Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease.
Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: 1TW7), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC50: 4.4nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6a against both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of (15)N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.
Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA.
Ravikiran S
RS
Yedidi
Joseck M
JM
Muhuhi
Zhigang
Z
Liu
Krisztina Z
KZ
Bencze
Kyriacos
K
Koupparis
Carrie E
CE
O'Connor
Iulia A
IA
Kovari
Mark R
MR
Spaller
Ladislau C
LC
Kovari
D000595:Amino Acid Sequence; D015195:Drug Design; D024921:Drug Resistance, Multiple, Viral; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D016333:HIV Protease / Q000235:genetics / Q000378:metabolism*; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D015497:HIV-1 / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics; D006801:Humans; D062105:Molecular Docking Simulation; D016296:Mutagenesis; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology*
D017320:HIV Protease Inhibitors; D019151:Peptide Library; D010455:Peptides; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
CA/p2; CA/p2-analogs; Capsid/short peptide; Chemical mutagenesis; FDA; FRET; HIV-1 protease; HIV/AIDS; HSQC; Multidrug-resistance; PI; Protease inhibitors; fluorescence resonance energy transfer; food and drug administration; heteronuclear single quantum coherence; protease inhibitors