ABSTRACT
A new class of small molecules that bind the HCV RNA IRES IIA subdomain with sub-micromolar affinity is reported. The benzimidazole 'hit' 1 with a KD approximately 100 microM to a 29-mer RNA model of Domain IIA was identified from a 180000-member library using mass spectrometry-based screening methods. Further MS-assisted SAR (structure-activity relationships) studies afforded benzimidazole derivatives with sub-micromolar binding affinity for the IIA RNA construct. The optimized benzimidazoles demonstrated activity in a cellular replicon assay at concentrations comparable to their KD for the RNA target.
Subject(s)
Benzimidazoles/chemistry , Hepacivirus/genetics , Models, Molecular , Quantitative Structure-Activity Relationship , RNA, Viral/chemistry , Ribosomes/drug effects , Base Sequence , Benzimidazoles/pharmacology , Benzimidazoles/toxicity , Binding Sites , Cell Line , Databases, Factual , Hepacivirus/physiology , Humans , Mass Spectrometry , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Viral/metabolism , Ribosomes/chemistry , Ribosomes/metabolism , Virus ReplicationABSTRACT
We report on lead optimization of a compound that was originally discovered to bind bacterial 23S rRNA near the L11 binding site and inhibit translation in vitro, but lacked detectable antibacterial activity. In this study, we were able to generate compounds with antibacterial activity against Gram-negative and Gram-positive pathogens, including a methicillin-resistant S. aureus strain.
Subject(s)
Anti-Bacterial Agents/chemical synthesis , Furans/chemical synthesis , Piperazines/chemical synthesis , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Furans/chemistry , Furans/pharmacology , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effects , Mass Spectrometry , Methicillin Resistance , Microbial Sensitivity Tests , Piperazines/chemistry , Piperazines/pharmacology , RNA, Ribosomal, 23S/metabolism , Structure-Activity RelationshipABSTRACT
A structure-activity relationship analysis was carried out on a high-throughput small molecule screening lead for HCV-IRES translation inhibition. The study led to the identification of a guanidine-based structure with low microM inhibitory activity.
Subject(s)
Antiviral Agents/chemistry , Guanidines/chemistry , Hepacivirus/genetics , Protein Biosynthesis/drug effects , Viral Proteins/antagonists & inhibitors , Antiviral Agents/pharmacology , Databases, Factual , Hepacivirus/metabolism , Ribosomes/drug effects , Ribosomes/genetics , Structure-Activity Relationship , Transcription, Genetic/drug effects , Viral Proteins/biosynthesisABSTRACT
Novel quinolone-macrocycle conjugates displayed submicromolar antibacterial activity against Escherichia coli and Staphylococcus aureus bacterial strains. An analogous open-chain structure was not active at 100 microM against the same pathogenic strains.
Subject(s)
Anti-Bacterial Agents/chemistry , Heterocyclic Compounds/pharmacology , Quinolones/pharmacology , Anti-Bacterial Agents/pharmacology , Escherichia coli/drug effects , Heterocyclic Compounds/chemistry , Microbial Sensitivity Tests , Quinolones/chemistry , Staphylococcus aureus/drug effects , Structure-Activity RelationshipABSTRACT
A mixture-based combinatorial library of 14-membered macrocycles was synthesized to target ribosomal RNA and uncover a new class of antibacterial agents. High-throughput screening identified a macrocyclic mixture that inhibited cell-free-coupled transcription/translation in Escherichia coli-derived extracts, with an IC(50) value in the 25-50 microM range. In a follow-up library of 64 single macrocycles, 8 gave IC(50) values ranging from 12 to 50 microM in the cell-free protein synthesis inhibition assay. Some of the macrocycles were screened in a translation inhibition assay, and IC(50) values generally paralleled those obtained in the uncoupled transcription/translation assay. Additional analogues were prepared in a preliminary structure-activity relationship study, and more potent macrocycles were identified with low micromolar activity (IC(50) values = 2-3 microM). Some of these macrocycles displayed antibacterial activity against lipopolysaccharide mutant E. coli bacterial cells (IC(50) values = 12-50 microM).
