Multiple receptor conformation docking, dock pose clustering and 3D QSAR studies on human poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors

References

• D’Amours D, Desnoyers S, D Silva I, Poirier GG. Poly(ADP-ribosyl) ation reactions in the regulation of nuclear functions. Biochem J 1999;342:249–68
   PubMed Web of Science ®Google Scholar
• de Murcia G, Menissier de Murcia J. Poly(ADP-ribose) polymerase: a molecular nick-sensor. Trends Biochem Sci 1994;19:172–6
   PubMed Web of Science ®Google Scholar
• Vira'g L, Szabo C. The therapeutic potential of poly(ADP-ribose) polymerase inhibitors. Pharmacol Rev 2002;54:375–429
   PubMed Web of Science ®Google Scholar
• Jagtap P, Szabo C. Poly(ADP-ribose) polymerase and the therapeutic effects of its inhibitors. Nat Rev Drug Discov 2005;4:421–40
   PubMed Web of Science ®Google Scholar
• Aguilar-Quesada R, Munoz-Gamez JA, Martin-Oliva D, et al. Modulation of transcription by PARP-1: consequences in carcinogenesis and inflammation. Curr Med Chem 2007;14:1179–87
   PubMed Web of Science ®Google Scholar
• Szabo C, Pacher P, Swanson RA. Novel modulators of poly(ADPribose) polymerase. Trends Pharmacol Sci 2006;27:626–30
   PubMed Web of Science ®Google Scholar
• Singh S, Makwana DK, Buckley T, et al. Clinical significance of PARP-1 inhibitors in cancer chemotherapy. Trans Clin Bio 2013;1:10–5
   Google Scholar
• Beneke S, Diefenbach J, Burkle A. Poly(ADP-ribosyl)ation inhibitors: promising drug candidates for a wide variety of pathophysiologic conditions. Int J Cancer 2004;111:813–8
   PubMed Web of Science ®Google Scholar
• McCabe N, Nicholas CT, Lord CJ, et al. Deficiency in the repair of DNA damage by homologous recombination and sensitivity to poly(ADP-ribose) polymerase inhibition. Cancer Res 2006;66:8109–15
   PubMed Web of Science ®Google Scholar
• Gudmundsdottir K, Ashworth A. The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability. Oncogene 2006;25:5864–74
   PubMed Web of Science ®Google Scholar
• Cramer RD, Patterson DE, Bunce JD. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids tocarrier proteins. J Am Chem Soc 1988;110:5959–67
   PubMed Web of Science ®Google Scholar
• Cramer RD 3rd, Patterson DE, Bunce JD. Crossvalidation bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant Struct Act Relat 1998;7:18–25
   Google Scholar
• Klebe G, Abraham U, Mietzner T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 1994;37:4130–46
   PubMed Web of Science ®Google Scholar
• Wold S, Johansson A, Cochi M. 3D-QSAR in drug design: theory, methods and application. In: Kubinyi H, ed. PLS-partial least squares projection tolatent structures. Leiden: ESCOM; 1993:523–50
   Google Scholar
• Park CH. PARP complexed with A861695. doi:10.2210/pdb2rd6/pdb. Available from: http://www.rcsb.org. pdbid: 2rd6
   Google Scholar
• Park CH. PARP complexed with A620223. doi:10.2210/pdb2rcw/pdb. Available from: http://www.rcsb.org. pdbid: 2rcw
   Google Scholar
• Miyashiro J, Woods KW, Park CH, et al. Synthesis and SAR of novel tricyclic quinoxalinone inhibitors of poly (ADP-ribose) polymerase-1 (PARP-1). Bioorg Med Chem Lett 2009;19:4050–4
   PubMed Web of Science ®Google Scholar
• Park CH. PARP complexed with A861696. doi:10.2210/pdb3gn7/pdb. Available from: http://www.rcsb.org, pdbid: 3gn7
   Google Scholar
• Gandhi VB, Luo Y, Liu X, et al. Discovery and SAR of substituted 3-oxoisoindoline-4-carboxamides as potent inhibitors of poly(ADP-ribose) polymerase (PARP) for the treatment of cancer. Bioorg Med Chem Lett 2010;20:1023–6
   PubMed Web of Science ®Google Scholar
• Penning TD, Zhu GD, Gong J, et al. Optimization of phenyl-substituted benzimidzole 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. J Med Chem 2010;53:3142–53
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739–49
   PubMed Web of Science ®Google Scholar
• Penning TD, Zhu GD, Gandhi VB, et al. Discovery of the poly(ADP-ribose) polymerase (PARP) inhibitor2-[(R)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-4-carboxamide (ABT-888) for the treatment of cancer. J Med Chem 2009;52:514–23
   PubMed Web of Science ®Google Scholar
• Penning TD, Zhu GD, Gong J, et al. 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. J Med Chem 2010;53:3142–53
   PubMed Web of Science ®Google Scholar
• Tong Y, Bouska JJ, Ellis PA, et al. Synthesis and evaluation of a new generation of orally efficacious benzimidazole-based poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors as anticancer agents. J Med Chem 2009;52:6803–13
   PubMed Web of Science ®Google Scholar
• Skalitzky DJ, Marakovits JT, Maegley KA, et al. Tricyclic benzimidazoles as potent poly(ADP-ribose) polymerase-1 inhibitors. J Med Chem 2003;46:210–3
   PubMed Web of Science ®Google Scholar
• Canan Koch SS, Thoresen LH, Tikhe JG, et al. Novel tricyclic poly(ADP-ribose) polymerase-1 inhibitors with potent anticancer chemopotentiating activity: design, synthesis, and X-ray cocrystal structure. J Med Chem 2002;45:4961–74
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739–49
   PubMed Web of Science ®Google Scholar
• Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron 1980;36:3219–28
   Web of Science ®Google Scholar
• Sivan SK, Manga V. Multiple receptor conformation docking and dock pose clustering as tool for CoMFA and CoMSIA analysis – a case study on HIV-1 protease inhibitors. J Mol Model 2012;18:569–82
   PubMed Web of Science ®Google Scholar
• Carlson HA, Masukawa KM, McCammon JA. Method for including the dynamic fluctuations of a protein in computer-aided drug design. J Phys Chem 1999;103:10213–9
   Web of Science ®Google Scholar
• Carlson HA, Masukawa KM, Rubins K, et al. Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem 2000;43:2100–14
   PubMed Web of Science ®Google Scholar
• Kanth SS, Vijjulatha M. Tetrahydroxy cyclic urea-potent inhibitor for HIV-1 protease wild type and mutant type – a computational design. E-J Chem 2008;5:584–92
   Google Scholar