References
- Bajusz, D., Ferenczy, G. G., & Keseru, G. M. (2017). Structure-based virtual screening approaches in kinase-directed drug discovery. Current Topics in Medicinal Chemistry, 17(20), 2235–2259. https://doi.org/https://doi.org/10.2174/1568026617666170224121313
- Banoth, S., Boda, S., Perugu, S., Balabadra, S., & Manga, V. (2018). Design, synthesis, biological evaluation and in silico molecular docking studies of novel benzochromeno[2,3-d]thiazolopyrimidine derivatives. Research on Chemical Intermediates, 44(3), 1833–1846. https://doi.org/https://doi.org/10.1007/s11164-017-3201-3
- Bensinger, D., Stubba, D., Cremer, A., Kohl, V., Waßmer, T., Stuckert, J., Engemann, V., Stegmaier, K., Schmitz, K., & Schmidt, B. (2019). Virtual screening identifies irreversible FMS-like tyrosine kinase 3 inhibitors with activity toward resistance-conferring mutations. Journal of Medicinal Chemistry, 62(5), 2428–2446. https://doi.org/https://doi.org/10.1021/acs.jmedchem.8b01714
- Burness, C. B., & Mckeage, K. (2012). Dabigatran etexilate: A review of its use for the prevention of venous thromboembolism after total hip or knee replacement surgery. Drugs, 72(7), 963–986. https://doi.org/https://doi.org/10.2165/11209080-000000000-00000
- Caballero, J. (2010). 3D-QSAR (CoMFA and CoMSIA) and pharmacophore (GALAHAD) studies on the differential inhibition of aldose reductase by flavonoid compounds. Journal of Molecular Graphics & Modelling, 29(3), 363–371. https://doi.org/https://doi.org/10.1016/j.jmgm.2010.08.005
- Cai, Z. Q., Hou, X., Zhang, B., & Liu, R. C. (2015). Synthesis and anticoagulant activities of novel benzimidazole derivatives. Chinese Journal of Synthetic Chemistry, 41(52), 908–912. https://doi.org/https://doi.org/10.15952/j.cnki.cjsc.1005-1511.2015.10.0908
- Chen, H. F., Dong, M.-H., Ren, Y.-J., & Wang, F. (2016). Design, synthesis, biological evaluation and molecular docking studies of dabigatran analogs as potential thrombin inhibitors. Journal of the Iranian Chemical Society, 13(2), 347–357. https://doi.org/https://doi.org/10.1007/s13738-015-0743-4
- Chen, D., Shi, J., Chen, Q., Zhang, R Ui, Gong, G., Xu, Y., & Zhu, Q. (2017). Design, synthesis and biological evaluation of thrombin inhibitors with 1, 2, 3, 4-tetrahydrobenzo[4, 5]imidazo[1, 2-a]pyrazine Nucleus. Chemical Journal of Chinese Universities, 38(6), 1059–1067. https://doi.org/https://doi.org/10.7503/cjcu20160797
- Choudhury, A., Goyal, D., & Lip, G. Y. (2006). Ximelagatran. Drugs of Today (Barcelona, Spain : 1998)), 42(1), 3–19. https://doi.org/https://doi.org/10.1358/dot.2006.42.1.893611
- Clark, M., Cramer, R. D., Opdenbosch, N., & Van, & R. D. C. III, (1989). Validation of the general purpose TRIPOS 5.2 force field. Journal of Computational Chemistry, 10(8), 982–1012. https://doi.org/https://doi.org/10.1002/jcc.540100804
- Costanzi, S., Cohen, A., Danfora, A., & Dolatmoradi, M. (2019). Influence of the structural accuracy of homology models on their applicability to docking-based virtual screening: The β2 adrenergic receptor as a case study. Journal of Chemical Information and Modeling, 59(7), 3177–3190. https://doi.org/https://doi.org/10.1021/acs.jcim.9b00380
- da Silva Rocha, S. F. L., Olanda, C. G., Fokoue, H. H., & Sant’Anna, C. M. R. (2019). Virtual screening techniques in drug discovery: Review and recent applications. Current Topics in Medicinal Chemistry, 19(19), 1751–1767. https://doi.org/https://doi.org/10.2174/1568026619666190816101948
- Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717–42427. https://doi.org/https://doi.org/10.1038/srep42717
- De Vivo, M., Masetti, M., Bottegoni, G., & Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9), 4035–4061. https://doi.org/https://doi.org/10.1021/acs.jmedchem.5b01684
- Ding, H. G., Cai, Z. Q., Jin, Z. S., & Zhang, L. J. (2017). Synthesis and anticoagulant activities of dabigatran etexilate derivatives. Chinese Journal of Synthetic Chemistry, 25(12), 957–962. https://doi.org/https://doi.org/10.15952/j.cnki.cjsc.1005-1511.2017.12.17228
- Doman, T. N., McGovern, S. L., Witherbee, B. J., Kasten, T. P., Kurumbail, R., Stallings, W. C., Connolly, D. T., & Shoichet, B. K. (2002). Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. Journal of Medicinal Chemistry, 45(11), 2213–2221. https://doi.org/https://doi.org/10.1021/jm010548w
- Ferrand, S., Schmid, A., Engeloch, C., & Glickman, J. F. (2005). Statistical evaluation of a self-deconvoluting matrix strategy for high-throughput screening of the CXCR3 receptor. Assay and Drug Development Technologies, 3(4), 413–424. https://doi.org/https://doi.org/10.1089/adt.2005.3.413
- Grepin, C., & Pernelle, C. (2000). High-throughput screening. Drug Discovery Today., 5(5), 212–214. https://doi.org/https://doi.org/10.1016/S1359-6446(00)01491-4
- Guedes, I. A., C. S., de, M., & Dardenne, L. E. (2014). Receptor-ligand molecular docking. Biophysical Reviews, 6(1), 75–87. https://doi.org/https://doi.org/10.1007/s12551-013-0130-2
- Guner, O. F. (2002). History and evolution of the pharmacophore concept in computer-aided drug design. Current Topics in Medicinal Chemistry, 2(12), 1321–1332. https://doi.org/https://doi.org/10.2174/1568026023392940
- Hauel, N. H., Nar, H., Priepke, H., Ries, U., Stassen, J.-M., & Wienen, W. (2002). Structure-based design of novel potent nonpeptide thrombin inhibitors. Journal of Medicinal Chemistry, 45(9), 1757–1766. https://doi.org/https://doi.org/10.1021/jm0109513
- Irene, R. K., Antonello, M., Concetta, G., Antonio, R., Lelio, M., & Filomena, S. (2011). Thrombin–aptamer recognition: A revealed ambiguity. Nucleic Acids Research, 17, 17. https://doi.org/https://doi.org/10.1093/nar/gkr522
- Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. https://doi.org/https://doi.org/10.1021/ci3001277
- Kothandan, G., Madhavan, T., Gadhe, C. G., & Cho, S. J. (2013). A combined 3D QSAR and pharmacophore-based virtual screening for the identification of potent p38 MAP kinase inhibitors: An in silico approach. Medicinal Chemistry Research, 22(4), 1773–1787. https://doi.org/https://doi.org/10.1007/s00044-012-0179-7
- Li, C. L., Dong, M. H., Ren, Y. J., & Li, L. H. (2015). Design, synthesis, biological evaluation and molecular docking of novel dabigatran derivatives as potential thrombin inhibitors. RSC Advances, 5(30), 23737–23748. https://doi.org/https://doi.org/10.1039/C5RA01828E
- Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/https://doi.org/10.1016/j.addr.2012.09.019
- Lip, G. Y. H., Rasmussen, L. H., Olsson, S. B., Jensen, E. C., Persson, A. L., Eriksson, U., & Wahlander, K. F. C. (2009). Oral direct thrombin inhibitor AZD0837 for the prevention of stroke and systemic embolism in patients with non-valvular atrial fibrillation: A randomized dose-guiding, safety, and tolerability study of four doses of AZD0837 vs. vitamin K antagonists. European Heart Journal, 30(23), 2897–2907. https://doi.org/https://doi.org/10.1093/eurheartj/ehp318
- Li, C. L., & Ren, Y. J. (2016). Synthesis and biological evaluation of novel dabigatran derivatives as thrombin inhibitors. Research on Chemical Intermediates, 42(2), 735–752. https://doi.org/https://doi.org/10.1007/s11164-015-2053-y
- Li, M. L., Ren, Y.-J., Dong, M.-H., & Ren, W.-X. (2015). Design, synthesis and structural exploration of novel fluorinated dabigatran derivatives as direct thrombin inhibitors. European Journal of Medicinal Chemistry, 96, 122–138. https://doi.org/https://doi.org/10.1016/j.ejmech.2015.04.012
- Liu, X., Shi, D., Zhou, S., Liu, H., Liu, H., & Yao, X. (2018). Molecular dynamics simulations and novel drug discovery. Expert Opinion on Drug Discovery, 13(1), 23–37. https://doi.org/https://doi.org/10.1080/17460441.2018.1403419
- Mckeage, K., & Plosker, G. L. (2001). Argatroban. Drugs, 61(4), 515–522. https://doi.org/https://doi.org/10.2165/00003495-200161040-00005
- Meilin, L., & Yujie, R. (2015). Synthesis and biological evaluation of some new 2,5-substituted 1-ethyl-1H-benzoimidazole fluorinated derivatives as direct thrombin inhibitors. Archiv Der Pharmazie, 348(5), 353–365. https://doi.org/https://doi.org/10.1002/ardp.201400463
- Mohapatra, R., Tran, M., Gore, J. M., Spencer, F. A. (2005). A review of the oral direct thrombin inhibitor ximelagatran: Not yet the end of the warfarin era…. American Heart Journal, 150(1), 19–26. https://doi.org/https://doi.org/10.1016/j.ahj.2005.02.012
- Muegge, I. (2003). Selection criteria for drug-like compounds. Medicinal Research Reviews, 23(3), 302–321. https://doi.org/https://doi.org/10.1002/med.10041
- Niedeggen, A., Lejczyk, J., Kröner, S., Stortz, C., Reith, S., & Janssens, U. (2008). Treatment of intracardiac thrombi with argatroban. Acute Cardiac Care, 10(4), 221–226. https://doi.org/https://doi.org/10.1080/17482940802262384
- Obergrussberger, A., Goetze, T. A., Brinkwirth, N., Becker, N., Friis, S., Rapedius, M., Haarmann, C., Rinke-Weiß, I., Stölzle-Feix, S., Brüggemann, A., George, M., & Fertig, N. (2018). An update on the advancing high-throughput screening techniques for patch clamp-based ion channel screens: Implications for drug discovery. Expert Opinion on Drug Discovery, 13(3), 269–277. https://doi.org/https://doi.org/10.1080/17460441.2018.1428555
- Persico, M., Dato, A., Orteca, N., Fattorusso, C., Novellino, E., Andreoli, M., & Ferlini, C. (2015). From protein communication to drug discovery. Current Topics in Medicinal Chemistry, 15(20), 2019–2031. https://doi.org/https://doi.org/10.2174/1568026615666150519102257
- Pozmogova, G. E., Zaitseva, M. A., Smirnov, I. P., Shvachko, A. G., Murina, M. A., & Sergeenko, V. I. (2010). Anticoagulant effects of thioanalogs of thrombin-binding DNA-aptamer and their stability in the plasma. Bulletin of Experimental Biology and Medicine, 150(2), 180–184. https://doi.org/https://doi.org/10.1007/s10517-010-1099-5
- Ren, W., Ren, Y., Dong, M., & Gao, Y. (2016). Design, synthesis, and thrombin inhibitory activity evaluation of some novel benzimidazole derivatives. Helvetica Chimica Acta, 99(4), 325–332. https://doi.org/https://doi.org/10.1002/hlca.201500527
- Richmond, N. J., Abrams, C. A., Wolohan, P. R. N., Abrahamian, E., Willett, P., & Clark, R. D. (2006). GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D. Journal of Computer-Aided Molecular Design, 20(9), 567–587. https://doi.org/https://doi.org/10.1007/s10822-006-9082-y
- Squizzato, A., Dentali, F., Steidl, L., & Ageno, W. (2009). New direct thrombin inhibitors. Internal and Emergency Medicine, 4(6), 479–484. https://doi.org/https://doi.org/10.1007/s11739-009-0314-8
- Stangier, D. J. (2008). Clinical pharmacokinetics and pharmacodynamics of the oral direct thrombin inhibitor dabigatran etexilate. Clinical Pharmacokinetics, 47(5), 285–295. https://doi.org/https://doi.org/10.2165/00003088-200847050-00001
- Timmis, A., Townsend, N., Gale, C., Grobbee, R., Maniadakis, N., Flather, M., Wilkins, E., Wright, L., Vos, R., Bax, J., Blum, M., Pinto, F., & Vardas, P. (2018). European society of cardiology: Cardiovascular disease statistics 2017. European Heart Journal, 39(7), 508–579. https://doi.org/https://doi.org/10.1093/eurheartj/ehx628
- Wang, F., Ren, Y.-J., & Dong, M.-H. (2016). Molecular design, synthesis and anticoagulant activity evaluation of fluorinated dabigatran analogues. Bioorganic & Medicinal Chemistry, 24(12), 2739–2753. https://doi.org/https://doi.org/10.1016/j.bmc.2016.04.038
- Xiao, J., Melvin, R. L., & Salsbury, F. R. (2017). Mechanistic insights into thrombin’s switch between “slow” and “fast” forms. Physical Chemistry Chemical Physics : PCCP, 19(36), 24522–24533. https://doi.org/https://doi.org/10.1039/c7cp03671j
- Xiao, J., Melvin, R. L., & Salsbury, F. R. (2019). Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning probing light chain mutation effects on thrombin via. Journal of Biomolecular Structure & Dynamics, 37(4), 982–953. https://doi.org/https://doi.org/10.1080/07391102.2018.1445032
- Xiao, J., & Salsbury, F. R. (2017). Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. Journal of Biomolecular Structure & Dynamics, 35(15), 3354–3351. https://doi.org/https://doi.org/10.1080/07391102.2016.1254682
- Xie, H., Qiu, K., & Xie, X. (2015). Pharmacophore modeling, virtual screening, and 3D-QSAR studies on a series of non-steroidal aromatase inhibitors. Medicinal Chemistry Research, 24(5), 1901–1905. https://doi.org/https://doi.org/10.1007/s00044-014-1257-9
- Yu, Z., Chen, Y., Zhao, W., Li, J., Liu, J., & Chen, F. (2018). Identification and molecular docking study of novel angiotensin-converting enzyme inhibitory peptides from Salmo salar using in silico methods . Journal of the Science of Food and Agriculture, 98(10), 3907–3914. https://doi.org/https://doi.org/10.1002/jsfa.8908
- Zhong, H., & Bowen, J. P. (2007). GALAHAD Tripos, Inc., 1699 South Hanley Road, St. Louis, MO 63144-2319. www.tripos.com. Contact company for pricing information. Journal of the American Chemical Society, 129(17), 5780. https://doi.org/https://doi.org/10.1021/ja069815j