ABSTRACT
Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.
Subject(s)
COVID-19 , Coronavirus 3C Proteases , SARS-CoV-2 , Humans , Peptides/pharmacology , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Protease Inhibitors/pharmacology , Protease Inhibitors/chemistry , Molecular Docking SimulationABSTRACT
Methionine aminopeptidase-2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. This step is required before they will fold or function correctly. Pre-clinical and clinical studies with a MetAP2 inhibitor suggest that they could be used as a novel treatment for obesity. Herein we describe the discovery of a series of pyrazolo[4,3-b]indoles as reversible MetAP2 inhibitors. A fragment-based drug discovery (FBDD) approach was used, beginning with the screening of fragment libraries to generate hits with high ligand-efficiency (LE). An indazole core was selected for further elaboration, guided by structural information. SAR from the indazole series led to the design of a pyrazolo[4,3-b]indole core and accelerated knowledge-based fragment growth resulted in potent and efficient MetAP2 inhibitors, which have shown robust and sustainable body weight loss in DIO mice when dosed orally.
Subject(s)
Aminopeptidases/antagonists & inhibitors , Body Weight/drug effects , Drug Discovery , Enzyme Inhibitors/pharmacology , Glycoproteins/antagonists & inhibitors , Indoles/pharmacology , Obesity/drug therapy , Pyrazoles/pharmacology , Administration, Oral , Aminopeptidases/metabolism , Animals , Dose-Response Relationship, Drug , Enzyme Inhibitors/administration & dosage , Enzyme Inhibitors/chemistry , Glycoproteins/metabolism , Humans , Indoles/administration & dosage , Indoles/chemistry , Methionyl Aminopeptidases , Mice , Mice, Obese , Models, Molecular , Molecular Structure , Pyrazoles/administration & dosage , Pyrazoles/chemistry , Structure-Activity RelationshipABSTRACT
Methionine aminopeptidase 2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. Pre-clinical and clinical studies suggest that MetAP2 inhibitors could be used as a novel treatment for obesity. Herein we describe our use of fragment screening methods and structural biology to quickly identify and elaborate an indazole fragment into a series of reversible MetAP2 inhibitors with <10nM potency, excellent selectivity, and favorable in vitro safety profiles.
Subject(s)
Aminopeptidases/antagonists & inhibitors , Body Weight/drug effects , Drug Discovery , Enzyme Inhibitors/pharmacology , Glycoproteins/antagonists & inhibitors , Indazoles/pharmacology , Obesity/drug therapy , Administration, Oral , Aminopeptidases/metabolism , Animals , Dose-Response Relationship, Drug , Enzyme Inhibitors/administration & dosage , Enzyme Inhibitors/chemistry , Glycoproteins/metabolism , Humans , Indazoles/chemical synthesis , Indazoles/chemistry , Methionyl Aminopeptidases , Mice , Mice, Obese , Models, Molecular , Molecular Structure , Structure-Activity RelationshipABSTRACT
The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and characterize its binding mode in the ATP binding site of Btk. Optimization of the fragment hit resulted in the identification of a lead compound which reduced paw swelling in a dose- and exposure-dependent fashion in a rat model of collagen-induced arthritis.
Subject(s)
Drug Discovery , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Protein-Tyrosine Kinases/antagonists & inhibitors , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Adenosine Triphosphate/metabolism , Agammaglobulinaemia Tyrosine Kinase , Animals , Arthritis/chemically induced , Arthritis/drug therapy , Binding Sites , Collagen/adverse effects , Dogs , Female , Ligands , Male , Mice , Models, Molecular , Protein Conformation , Protein Kinase Inhibitors/therapeutic use , Protein-Tyrosine Kinases/chemistry , Protein-Tyrosine Kinases/metabolism , Rats , Small Molecule Libraries/therapeutic useABSTRACT
A hit-to-lead optimization process was carried out on the high throughput screening hit compound 1 resulting in the identification of several potent and selective CCR1 receptor antagonists. Compound 37 shows the best overall profile with IC(50) values of <100 nM in binding and functional assays.
Subject(s)
Piperidines/chemistry , Piperidines/pharmacology , Receptors, CCR1/antagonists & inhibitors , Calcium/metabolism , Cell Line , Cell Movement/drug effects , Chemokine CCL3/metabolism , Chemotaxis/drug effects , Humans , Molecular Structure , Monocytes/cytology , Monocytes/drug effects , Monocytes/metabolism , Piperidines/chemical synthesis , Structure-Activity RelationshipABSTRACT
Design and synthesis of a series of 3-amino-4-(2-(2-(4-benzylpiperazin-1-yl)-2-oxoethoxy)phenylamino)cyclobutenedione derivatives as novel CCR1 antagonists are described. Structure-activity relationship studies led to the identification of compound 22, which demonstrated potent binding activity, functional antagonism of CCR1 as well as good species cross-reactivity. In addition, compound 22 also showed desirable pharmacokinetic profiles and was selected for in vivo studies in the mouse collagen-induced arthritis model.
