Focusing on shared subpockets – new developments in fragment-based drug discovery

References

• Gkeka P, Eleftheratos S, Kolocouris A, et al. Free energy calculations reveal the origin of binding preference for aminoadamantane blockers of influenza A/M2TM pore. J Chem Theor Comp 2013;9(2):1272–81
   Web of Science ®Google Scholar
• Warren GL, Andrews CW, Capelli AM, et al. A critical assessment of docking programs and scoring functions. J Med Chem 2006;49:5912–31
   PubMed Web of Science ®Google Scholar
• Koes DR, Baumgartner MP, Camacho CJ. Lessons Learned in Empirical Scoring with smina from the CSAR. 2011 Benchmarking Exercise. J Chem Inf Model 2013;53:1893–904
   PubMed Web of Science ®Google Scholar
• Smith RD, et al. CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. J Chem Inf Model 2011;51:2115–31
   PubMed Web of Science ®Google Scholar
• Damm-Ganamet KL, Smith RD, Dunbar JB, et al. Csar benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model 2013;53:1853–70
   PubMed Web of Science ®Google Scholar
• Cheng T, Li X, Li Y, et al. Comparative Assessment of Scoring Functions on a Diverse Test Set. J Chem Inf Model 2009;49:1079–93
   PubMed Web of Science ®Google Scholar
• 241st ACS National Meeting. Computer-aided drug design: A personal perspective on tools, mindsets, and on what we could do next. 241st ACS National Meeting, Anaheim: 2011
   Google Scholar
• Kumar A, Voet A, Zhang KY. Fragment Based Drug Design: From Experimental to Computational Approaches. Curr Med Chem 2012;19(30):5128–47
   PubMed Web of Science ®Google Scholar
• Brenke R, Kozakov D, Chuang G, et al. Fragment-based identification of druggable “hot spots” of proteins using Fourier domain correlation techniques. Bioinformatics 2009;25:621–7
   PubMed Web of Science ®Google Scholar
• Koes DR, Camacho CJ. PocketQuery: protein–protein interaction inhibitor starting points from protein–protein interaction structure. Nucleic Acids Res 2012;40:W387–92
   PubMed Web of Science ®Google Scholar
• Buckley DL, Van Molle I, Gareiss PC, et al. Targeting the von Hippel−Lindau E3 Ubiquitin Ligase Using SmallMolecules To Disrupt the VHL/HIF-1α Interaction. J Am Chem Soc 2012;134:4465–8
   PubMed Web of Science ®Google Scholar
• Van Molle I, Thomann A, Buckley DL, et al. Dissecting fragment-basedlead discoveryat the von hippel-lindau protein:hypoxia inducible factor 1a protein-proteininterface. Chem Biol 2012;19:1300–12
   PubMed Web of Science ®Google Scholar
• POCKETQUERY. Available from: http://pocketquery.csb.pitt.edu
   Google Scholar
• Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005;21:2534–6
   PubMed Web of Science ®Google Scholar
• Camacho CJ, Ma H, Champ PC. Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions. Proteins 2006;63:868–77
   PubMed Web of Science ®Google Scholar
• Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM:a program for macromolecularenergy, minimization, and dynamic calculations. J Comput Chem 1983;4:187–217
   Web of Science ®Google Scholar
• Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure. Bioinformatics 2012;28(6):784–91
   PubMed Web of Science ®Google Scholar
• Koes DR, Camacho CJ. ZINC Pharmer: pharmacophore search of the ZINC database. Nucleic Acids Res 2012;40(W1):W409–14
   PubMed Web of Science ®Google Scholar
• Koes DR, Dömling A, Camacho CJ, et al. Enabling large-scale design, synthesis and validation of small moleculeprotein-protein antagonists. PLoS One 2012;7:e32839
   PubMed Web of Science ®Google Scholar
• Dömling A. Recent developments in isocyanide based multicomponent reactions in applied chemistry. Chem Rev 2006;106:17–89
   PubMed Web of Science ®Google Scholar
• Dömling A, Wei W, Kan W. Chemistry and Biology of Multicomponent Reactions. Chem Rev 2012;112:3083–135
   PubMed Web of Science ®Google Scholar
• Alicia PH, Adrian S, Richard JB, et al. What Can We Learn from the Evolution of Protein-Ligand Interactions to Aid the Design of New Therapeutics? PLoS ONE 2012;7(12):e51742
   PubMed Web of Science ®Google Scholar
• Björn O, Patrick Mc, Per A, et al. Impact of Stereospecific Intramolecular Hydrogen Bonding on Cell Permeability and Physicochemical Properties. J Med Chem 2014;57:2746–54
   PubMed Web of Science ®Google Scholar
• Dömling A. Recent advances in isocyanide-based multicomponent chemistry. Curr Opin Chem Biol 2002;6:306–13
   PubMed Web of Science ®Google Scholar
• Frank L, Jack B, Christine H. Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success. J Med Chem 2009;52:6752–6
   PubMed Web of Science ®Google Scholar
• Miquel DF, Roberto M, Patrick A. Structural systems pharmacology: the role of 3D structures in next-generation drug development. Chem Bio 2013;20:674–84
   PubMed Web of Science ®Google Scholar
• Meireles L, Dömling A, Camacho CJ. ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res 2010;38:W407
   PubMed Web of Science ®Google Scholar
• ANCHORQUERY. Available from: http://anchorquery.csb.pitt.edu/
   Google Scholar
• Stanislava U, Dusan U, Helen P, et al. Structure of Free MDM2 N-terminal Domain Reveals Conformational Adjustments that Accompany p53-binding. J Mol Biol 2005;350:587–98
   PubMed Web of Science ®Google Scholar
• Susanne E, Volkhard H. Transient Pockets on Protein Surfaces Involved in Protein-Protein Interaction. J Med Chem 2007;50:3457–64
   PubMed Web of Science ®Google Scholar
• Camacho CJ, Holak TA, Dömling A. Exhaustive fluorine scanningtoward potent p53-MDM2 antagonists. Chem Med Chem 2012;7:49–52
   Web of Science ®Google Scholar
• Yijun H, Holak TA, Dömling A. Discovery of highly potent p53-MDM2 antagonists and structural basis for anti-acute myeloid leukemia activities. ACS Chem Biol 2014;9:802–11
   PubMed Web of Science ®Google Scholar
• Czarna A, Holak TA, Dömling A. Robustgeneration of lead compounds for protein−protein interactions bycomputational and MCR chemistry: p53/HDM2 antagonists. Angew Chem Int Ed 2010;49:5352–6
   PubMed Web of Science ®Google Scholar
• Dömling A, Ugi I. Multicomponent reactions with isocyanides. Angew Chem Int Ed 2000;39:3169–210
   Web of Science ®Google Scholar
• Jorgensen WL. The Many Roles of Computation in Drug Discovery. Science 2004;303:1813–18
   PubMed Web of Science ®Google Scholar
• Kitchen DB, Decornez H, Furr JR, et al. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004;3:935–49
   PubMed Web of Science ®Google Scholar
• Edwards AM, Isserlin R, Bader GD, et al. Too many roads not taken. Nature 2011;470:163–5
   PubMed Web of Science ®Google Scholar
• Kussie PH, Gorina S, Marechal V, et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 1996;274(5289):948–53
   PubMed Web of Science ®Google Scholar
• Masaki M, Hiroyuki N, Yuuichi S. Synthesis and evaluation of novel orally active p53–MDM2 interaction inhibitors. Bioorg Med Chem 2013;21:4319–31
   PubMed Web of Science ®Google Scholar
• Ana ZG, John E, Michael DB. Selective and potent morpholinone inhibitors of the MDM2−p53 protein−protein interaction. J Med Chem 2014;57:2472–88
   PubMed Web of Science ®Google Scholar
• Qingjie D, Zhuming Z, Jin-Jun L. Discovery of RG7388, a Potent and Selective p53−MDM2 Inhibitor in Clinical Development. J Med Chem 2013;56:5979–83
   PubMed Web of Science ®Google Scholar
• Popowicz GM, Czarna A, Dömling A. Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery. Cell Cycle 2010;9(6):1104–11
   PubMed Web of Science ®Google Scholar
• Changyou Z, Le Z, Xiaoli W. An Ultrahigh Affinity D-Peptide Antagonist of MDM2. J Med Chem 2012;55:6237–41
   PubMed Web of Science ®Google Scholar
• Sohee B, Peter SK, Gregory LV. Structure of the Stapled p53 Peptide Bound to Mdm2. J Am Chem Soc 2012;134:103–6
   PubMed Web of Science ®Google Scholar
• Kwon HJ, Lagace TA, McNutt MC, et al. Molecular basis for LDL receptor recognition by PCSK9. Proc Nat Acad Sci USA 2008;105:1820–5
   PubMed Web of Science ®Google Scholar
• Liu S, Song X, Chrunyk BA, et al. Crystal structures of interleukin 17A and its complex with IL-17 receptor A. Nat Commun 2013;4:1888–8
   PubMed Web of Science ®Google Scholar
• John JI, Teague S, Michael MM, et al. ZINC: A free tool to discover chemistry for biology. J Chem Inf Model 2012;52:1757–68
   PubMed Web of Science ®Google Scholar
• Mantosh KS, Khoury K, Dömling A, et al. Various cyclization scaffolds by a truly Ugi 4-CR. Org Biomol Chem 2013;11:4792–6
   PubMed Web of Science ®Google Scholar