ABSTRACT
The discovery of a highly potent and selective small molecule inhibitor 9 for in vitro target validation of MNK1/2 kinases is described. The aminopyrazine benzimidazole series was derived from an HTS hit and optimized by utilization of a docking model, conformation analysis, and binding pocket comparison against antitargets.
Subject(s)
Intracellular Signaling Peptides and Proteins/antagonists & inhibitors , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/antagonists & inhibitors , Binding Sites , Caco-2 Cells/drug effects , Drug Design , High-Throughput Screening Assays/methods , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Molecular Docking Simulation , Permeability , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/metabolism , Solubility , Structure-Activity RelationshipABSTRACT
A series of structure based drug design hypotheses and focused screening efforts led to the identification of tetrahydropyrrolo-diazepenones with striking potency against ERK2 kinase. The role of fluorination in mitigating microsomal clearance was systematically explored. Ultimately, it was found that fluorination of a cyclopentanol substructure provided significant improvement in both potency and human metabolic stability.
Subject(s)
Azepines/pharmacology , Heterocyclic Compounds, 2-Ring/pharmacology , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Pyrroles/pharmacology , Azepines/chemistry , Crystallography, X-Ray , Dose-Response Relationship, Drug , Heterocyclic Compounds, 2-Ring/chemistry , Humans , Mitogen-Activated Protein Kinase 1/metabolism , Models, Molecular , Molecular Structure , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry , Pyrroles/chemistry , Structure-Activity RelationshipABSTRACT
The current standard of care for hepatitis C virus (HCV) infection, pegylated alpha interferon in combination with ribavirin, has a limited response rate and adverse side effects. Drugs targeting viral proteins are in clinical development, but they suffer from the development of high viral resistance. The inhibition of cellular proteins that are essential for viral amplification is thought to have a higher barrier to the emergence of resistance. Three cyclophilin inhibitors, the cyclosporine analogs DEBIO-025, SCY635, and NIM811, have shown promising results for the treatment of HCV infection in early clinical trials. In this study, we investigated the frequency and mechanism of resistance to cyclosporine (CsA), NIM811, and a structurally unrelated cyclophilin inhibitor, SFA-1, in replicon-containing Huh7 cells. Cross-resistance between all clones was observed. NIM811-resistant clones were selected only after obtaining initial resistance to either CsA or SFA-1. The time required to select resistance against cyclophilin inhibitors was significantly longer than that required for resistance selection against viral protein inhibitors, and the achievable resistance level was substantially lower. Resistance to cyclophilin inhibitors was mediated by amino acid substitutions in NS3, NS5A, and NS5B, with NS5A mutations conferring the majority of resistance. Mutation D320E in NS5A mediated most of the resistance conferred by NS5A. Taken together, the results indicate that there is a very low frequency and level of resistance to cyclophilin-binding drugs mediated by amino acid substitutions in three viral proteins. The interaction of cyclophilin with NS5A seems to be the most critical, since the NS5A mutations have the largest impact on resistance.
Subject(s)
Cyclophilins/antagonists & inhibitors , Cyclosporine/pharmacology , Drug Resistance, Viral/physiology , Hepacivirus/genetics , Replicon/genetics , Antiviral Agents/pharmacology , Cell Line , Cyclosporins/pharmacology , Enzyme Inhibitors/pharmacology , Hepacivirus/growth & development , Hepacivirus/metabolism , Humans , Lactones/pharmacology , Mutagenesis, Site-Directed , RNA, Viral/metabolism , Spiro Compounds/pharmacology , Transfection , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolismABSTRACT
6-Substituted 8,9-dimethoxy-2,3-methylenedioxy-6H-dibenzo[c,h][2,6]naphthyridin-5-ones were synthesized and evaluated for topoisomerase I-targeting activity and cytotoxicity. Several of these reversed lactam analogues of ARC-111 exhibited exceptional cytotoxicity with IC50 values ranging from 0.5 to 3.0 nM. In contrast to topotecan, no resistance was observed with several of these reversed lactam analogues in tumor cell lines that overexpressed the efflux transporters MDR1 or BCRP.
Subject(s)
Benzene/chemistry , DNA Topoisomerases, Type I/metabolism , Lactams/chemistry , Naphthyridines/chemistry , Naphthyridines/pharmacology , Topoisomerase I Inhibitors , Amides/chemistry , Camptothecin/pharmacology , Cell Line , Cell Proliferation/drug effects , DNA/metabolism , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/toxicity , Humans , Molecular Structure , Naphthyridines/chemical synthesis , Naphthyridines/toxicity , Structure-Activity RelationshipABSTRACT
The exceptional topoisomerase I-targeting activity and antitumor activity of 5-(2-N,N-dimethylamino)ethyl-8,9-dimethoxy-2,3-methylenedioxy-5H-dibenzo[c,h][1,6]naphthyridin-6-one (ARC-111, topovale) prompted studies on similarly substituted benzo[i]phenanthridine-12-carboxylic ester and amide derivatives. Among the benzo[i]phenanthridine-12-carboxylic esters evaluated, the 2-(N,N-dimethylamino)ethyl, 2-(N,N-dimethylamino)-1-methylethyl, and 2-(N,N-dimethylamino)-1,1-dimethylethyl esters possessed similar cytotoxicity, ranging from 30 to 55 nM in RPMI8402 and KB3-1 cells. Several of the carboxamide derivatives possess potent topoisomerase I-targeting activity and cytotoxicity. The 2-(N,N-dimethylamino)ethyl, 2-(N,N-diethylamino)ethyl, and 2-(pyrrolidin-1-yl)ethyl amides were among the more cytotoxic benzo[i]phenanthridine-12-carboxylic derivatives, with IC50 values ranging from 0.4 to 5.0 nM in RPMI8402 and KB3-1 cells.
Subject(s)
Amides/chemistry , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/toxicity , Esters/chemistry , Topoisomerase I Inhibitors , Camptothecin/analogs & derivatives , Camptothecin/chemistry , Cell Line , Cell Survival/drug effects , DNA/metabolism , DNA Topoisomerases, Type I/metabolism , Enzyme Inhibitors/chemical synthesis , Humans , Inhibitory Concentration 50 , Irinotecan , Molecular Structure , Topotecan/chemistryABSTRACT
The exceptional TOP1-targeting activity and antitumor activity of ARC-111, 1, prompted studies on similarly substituted benzo[i]phenanthridine-12-carboxylic ester and amide derivatives. These studies were extended to include 6-substituted 8,9-dimethoxy-2,3-methylenedioxy-dibenzo[c,h][2,6]naphthyridin-5-ones, which represent reversed lactam analogues of 1. Several of these analogues retained the potent TOP1-targeting activity and cytotoxicity observed for ARC-111.