Design, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents

References

• Accelrys Software Inc. (2012). Discovery studio 3.5 client. Accelrys Inc.
   Google Scholar
• Advanced Chemistry Development Inc. (2001). ACD/ChemSketch.
   Google Scholar
• Afriza, D., Suriyah, W. H., & Ichwan, S. J. A. (2018). In silico analysis of molecular interactions between the anti-apoptotic protein survivin and dentatin, nordentatin, and quercetin. Journal of Physics: Conference Series, 1073(3), 032001. https://doi.org/10.1088/1742-6596/1073/3/03200.)
   Google Scholar
• Aggarwal, A., Parai, M. K., Shetty, N., Wallis, D., Woolhiser, L., Hastings, C., Dutta, N. K., Galaviz, S., Dhakal, R. C., Shrestha, R., Wakabayashi, S., Walpole, C., Matthews, D., Floyd, D., Scullion, P., Riley, J., Epemolu, O., Norval, S., Snavely, T., … Sacchettini, J. C. (2017). Development of a novel lead that targets m. tuberculosis polyketide synthase 13. Cell, 170(2), 249–259.e25. https://doi.org/10.1016/j.cell.2017.06.025
   PubMed Web of Science ®Google Scholar
• Ahn, S., Lee, M., An, S., Hyun, S., Hwang, J., Lee, J., & Noh, M. (2018). 2-Formyl-komarovicine promotes adiponectin production in human mesenchymal stem cells through PPARγ partial agonism. Bioorganic & Medicinal Chemistry, 26(5), 1069–1075. https://doi.org/10.1016/j.bmc.2018.01.019
   PubMed Web of Science ®Google Scholar
• Akinpelu, O. I., Lawal, M. M., Kumalo, H. M., & Mhlongo, N. N. (2020a). Computational studies of the properties and activities of selected trisubstituted benzimidazoles as potential antitubercular drugs inhibiting MTB-FtsZ polymerization. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1830176
   Google Scholar
• Akinpelu, I. O., Monsurat, M. L., Hezekiel, M. K., & Ndumiso, N. M. (2020b). Drug repurposing: Fusidic acid as a potential inhibitor of M. tuberculosis FtsZ polymerization – Insight from DFT calculations, molecular docking and molecular dynamics simulations. Tuberculosis (Edinburgh, Scotland), 121, 101920. https://doi.org/10.1016/j.tube.2020.101920
   PubMed Web of Science ®Google Scholar
• Akpa, S. J., Say, M. V., Zoakouma, R. S. P., Fanté, B., Sissouma, D., & Adjou, A. (2016). Synthesis of 2-(benzylthio)benzimidazole, 2-[(benzimidazol-2-yl)methylthio]benzimidazole and structural analogues against Haemoncus contortus, Afr. Journal of Pharmacy and Pharmacology., 10, 670–680. https://doi.org/10.5897/AJPP2016.4557
   Google Scholar
• Alderwick, L. J., Lloyd, G. S., Ghadbane, H., May, J. W., Bhatt, A., Eggeling, L., Fütterer, K., & Besra, G. S. (2011). The C-terminal domain of the arabinosyltransferase mycobacterium tuberculosis EmbC is a lectin-like carbohydrate binding module. PLoS Pathogens, 7(2), e1001299. https://doi.org/10.1371/journal.ppat.1001299
   PubMed Web of Science ®Google Scholar
• Anandakrishnan, R., Drozdetski, A., Walker, R. C., & Onufriev, A. V. (2015). Speed of conformational change: Comparing explicit and implicit solvent molecular dynamics simulations. Biophysical Journal, 108(5), 1153–1164. https://doi.org/10.1016/j.bpj.2014.12.047
   PubMed Web of Science ®Google Scholar
• Ansari, S. A., Jafri, M. A., Satar, R., Ahmad, S. I., & Chibber, S. (2018). Molecular docking as a computational tool for analyzing product mediated inhibition for β-galactosidase immobilized on glutaraldehyde modified matrices. Oriental Journal of Chemistry, 34(2), 820–824. https://doi.org/10.13005/ojc/340227
   Web of Science ®Google Scholar
• Ayaz, F., Ersan, R. H., Kuzu, B., & Algul, O. (2020). New-generation benzimidazole-based plasmid delivery reagents with high transfection efficiencies on the mammalian cells. In Vitro Cellular & Developmental Biology. Animal, 56(1), 34–41. https://doi.org/10.1007/s11626-019-00418-4
   PubMed Web of Science ®Google Scholar
• Bai, Q., Shao, Y., Pan, D., Zhang, Y., Liu, H., & Yao, X. (2014). Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations. PLoS One, 9(9), e107837. https://doi.org/10.1371/journal.pone.0107837
   PubMed Web of Science ®Google Scholar
• Batt, S. M., Jabeen, T., Bhowruth, V., Quill, L., Lund, P. A., Eggeling, L., Alderwick, L. J., Fütterer, K., & Besra, G. S. (2012). Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 109(28), 11354–11359. https://doi.org/10.1073/pnas.1205735109
   PubMed Web of Science ®Google Scholar
• Boggu, P. R., Venkateswararao, E., Manickam, M., Kwak, D., Kim, Y., & Jung, S. (2016). Exploration of 2-benzylbenzimidazole scaffold as novel inhibitor of NF-κB. Bioorganic & Medicinal Chemistry, 24(8), 1872–1878. https://doi.org/10.1016/j.bmc.2016.03.012
   PubMed Web of Science ®Google Scholar
• Burmaoglu, S., Algul, O., Gobek, A., Aktas Anil, D., Ulger, M., Erturk, B. G., Kaplan, E., Dogen, A., & Aslan, G. (2017). Design of potent fluoro-substituted chalcones as antimicrobial agents. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 490–495. https://doi.org/10.1080/14756366.2016.1265517
   PubMed Web of Science ®Google Scholar
• Carugo, O., & Pongor, S. (2001). A Normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science: A Publication of the Protein Society, 10(7), 1470–1473. doi: 10.1110/ps.690101.).
   PubMed Web of Science ®Google Scholar
• Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham, T. E., Darden, T. A., Duke, R. E., Gohlke, H., Goetz, A. W., Gusarov, S., Homeyer, N., Janowski, P., Kaus, J., Kolossváry, I., Kovalenko, A., Lee, T. S., LeGrand, S. … Kollman, P. A. (2014). AMBER 14. University of California.
   Google Scholar
• Clinical and Laboratory Standards Institute (CLSI) (formerly NCCLS). (2002). Antimycobacterial susceptibility testing for M. tuberculosis: Tentative standard NCCLS document M24-T, Villanova, Pennsylvania.
   Google Scholar
• Djemoui, A., Naouri, A., Ouahrani, M. R., Djemoui, D., Lahcene, S., Lahrech, M. B., Boukenna, L., Albuquerque, H. M. T., Saher, L., Rocha, D. H. A., Monteiro, F. L., Helguero, L. A., Bachari, K., Talhi, O., & Silva, A. M. S. (2020). A step-by-step synthesis of triazole-benzimidazole-chalcone hybrids: Anticancer activity in human cells+. Journal of Molecular Structure., 1204, 127487. https://doi.org/10.1016/j.molstruc.2019.127487
   Web of Science ®Google Scholar
• Duran, G. G., Küçük, M. U., Algül, Ö., & Terzi, M. Y. (2020). Investigation of new benzimidazole derivative compounds' effects on A549 cell line. Brazilian Archives of Biology and Technology, 63, e20190364. https://doi.org/10.1590/1678-4324-2020190364
   Google Scholar
• Ersan, R. H., Alagoz, M. A., Ertan-Bolelli, T., Duran, N., Burmaoglu, S., & Algul, O. (2020). Head-to-head bisbenzazole derivatives as antiproliferative agents: Design, synthesis, in vitro activity, and SAR analysis. Mol. Divers. 25(4), 2247–2259. https://doi.org/10.1007/s11030-020-10115-0
   PubMed Web of Science ®Google Scholar
• Ersan, R. H., Yuksel, A., Ertan-Bolelli, T., Dogen, A., Burmaoglu, S., & Algul, O. (2021). One‐pot synthesis of novel benzimidazoles with a naphthalene moiety as antimicrobial agents and molecular docking studies. Journal of the Chinese Chemical Society, 68(2), 374–383. https://doi.org/10.1002/jccs.202000125
   Web of Science ®Google Scholar
• Foo, C. S., Lechartier, B., Kolly, G. S., Boy-Röttger, S., Neres, J., Rybniker, J., Lupien, A., Sala, C., Piton, J., & Cole, S. T. (2016). Characterization of DprE1-mediated benzothiazinone resistance in mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 60(11), 6451–6459. https://doi.org/10.1128/AAC.01523-16
   PubMed Web of Science ®Google Scholar
• Gawad, J., & Bonde, C. (2018). Decaprenyl-phosphoryl-ribose 2'-epimerase (DprE1): Challenging target for antitubercular drug discovery. Chemistry Central Journal, 12(1), 72. https://doi.org/10.1186/s13065-018-0441-2
   PubMedGoogle Scholar
• Genheden, S., Luchko, T., Gusarov, S., Kovalenko, A., & Ryde, U. (2010). An MM/3D-RISM Approach for Ligand Binding Affinities. The Journal of Physical Chemistry. B, 114(25), 8505–8516. https://doi.org/10.1021/jp101461s
   PubMed Web of Science ®Google Scholar
• Götz, A. W., Williamson, M. J., Xu, D., Poole, D., Le Grand, S., & Walker, R. C. (2012). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. Journal of Chemical Theory and Computation, 8(5), 1542–1555. https://doi.org/10.1021/ct200909j
   PubMed Web of Science ®Google Scholar
• Gozelle, M., Süloğlu, A. K., Selmanoğlu, G., Ramazanoğlu, N., Açık, L., & Gümüş, F. (2019). Studies on the synthesis, characterization, cytotoxic activities and plasmid DNA binding of platinum(II) complexes having 2-subsituted benzimidazole ligands. Polyhedron, 161, 298–308. https://doi.org/10.1016/j.poly.2019.01.028
   Web of Science ®Google Scholar
• Grundner, C., Perrin, D., van Huijsduijnen, R. H., Swinnen, D., Gonzalez, J., Gee, C. L., Wells, T. N., & Alber, T. (2007). Structural basis for selective inhibition of mycobacterium tuberculosis protein tyrosine phosphatase PtpB. Structure (London, England : 1993), 15(4), 499–509. https://doi.org/10.1016/j.str.2007.03.003
   PubMed Web of Science ®Google Scholar
• Gümüs, F., Altuntas, T. G., Saygun, N., Ozden, T., & Ozden, S. (1989). In vitro tuberculostatic activities of some 2-benzylbenzimidazole and 2-phenoxymethylbenzimidazole derivatives. Journal de Pharmacie de Belgique, 44(6), 398–402.
   PubMed Web of Science ®Google Scholar
• Hall, L., Jude, K. P., Clark, S. L., & Wengenack, N. L. (2011). Antimicrobial susceptibility testing of Mycobacterium tuberculosis complex for first and second line drugs by broth dilution in a microtiter plate format. Journal of Visualized Experiments, 52, 3094. https://doi.org/10.3791/3094
   Google Scholar
• Harding, E. (2020). WHO global progress report on tuberculosis elimination. The Lancet Respiratory Medicine, 8(1), 19. https://doi.org/10.1016/S2213-2600(19)30418-7
   PubMed Web of Science ®Google Scholar
• https://www.who.int/publications/i/item/global-tuberculosis-report-2019.
   Google Scholar
• Kopel, P., Wawrzak, D., Langer, V., Cihalova, K., Chudobova, D., Vesely, R., Adam, V., & Kizek, R. (2015). Biological activity and molecular structures of bis(benzimidazole) and trithiocyanurate complexes. Molecules (Basel, Switzerland), 20(6), 10360–10376. https://doi.org/10.3390/molecules200610360
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Leung, A. K. W., White, E. L., Ross, L. J., Reynolds, R. C., Devito, J. A., & Borhani, D. W. (2004). Structure of mycobacterium tuberculosis FtsZ reveals unexpected, G protein-like conformational switches. Journal of Molecular Biology, 342(3), 953–970. https://doi.org/10.1016/j.jmb.2004.07.061
   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. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Mahajan, P., Wadhwa, B., Barik, M. R., Malik, F., & Nargotra, A. (2020). Combining ligand- and structure-based in silico methods for the identification of natural product-based inhibitors of Akt1 . Molecular Diversity, 24(1), 45–60. https://doi.org/10.1007/s11030-019-09924-9
   PubMed Web of Science ®Google Scholar
• Maharaj, Y., Bhakat, S., & Soliman, M. (2015). Computer-aided identification of novel DprE1 inhibitors as potential anti-TB lead compounds: A hybrid virtual-screening and molecular dynamics approach. Letters in Drug Design & Discovery, 12(4), 302–313. https://doi.org/10.2174/1570180811666141001005536
   Web of Science ®Google Scholar
• Maia, M. S., de Sousa, N. F., Rodrigues, G. C. S., Monteiro, A. F. M., Scotti, M. T., & Scotti, L. (2020). Lignans and neolignans anti-tuberculosis identified by QSAR and molecular modeling. Combinatorial Chemistry & High Throughput Screening, 23(6), 504–516. https://doi.org/10.2174/1386207323666200226094940
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Makarov, V., Manina, G., Mikusova, K., Möllmann, U., Ryabova, O., Saint-Joanis, B., Dhar, N., Pasca, M. R., Buroni, S., Lucarelli, A. P., Milano, A., De Rossi, E., Belanova, M., Bobovska, A., Dianiskova, P., Kordulakova, J., Sala, C., Fullam, E., Schneider, P., … Cole, S. T. (2009). Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis. Science (New York, N.Y.), 324(5928), 801–804. https://doi.org/10.1126/science.1171583
   PubMed Web of Science ®Google Scholar
• Manjunatha, M. R., Randa, S., Manoranjan, P., Clair, S., Anisha, A., Vijender, P., Naveen, K., Jyothi , M., Sreenivasaiah, M., Narayan, A., Supreeth, G., Sreevalli, S., Vasan, K. S., Vasanthi, R., Meenakshi, M., Cooper, C., Khisi, M., Scott, B., Ruben, T., … Shirude, P. S. (2019). Scaffold morphing to identify novel DprE1 inhibitors with antimycobacterial activity. ACS Medicinal Chemistry Letters, 10(10), 1480–1485. https://doi.org/10.1021/acsmedchemlett.9b00343
   PubMed Web of Science ®Google Scholar
• National Committee for Clinical Laboratory Standards. (2003). Susceptibility testing of mycobacteria, nocardia, and other aerobic actinomycetes: Approved standard NCCLS document M24-A, Wayne, Pennsylvania.
   Google Scholar
• Neres, J., & Cole, S. T. (2016). Non-mutagenic nitrobenzothiazoles as novel anti-tubercular agents: A balance between potency and electron affinity. https://doi.org/10.2210/pdb4p8h/pdb
   Google Scholar
• Nguyen, N. T., Nguyen, T. H., Han Pham, T. N., Huy, N. T., Bay, M. V., Pham, M. Q., Nam, P. C., Vu, V. V., & Ngo, S. T. (2020). Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity. Journal of Chemical Information and Modeling, 60(1), 204–211. doi: 10.1021/acs.jcim.9b00778.).
   PubMed Web of Science ®Google Scholar
• Niknam, K., & Fatehi-Raviz, A. (2007). Synthesis of 2-substituted benzimidazoles and bis-benzimidazoles by microwave in the presence of alumina-methanesulfonic acid. Journal of the Iranian Chemical Society, 4(4), 438–443. https://doi.org/10.1007/BF03247230
   Web of Science ®Google Scholar
• Nisha, D., Kumar Jena, P., & Kumar Pradhan, S. (2020). Arabinosyltransferase C enzyme of mycobacterium tuberculosis, a potential drug target: An insight from molecular docking study. Heliyon, 6(2), e02693. doi: 10.1016/j.heliyon.2019.e02693.)
   PubMed Web of Science ®Google Scholar
• Oren, I., Temiz, O., Yalcin, I., Sener, E., Akin, A., & Uçartürk, N. (1997). Synthesis and microbiological activity of 5 (or 6)-methyl-2-substituted benzoxazole and benzimidazole derivatives. Arzneimittel-Forschung, 47(12), 1393–1397.
   PubMed Web of Science ®Google Scholar
• Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: A review. Biophysical Reviews, 9(2), 91–102. https://doi.org/10.1007/s12551-016-0247-1
   PubMedGoogle Scholar
• Panda, M., Ramachandran, S., Ramachandran, V., Shirude, P. S., Humnabadkar, V., Nagalapur, K., Sharma, S., Kaur, P., Guptha, S., Narayan, A., Mahadevaswamy, J., Ambady, A., Hegde, N., Rudrapatna, S. S., Hosagrahara, V. P., Sambandamurthy, V. K., & Raichurkar, A. (2014). Discovery of pyrazolopyridones as a novel class of noncovalent DprE1 inhibitor with potent anti-mycobacterial activity. Journal of Medicinal Chemistry, 57(11), 4761–4771. https://doi.org/10.1021/jm5002937
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phillips, M. A. (1928). The formation of 2-substituted benziminazoles. Journal of the Chemical Society., 1928, 2393–2399. https://doi.org/10.1039/JR9280002393
   Google Scholar
• Prakash, A., & Luthra, P. M. (2012). Insilico study of the A(2A)R-D (2)R kinetics and interfacial contact surface for heteromerization. Amino Acids, 43(4), 1451–1464. https://doi.org/10.1007/s00726-012-1218-x
   PubMed Web of Science ®Google Scholar
• Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., & Sanner, M. F. (2015). AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility. PLOS Computational Biology, 11(12), e1004586. https://doi.org/10.1371/journal.pcbi.1004586
   PubMed Web of Science ®Google Scholar
• Riccardi, G., Pasca, M. R., Chiarelli, L. R., Manina, G., Mattevi, A., & Binda, C. (2013). The DprE1 enzyme, one of the most vulnerable targets of Mycobacterium tuberculosis. Applied Microbiology and Biotechnology, 97(20), 8841–8848. https://doi.org/10.1007/s00253-013-5218-x
   PubMed Web of Science ®Google Scholar
• Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888. https://doi.org/10.1021/ct400314y
   PubMed Web of Science ®Google Scholar
• Sarkar, P., Yarlagadda, V., Ghosh, C., & Haldar, J. (2017). A review on cell wall synthesis inhibitors with an emphasis on glycopeptide antibiotics. MedChemComm, 8(3), 516–533. doi: 10.1039/c6md00585c.).
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Sayed, A. M., Alhadrami, H. A., El‐Hawary, S. S., Mohammed, R., Hassan, H. M., Rateb, M. E., Abdelmohsen, U. R., & Bakeer, W. (2020). Discovery of two brominated oxindole alkaloids as staphylococcal DNA gyrase and pyruvate kinase inhibitors via inverse virtual screening. Microorganisms, 8(2), 293. https://doi.org/10.3390/microorganisms8020293
   PubMed Web of Science ®Google Scholar
• Singh, S., Kumar Srivastava, H., Kishor, G., Singh, H., Agrawal, P., & Raghava, G. P. S. (2017). Evaluation of protein-ligand docking methods on peptide-ligand complexes for docking small ligands to peptides. BioRxiv, 212514. https://doi.org/10.1101/212514
   Google Scholar
• Sparks, R. B., Polam, P., Zhu, W., Crawley, M. L., Takvorian, A., McLaughlin, E., Wei, M., Ala, P. J., Gonneville, L., Taylor, N., Li, Y., Wynn, R., Burn, T. C., Liu, P. C. C., & Combs, A. P. (2007). Benzothiazole benzimidazole (S)-isothiazolidinone derivatives as protein tyrosine phosphatase-1B inhibitors. Bioorganic & Medicinal Chemistry Letters, 17(3), 736–740. https://doi.org/10.1016/j.bmcl.2006.10.079
   PubMed Web of Science ®Google Scholar
• Spyrakis, F., Cozzini, P., & Kellogg, G. E. (2016). Applying computational scoring functions to assess biomolecular interactions in food science: Applications to the estrogen receptors. NuRR, 3, 1–21. https://doi.org/10.11131/2016/101202.
   Google Scholar
• Stanley, S. A., Grant, S. S., Kawate, T., Iwase, N., Shimizu, M., Wivagg, C., Melanie, S., Kazyanskaya, E., Aquadro, J., Golas, A., Fitzgerald, M., Dai, H., Zhang, L., & Hung, D. T. (2012). Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening. ACS Chemical Biology, 7(8), 1377–1384. doi: 10.1021/acsmedchemlett.9b00343
   PubMed Web of Science ®Google Scholar
• Thanh, N. D., Do, H. S., Nguyen, T. T. H., Do, T. T., Cao, T. L., Hoang, T. K. V., Ngoc Toan, V., Ngoc Toan, D., & Dang, L. H. (2019). Synthesis, biological evaluation and molecular docking study of 1,2,3-1H-triazoles having 4H-pyrano[2,3-d]pyrimidine as potential mycobacterium tuberculosis protein tyrosine phosphatase B inhibitors. Bioorganic & Medicinal Chemistry Letters, 29(2), 164–171. https://doi.org/10.1016/j.bmcl.2018.12.009
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi: 10.1002/jcc.21334.AutoDock.
   PubMed Web of Science ®Google Scholar
• Verma, H., Choudhary, S., Kumar, M., & Silakari, O. (2021). In silico guided design of non-covalent inhibitors of DprE1: Synthesis and biological evaluation. SAR and QSAR in Environmental Research, 32(4), 333–352. https://doi.org/10.1080/1062936X.2021.1900390
   PubMed Web of Science ®Google Scholar
• Wang, J., & Hou, T. (2012). Develop and test a solvent accessible surface area-based model in conformational entropy calculations. Journal of Chemical Information and Modeling, 52(5), 1199–1212. https://doi.org/10.1021/ci300064d
   PubMed Web of Science ®Google Scholar
• Wang, Y., Sarris, K., Sauer, D. R., & Djuric, S. W. (2006). A simple and efficient one step synthesis of benzoxazoles and benzimidazoles from carboxylic acids. Tetrahedron Letters, 47(28), 4823–4826. https://doi.org/10.1016/j.tetlet.2006.05.052
   Web of Science ®Google Scholar
• Warrier, T., Kapilashrami, K., Argyrou, A., Ioerger, T. R., Little, D., Murphy, K. C., Nandakumar, M., Park, S., Gold, B., Mi, J., Zhang, T., Meiler, E., Rees, M., Somersan-Karakaya, S., Porras-De Francisco, E., Martinez-Hoyos, M., Burns-Huang, K., Roberts, J., Ling, Y., … Nathan, C. F. (2016). N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 113(31), E4523-30. https://doi.org/10.1073/pnas.1606590113
   PubMed Web of Science ®Google Scholar
• Yamashita, F. Y., & Hashida, M. H. (2004). In Silico Approaches for Predicting ADME Properties of Drugs. Drug Metabolism and Pharmacokinetics, 19(5), 327–338. https://doi.org/10.2133/dmpk.19.327
   PubMedGoogle Scholar
• Yuan, Y., Hu, Z., Bao, M., Sun, R., Long, X., Long, L., Li, J., Wu, C., & Bao, J. (2019). Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach. Journal of Biomolecular Structure & Dynamics, 37(15), 4092–4103. https://doi.org/10.1080/07391102.2018.1541141
   PubMed Web of Science ®Google Scholar