The exploration of macrocycles for drug discovery — an underexploited structural class

Macrocyclic natural products have evolved to fulfil numerous biochemical functions, and their profound pharmacological properties have led to their development as drugs. A macrocycle provides diverse functionality and stereochemical complexity in a conformationally pre-organized ring structure. This can result in high affinity and selectivity for protein targets, while preserving sufficient bioavailability to reach intracellular locations. Despite these valuable characteristics, and the proven success of more than 100 marketed macrocycle drugs derived from natural products, this structural class has been poorly explored within drug discovery. This is in part due to concerns about synthetic intractability and non-drug-like properties. This Review describes the growing body of data in favour of macrocyclic therapeutics, and demonstrates that this class of compounds can be both fully drug-like in its properties and readily prepared owing to recent advances in synthetic medicinal chemistry.

[1]  Marilyn A. Anderson,et al.  Discovery of Cyclotide-Like Protein Sequences in Graminaceous Crop Plants: Ancestral Precursors of Circular Proteins?[W] , 2006, The Plant Cell Online.

[2]  Pravin Chaturvedi,et al.  Design principles for orally bioavailable drugs , 1996 .

[3]  R. Gussio,et al.  Comparison of the Activities of the Truncated Halichondrin B Analog NSC 707389 (E7389) with Those of the Parent Compound and a Proposed Binding Site on Tubulin , 2006, Molecular Pharmacology.

[4]  S. Beauchemin,et al.  Discovery of a new class of macrocyclic antagonists to the human motilin receptor. , 2006, Journal of medicinal chemistry.

[5]  M. Faul,et al.  (S)-13-[(dimethylamino)methyl]-10,11,14,15-tetrahydro-4,9:16, 21-dimetheno-1H, 13H-dibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecene-1,3(2H)-d ione (LY333531) and related analogues: isozyme selective inhibitors of protein kinase C beta. , 1996, Journal of medicinal chemistry.

[6]  J. Sanglier,et al.  Antascomicins A, B, C, D and E. Novel FKBP12 binding compounds from a Micromonospora strain. , 1996, The Journal of antibiotics.

[7]  D. Pei,et al.  Macrocyclic inhibitors for peptide deformylase: a structure-activity relationship study of the ring size. , 2004, Journal of medicinal chemistry.

[8]  M. Spaller,et al.  Bridged peptide macrocycles as ligands for PDZ domain proteins. , 2005, Organic letters.

[9]  William Fenical,et al.  Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora , 2006, Applied and Environmental Microbiology.

[10]  S. Schreiber,et al.  Macrolactones in diversity-oriented synthesis: preparation of a pilot library and exploration of factors controlling macrocyclization. , 2004, Journal of combinatorial chemistry.

[11]  E. Katz,et al.  The peptide antibiotics of Bacillus: chemistry, biogenesis, and possible functions. , 1977, Bacteriological reviews.

[12]  S. Matthews,et al.  Resisting degradation by human elastase: commonality of design features shared by 'canonical' plant and bacterial macrocyclic protease inhibitor scaffolds. , 2007, Bioorganic & medicinal chemistry.

[13]  M. Katharine Holloway,et al.  Macrocyclic Inhibitors of β-Secretase: Functional Activity in an Animal Model. , 2006 .

[14]  Hatsuo Aoki,et al.  FK-506, a novel immunosuppressant isolated from a Streptomyces. I. Fermentation, isolation, and physico-chemical and biological characteristics. , 1987 .

[15]  W. Greenlee,et al.  Macrocyclic renin inhibitors : synthesis of a subnanomolar, orally active cysteine derived inhibitor , 1993 .

[16]  K. Giuliano,et al.  Tubulin assembly, taxoid site binding, and cellular effects of the microtubule-stabilizing agent dictyostatin. , 2005, Biochemistry.

[17]  J. Clardy Structural studies on FK-506, cyclosporin A and their immunophilin complexes , 1994 .

[18]  W. DeGrado,et al.  Template-Constrained Cyclic Peptides: Design of High-Affinity Ligands for GPIIb/IIIa , 1994 .

[19]  Ronald J Quinn,et al.  A common protein fold topology shared by flavonoid biosynthetic enzymes and therapeutic targets. , 2006, Journal of natural products.

[20]  B. Brandhuber,et al.  750 Preclinical characteristics of ITMN-B, an orally active inhibitor of the HCV NS3/4A protease nominated for preclinical development , 2006 .

[21]  R A Stearns,et al.  Highly potent, orally active diester macrocyclic human renin inhibitors. , 1992, Journal of medicinal chemistry.

[22]  S. Schreiber,et al.  STRUCTURAL BASIS FOR PEPTIDOMIMICRY BY A NATURAL PRODUCT , 1994 .

[23]  P. Ruggli Über einen Ring mit dreifacher Bindung , 1912 .

[24]  L. Wessjohann Synthesis of natural-product-based compound libraries. , 2000, Current opinion in chemical biology.

[25]  Matthew P Jacobson,et al.  Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. , 2006, Journal of the American Chemical Society.

[26]  E. Nogales,et al.  Structure of tubulin at 6.5 Å and location of the taxol-binding site , 1995, Nature.

[27]  David J Newman,et al.  Natural products as sources of new drugs over the period 1981-2002. , 2003, Journal of natural products.

[28]  Derek S. Tan,et al.  Exploiting ligand conformation in selective inhibition of non-ribosomal peptide synthetase amino acid adenylation with designed macrocyclic small molecules. , 2007, Journal of the American Chemical Society.

[29]  L. Wessjohann,et al.  What Can a Chemist Learn from Nature′s Macrocycles? A Brief, Conceptual View , 2005 .

[30]  Bruce E Maryanoff Inhibitors of serine proteases as potential therapeutic agents: the road from thrombin to tryptase to cathepsin G. , 2004, Journal of medicinal chemistry.

[31]  Chang Park,et al.  Structure-based design, synthesis, and biological evaluation of potent and selective macrocyclic checkpoint kinase 1 inhibitors. , 2007, Journal of medicinal chemistry.

[32]  Douglas A. Horton,et al.  Difficult macrocyclizations: new strategies for synthesizing highly strained cyclic tetrapeptides. , 2003, Organic letters.

[33]  D. Fairlie,et al.  Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease. , 2000, Journal of medicinal chemistry.

[34]  Martin Poirier,et al.  Structure-activity study on a novel series of macrocyclic inhibitors of the hepatitis C virus NS3 protease leading to the discovery of BILN 2061. , 2004, Journal of medicinal chemistry.

[35]  H. Briem,et al.  Macrocyclic Aminopyrimidines as Multitarget CDK and VEGF‐R Inhibitors with Potent Antiproliferative Activities , 2007, ChemMedChem.

[36]  Martin J Scanlon,et al.  Conformationally constrained macrocycles that mimic tripeptide beta-strands in water and aprotic solvents. , 2002, Journal of the American Chemical Society.

[37]  F. Schluenzen,et al.  Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria , 2001, Nature.

[38]  T. Nicas,et al.  Mechanism of action of oritavancin and related glycopeptide antibiotics. , 2003, FEMS microbiology reviews.

[39]  J. Nielsen,et al.  Combinatorial synthesis of natural products. , 2002, Current opinion in chemical biology.

[40]  Y. Kook,et al.  Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences. , 2004, International journal of systematic and evolutionary microbiology.

[41]  D. Williams,et al.  Why are secondary metabolites (natural products) biosynthesized? , 1989, Journal of natural products.

[42]  A. Krantz,et al.  Synthesis and activity of conformationally-constrained macrocyclic norstatine-based inhibitors of HIV protease , 1996 .

[43]  G. Kroemer,et al.  Current development of mTOR inhibitors as anticancer agents , 2006, Nature Reviews Drug Discovery.

[44]  A. Kwong,et al.  Preclinical Profile of VX-950, a Potent, Selective, and Orally Bioavailable Inhibitor of Hepatitis C Virus NS3-4A Serine Protease , 2006, Antimicrobial Agents and Chemotherapy.

[45]  B. Maryanoff,et al.  Macrocyclic inhibitors of serine proteases , 1997 .

[46]  C. Verlinde,et al.  Structure-based design of a macrocyclic inhibitor for peptide deformylase. , 2003, Journal of medicinal chemistry.

[47]  S. Schreiber,et al.  Synthesis and analysis of 506BD, a high-affinity ligand for the immunophilin FKBP , 1991 .

[48]  Mark S Butler,et al.  Natural products to drugs: natural product derived compounds in clinical trials. , 2005, Natural product reports.

[49]  Paul H. Axelsen,et al.  Simultaneous Recognition of a Carboxylate-Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer , 1997 .

[50]  L. Wessjohann,et al.  Strategies for Total and Diversity-Oriented Synthesis of Natural Product(-like) Macrocycles , 2005 .

[51]  P. Bonneau,et al.  An NS 3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus , 2003 .

[52]  L. Wessjohann,et al.  Macrocycles Rapidly Produced by Multiple Multicomponent Reactions Including Bifunctional Building Blocks (MiBs) , 2005 .

[53]  Arun K. Ghosh,et al.  Synergistic Effects of Peloruside A and Laulimalide with Taxoid Site Drugs, but Not with Each Other, on Tubulin Assembly , 2006, Molecular Pharmacology.

[54]  D. Williams,et al.  On the evolution of functional secondary metabolites (natural products) , 1992, Molecular microbiology.

[55]  H. Hirai,et al.  Structure-based drug design of a highly potent CDK1,2,4,6 inhibitor with novel macrocyclic quinoxalin-2-one structure. , 2006, Bioorganic & medicinal chemistry letters.

[56]  W. DeGrado,et al.  Macrocyclic amino carboxylates as selective MMP-8 inhibitors. , 1998, Journal of medicinal chemistry.

[57]  A. Gradillas,et al.  Macrocyclization by ring-closing metathesis in the total synthesis of natural products: reaction conditions and limitations. , 2006, Angewandte Chemie.

[58]  Terry Walsh,et al.  Countering cooperative effects in protease inhibitors using constrained beta-strand-mimicking templates in focused combinatorial libraries. , 2004, Journal of medicinal chemistry.

[59]  R. Hughes,et al.  Solid- and solution-phase synthesis of vancomycin and vancomycin analogues with activity against vancomycin-resistant bacteria. , 2001, Chemistry.

[60]  William Fenical,et al.  Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica , 2007, Proceedings of the National Academy of Sciences.

[61]  J. Blondeau The evolution and role of macrolides in infectious diseases , 2002, Expert opinion on pharmacotherapy.

[62]  K. Altmann,et al.  Epothilones as lead structures for the synthesis-based discovery of new chemotypes for microtubule stabilization. , 2008, Accounts of chemical research.

[63]  Amitha K. Hewavitharana,et al.  Discovery of a New Source of Rifamycin Antibiotics in Marine Sponge Actinobacteria by Phylogenetic Prediction , 2006, Applied and Environmental Microbiology.

[64]  R. Hughes,et al.  Synthesis and biological evaluation of vancomycin dimers with potent activity against vancomycin-resistant bacteria: target-accelerated combinatorial synthesis. , 2001, Chemistry.

[65]  Herbert Waldmann,et al.  From protein domains to drug candidates-natural products as guiding principles in the design and synthesis of compound libraries. , 2002, Angewandte Chemie.

[66]  R J Lynch,et al.  Design and synthesis of P2-P1'-linked macrocyclic human renin inhibitors. , 1991, Journal of medicinal chemistry.

[67]  P. Wender,et al.  The design, computer modeling, solution structure, and biological evaluation of synthetic analogs of bryostatin 1. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Herbert Waldmann,et al.  From protein domains to drug candidates – natural products as guiding principles in , 2002 .

[69]  A L Demain,et al.  The natural functions of secondary metabolites. , 2000, Advances in biochemical engineering/biotechnology.

[70]  Steven R. LaPlante,et al.  An NS3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus , 2003, Nature.

[71]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[72]  Paul A Clemons,et al.  Relationship of stereochemical and skeletal diversity of small molecules to cellular measurement space. , 2004, Journal of the American Chemical Society.

[73]  D. Rich,et al.  Peptidomimetics derived from natural products , 1993, Medicinal research reviews.

[74]  Dajun Yang,et al.  A novel macrocyclic tetrapeptide mimetic that exhibits low-picomolar Grb2 SH2 domain-binding affinity. , 2003, Biochemical and biophysical research communications.

[75]  Andrew G. Leach,et al.  Comparison of the ATP binding sites of protein kinases using conformationally diverse bisindolylmaleimides. , 2005, Journal of the American Chemical Society.

[76]  A. Krantz,et al.  Design, synthesis, and activity of conformationally-constrained macrocyclic peptide-based inhibitors of HIV protease , 1994 .

[77]  S. Matsunaga,et al.  Bioactive marine metabolites. 33. Cyclotheonamides, potent thrombin inhibitors, from a marine sponge Theonella sp , 1990 .

[78]  R J Lynch,et al.  Renin inhibitors containing conformationally restricted P1-P1' dipeptide mimetics. , 1991, Journal of medicinal chemistry.

[79]  D. Pei,et al.  High-throughput synthesis and screening of cyclic peptide antibiotics. , 2007, Journal of medicinal chemistry.

[80]  S. Schreiber,et al.  The mechanism of action of cyclosporin A and FK506. , 1992, Immunology today.

[81]  É. Marsault,et al.  Potent macrocyclic antagonists to the motilin receptor presenting novel unnatural amino acids. , 2007, Bioorganic & medicinal chemistry letters.

[82]  Måns Ehrenberg,et al.  The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. , 2003, Journal of molecular biology.

[83]  Stuart L. Schreiber,et al.  Structure of the FKBP12-Rapamycin Complex Interacting with Binding Domain of Human FRAP , 1996, Science.

[84]  David R. Liu,et al.  DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles , 2004, Science.

[85]  B. Podlogar,et al.  Design, synthesis, and conformational analysis of a novel macrocyclic HIV-protease inhibitor. , 1994, Journal of medicinal chemistry.

[86]  K. Stankunas,et al.  Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity. , 2006, Chemistry & biology.

[87]  Rolf Müller,et al.  Evolutionary implications of bacterial polyketide synthases. , 2005, Molecular biology and evolution.

[88]  Matthew P Jacobson,et al.  Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. , 2006, Journal of the American Chemical Society.

[89]  J. Huff,et al.  Conformational restriction of flexible ligands guided by the transferred noe experiment: potent macrocyclic inhibitors of farnesyltransferase. , 2001, Journal of the American Chemical Society.

[90]  F. Koehn,et al.  The evolving role of natural products in drug discovery , 2005, Nature Reviews Drug Discovery.

[91]  P. Bonneau,et al.  Macrocyclic inhibitors of the NS3 protease as potential therapeutic agents of hepatitis C virus infection. , 2003, Angewandte Chemie.

[92]  P. Nghiem,et al.  Tacrolimus and pimecrolimus: from clever prokaryotes to inhibiting calcineurin and treating atopic dermatitis. , 2002, Journal of the American Academy of Dermatology.

[93]  S. Schreiber Immunophilin-sensitive protein phosphatase action in cell signaling pathways , 1992, Cell.

[94]  Wim J. N. Meester,et al.  Intramolecular Staudinger ligation: a powerful ring-closure method to form medium-sized lactams. , 2003, Angewandte Chemie.

[95]  N. Matsumori,et al.  Amphotericin B covalent dimers forming sterol-dependent ion-permeable membrane channels. , 2002, Journal of the American Chemical Society.

[96]  Dajun Yang,et al.  Development of a phosphatase-stable phosphotyrosyl mimetic suitably protected for the synthesis of high-affinity Grb2 SH2 domain-binding ligands. , 2002, Bioorganic & medicinal chemistry letters.

[97]  H. Ye,et al.  Novel bis(indolyl)maleimide pyridinophanes that are potent, selective inhibitors of glycogen synthase kinase-3. , 2007, Bioorganic & medicinal chemistry letters.

[98]  A. D. Rodrigues,et al.  3-Aminopyrrolidinone farnesyltransferase inhibitors: design of macrocyclic compounds with improved pharmacokinetics and excellent cell potency. , 2002, Journal of medicinal chemistry.

[99]  Dudley H. Williams,et al.  The Vancomycin Group of Antibiotics and the Fight Against Resistant Bacteria , 1999 .