ABSTRACT
Inhibition of soluble epoxide hydrolase (sEH) has recently emerged as a new approach to treat cardiovascular disease and respiratory disease. Inhibitors based on 1,3,5-triazine chemotype were discovered through affinity selection against two triazine-based DNA-encoded libraries. The structure and activity relationship study led to the expansion of the original 1,4-cycloalkyl series to related aniline, piperidine, quinoline, aryl-ether and benzylic series. The 1,3-cycloalkyl chemotype led to the discovery of a clinical candidate (GSK2256294) for COPD.
Subject(s)
Cyclohexylamines/pharmacology , Epoxide Hydrolases/antagonists & inhibitors , Triazines/pharmacology , Cyclohexylamines/chemistry , Drug Discovery , Humans , Molecular Structure , Pulmonary Disease, Chronic Obstructive/drug therapy , Small Molecule Libraries , Triazines/chemistryABSTRACT
DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).
Subject(s)
DNA/chemistry , Iodobenzoates/chemistry , Phosphatidylinositol 3-Kinases/chemistry , Small Molecule Libraries/chemical synthesis , Acylation , Amination , Combinatorial Chemistry Techniques , Humans , Ligands , Structure-Activity RelationshipABSTRACT
The aggrecan degrading metalloprotease ADAMTS-4 has been identified as a novel therapeutic target for osteoarthritis. Here, we use DNA-encoded Library Technology (ELT) to identify novel ADAMTS-4 inhibitors from a DNA-encoded triazine library by affinity selection. Structure-activity relationship studies based on the selection information led to the identification of potent and highly selective inhibitors. For example, 4-(((4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-6-(((4-methylpiperazin-1-yl)methyl)amino)-1,3,5-triazin-2-yl)amino)methyl)-N-ethyl-N-(m-tolyl)benzamide has IC50 of 10 nM against ADAMTS-4, with >1000-fold selectivity over ADAMT-5, MMP-13, TACE, and ADAMTS-13. These inhibitors have no obvious zinc ligand functionality.
ABSTRACT
In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.
ABSTRACT
The inhibition of protein-protein interactions remains a challenge for traditional small molecule drug discovery. Here we describe the use of DNA-encoded library technology for the discovery of small molecules that are potent inhibitors of the interaction between lymphocyte function-associated antigen 1 and its ligand intercellular adhesion molecule 1. A DNA-encoded library with a potential complexity of 4.1 billion compounds was exposed to the I-domain of the target protein and the bound ligands were affinity selected, yielding an enriched small-molecule hit family. Compounds representing this family were synthesized without their DNA encoding moiety and found to inhibit the lymphocyte function-associated antigen 1/intercellular adhesion molecule-1 interaction with submicromolar potency in both ELISA and cell adhesion assays. Re-synthesized compounds conjugated to DNA or a fluorophore were demonstrated to bind to cells expressing the target protein.
Subject(s)
Drug Discovery , Lymphocyte Function-Associated Antigen-1/metabolism , Small Molecule Libraries/pharmacology , Cell Adhesion/drug effects , Dose-Response Relationship, Drug , Humans , Jurkat Cells , Ligands , Molecular Structure , Protein Binding/drug effects , Small Molecule Libraries/chemical synthesis , Small Molecule Libraries/chemistry , Structure-Activity RelationshipABSTRACT
The metalloprotease ADAMTS-5 is considered a potential target for the treatment of osteoarthritis. To identify selective inhibitors of ADAMTS-5, we employed encoded library technology (ELT), which enables affinity selection of small molecule binders from complex mixtures by DNA tagging. Selection of ADAMTS-5 against a four-billion member ELT library led to a novel inhibitor scaffold not containing a classical zinc-binding functionality. One exemplar, (R)-N-((1-(4-(but-3-en-1-ylamino)-6-(((2-(thiophen-2-yl)thiazol-4-yl)methyl)amino)-1,3,5-triazin-2-yl)pyrrolidin-2-yl)methyl)-4-propylbenzenesulfonamide (8), inhibited ADAMTS-5 with IC(50) = 30 nM, showing >50-fold selectivity against ADAMTS-4 and >1000-fold selectivity against ADAMTS-1, ADAMTS-13, MMP-13, and TACE. Extensive SAR studies showed that potency and physicochemical properties of the scaffold could be further improved. Furthermore, in a human osteoarthritis cartilage explant study, compounds 8 and 15f inhibited aggrecanase-mediated (374)ARGS neoepitope release from aggrecan and glycosaminoglycan in response to IL-1ß/OSM stimulation. This study provides the first small molecule evidence for the critical role of ADAMTS-5 in human cartilage degradation.
Subject(s)
ADAM Proteins/antagonists & inhibitors , Cartilage, Articular/drug effects , Databases, Chemical , Osteoarthritis/pathology , Sulfonamides/chemical synthesis , Triazines/chemical synthesis , ADAMTS5 Protein , Aggrecans/metabolism , Animals , Cartilage, Articular/metabolism , Cartilage, Articular/pathology , Endopeptidases/metabolism , Epitopes , Glycosaminoglycans/metabolism , Humans , In Vitro Techniques , Male , Middle Aged , Osteoarthritis/drug therapy , Rats , Rats, Sprague-Dawley , Small Molecule Libraries , Stereoisomerism , Structure-Activity Relationship , Sulfonamides/pharmacokinetics , Sulfonamides/pharmacology , Triazines/pharmacokinetics , Triazines/pharmacologyABSTRACT
Inhibition of methionine aminopeptidase-2 (MetAP2) represents a novel approach to antiangiogenic therapy. We describe the synthesis and activity of fumagillin analogues that address the pharmacokinetic and safety liabilities of earlier candidates in this compound class. Two-step elaboration of fumagillol with amines yielded a diverse series of carbamates at C6 of the cyclohexane spiroepoxide. The most potent of these compounds exhibited subnanomolar inhibition of cell proliferation in HUVEC and BAEC assays. Although a range of functionalities were tolerated at this position, alpha-trisubstituted amines possessed markedly decreased inhibitory activity, and this could be rationalized by modeling based on the known fumagillin-MetAP2 crystal structure. The lead compound resulting from these studies, (3R,4S,5S,6R)-5-methoxy-4-((2R,3R)-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl)-1-oxaspiro[2.5]octan-6-yl (R)-1-amino-3-methyl-1-oxobutan-2-ylcarbamate, (PPI-2458), demonstrated an improved pharmacokinetic profile relative to the earlier clinical candidate TNP-470, and has advanced into phase I clinical studies in non-Hodgkin's lymphoma and solid cancers.
Subject(s)
Aminopeptidases/antagonists & inhibitors , Carbamates/chemistry , Carbamates/pharmacology , Cyclohexanes/chemistry , Cyclohexanes/pharmacology , Fatty Acids, Unsaturated/chemistry , Fatty Acids, Unsaturated/pharmacology , Metalloendopeptidases/antagonists & inhibitors , Amino Acids/chemistry , Animals , Cattle , Cell Growth Processes/drug effects , Endothelial Cells/cytology , Endothelial Cells/drug effects , Humans , Models, Molecular , Sesquiterpenes/chemistry , Sesquiterpenes/pharmacology , Structure-Activity RelationshipABSTRACT
Fumagillin, an irreversible inhibitor of MetAP2, has been shown to potently inhibit growth of malaria parasites in vitro. Here, we demonstrate activity of fumagillin analogs with an improved pharmacokinetic profile against malaria parasites, trypanosomes, and amoebas. A subset of the compounds showed efficacy in a murine malaria model. The observed SAR forms a basis for further optimization of fumagillin based inhibitors against parasitic targets by inhibition of MetAP2.
Subject(s)
Aminopeptidases/antagonists & inhibitors , Antimalarials/chemistry , Cyclohexanes/chemistry , Fatty Acids, Unsaturated/chemistry , Metalloendopeptidases/antagonists & inhibitors , Administration, Oral , Aminopeptidases/metabolism , Animals , Antimalarials/chemical synthesis , Antimalarials/pharmacology , Cyclohexanes/chemical synthesis , Cyclohexanes/pharmacology , Fatty Acids, Unsaturated/chemical synthesis , Fatty Acids, Unsaturated/pharmacology , Metalloendopeptidases/metabolism , Mice , Parasitic Sensitivity Tests , Sesquiterpenes/chemical synthesis , Sesquiterpenes/chemistry , Sesquiterpenes/pharmacologyABSTRACT
Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a long-sought goal. We report the synthesis and interrogation of an 800-million-member DNA-encoded library in which small molecules are covalently attached to an encoding oligonucleotide. The library was assembled by a combination of chemical and enzymatic synthesis, and interrogated by affinity selection. We describe methods for the selection and deconvolution of the chemical display library, and the discovery of inhibitors for two enzymes: Aurora A kinase and p38 MAP kinase.