ABSTRACT
Zika virus (ZIKV) is a member of the Flaviviridae family that can cause neurological disorders and congenital malformations. The NS2B-NS3 viral serine protease is an attractive target for the development of new antiviral agents against ZIKV. We report here a SAR study on a series of substrate-like linear tripeptides that inhibit in a non-covalent manner the NS2B-NS3 protease. Optimization of the residues at positions P1, P2, P3 and of the N-terminal and C-terminal portions of the tripeptide allowed the identification of inhibitors with sub-micromolar potency with phenylglycine as arginine-mimicking group and benzylamide as C-terminal fragment. Further SAR exploration and application of these structural changes to a series of peptides having a 4-substituted phenylglycine residue at the P1 position led to potent compounds showing double digit nanomolar inhibition of the Zika protease (IC50 = 30 nM) with high selectivity against trypsin-like proteases and the proteases of other flavivirus, such as Dengue 2 virus (DEN2V) and West Nile virus (WNV).
Subject(s)
Antiviral Agents/pharmacology , Peptides/pharmacology , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Zika Virus/drug effects , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Dengue Virus/drug effects , Dose-Response Relationship, Drug , Humans , Microbial Sensitivity Tests , Molecular Structure , Peptides/chemical synthesis , Peptides/chemistry , Protease Inhibitors/chemical synthesis , Protease Inhibitors/chemistry , RNA Helicases/antagonists & inhibitors , RNA Helicases/metabolism , Serine Endopeptidases/metabolism , Structure-Activity Relationship , Viral Nonstructural Proteins/metabolism , West Nile virus/drug effects , Zika Virus/enzymologyABSTRACT
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral genome and has been a prime target for drug discovery efforts. Here, we report on the further development of tetracyclic indole inhibitors, binding to an allosteric site on the thumb domain. Structure-activity relationship (SAR) studies around an indolo-benzoxazocine scaffold led to the identification of compound 33 (MK-3281), an inhibitor with good potency in the HCV subgenomic replication assay and attractive molecular properties suitable for a clinical candidate. The compound caused a consistent decrease in viremia in vivo using the chimeric mouse model of HCV infection.
Subject(s)
Antiviral Agents/chemical synthesis , Hepacivirus/drug effects , Indoles/chemical synthesis , Oxazocines/chemical synthesis , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Viral Nonstructural Proteins/antagonists & inhibitors , Administration, Oral , Animals , Antiviral Agents/pharmacokinetics , Antiviral Agents/pharmacology , Biological Availability , Cell Line, Tumor , Crystallography, X-Ray , Dogs , Hepacivirus/enzymology , Hepacivirus/physiology , Humans , Indoles/pharmacokinetics , Indoles/pharmacology , Macaca mulatta , Mice , Mice, SCID , Mice, Transgenic , Models, Molecular , Molecular Structure , Oxazocines/pharmacokinetics , Oxazocines/pharmacology , Rats , Rats, Sprague-Dawley , Stereoisomerism , Structure-Activity Relationship , Viremia/drug therapy , Viremia/virology , Virus Replication/drug effectsABSTRACT
The RNA replication machinery of HCV is a multi-subunit membrane-associated complex. NS5A has emerged as an active component of HCV replicase, possibly involved in regulation of viral replication and resistance to the antiviral effect of interferon. We report here substituted piperazinyl-N-(aryl)benzamides as potent inhibitors of HCV replication exerted via modulation of the dimerization of NS5A.
Subject(s)
Benzamides/chemical synthesis , Hepacivirus/genetics , Hepatitis C/drug therapy , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Antiviral Agents/chemistry , Benzamides/pharmacology , Crystallography, X-Ray/methods , Dimerization , Hepacivirus/physiology , Humans , Interferons/chemistry , Models, Chemical , Molecular Conformation , Mutation , Structure-Activity RelationshipABSTRACT
We report the evolutionary path from an open-chain series to conformationally constrained tetracyclic indole inhibitors of HCV NS5B-polymerase, where the C2 aromatic is tethered to the indole nitrogen. SAR studies led to the discovery of zwitterionic compounds endowed with good intrinsic enzyme affinity and cell-based potency, as well as superior DMPK profiles to their acyclic counterparts, and ultimately to the identification of a pre-clinical candidate with an excellent predicted human pharmacokinetic profile.
Subject(s)
Chemistry, Pharmaceutical/methods , Enzyme Inhibitors/chemical synthesis , Viral Nonstructural Proteins/antagonists & inhibitors , Allosteric Site , Animals , Drug Design , Enzyme Inhibitors/pharmacology , Hepacivirus , Humans , Hydrolysis , Indoles/chemistry , Models, Chemical , Nitrogen/chemistry , Protein Conformation , Rats , Structure-Activity RelationshipABSTRACT
Allosteric inhibition of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase enzyme has recently emerged as a viable strategy toward blocking replication of viral RNA in cell-based systems. We report here 2 series of indole-N-acetamides, bearing physicochemically diverse carboxylic acid replacements, which show potent affinity for the NS5B enzyme with reduced potential for formation of glucuronide conjugates. Preliminary optimization of these series furnished compounds that are potent in the blockade of subgenomic HCV RNA replication in HUH-7 cells.
Subject(s)
Carboxylic Acids/chemistry , Enzyme Inhibitors/chemistry , Indoleacetic Acids/chemistry , Indoleacetic Acids/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Cell Line , Enzyme Inhibitors/pharmacology , HumansABSTRACT
Thieno[3,2-b]pyrroles are a novel class of allosteric inhibitors of HCV NS5B RNA-dependent RNA polymerase which show potent affinity for the NS5B enzyme. Introduction of a polar substituent in the position N1 led to a compound that efficiently blocks subgenomic HCV RNA replication in HUH-7 cells with an EC50 of 2.9 microM.
Subject(s)
Protease Inhibitors/chemistry , Pyrroles/chemistry , Viral Nonstructural Proteins/antagonists & inhibitors , Allosteric Regulation , Protease Inhibitors/pharmacology , Pyrroles/pharmacologyABSTRACT
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral RNA. We recently disclosed dihydroxypyrimidine carboxylates 2 as novel, reversible inhibitors of the HCV NS5B polymerase. This series was further developed into 5,6-dihydroxy-2-(2-thienyl)pyrimidine-4-carboxylic acids such as 34 (EC50 9.3 microM), which now show activity in the cell-based HCV replication assay. The structure-activity relationship of these inhibitors is discussed in the context of their physicochemical properties and of the polymerase crystal structure. We also report the results of mutagenesis experiments which support the proposed binding model, which involves pyrophosphate-like chelation of the active site Mg ions.
Subject(s)
Antiviral Agents/chemical synthesis , Hepacivirus/drug effects , Hepacivirus/enzymology , Methylurea Compounds/chemical synthesis , Models, Molecular , Pyrimidines/chemical synthesis , Thiophenes/chemical synthesis , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/genetics , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Binding Sites , Cell Line , Chelating Agents/chemistry , Crystallization , Humans , Methylurea Compounds/chemistry , Methylurea Compounds/pharmacology , Mutagenesis , Protein Conformation , Pyrimidines/chemistry , Pyrimidines/pharmacology , Structure-Activity Relationship , Thiophenes/chemistry , Thiophenes/pharmacology , Viral Nonstructural Proteins/chemistry , Virus Replication/drug effectsABSTRACT
The design of a series of peptidomimetic inhibitors of the hepatitis C virus NS3 protease is described. These inhibitors feature an indoline-2-carboxamide as a novel heterocyclic replacement for the P3 amino acid residue and N-terminal capping group of tripeptide based inhibitors. The crystal structure of the ternary NS3/NS4A/inhibitor complex for the most active molecule in this series highlights its suitability as an N-terminal capping group of a dipeptide inhibitor of the NS3 protease.
Subject(s)
Antiviral Agents/chemical synthesis , Hepacivirus/enzymology , Indoles/chemical synthesis , Oligopeptides/chemistry , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Antiviral Agents/chemistry , Crystallography, X-Ray , Indoles/chemistry , Models, Molecular , Molecular Mimicry , Molecular Structure , Protein Binding , StereoisomerismABSTRACT
N-terminal truncation of the hexapeptide ketoacid 1 gave rise to potent tripeptide inhibitors of the hepatitis C virus NS3 protease/NS4A cofactor complex. Optimization of these tripeptides led to ketoacid 30 with an IC50 of 0.38 microM. The SAR of these tripeptides is discussed in the light of the recently published crystal structures of a ternary tripetide/NS3/NS4A complexes.
