ABSTRACT
A novel series of non-nucleoside small molecules containing a tricyclic dihydropyridinone structural motif was identified as potent HCV NS5B polymerase inhibitors. Driven by structure-based design and building on our previous efforts in related series of molecules, we undertook extensive SAR studies, in which we identified a number of metabolically stable and very potent compounds in genotype 1a and 1b replicon assays. This work culminated in the discovery of several inhibitors, which combined potent in vitro antiviral activity against both 1a and 1b genotypes, metabolic stability, good oral bioavailability, and high C(12) (PO)/EC(50) ratios.
Subject(s)
Biological Availability , Drug Design , Structure-Activity Relationship , Antiviral Agents/pharmacokinetics , Chemistry, Pharmaceutical , Crystallography, X-Ray , Drug Evaluation, Preclinical , Genotype , Hepacivirus/drug effects , Hepatitis C , Molecular Structure , RNA-Dependent RNA Polymerase , Viral Nonstructural Proteins/antagonists & inhibitorsABSTRACT
Hexahydro-pyrrolo- and hexahydro-1H-pyrido[1,2-b]pyridazin-2-one analogs were discovered as a novel class of inhibitors of genotype 1 HCV NS5B polymerase. Among these, compound 4c displayed potent inhibitory activities in biochemical and replicon assays (IC(50) (1b) <10 nM; EC(50) (1b)=34 nM) as well as good stability towards human liver microsomes (HLM t(1/2) =59 min).
Subject(s)
Antiviral Agents/chemical synthesis , Antiviral Agents/pharmacology , Hepacivirus/drug effects , Microsomes, Liver/drug effects , Pyridazines/chemical synthesis , Pyridazines/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Antiviral Agents/chemistry , Combinatorial Chemistry Techniques , Crystallography, X-Ray , Drug Design , Humans , Molecular Structure , Pyridazines/chemistry , Structure-Activity RelationshipABSTRACT
A novel series of HCV NS5B polymerase inhibitors comprising 1,1-dioxoisothiazoles and benzo[b]thiophene-1,1-dioxides were designed, synthesized, and evaluated. SAR studies guided by structure-based design led to the identification of a number of potent NS5B inhibitors with nanomolar IC(50) values. The most potent compound exhibited IC(50) less than 10nM against the genotype 1b HCV polymerase and EC(50) of 70 nM against a genotype 1b replicon in cell culture. The DMPK properties of selected compounds were also evaluated.
Subject(s)
Antiviral Agents/chemical synthesis , Antiviral Agents/pharmacokinetics , Enzyme Inhibitors/pharmacokinetics , Thiazoles/chemical synthesis , Thiophenes/chemical synthesis , Viral Nonstructural Proteins/antagonists & inhibitors , Chemistry, Pharmaceutical/methods , Crystallography, X-Ray/methods , Drug Design , Genotype , Humans , Inhibitory Concentration 50 , Models, Chemical , Molecular Conformation , RNA, Viral/metabolism , Structure-Activity Relationship , Thiazoles/pharmacokinetics , Thiophenes/pharmacokineticsABSTRACT
5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. Lead optimization led to the discovery of compound 3a, which displayed potent inhibitory activities in biochemical and replicon assays [IC(50) (1b)<10nM; IC(50) (1a)=22 nM; EC(50) (1b)=5nM], good stability toward human liver microsomes (HLM t(1/2)>60 min), and high ratios of liver to plasma concentrations 12h after a single oral administration to rats.
Subject(s)
Antiviral Agents/chemical synthesis , Antiviral Agents/pharmacokinetics , Hepacivirus/drug effects , Pyridazines/chemical synthesis , Pyridazines/pharmacokinetics , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Viral Nonstructural Proteins/antagonists & inhibitors , Administration, Oral , Animals , Antiviral Agents/blood , Antiviral Agents/chemistry , Combinatorial Chemistry Techniques , Drug Design , Humans , Microsomes, Liver/drug effects , Molecular Structure , Pyridazines/blood , Pyridazines/chemistry , Rats , Structure-Activity RelationshipABSTRACT
Aminoglycoside antibiotics target an internal RNA loop within the bacterial ribosomal decoding site. Here, we describe the synthesis and SAR of novel 3,5-diamino-piperidine derivatives as aminoglycoside mimetics, and show they act as inhibitors of bacterial translation and growth.
Subject(s)
Anti-Bacterial Agents/chemical synthesis , Piperidines/chemical synthesis , Piperidines/pharmacology , Aminoglycosides , Anti-Bacterial Agents/pharmacology , Molecular Mimicry , Protein Biosynthesis/drug effects , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/growth & development , Structure-Activity RelationshipABSTRACT
We report the structure-guided discovery, synthesis, and initial characterization of 3,5-diamino-piperidinyl triazines (DAPT), a novel translation inhibitor class that targets bacterial rRNA and exhibits broad-spectrum antibacterial activity. DAPT compounds were designed as structural mimetics of aminoglycoside antibiotics which bind to the bacterial ribosomal decoding site and thereby interfere with translational fidelity. We found that DAPT compounds bind to oligonucleotide models of decoding-site RNA, inhibit translation in vitro, and induce translation misincorporation in vivo, in agreement with a mechanism of action at the ribosomal decoding site. The novel DAPT antibacterials inhibit growth of gram-positive and gram-negative bacteria, including the respiratory pathogen Pseudomonas aeruginosa, and display low toxicity to human cell lines. In a mouse protection model, an advanced DAPT compound demonstrated efficacy against an Escherichia coli infection at a 50% protective dose of 2.4 mg/kg of body weight by single-dose intravenous administration.
Subject(s)
Aminoglycosides/pharmacology , Protein Biosynthesis/drug effects , Anti-Bacterial Agents/pharmacology , Biomimetic Materials/chemistry , Biomimetic Materials/pharmacology , Drug Design , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effects , Piperidines/pharmacology , Protein Conformation , Ribosomes/drug effects , Structure-Activity Relationship , Triazines/pharmacologyABSTRACT
Syntheses of dehydroalanine derivatives via a solid-support route, starting from selenocystein, and via conventional solution phase chemistry are described along with initial biological testing. The target compounds were designed as mimetics of the dehydroalanine side chain of the macrocyclic antibiotic thiostrepton that acts on the bacterial ribosome.
Subject(s)
Alanine/analogs & derivatives , Molecular Mimicry , Thiostrepton/chemistry , Alanine/chemical synthesis , Chromatography, Liquid , Magnetic Resonance Spectroscopy , Mass Spectrometry , Thiostrepton/pharmacologySubject(s)
RNA, Bacterial/chemistry , Ribosomes/chemistry , 2-Aminopurine/chemistry , Aminoglycosides/chemical synthesis , Anti-Bacterial Agents/chemical synthesis , Crystallization , Crystallography, X-Ray , Gene Targeting , Models, Molecular , Nucleic Acid Conformation , Oligonucleotides/chemistry , RNA, Bacterial/biosynthesis , RNA, Bacterial/drug effects , Ribosomes/drug effects , Spectrometry, Fluorescence , Spectrophotometry, UltravioletABSTRACT
RNA recognition by natural aminoglycoside antibiotics depends on the 2-deoxystreptamine (2-DOS) scaffold which participates in specific hydrogen bonds with the ribosomal decoding-site target. Three-dimensional structure information has been used for the design of azepane-monoglycosides, building blocks for novel antibiotics in which 2-DOS is replaced by a heterocyclic scaffold. Azepane-glycosides showed target binding and translation inhibition in the low micromolar range and inhibited growth of Staphylococcus aureus, including aminoglycoside-resistant strains.
Subject(s)
Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Azepines/chemistry , Azepines/pharmacology , RNA, Ribosomal/antagonists & inhibitors , Staphylococcus aureus/drug effects , Staphylococcus aureus/growth & development , Aminoglycosides/adverse effects , Aminoglycosides/chemistry , Anti-Bacterial Agents/chemistry , Azepines/metabolism , Drug Design , Glycosides/chemistry , Glycosides/metabolism , Glycosides/pharmacology , Heterocyclic Compounds/chemistry , Heterocyclic Compounds/metabolism , Heterocyclic Compounds/pharmacology , Nucleic Acid Conformation , Paromomycin , Protein Biosynthesis/drug effects , RNA, Bacterial/antagonists & inhibitors , RNA, Ribosomal/chemistry , Structure-Activity RelationshipSubject(s)
Aminoglycosides/chemistry , Anti-Bacterial Agents/chemistry , Hexosamines/chemistry , RNA, Bacterial/metabolism , RNA, Ribosomal/metabolism , Aminoglycosides/metabolism , Aminoglycosides/pharmacology , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Binding Sites , Escherichia coli/drug effects , Escherichia coli/metabolism , Hexosamines/metabolism , Hexosamines/pharmacology , Microbial Sensitivity Tests , Models, Molecular , Molecular Structure , Staphylococcus aureus/drug effects , Staphylococcus aureus/metabolism , Structure-Activity RelationshipSubject(s)
Anti-Bacterial Agents/chemistry , Glycosides/chemistry , Piperidines/chemistry , RNA, Bacterial/metabolism , RNA, Ribosomal/metabolism , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Binding Sites , Escherichia coli/drug effects , Escherichia coli/metabolism , Glycosides/metabolism , Glycosides/pharmacology , Inhibitory Concentration 50 , Models, Molecular , Molecular Structure , Piperidines/metabolism , Piperidines/pharmacology , Staphylococcus aureus/drug effects , Staphylococcus aureus/metabolism , Structure-Activity RelationshipABSTRACT
Natural aminoglycoside antibiotics recognize an internal loop of bacterial ribosomal-decoding-site RNA by binding to the deep groove of the RNA structure. We have designed, synthesized, and tested RNA-targeted paromamine derivatives that exploit additional interactions on the shallow groove face of the decoding-site RNA. An in vitro transcription-translation assay of a series of 6'-derivatives showed the 6'-position to be very sensitive to substitution. This result suggests that the group at the 6'-position plays a pivotal role in RNA target recognition.
Subject(s)
Aminoglycosides/chemical synthesis , Aminoglycosides/pharmacology , RNA, Ribosomal/antagonists & inhibitors , Aminoglycosides/chemistry , Anti-Bacterial Agents/chemistry , Binding Sites , Cell-Free System , Drug Design , Protein Biosynthesis/drug effects , RNA, Bacterial/antagonists & inhibitors , RNA, Ribosomal/chemistry , RNA, Ribosomal/ultrastructure , Structure-Activity RelationshipABSTRACT
The ribosomal decoding site is the target of aminoglycoside antibiotics that specifically recognize an internal loop RNA structure. We synthesized RNA-targeted 2,5-dideoxystreptamine-4-amides in which a sugar moiety in natural aminoglycosides is replaced by heterocycles.