title: Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains.
abstract: Protease inhibitors (PIs) are an important class of drugs for the treatment of HIV infection. However, in the course of treatment, resistant viral variants with reduced sensitivity to PIs often emerge and become a major obstacle to successful control of viral load. On the basis of a compound equipotently inhibiting HIV-1 and 2 proteases (PR), we have designed a pseudopeptide inhibitor, QF34, that efficiently inhibits a wide variety of PR variants. In order to analyze the potency of the inhibitor, we constructed PR species harboring the typical (signature) mutations that confer resistance to commercially available PIs. Kinetic analyses showed that these mutated PRs were inhibited up to 1,000-fold less efficiently by the clinically approved PIs. In contrast, all PR species were effectively inhibited by QF34. In a clinical study, we have monitored 30 HIV-positive patients in the Czech Republic undergoing highly active antiretroviral therapy, and have identified highly PI resistant variants. Kinetic analyses revealed that QF34 retained its subnanomolar potency against multi-drug resistant PR variants. X-ray crystallographic analysis and molecular modeling experiments explained the wide specificity of QF34: this inhibitor binds to the PR in an unusual manner, thus avoiding contact sites that are mutated upon resistance development, and the unusual binding mode and consequently the binding energy is therefore preserved in the complex with a resistant variant. These results suggest a promising route for the design of second-generation PIs that are active against a variety of resistant PR variants.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Protease of Human Pathogens, Flemingovo n. 2, CZ-16610 Praha 6, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Weber
authors.forename: Jeroen R
authors.initials: JR
authors.lastname: Mesters
authors.forename: Martin
authors.initials: M
authors.lastname: Lepsík
authors.forename: Jana
authors.initials: J
authors.lastname: Prejdová
authors.forename: Martin
authors.initials: M
authors.lastname: Svec
authors.forename: Jana
authors.initials: J
authors.lastname: Sponarová
authors.forename: Petra
authors.initials: P
authors.lastname: Mlcochová
authors.forename: Kristina
authors.initials: K
authors.lastname: Skalická
authors.forename: Kvido
authors.initials: K
authors.lastname: Strísovský
authors.forename: Tána
authors.initials: T
authors.lastname: Uhlíková
authors.forename: Milan
authors.initials: M
authors.lastname: Soucek
authors.forename: Ladislav
authors.initials: L
authors.lastname: Machala
authors.forename: Marie
authors.initials: M
authors.lastname: Stanková
authors.forename: Jirí
authors.initials: J
authors.lastname: Vondrásek
authors.forename: Thomas
authors.initials: T
authors.lastname: Klimkait
authors.forename: Hans Georg
authors.initials: HG
authors.lastname: Kraeusslich
authors.forename: Rolf
authors.initials: R
authors.lastname: Hilgenfeld
authors.forename: Jan
authors.initials: J
authors.lastname: Konvalinka
mesh_terms: D019943:Amino Acid Substitution; D023241:Antiretroviral Therapy, Highly Active; D001665:Binding Sites; D018360:Crystallography, X-Ray; D015195:Drug Design; D004352:Drug Resistance, Microbial / Q000235:genetics; D018432:Drug Resistance, Multiple / Q000235:genetics; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D017320:HIV Protease Inhibitors / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008297:Male; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D009154:Mutation; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D011487:Protein Conformation; D015202:Protein Engineering; D011994:Recombinant Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology
chemical_list: D017320:HIV Protease Inhibitors; D009842:Oligopeptides; C470354:QF34 pseudopeptide; D011994:Recombinant Proteins; D018894:Reverse Transcriptase Inhibitors