doi:10.1016/j.cbi.2006.12.006
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9, 646. doi:10.1038/nsb0902-646
   PubMedGoogle Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. doi:10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Koschtzki, D., & Schreiber, F. (2008). Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regulation and Systems Biology, 2, GRSB.S702 doi:10.4137/GRSB.S702
   Google Scholar
• Li, D.-Q., Nair, S. S., Ohshiro, K., Kumar, A., Nair, V. S., Pakala, S. B., Reddy, S. D. N., Gajula, R. P., Eswaran, J., Aravind, L., Kumar, R. (2012). MORC2 signaling integrates phosphorylation-dependent, ATPase-coupled chromatin remodeling during the DNA damage response. Cell Reports, 2(6), 1657–1669. doi:10.1016/j.celrep.2012.11.018
   PubMed Web of Science ®Google Scholar
• Li, X., O’Brien, C. P., Collier, G., Vellore, N. A., Wang, F., Latour, R. A., Bruce, D. A., Stuart, S. J. (2007). An improved replica-exchange sampling method: Temperature intervals with global energy reassignment. The Journal of Chemical Physics, 127(16), 164116. doi:10.1063/1.2780152
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. doi:10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Lu, H., Lei, M., & Schulze-Gahmen, U. Crystal Structure of the Complex Between Human Pak1-kinase and 3-Hydroxystaurosporine.
   Google Scholar
• Lybrand, T. P. (1995). Ligand-protein docking and rational drug design. Current Opinion in Structural Biology, 5(2), 224–228. DOI:. doi:10.1016/0959-440X(95)80080-8
   PubMed Web of Science ®Google Scholar
• Malvia, S., Bagadi, S. A., Dubey, U. S., & Saxena, S. (2017). Epidemiology of breast cancer in Indian women. Asia-Pacific Journal of Clinical Oncology, 13(4), 289–295. doi:10.1111/ajco.12661
   PubMed Web of Science ®Google Scholar
• Nair, M. S., & Shukla, A. (2019). Molecular modeling, simulation and principal component analysis of binding of resveratrol and its analogues with DNA. Journal of Biomolecular Structure and Dynamics, 1–11. DOI:. doi:10.1080/07391102.2019.1662849
   PubMed Web of Science ®Google Scholar
• Ozgur, A., Vu, T., Erkan, G., & Radev, D. R. (2008). Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics, 24(13), i277–i285. doi:10.1093/bioinformatics/btn182
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. doi:10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Piro, R. M., & Di Cunto, F. (2012). Computational approaches to disease gene prediction: Rationale, classification and successes. FEBS Journal, 279(5), 678–696. doi:10.1111/j.1742-4658.2012.08471.x
   PubMed Web of Science ®Google Scholar
• Redelman-Sidi, G., Iyer, G., Solit, D. B., & Glickman, M. S. (2013). Oncogenic activation of Pak1-dependent pathway of macropinocytosis determines BCG entry into bladder cancer cells. Cancer Research, 73(3), 1156–1167. doi:10.1158/0008-5472.CAN-12-1882
   PubMed Web of Science ®Google Scholar
• Reva, B. A., Finkelstein, A. V., & Skolnick, J. (1998). What is the probability of a chance prediction of a protein structure with an rmsd of 6 Ã¥? Folding and Design, 3(2), 141–147. doi:10.1016/S1359-0278(98)00019-4
   PubMedGoogle Scholar
• Roe, D. R., & Cheatham, III, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. doi:10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2020-1: Canvas, Schrödinger, LLC, New York, NY, 2020.
   Google Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. doi:10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Shukla, A., Tyagi, R., Meena, S., Datta, D., Srivastava, S. K., & Khan, F. (2020). 2D-and 3D-QSAR modelling, molecular docking and in vitro evaluation studies on 18Î2-glycyrrhetinic acid derivatives against triple-negative breast cancer cell line. Journal of Biomolecular Structure and Dynamics, 38(1), 168–185. doi:10.1080/07391102.2019.1570868
   PubMed Web of Science ®Google Scholar
• Siddani, B. R., Pochineni, L. P., & Palanisamy, M. (2013). Candidate gene identification for systemic lupus erythematosus using network centrality measures and gene ontology. PLoS One, 8(12), e81766. doi:10.1371/journal.pone.0081766
   PubMed Web of Science ®Google Scholar
• Simossis, V. A., & Heringa, J. (2005). PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Research, 33(Web Server), W289–W294. doi:10.1093/nar/gki390
   PubMed Web of Science ®Google Scholar
• Sivakumar, M., Saravanan, K., Saravanan, V., Sugarthi, S., Kumar, S. M., Alhaji Isa, M., Rajakumar, P., Aravindhan, S. (2019). Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics. Journal of Biomolecular Structure and Dynamics, 1–15. DOI:. doi:10.1080/07391102.2019.1620128
   PubMed Web of Science ®Google Scholar
• Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. doi:10.1124/pr.112.007336
   PubMed Web of Science ®Google Scholar
• Stitou, M., Toufik, H., Bouachrine, M., & Lamchouri, F. (2019). Quantitative structure-activity relationships analysis, homology modeling, docking and molecular dynamics studies of triterpenoid saponins as Kirsten rat sarcoma inhibitors. Journal of Biomolecular Structure and Dynamics, 1–19. doi:10.1080/07391102.2019.1707122
   Web of Science ®Google Scholar
• Tang, Z., Li, C., Kang, B., Gao, G., Li, C., & Zhang, Z. (2017). GEPIA: A web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Research, 45(W1), W98–W102. doi:10.1093/nar/gkx247
   PubMed Web of Science ®Google Scholar
• Thomson, D. W., Bracken, C. P., & Goodall, G. J. (2011). Experimental strategies for microRNA target identification. Nucleic Acids Research, 39(16), 6845–6853. doi:10.1093/nar/gkr330
   PubMed Web of Science ®Google Scholar
• Turkey, C., Demir, Y., & Beydemir, C. (2020). Calcium channel blockers: Molecular docking and inhibition studies on carbonic anhydrase I and II isoenzymes. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2020.1736631
   Web of Science ®Google Scholar
• UniProt, C. (2009). The universal protein resource (UniProt) in 2010. Nucleic Acids Research, 38, D142–D148. doi:10.1093/nar/gkp846
   PubMed Web of Science ®Google Scholar
• Wang, G., Zhang, Q., Song, Y., Wang, X., Guo, Q., Zhang, J. … (2015). PAK1 regulates RUFY3-mediated gastric cancer cell migration and invasion. Cell Death & Disease, 6, e1682. doi:10.1038/cddis.2015.50
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Yang, L., Song, G., & Jernigan, R. L. (2009). Comparisons of experimental and computed protein anisotropic temperature factors. Proteins: Structure, Function, and Bioinformatics, 76(1), 164–175. doi:10.1002/prot.22328
   PubMed Web of Science ®Google Scholar
• Zhang, X., Yan, J., Wang, H., Wang, Y., Wang, J., & Zhao, D. (2019). Molecular docking, 3D-QSAR, and molecular dynamics simulations of thieno [3,2-b] pyrrole derivatives against anticancer targets of KDM1A/LSD1. Journal of Biomolecular Structure and Dynamics, 1–24. doi:10.1080/07391102.2020.1726819
   Web of Science ®Google Scholar