ABSTRACT
The p38α mitogen-activated protein kinase regulates the synthesis of pro-inflammatory cytokines in response to stimulation by a diverse set of stress signals. Various different chemotypes and clinical candidates that inhibit p38α function have been reported over the years. In this publication, the novel structure of p38α cocrystallized with the clinical candidate TAK-715 is reported. Owing to the impact of crystallization conditions on the conformation of protein kinases (and in particular p38α), the structures of complexes of p38α with SB-203580, SCIO-469 and VX-745 have also been determined to enable in-depth comparison of ligand-induced protein conformations. The impact of experimental conditions on p38α-inhibitor complex structures, most importantly soaking versus cocrystallization, is discussed. Analysis of the structures and quantification of the protein-ligand interactions couples ligand-induced protein conformations to the number of interactions and to inhibitor selectivity against the human kinome. This shows that for the design of novel kinase inhibitors, selectivity is best obtained through maximization of the number of interactions throughout the ATP pocket and the exploitation of specific features in the active site.
Subject(s)
Benzamides/pharmacology , Thiazoles/pharmacology , p38 Mitogen-Activated Protein Kinases/chemistry , Adenosine Triphosphate/chemistry , Catalytic Domain , Cloning, Molecular , Crystallization , Crystallography, X-Ray/methods , Humans , Imidazoles/pharmacology , Indoles/pharmacology , Ligands , Protein Binding , Protein Conformation , Protein Kinase Inhibitors/pharmacology , Pyridazines/pharmacology , Pyridines/pharmacology , Pyrimidines/pharmacology , Structure-Activity RelationshipABSTRACT
MK2 kinase is a promising drug discovery target for the treatment of inflammatory diseases. Here, we describe the discovery of novel MK2 inhibitors using X-ray crystallography and structure-based drug design. The lead has in vivo efficacy in a short-term preclinical model.
Subject(s)
Adenosine Triphosphate , Drug Design , Intracellular Signaling Peptides and Proteins/antagonists & inhibitors , Protein Kinase Inhibitors/chemical synthesis , Protein Serine-Threonine Kinases/antagonists & inhibitors , Adenosine Triphosphate/chemistry , Animals , Binding, Competitive , Caco-2 Cells , Crystallography, X-Ray , Disease Models, Animal , Humans , Inhibitory Concentration 50 , Intracellular Signaling Peptides and Proteins/chemistry , Models, Molecular , Molecular Structure , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/chemistry , Rats , Structure-Activity RelationshipABSTRACT
The identification of a potent, selective, and orally available MK2 inhibitor series is described. The initial absence of oral bioavailability was successfully tackled by moving the basic nitrogen of the spiro-4-piperidyl moiety towards the electron-deficient pyrrolepyridinedione core, thereby reducing the pK(a) and improving Caco-2 permeability. The resulting racemic spiro-3-piperidyl analogues were separated by chiral preparative HPLC, and the activity towards MK2 inhibition was shown to reside mostly in the first eluting stereoisomer. This led to the identification of new MK2 inhibitors, such as (S)-23, with low nanomolar biochemical inhibition (EC(50) 7.4 nM) and submicromolar cellular target engagement activity (EC(50) 0.5 µM).
Subject(s)
Drug Discovery , Intracellular Signaling Peptides and Proteins/antagonists & inhibitors , Piperidines/chemical synthesis , Protein Serine-Threonine Kinases/antagonists & inhibitors , Spiro Compounds/chemical synthesis , Administration, Oral , Animals , Binding, Competitive , Biological Availability , Caco-2 Cells , Chromatography, High Pressure Liquid , Crystallography, X-Ray , Disease Models, Animal , Enzyme Activation/drug effects , Humans , Inhibitory Concentration 50 , Intracellular Signaling Peptides and Proteins/chemistry , Molecular Structure , Piperidines/chemistry , Piperidines/pharmacology , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/chemistry , Rats , Spiro Compounds/chemistry , Spiro Compounds/pharmacology , Stereoisomerism , Structure-Activity Relationship , Substrate SpecificityABSTRACT
The trifluoromethylphenyl P2 motif from previously reported heteroarylnitrile series has been successfully applied for the design and synthesis of highly potent novel ketoamide-based cathepsin S inhibitors. The key in this process is the change of the torsion angle between the P2 phenyl ring and the attached secondary amide by adding a small Cl, F, or Me group at the 2-position.
Subject(s)
Aniline Compounds/chemical synthesis , Cathepsins/antagonists & inhibitors , Cysteine Proteinase Inhibitors/chemical synthesis , Amides/chemical synthesis , Amides/pharmacology , Aniline Compounds/pharmacology , Animals , Cysteine Proteinase Inhibitors/pharmacology , Fluorine , Humans , Ketones , Structure-Activity RelationshipABSTRACT
Several structure-guided optimisation strategies were explored in order to improve the hERG selectivity profile of cathepsin K inhibitor 1, whilst maintaining its otherwise excellent in vitro and in vivo profile. Ultimately, attenuation of clogP and pK(a) properties proved a successful approach and led to the discovery of a potent analogue 23, which, in addition to the desired selectivity over hERG (>1000-fold), displayed a highly attractive overall profile.
Subject(s)
Cathepsin K/antagonists & inhibitors , Ether-A-Go-Go Potassium Channels/drug effects , Nitriles/chemical synthesis , Nitriles/pharmacology , Potassium Channel Blockers/chemical synthesis , Potassium Channel Blockers/pharmacology , Pyrimidines/chemical synthesis , Pyrimidines/pharmacology , Drug Design , Drug Discovery , Indicators and Reagents , Models, Molecular , ROC Curve , Structure-Activity Relationship , Torsades de Pointes/drug therapyABSTRACT
Starting from previously disclosed equally potent cathepsin K and S inhibitor 4-propyl-6-(3-trifluoromethylphenyl)pyrimidine-2-carbonitrile 1, a novel 2-phenyl-9H-purine-6-carbonitrile scaffold was identified to provide potent and selective cathepsin S inhibitors.
Subject(s)
Cathepsins/antagonists & inhibitors , Nitriles/chemistry , Protease Inhibitors/chemistry , Purines/chemistry , Catalytic Domain , Cathepsin K/antagonists & inhibitors , Cathepsin K/metabolism , Cathepsins/metabolism , Cell Line , Computer Simulation , Humans , Nitriles/chemical synthesis , Nitriles/pharmacology , Protease Inhibitors/chemical synthesis , Protease Inhibitors/pharmacology , Purines/chemical synthesis , Purines/pharmacology , Pyrimidines/chemistryABSTRACT
6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile analogues were identified as potent and selective cathepsin S inhibitor against both purified enzyme and in human JY cell based cellular assays. This core has a very stable thio-trapping nitrile war-head in comparison with the well reported pyrimidine-2-carbonitrile cysteine cathepsin inhibitors. Compound 47 is also very potent in in vivo mouse spleenic Lip10 accumulation assays.
Subject(s)
Cathepsins/antagonists & inhibitors , Nitriles/chemistry , Protease Inhibitors/chemistry , Pyridines/chemistry , Animals , Binding Sites , Cathepsins/metabolism , Cell Line , Crystallography, X-Ray , Humans , Mice , Nitriles/chemical synthesis , Nitriles/pharmacokinetics , Protease Inhibitors/chemical synthesis , Protease Inhibitors/pharmacokinetics , Pyridines/chemical synthesis , Pyridines/pharmacokinetics , Structure-Activity RelationshipABSTRACT
Using computer aided modelling studies, a new extended P2/S2 interaction was identified. This extended region can accommodate a variety of functional groups, such as aryls and basic amines. It was discovered that the N3 nitrogen of the pyrimidine-2-carbonitrile is critical for its cathepsin cysteine protease inhibition. N1 nitrogen also contributes to the inhibitory activity, but to a very limited degree. An 'in situ double activation' mechanism was proposed to explain these results.
Subject(s)
Cathepsins/antagonists & inhibitors , Nitriles/chemistry , Protease Inhibitors/chemistry , Pyrimidines/chemistry , Binding Sites , Cathepsins/metabolism , Computer Simulation , Humans , Models, Molecular , Nitriles/chemical synthesis , Nitriles/pharmacology , Protease Inhibitors/chemical synthesis , Protease Inhibitors/pharmacologyABSTRACT
Morphing structural features of HTS-derived chemotypes led to the discovery of novel 2-cyano-pyrimidine inhibitors of cathepsin K with good pharmacokinetic profiles, for example, compound 20 showed high catK potency (IC(50)=4nM), >580-fold selectivity over catL and catB, and oral bioavailability in the rat of 52%.
Subject(s)
Cathepsin K/antagonists & inhibitors , Cysteine Proteinase Inhibitors/chemistry , Pyrimidines/chemistry , Administration, Oral , Animals , Binding Sites , Cathepsin K/metabolism , Cell Line , Crystallography, X-Ray , Cysteine Proteinase Inhibitors/chemical synthesis , Cysteine Proteinase Inhibitors/pharmacokinetics , Drug Design , High-Throughput Screening Assays , Humans , Pyrimidines/chemical synthesis , Pyrimidines/pharmacokinetics , Rats , Rats, Sprague-Dawley , Structure-Activity RelationshipABSTRACT
A novel dioxo-triazine series of cathepsin K inhibitors was identified from HTS. A rapid exploratory programme led to the discovery of potent and selective cathepsin K inhibitors, typified by compound 24 which displayed IC(50) values of 17nM against catK and >10,000nM in catL, catB and catS assays.
