Integrated support vector machine and pharmacophore based virtual screening driven identification of thiophene carboxamide scaffold containing compound as potential PARP1 inhibitor

References

• Alemasova, E. E., & Lavrik, O. I. (2019). Poly(ADP-ribosyl)ation by PARP1: Reaction mechanism and regulatory proteins. Nucleic Acids Research, 47(8), 3811–3827. https://doi.org/10.1093/nar/gkz120
   PubMed Web of Science ®Google Scholar
• Baptista, S. J., Silva, M. M., Moroni, E., Meli, M., Colombo, G., Dinis, T. C., & Salvador, J. A. (2017). Novel PARP-1 Inhibitor Scaffolds Disclosed by a Dynamic Structure-Based Pharmacophore Approach. PLoS One, 12(1), e0170846p. https://doi.org/10.1371/journal.pone.0170846
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Best, R. B., Zhu, X., Shim, J., Lopes, P. E., Mittal, J., Feig, M., & Mackerell, A. D. Jr. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. Journal of Chemical Theory and Computation, 8(9), 3257–3273. https://doi.org/10.1021/ct300400x
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101p
   PubMed Web of Science ®Google Scholar
• Canan Koch, S. S., Thoresen, L. H., Tikhe, J. G., Maegley, K. A., Almassy, R. J., Li, J., Yu, X.-H., Zook, S. E., Kumpf, R. A., Zhang, C., Boritzki, T. J., Mansour, R. N., Zhang, K. E., Ekker, A., Calabrese, C. R., Curtin, N. J., Kyle, S., Thomas, H. D., Wang, L.-Z., … Hostomsky, Z. (2002). Novel Tricyclic Poly(ADP-ribose) Polymerase-1 Inhibitors with Potent Anticancer Chemopotentiating Activity: Design, Synthesis, and X-ray Cocrystal structure. J Med Chem, 45(23), 4961–4974. https://doi.org/10.1021/jm020259n
   PubMed Web of Science ®Google Scholar
• Cao, R. (2016). Free energy calculation provides insight into the action mechanism of selective PARP-1 inhibitor. Journal of Molecular Modeling, 22(4), 74p. https://doi.org/10.1007/s00894-016-2952-x
   PubMed Web of Science ®Google Scholar
• Carpenter, K. A., & Huang, X. (2018). Machine Learning-based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review. Curr Pharm Des, 24(28), 3347–3358. https://doi.org/10.2174/1381612824666180607124038
   PubMed Web of Science ®Google Scholar
• ChemAxon. (2016). Marvin was used for drawing, displaying and characterizing chemical structures, substructures and reactions (Version Marvin 16.9.12).
   Google Scholar
• Cincinelli, R., Musso, L., Merlini, L., Giannini, G., Vesci, L., Milazzo, F. M., Carenini, N., Perego, P., Penco, S., Artali, R., Zunino, F., Pisano, C., & Dallavalle, S. (2014). 7-Azaindole-1-carboxamides as a new class of PARP-1 inhibitors. Bioorganic & Medicinal Chemistry, 22(3), 1089–1103. https://doi.org/10.1016/j.bmc.2013.12.031
   PubMed Web of Science ®Google Scholar
• Cockcroft, X.-L., Dillon, K. J., Dixon, L., Drzewiecki, J., Kerrigan, F., Loh, V. M., Martin, N. M. B., Menear, K. A., & Smith, G. C. M. (2006). Phthalazinones 2: Optimisation and synthesis of novel potent inhibitors of poly(ADP-ribose)polymerase. Bioorganic & Medicinal Chemistry Letters, 16(4), 1040–1044. https://doi.org/10.1016/j.bmcl.2005.10.081
   PubMed Web of Science ®Google Scholar
• Costantino, G., Macchiarulo, A., Camaioni, E., & Pellicciari, R. (2001). Modeling of Poly(ADP-ribose)polymerase (PARP) Inhibitors. Docking of Ligands and Quantitative structure-activity relationship analysis . Journal of Medicinal Chemistry, 44(23), 3786–3794. https://doi.org/10.1021/jm010116l
   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. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L., & Overington, J. P. (2015). ChEMBL web services: Streamlining access to drug discovery data and utilities. Nucleic Acids Research, 43(W1), W612–620. https://doi.org/10.1093/nar/gkv352
   PubMed Web of Science ®Google Scholar
• Dixon, S. L., Smondyrev, A. M., & Rao, S. N. (2006). PHASE: A novel approach to pharmacophore modeling and 3D database searching. Chemical Biology & Drug Design, 67(5), 370–372. https://doi.org/10.1111/j.1747-0285.2006.00384.x
   PubMed Web of Science ®Google Scholar
• Durant, J. L., Leland, B. A., Henry, D. R., & Nourse, J. G. (2002). Reoptimization of MDL keys for use in drug discovery. Journal of Chemical Information and Computer Sciences, 42(6), 1273–1280. https://doi.org/10.1021/ci010132r
   PubMedGoogle Scholar
• Ekhteiari Salmas, R., Unlu, A., Bektaş, M., Yurtsever, M., Mestanoglu, M., & Durdagi, S. (2017). Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: Combination of in silico and in vitro studies. Journal of Biomolecular Structure & Dynamics, 35(9), 1899–1915. https://doi.org/10.1080/07391102.2016.1199328
   PubMed Web of Science ®Google Scholar
• Elmasry, G. F., Aly, E. E., Awadallah, F. M., & El-Moghazy, S. M. (2019). Design and synthesis of novel PARP-1 inhibitors based on pyridopyridazinone scaffold. Bioorganic Chemistry, 87, 655–666. https://doi.org/10.1016/j.bioorg.2019.03.068
   PubMed Web of Science ®Google Scholar
• Eltze, T., Boer, R., Wagner, T., Weinbrenner, S., McDonald, M. C., Thiemermann, C., Bürkle, A., & Klein, T. (2008). Imidazoquinolinone, imidazopyridine, and isoquinolindione derivatives as novel and potent inhibitors of the poly(ADP-ribose) polymerase (PARP): A comparison with standard PARP inhibitors. Molecular Pharmacology, 74(6), 1587–1598. https://doi.org/10.1124/mol.108.048751
   PubMed Web of Science ®Google Scholar
• Fang, J., Yang, R., Gao, L., Zhou, D., Yang, S., Liu, A. L., & Du, G. H. (2013). Predictions of BuChE inhibitors using support vector machine and naive Bayesian classification techniques in drug discovery. Journal of Chemical Information and Modeling, 53(11), 3009–3020. https://doi.org/10.1021/ci400331p
   PubMed Web of Science ®Google Scholar
• Ferraris, D. V. (2010). Evolution of poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors. From concept to clinic. Journal of Medicinal Chemistry, 53(12), 4561–4584. https://doi.org/10.1021/jm100012m
   PubMed Web of Science ®Google Scholar
• Ferraris, D., Ficco, R. P., Dain, D., Ginski, M., Lautar, S., Lee-Wisdom, K., Liang, S., Lin, Q., Lu, M. X.-C., Morgan, L., Thomas, B., Williams, L. R., Zhang, J., Zhou, Y., & Kalish, V. J. (2003). Design and synthesis of poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors. part 4: Biological evaluation of imidazobenzodiazepines as potent PARP-1 inhibitors for treatment of ischemic injuries. Bioorganic & Medicinal Chemistry, 11(17), 3695–3707. https://doi.org/10.1016/s0968-0896(03)00333-x
   PubMed Web of Science ®Google Scholar
• Ferraris, D., Ficco, R. P., Pahutski, T., Lautar, S., Huang, S., Zhang, J., & Kalish, V. (2003). Design and synthesis of poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors. Part 3: In vitro evaluation of 1,3,4,5-Tetrahydro-benzo[c][1,6]- and [c][1,7]-naphthyridin-6-ones. Bioorganic and Medicinal Chemistry Letters., 13(15), 2513–2518. https://doi.org/10.1016/S0960-894X(03)00465-7
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Greenwood, J. R., Calkins, D., Sullivan, A. P., & Shelley, J. C. (2010). Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. Journal of Computer-Aided Molecular Design, 24(6-7), 591–604. https://doi.org/10.1007/s10822-010-9349-1
   PubMed Web of Science ®Google Scholar
• Halder, A. K., Saha, A., Saha, K. D., & Jha, T. (2015). Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics, 33(8), 1756–1779. https://doi.org/10.1080/07391102.2014.969772
   PubMed Web of Science ®Google Scholar
• Hannigan, K., Kulkarni, S. S., Bdzhola, V. G., Golub, A. G., Yarmoluk, S. M., & Talele, T. T. (2013). Identification of novel PARP-1 inhibitors by structure-based virtual screening. Bioorganic & Medicinal Chemistry Letters, 23(21), 5790–5794. https://doi.org/10.1016/j.bmcl.2013.09.007
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(sici)1096-987x(199709)18:12 < 1463::aid-jcc4 > 3.0.co;2-h
   Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27-38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Inbar-Rozensal, D., Castiel, A., Visochek, L., Castel, D., Dantzer, F., Izraeli, S., & Cohen-Armon, M. (2009). A selective eradication of human nonhereditary breast cancer cells by phenanthridine-derived polyADP-ribose polymerase inhibitors. Breast Cancer Research : BCR, 11(6), R78phttps://doi.org/10.1186/bcr2445
   PubMed Web of Science ®Google Scholar
• Ivanenkov, Y. A., Zhavoronkov, A., Yamidanov, R. S., Osterman, I. A., Sergiev, P. V., Aladinskiy, V. A., Aladinskaya, A. V., Terentiev, V. A., Veselov, M. S., Ayginin, A. A., Kartsev, V. G., Skvortsov, D. A., Chemeris, A. V., Baimiev, A. K., Sofronova, A. A., Malyshev, A. S., Filkov, G. I., Bezrukov, D. S., Zagribelnyy, B. A., … Dontsova, O. A. (2019). Identification of Novel Antibacterials Using Machine Learning Techniques. [Original Research. Front Pharmacol, 10(913), 913]. https://doi.org/10.3389/fphar.2019.00913
   PubMedGoogle Scholar
• Iwashita, A., Hattori, K., Yamamoto, H., Ishida, J., Kido, Y., Kamijo, K., Murano, K., Miyake, H., Kinoshita, T., Warizaya, M., Ohkubo, M., Matsuoka, N., & Mutoh, S. (2005). Discovery of quinazolinone and quinoxaline derivatives as potent and selective poly(ADP-ribose) polymerase-1/2 inhibitors. FEBS Lett, 579(6), 1389–1393. https://doi.org/10.1016/j.febslet.2005.01.036
   PubMed Web of Science ®Google Scholar
• Jagtap, P. G., Southan, G. J., Baloglu, E., Ram, S., Mabley, J. G., Marton, A., Salzman, A., & Szabó, C. (2004). The discovery and synthesis of novel adenosine substituted 2,3-dihydro-1H-isoindol-1-ones: Potent inhibitors of poly(ADP-ribose) polymerase-1 (PARP-1). Bioorganic & Medicinal Chemistry Letters, 14(1), 81–85. https://doi.org/10.1016/j.bmcl.2003.10.007
   PubMed Web of Science ®Google Scholar
• Jain, P. G., & Patel, B. D. (2019). Medicinal chemistry approaches of poly ADP-Ribose polymerase 1 (PARP1) inhibitors as anticancer agents - A recent update. European Journal of Medicinal Chemistry, 165, 198–215. https://doi.org/10.1016/j.ejmech.2019.01.024
   PubMed Web of Science ®Google Scholar
• Jones, P., Altamura, S., Boueres, J., Ferrigno, F., Fonsi, M., Giomini, C., Lamartina, S., Monteagudo, E., Ontoria, J. M., Orsale, M. V., Palumbi, M. C., Pesci, S., Roscilli, G., Scarpelli, R., Schultz-Fademrecht, C., Toniatti, C., & Rowley, M. (2009). Discovery of 2-{4-[(3S)-Piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide (MK-4827): A Novel Oral Poly(ADP-ribose)polymerase (PARP) Inhibitor Efficacious in BRCA-1 and -2 Mutant Tumors. Journal of Medicinal Chemistry, 52(22), 7170–7185. https://doi.org/10.1021/jm901188v
   PubMed Web of Science ®Google Scholar
• Jones, P., Wilcoxen, K., Rowley, M., & Toniatti, C. (2015). Niraparib: A Poly(ADP-ribose) Polymerase (PARP) Inhibitor for the Treatment of Tumors with Defective Homologous Recombination. Journal of Medicinal Chemistry, 58(8), 3302–3314. https://doi.org/10.1021/jm5018237
   PubMed Web of Science ®Google Scholar
• Ko, H. L., & Ren, E. C. (2012). Functional Aspects of PARP1 in DNA Repair and Transcription. Biomolecules, 2(4), 524–548. https://doi.org/10.3390/biom2040524
   PubMedGoogle Scholar
• Kuldeep, J. R., K., Kaur, P., Goyal, N., & Siddiqi, M. I. (2020). Identification of potential anti-leishmanial agents using computational investigation and biological evaluation against trypanothione reductase. Journal of Biomolecular Structure and Dynamics, 39(3), 960–969. https://doi.org/10.1080/07391102.2020.1721330
   Google Scholar
• Kumar, V., Khan, S., Gupta, P., Rastogi, N., Mishra, D. P., Ahmed, S., & Siddiqi, M. I. (2014). Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents. Journal of Computer-Aided Molecular Design, 28(12), 1247–1256. https://doi.org/10.1007/s10822-014-9800-9
   PubMed Web of Science ®Google Scholar
• Kumar, V., Krishna, S., & Siddiqi, M. I. (2015). Virtual screening strategies: Recent advances in the identification and design of anti-cancer agents. Methods (San Diego, Calif.), 71, 64–70. https://doi.org/10.1016/j.ymeth.2014.08.010
   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
• Loh, V. M., Cockcroft, X-l., Dillon, K. J., Dixon, L., Drzewiecki, J., Eversley, P. J., Gomez, S., Hoare, J., Kerrigan, F., Matthews, I. T. W., Menear, K. A., Martin, N. M. B., Newton, R. F., Paul, J., Smith, G. C. M., Vile, J., & Whittle, A. J. (2005). Phthalazinones. Part 1: The design and synthesis of a novel series of potent inhibitors of poly(ADP-ribose)polymerase. Bioorganic & Medicinal Chemistry Letters, 15(9), 2235–2238. https://doi.org/10.1016/j.bmcl.2005.03.026
   PubMed Web of Science ®Google Scholar
• Malyuchenko, N. V., Kotova, E. Y., Kulaeva, O. I., Kirpichnikov, M. P., & Studitskiy, V. M. (2015). PARP1 Inhibitors: Antitumor drug design. Acta Naturae, 7(3), 27–37.
   PubMed Web of Science ®Google Scholar
• Mathworks. https://in.mathworks.com/products/matlab.html. Version 9.3.
   Google Scholar
• Maybridge. https://www.thermofisher.in/chemicals/en/brands/maybridge.html
   Google Scholar
• McGonigle, S., Chen, Z., Wu, J., Chang, P., Kolber-Simonds, D., Ackermann, K., Twine, N. C., Shie, J.-L., Miu, J. T., Huang, K.-C., Moniz, G. A., & Nomoto, K. (2015). E7449: A dual inhibitor of PARP1/2 and tankyrase1/2 inhibits growth of DNA repair deficient tumors and antagonizes Wnt signaling. Oncotarget, 6(38), 41307–41323. https://doi.org/10.18632/oncotarget.5846
   PubMed Web of Science ®Google Scholar
• Menear, K. A., Adcock, C., Boulter, R., Cockcroft, X-l., Copsey, L., Cranston, A., Dillon, K. J., Drzewiecki, J., Garman, S., Gomez, S., Javaid, H., Kerrigan, F., Knights, C., Lau, A., Loh, V. M., Matthews, I. T. W., Moore, S., O'Connor, M. J., Smith, G. C. M., & Martin, N. M. B. (2008). 4-[3-(4-cyclopropanecarbonylpiperazine-1-carbonyl)-4-fluorobenzyl]-2H-phthalazin-1-one: A novel bioavailable inhibitor of poly(ADP-ribose) polymerase-1. Journal of Medicinal Chemistry, 51(20), 6581–6591. https://doi.org/10.1021/jm8001263
   PubMed Web of Science ®Google Scholar
• Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/10.1021/jm300687e
   PubMed Web of Science ®Google Scholar
• Nakajima, H., Kakui, N., Ohkuma, K., Ishikawa, M., & Hasegawa, T. (2005). A newly synthesized poly(ADP-ribose) polymerase inhibitor, DR2313 [2-methyl-3,5,7,8-tetrahydrothiopyrano[4,3-d]-pyrimidine-4-one]: Pharmacological profiles, neuroprotective effects, and therapeutic time window in cerebral ischemia in rats. The Journal of Pharmacology and Experimental Therapeutics, 312(2), 472–481. https://doi.org/10.1124/jpet.104.075465
   PubMed Web of Science ®Google Scholar
• Niu, M., & Gu, Y. (2015). An in silico protocol for identifying potential poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors from chemical databases. New Journal of Chemistry, 39(2), 1060–1066. https://doi.org/10.1039/C4NJ01387E
   Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33p. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Papeo, G., Posteri, H., Borghi, D., Busel, A. A., Caprera, F., Casale, E., Ciomei, M., Cirla, A., Corti, E., D'Anello, M., Fasolini, M., Forte, B., Galvani, A., Isacchi, A., Khvat, A., Krasavin, M. Y., Lupi, R., Orsini, P., Perego, R., … Montagnoli, A. (2015). Discovery of 2-[1-(4,4-Difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide (NMS-P118): A Potent, Orally Available, and Highly Selective PARP-1 Inhibitor for Cancer Therapy. J Med Chem, 58(17), 6875–6898. https://doi.org/10.1021/acs.jmedchem.5b00680
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1980). Crystal Structure and Pair Potentials: A Molecular-Dynamics Study. Physical Review Letters, 45(14), 1196–1199. https://doi.org/10.1103/PhysRevLett.45.1196
   Web of Science ®Google Scholar
• Penning, T. D., Zhu, G.-D., Gandhi, V. B., Gong, J., Liu, X., Shi, Y., Klinghofer, V., Johnson, E. F., Donawho, C. K., Frost, D. J., Bontcheva-Diaz, V., Bouska, J. J., Osterling, D. J., Olson, A. M., Marsh, K. C., Luo, Y., & Giranda, V. L. (2009). Discovery of the Poly(ADP-ribose) polymerase (PARP) inhibitor 2-[(R)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-4-carboxamide (ABT-888) for the treatment of cancer. Journal of Medicinal Chemistry, 52(2), 514–523. https://doi.org/10.1021/jm801171j
   PubMed Web of Science ®Google Scholar
• Penning, T. D., Zhu, G.-D., Gong, J., Thomas, S., Gandhi, V. B., Liu, X., Shi, Y., Klinghofer, V., Johnson, E. F., Park, C. H., Fry, E. H., Donawho, C. K., Frost, D. J., Buchanan, F. G., Bukofzer, G. T., Rodriguez, L. E., Bontcheva-Diaz, V., Bouska, J. J., Osterling, D. J., … Giranda, V. L. (2010). Optimization of phenyl-substituted benzimidazole carboxamide poly(ADP-ribose) polymerase inhibitors: Identification of (S)-2-(2-fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (A-966492), a highly potent and efficacious inhibitor. Journal of Medicinal Chemistry, 53(8), 3142–3153. https://doi.org/10.1021/jm901775y
   PubMed Web of Science ®Google Scholar
• Pescatore, G., Branca, D., Fiore, F., Kinzel, O., Bufi, L. L., Muraglia, E., Orvieto, F., Rowley, M., Toniatti, C., Torrisi, C., & Jones, P. (2010). Identification and SAR of novel pyrrolo[1,2-a]pyrazin-1(2H)-one derivatives as inhibitors of poly(ADP-ribose) polymerase-1 (PARP-1). Bioorganic & Medicinal Chemistry Letters, 20(3), 1094–1099. https://doi.org/10.1016/j.bmcl.2009.12.026
   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
• Purnell, M. R., & Whish, W. J. (1980). Novel inhibitors of poly(ADP-ribose) synthetase. The Biochemical Journal, 185(3), 775–777. https://doi.org/10.1042/bj1850775
   PubMed Web of Science ®Google Scholar
• Ramadan, S. K., Elrazaz, E. Z., Abouzid, K. A. M., & El-Naggar, A. M. (2020). Design, synthesis and in silico studies of new quinazolinone derivatives as antitumor PARP-1 inhibitors. RSC Advances, 10(49), 29475–29492. https://doi.org/10.1039/D0RA05943A
   PubMed Web of Science ®Google Scholar
• Rodríguez, M. I., Majuelos-Melguizo, J., Martí Martín-Consuegra, J. M., Ruiz de Almodóvar, M., López-Rivas, A., & Javier Oliver, F. (2015). Deciphering the insights of poly(ADP-ribosylation) in tumor progression. Medicinal Research Reviews, 35(4), 678–697. https://doi.org/10.1002/med.21339
   PubMed Web of Science ®Google Scholar
• Ruf, A., de Murcia, G., & Schulz, G. E. (1998). Inhibitor and NAD + binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. Biochemistry, 37(11), 3893–3900. https://doi.org/10.1021/bi972383s
   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
• Schrödinger Release 2018-2: LigPrep. (2018). Schrödinger Release 2018-2: LigPrep, S., LLC, New York, NY.
   Google Scholar
• Schrödinger Release 2018-2: Maestro. (2018). Schrödinger Release 2018-2: Maestro, S., LLC, New York, NY.
   Google Scholar
• Schrödinger Release 2018-2: QikProp. (2018). Schrödinger Release 2018-2: QikProp, S., LLC, New York, NY.
   Google Scholar
• Singh, N., Tiwari, S., Srivastava, K. K., & Siddiqi, M. I. (2015). Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation. Journal of Chemical Information and Modeling, 55(6), 1120–1129. https://doi.org/10.1021/acs.jcim.5b00150
   PubMed Web of Science ®Google Scholar
• Singh, S. S., Sarma, J. A., Narasu, L., Dayam, R., Xu, S., & Neamati, N. (2014). A review on PARP1 inhibitors: Pharmacophore modeling, virtual and biological screening studies to identify novel PARP1 inhibitors. Current Topics in Medicinal Chemistry, 14(17), 2020–2030. https://doi.org/10.2174/1568026614666140929152123
   PubMed Web of Science ®Google Scholar
• Slade, D. (2020). PARP and PARG inhibitors in cancer treatment. Genes & Development, 34(5-6), 360–394. https://doi.org/10.1101/gad.334516.119
   PubMed Web of Science ®Google Scholar
• Steffen, J. D., Brody, J. R., Armen, R. S., & Pascal, J. M. (2013). Structural Implications for Selective Targeting of PARPs. Frontiers in Oncology, 3, 301p. https://doi.org/10.3389/fonc.2013.00301
   PubMedGoogle Scholar
• Thomas, H. D., Calabrese, C. R., Batey, M. A., Canan, S., Hostomsky, Z., Kyle, S., Maegley, K. A., Newell, D. R., Skalitzky, D., Wang, L.-Z., Webber, S. E., & Curtin, N. J. (2007). Preclinical selection of a novel poly(ADP-ribose) polymerase inhibitor for clinical trial. Mol Cancer Ther, 6(3), 945–956. https://doi.org/10.1158/1535-7163.mct-06-0552
   PubMed Web of Science ®Google Scholar
• Torrisi, C., Bisbocci, M., Ingenito, R., Ontoria, J. M., Rowley, M., Schultz-Fademrecht, C., Toniatti, C., & Jones, P. (2010). Discovery and SAR of novel, potent and selective hexahydrobenzonaphthyridinone inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1). Bioorganic & Medicinal Chemistry Letters, 20(2), 448–452. https://doi.org/10.1016/j.bmcl.2009.12.002
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wang, B., Chu, D., Feng, Y., Shen, Y., Aoyagi-Scharber, M., & Post, L. E. (2016). Discovery and Characterization of (8S,9R)-5-Fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one (BMN 673, Talazoparib), a Novel, Highly Potent, and Orally Efficacious Poly(ADP-ribose) Polymerase-1/2 Inhibitor, as an Anticancer Agent. Journal of Medicinal Chemistry, 59(1), 335–357. https://doi.org/10.1021/acs.jmedchem.5b01498
   PubMed Web of Science ®Google Scholar
• Wang, L., Liu, F., Jiang, N., Zhou, W., Zhou, X., & Zheng, Z. (2016). Design, Synthesis, and Biological Evaluation of Novel PARP-1 Inhibitors Based on a 1H-Thieno[3,4-d] Imidazole-4-Carboxamide Scaffold. Molecules, 21(6), 772. https://doi.org/10.3390/molecules21060772
   PubMed Web of Science ®Google Scholar
• Welcsh, P. L., & King, M. C. (2001). BRCA1 and BRCA2 and the genetics of breast and ovarian cancer. Human Molecular Genetics, 10(7), 705–713. https://doi.org/10.1093/hmg/10.7.705
   PubMed Web of Science ®Google Scholar
• Yap, C. W. (2011). PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry, 32(7), 1466–1474. https://doi.org/10.1002/jcc.21707
   PubMed Web of Science ®Google Scholar
• Ye, N., Chen, C.-H., Chen, T., Song, Z., He, J.-X., Huan, X.-J., Song, S.-S., Liu, Q., Chen, Y., Ding, J., Xu, Y., Miao, Z.-H., & Zhang, A. (2013). Design, Synthesis, and Biological Evaluation of a Series of Benzo[de][1,7]naphthyridin-7(8H)-ones Bearing a Functionalized Longer Chain Appendage as Novel PARP1 Inhibitors. Journal of Medicinal Chemistry, 56(7), 2885–2903. https://doi.org/10.1021/jm301825t
   PubMed Web of Science ®Google Scholar
• Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816
   PubMed Web of Science ®Google Scholar