When analoging is not enough: scaffold discovery in medicinal chemistry

Bibliography

• Newman DJ, Cragg GM. Natural products as sources of new drugs over the last 25 years. J Nat Prod 2007;70:461-77
   PubMed Web of Science ®Google Scholar
• Jhoti H, Leach AR. Structure-based drug discovery. Springer, Dordrecht; 2007
   Google Scholar
• Brown N, Jacoby E. On scaffolds and hopping in medicinal chemistry. Mini Rev Med Chem 2006;6:1217-29
   PubMed Web of Science ®Google Scholar
• Schneider G, Schneider P, Renner S. Scaffold-hopping: how far can you jump? QSAR Comb Sci 2006;25:1162-71
   Google Scholar
• Hajduk PJ, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 2007;6:211-19
   PubMed Web of Science ®Google Scholar
• Congreve M, Chessari G, Tisi D, Recent developments in fragment-based drug discovery. J Med Chem 2008;51:3661-80
   PubMed Web of Science ®Google Scholar
• Aronov AM, McClain B, Moody CS, Kinase-likeness and kinase-privileged fragments: toward virtual polypharmacology. J Med Chem 2008;51:1214-22
   PubMed Web of Science ®Google Scholar
• van der Horst E, Okuno Y, Bender A, Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner. J Chem Inf Model 2009;9:348-60
   Google Scholar
• Zhao H. Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective. Drug Discov Today 2007;12:149-55
   PubMed Web of Science ®Google Scholar
• Oprea TI, Davis AM, Teague SJ, Is there a difference between leads and drugs? A historical perspective. J Chem Info Comput Sci 2001;41:1308-15
   PubMedGoogle Scholar
• Proudfoot JR. Drugs, leads, and drug-likeness: an analysis of some recently launched drugs. Bioorg Med Chem Lett 2002;12:1647-50
   PubMed Web of Science ®Google Scholar
• Reich HJ, Cram DJ. Macro rings. XXXVII. Multiple electrophilic substitution reactions of [2.2]paracyclophanes and interconversions of polysubstituted derivatives. J Am Chem Soc 1969;91:3527-33
   Web of Science ®Google Scholar
• Vieth M, Sutherland JJ. Dependence of molecular properties on proteomic family for marketed oral drugs. J Med Chem 2006;49:3451-3
   PubMed Web of Science ®Google Scholar
• Lombardino JG, Lowe JA. The role of the medicinal chemist in drug discovery — then and now. Nat Rev Drug Discov 2004;3:853-62
   PubMed Web of Science ®Google Scholar
• Adams C, Brantner VV. Estimating the cost of new drug development: is it really $802 million? Health Aff 2006;2:420-8
   Google Scholar
• Warr WA. Fragment-based drug discovery. J Comput Aided Mol Des 2009;23:453-8
   PubMed Web of Science ®Google Scholar
• Keserü GM, Makara GM. The influence of lead discovery strategies on the properties of drug candidates. Nat Rev Drug Discov 2009;8:203-12
   PubMed Web of Science ®Google Scholar
• Fink T, Bruggesser H, Reymond JL. Virtual exploration of the small-molecule chemical universe below 160 Daltons. Angew Chem Int Ed Engl 2005;44:1504-8
   PubMed Web of Science ®Google Scholar
• Schuffenhauer A, Ruedisser S, Marzinzik A, Library design for fragment based screening. Curr Top Med Chem 2005;5:751-62
   PubMed Web of Science ®Google Scholar
• Orita M, Warizaya M, Amano Y, Advances in fragment-based drug discovery platforms. Exp Opin Drug Discov 2009;4:1125-44
   PubMed Web of Science ®Google Scholar
• Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2006;2:720-3
   PubMed Web of Science ®Google Scholar
• Arkin MR, Wells JA. Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004;3:301-17
   PubMed Web of Science ®Google Scholar
• Fuller JC, Burgoyne NJ, Jackson RM. Predicting druggable binding sites at the protein–protein interface. Drug Discov Today 2009;14:155-61
   PubMed Web of Science ®Google Scholar
• Oltersdorf T, Elmore SW, Shoemaker AR, An inhibitor of Bcl family proteins induces regression of solid tumours. Nature 2005;435:677-81
   PubMed Web of Science ®Google Scholar
• Wendt MD. Discovery of ABT-263, a Bcl-family protein inhibitor: observations on targeting a large protein–protein interaction. Exp Opin Drug Discov 2008;3:1123-43
   PubMed Web of Science ®Google Scholar
• Juin P, Geneste O, Raimbaud E, Shooting at survivors: Bcl-2 family members as drug targets for cancer. Biochim Biophys Acta 2004;1644:251-60
   PubMed Web of Science ®Google Scholar
• Petros AM, Dinges J, Augeri DA, Discovery of a potent inhibitor of the antiapoptotic protein Bcl-xL from NMR and parallel synthesis. J Med Chem 2006;49:656-63
   PubMed Web of Science ®Google Scholar
• Hopkins AL, Mason JS, Overington JP. Can we rationally design promiscuous drugs? Curr Opin Struct Biol 2006;16:127-36
   PubMed Web of Science ®Google Scholar
• Morphy R, Rankovic Z. Fragments, network biology and designing multiple ligands. Drug Discov Today 2007;12:156-60
   PubMed Web of Science ®Google Scholar
• Roth BL, Sheffler DJ, Kroeze WK. Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov 2004;3:353-9
   PubMed Web of Science ®Google Scholar
• Morphy R, Rankovic Z. The physicochemical challenges of designing multiple ligands. J Med Chem 2006;49:4961-70
   PubMed Web of Science ®Google Scholar
• Card GL, Blasdel L, England BP, A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat Biotechnol 2005;23:201-7
   PubMed Web of Science ®Google Scholar
• Artis DA, Lin JJ, Zhang C, Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent. Proc Natl Acad Sci USA 2009;106:262-7
   PubMed Web of Science ®Google Scholar
• Willson TM, Brown PJ, Sternbach DD, The PPARs: from orphan receptors to drug discovery. J Med Chem 2000;43:527-50
   PubMed Web of Science ®Google Scholar
• Schneider G, Neidhart W, Giller T, “Scaffold-hopping” by topological pharmacophore search: a contribution to virtual screening. Angew Chem Int Ed Engl 1999;38:2894-6
   PubMed Web of Science ®Google Scholar
• Xin Z, Zhao H, Serby MD, Discovery of piperidine-aryl urea-based stearoyl-CoA desaturase 1 inhibitors. Bioorg Med Chem Lett 2008;18:4298-302
   PubMed Web of Science ®Google Scholar
• Abreo M, Chafeev M, Chakka N, WO 2005/011655; 2005
   Google Scholar
• Liu G, Lynch JK, Freeman J, Discovery of potent, selective, orally bioavailable stearoyl-CoA desaturase 1 inhibitors. J Med Chem 2007;50:3086-100
   PubMed Web of Science ®Google Scholar
• Zhao H, Guo Z. Medicinal chemistry strategies in follow-on drug discovery. Drug Discov Today 2009;14:516-22
   PubMed Web of Science ®Google Scholar
• Sandner P, Ziegelbauer K. Product-related research: how research can contribute to successful life-cycle management. Drug Discov Today 2008;13:457-63
   PubMed Web of Science ®Google Scholar
• Nicholas KT, Andrew SB, David B, Sildenafil (VIAGRA™), a potent and selective inhibitor of type 5 cGMP phosphodiesterase with utility for the treatment of male erectile dysfunction. Bioorg Med Chem Lett 1996;6:1819-24
   Web of Science ®Google Scholar
• Haning H, Niewöhner U, Schenke T, Imidazo[5,1-f][1,2, and 4]triazin-4(3H)-ones, a new class of potent PDE 5 inhibitors. Bioorg Med Chem Lett 2002;12:865-8
   PubMed Web of Science ®Google Scholar
• Andricopulo AD, Salum1 LB, Abraham DJ. Structure-based drug design strategies in medicinal chemistry. Curr Top Med Chem 2009;9:771-90
   PubMed Web of Science ®Google Scholar
• Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 2005;4:649-63
   PubMed Web of Science ®Google Scholar
• Klebe G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2006;11:580-94
   PubMed Web of Science ®Google Scholar
• Clark DE. What has computer-aided molecular design ever done for drug discovery? Exp Opin Drug Discov 2006;1:103-10
   PubMed Web of Science ®Google Scholar
• Jorgensen WL. Efficient drug lead discovery and optimization. Acc Chem Res 2009;42:724-33
   PubMed Web of Science ®Google Scholar
• Nuti E, Panelli L, Casalini F, Design, synthesis, biological evaluation, and NMR studies of a new series of arylsulfones as selective and potent matrix metalloproteinase-12 inhibitors. J Med Chem 2009;52:6347-61
   PubMed Web of Science ®Google Scholar
• Zaliani A, Boda K, Seidel T, Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des 2009;23:593-602
   PubMed Web of Science ®Google Scholar
• Vieth M, Erickson J, Wang J, Kinase inihibitor data modeling and de novo inhibitor design with fragment approaches. J Med Chem 2009;52:6456-66
   PubMed Web of Science ®Google Scholar
• Bemis GW, Murcko MA. The properties of known drugs. 1. Molecular frameworks. J Med Chem 1996;39:2887-93
   PubMed Web of Science ®Google Scholar
• Wilson RM, Danishefsky SJ. Small molecule natural products in the discovery of therapeutic agents: the synthesis connection. J Org Chem 2006;71:8329-51
   PubMed Web of Science ®Google Scholar
• Borzilleri RM, Vite GD. Case history: discovery of ixabepilone (IXEMPRA™), a first-in-class epothilone analog for treatment of cancer. Ann Rep Med Chem 2008;44:301-22
   Web of Science ®Google Scholar
• Hert J, Irwin JJ, Laggner C, Quantifying biogenic bias in screening libraries. Nat Chem Biol 2009;5:479-83
   PubMed Web of Science ®Google Scholar
• Maibaum J, Feldman DL. Case history on Tekturna®/Rasilez® (Aliskiren), a highly efficacious direct oral rennin inhibitor as a new therapy for hypertension. Ann Rep Med Chem 2008;44:105-27
   Web of Science ®Google Scholar
• David E, Tramontin T, Zemmel R. Pharmaceutical R&D: the road to positive returns. Nat Rev Drug Discov 2009;8:609-10
   PubMed Web of Science ®Google Scholar
• Ruffolo RR. Why has R&D productivity declined in the pharmaceutical industry? Exp Opin Drug Discov 2006;1:99-102
   PubMed Web of Science ®Google Scholar