An allosteric mechanism for inhibiting HIV-1 integrase with a small molecule.
HIV-1 integrase (IN) is a validated target for developing antiretroviral inhibitors. Using affinity acetylation and mass spectrometric (MS) analysis, we previously identified a tetra-acetylated inhibitor (2E)-3-[3,4-bis(acetoxy)phenyl]-2-propenoate-N-[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propenyl]-L-serine methyl ester; compound 1] that selectively modified Lys173 at the IN dimer interface. Here we extend our efforts to dissect the mechanism of inhibition and structural features that are important for the selective binding of compound 1. Using a subunit exchange assay, we found that the inhibitor strongly modulates dynamic interactions between IN subunits. Restricting such interactions does not directly interfere with IN binding to DNA substrates or cellular cofactor lens epithelium-derived growth factor, but it compromises the formation of the fully functional nucleoprotein complex. Studies comparing compound 1 with a structurally related IN inhibitor, the tetra-acetylated-chicoric acid derivative (2R,3R)-2,3-bis[[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propen-1-yl]oxy]-butanedioic acid (compound 2), indicated striking mechanistic differences between these agents. The structures of the two inhibitors differ only in their central linker regions, with compounds 1 and 2 containing a single methyl ester group and two carboxylic acids, respectively. MS experiments highlighted the importance of these structural differences for selective binding of compound 1 to the IN dimer interface. Moreover, molecular modeling of compound 1 complexed to IN identified a potential inhibitor binding cavity and provided structural clues regarding a possible role of the central methyl ester group in establishing an extensive hydrogen bonding network with both interacting subunits. The proposed mechanism of action and binding site for the small-molecule inhibitor identified in the present study provide an attractive venue for developing allosteric inhibitors of HIV-1 IN.
Kessl
Jacques J
JJ
Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, the Ohio State University, Columbus, Ohio 43210, USA.
Eidahl
Jocelyn O
JO
Shkriabai
Nikolozi
N
Zhao
Zhuojun
Z
McKee
Christopher J
CJ
Hess
Sonja
S
Burke
Terrence R
TR
Kvaratskhelia
Mamuka
M
D000595:Amino Acid Sequence; D002850:Chromatography, Gel; D019427:HIV Integrase / Q000737:chemistry / Q000187:drug effects* / Q000378:metabolism; D019428:HIV Integrase Inhibitors / Q000494:pharmacology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000494:pharmacology; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D019428:HIV Integrase Inhibitors; D010455:Peptides; D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1