Structure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme

References

• Anderson, H. C. (1983). Rattle: A velocity version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52, 24–34.
   Web of Science ®Google Scholar
• Andres, C. J., Bronson, J. J., D., Andrea, S. V., Deshpande, M. S., Falk, P. J., Grant-Young, K. A., Harte, W. E., … Stock, D. (2000). 4-Thiazolidinones: Novel inhibitors of the bacterial enzyme MurB. Bioorganic & Medicinal Chemistry Letters, 10(8), 715–717. doi:10.1016/S0960-894X(00)00073-1
   PubMed Web of Science ®Google Scholar
• Arora, R., Issar, U., & Kakkar, R. (2018). Identification of novel urease inhibitors: Pharmacophore modeling, virtual screening and molecular docking studies. Journal of Biomolecular Structure and Dynamics, 37(16), 4312–4326.
   PubMed Web of Science ®Google Scholar
• Benson, T. E., Harris, M. S., Choi, G. H., Cialdella, J. I., Herberg, J. T., Martin, J. P., & Baldwin, E. T. (2001). A structural variation for MurB: X-ray crystal structure of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB). Biochemistry, 40(8), 2340–2350. doi:10.1021/bi002162d
   PubMed Web of Science ®Google Scholar
• Benson, T. E., Walsh, C. T., & Hogle, J. M. (1997). X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-Å resolution. Biochemistry, 36(4), 806–811. doi:10.1021/bi962221g
   PubMed Web of Science ®Google Scholar
• Bronson, J. J., Den Bleyker, K. L., Falk, P. J., Mate, R. A., Ho, H. T., Pucci, M. J., & Snyder, L. B. (2003). Discovery of the first antibacterial small molecule inhibitors of MurB. Bioorganic & Medicinal Chemistry Letters, 13(5), 873–875. doi:10.1016/S0960-894X(02)01076-4
   PubMed Web of Science ®Google Scholar
• Chen, M. W., Lohkamp, B., Schnell, R., Lescar, J., & Schneider, G. (2013). Substrate channel flexibility in Pseudomonas aeruginosa MurB accommodates two distinct substrates. PloS One, 8(6), e66936. doi:10.1371/journal.pone.0066936
   PubMed Web of Science ®Google Scholar
• Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(1), 71–80. doi:10.1186/1741-7007-9-71
   PubMed Web of Science ®Google Scholar
• El Zoeiby, A., Sanschagrin, F., & Levesque, R. C. (2003). Structure and function of the Mur enzymes: Development of novel inhibitors. Molecular Microbiology, 47(1), 1–12. doi:10.1046/j.1365-2958.2003.03289.x
   PubMed Web of Science ®Google Scholar
• Eniyan, K., Dharavath, S., Vijayan, R., Bajpai, U., & Gourinath, S. (2018). Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1866(3), 397–406. doi:10.1016/j.bbapap.2017.11.013
   PubMed Web of Science ®Google Scholar
• Foster, S. J., & Popham, D. L. (2002). Structure and synthesis of cell wall, spore cortex, teichoic acids, S-layers, and capsules. In Bacillus subtilis and its closest relatives (pp. 21–41). Washington, DC: American Society of Microbiology.
   Google Scholar
• Ghosh, S., Nie, A., An, J., & Huang, Z. (2006). Structure-based virtual screening of chemical libraries for drug discovery. Current Opinion in Chemical Biology, 10(3), 194–202. doi:10.1016/j.cbpa.2006.04.002
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Duffy, E. M. (2000). Prediction of drug solubility from Monte Carlo simulations. Bioorganic & Medicinal Chemistry Letters, 10(11), 1155–1158. doi:10.1016/s0960-894x(00)00172-4
   PubMed Web of Science ®Google Scholar
• Kakkar, R. (2011). Structure-based design of PDHK2 inhibitors from docking studies. International Journal of Pharmaceutics, 1, 50–58.
   Google Scholar
• Kishida, H., Unzai, S., Roper, D. I., Lloyd, A., Park, S. Y., & Tame, J. R. (2006). Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Biochemistry, 45(3), 783–792.
   PubMed Web of Science ®Google Scholar
• Kumari, T., Issar, U., & Kakkar, R. (2014). Docking modes of BB-3497 into the PDF active site-a comparison of the pure MM and QM/MM based docking strategies . Current Computer-Aided Drug Design, 10(4), 315–326. doi:10.2174/157340991004150518145522
   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
• Lyne, P. D. (2002). Structure-based virtual screening: An overview. Drug Discovery Today, 7(20), 1047–1055. doi:10.1016/S1359-6446(02)02483-2
   PubMed Web of Science ®Google Scholar
• Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. doi:10.1021/jm060522a
   PubMed Web of Science ®Google Scholar
• Mansour, T. S., Caufield, C. E., Rasmussen, B., Chopra, R., Krishnamurthy, G., Morris, K. M., … Antane, S. (2007). Naphthyl tetronic acids as multi‐target inhibitors of bacterial peptidoglycan biosynthesis. ChemMedChem, 2(10), 1414–1417. doi:10.1002/cmdc.200700094
   PubMed Web of Science ®Google Scholar
• Mishra, H., Singh, N., Lahiri, T., & Misra, K. (2009). A comparative study on the molecular descriptors for predicting drug-likeness of small molecules. Bioinformation, 3(9), 384–388. doi:10.6026/97320630003384
   PubMedGoogle Scholar
• Rao, S., Sanschagrin, P. C., Greenwood, J. R., Repasky, M. P., Sherman, W., & Farid, R. (2008). Improving database enrichment through ensemble docking. Journal of Computer-Aided Molecular Design, 22(9), 621–627. doi:10.1007/s10822-008-9182-y
   PubMed Web of Science ®Google Scholar
• Rastelli, G., Rio, A. D., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA. Journal of Computational Chemistry, 31(4), 797–810. doi:10.1002/jcc.21372
   PubMed Web of Science ®Google Scholar
• Sherman, W., Beard, H. S., & Farid, R. (2006). Use of an induced fit receptor structure in virtual screening. Chemical Biology & Drug Design, 67(1), 83–84. doi:10.1111/j.1747-0285.2005.00327.x
   PubMed Web of Science ®Google Scholar
• Sinko, W., Lindert, S., & McCammon, J. A. (2013). Accounting for receptor flexibility and enhanced sampling methods in computer‐aided drug design. Chemical Biology & Drug Design, 81(1), 41–49. doi:10.1111/cbdd.12051
   PubMed Web of Science ®Google Scholar
• Swope, W. C., Andersen, H. C., Berens, P. H., & Wilson, K. R. (1982). A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters. Journal of Chemical Physics, 76(1), 637–649. doi:10.1063/1.442716
   Web of Science ®Google Scholar
• Yang, J. M., Chen, Y. F., Shen, T. W., Kristal, B. S., & Hsu, D. F. (2005). Consensus scoring criteria for improving enrichment in virtual screening. Journal of Chemical Information and Modeling, 45(4), 1134–1146. doi:10.1021/ci050034w
   PubMed Web of Science ®Google Scholar
• Yang, Y., Severin, A., Chopra, R., Krishnamurthy, G., Singh, G., Hu, W., … Shlaes, D. M. (2006). 3,5-dioxopyrazolidines, novel inhibitors of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) with activity against gram-positive bacteria. Antimicrobial Agents and Chemotherapy, 50(2), 556–564. doi:10.1128/AAC.50.2.556-564.2006
   PubMed Web of Science ®Google Scholar