Insights into the mechanism of inhibition of CXCR4: identification of Piperidinylethanamine analogs as anti-HIV-1 inhibitors

• Published in: Antimicrobial agents and chemotherapy 2015-04, Vol.59 (4), p.1895-1904
• Main Authors: Das, Debananda, Maeda, Kenji, Hayashi, Yasuhiro, Gavande, Navnath, Desai, Darshan V, Chang, Simon B, Ghosh, Arun K, Mitsuya, Hiroaki
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acid Substitution; Anti-HIV Agents; Anti-HIV Agents - chemical synthesis; Anti-HIV Agents - pharmacology; Antiviral Agents; Cell Survival - drug effects; High-Throughput Screening Assays; HIV Fusion Inhibitors; HIV Fusion Inhibitors - chemical synthesis; HIV Fusion Inhibitors - pharmacology; HIV-1; HIV-1 - drug effects; Human immunodeficiency virus; Human immunodeficiency virus 1; Humans; Hydrogen Bonding; Mutagenesis, Site-Directed; Piperidines; Piperidines - chemical synthesis; Piperidines - pharmacology; Receptors, CXCR4; Receptors, CXCR4 - antagonists & inhibitors; Receptors, CXCR4 - chemistry; Small Molecule Libraries; Viral Envelope Proteins - metabolism
• ISSN: 0066-4804; 1098-6596
• DOI: 10.1128/AAC.04654-14

The cellular entry of HIV-1 into CD4(+) T cells requires ordered interactions of HIV-1 envelope glycoprotein with C-X-C chemokine receptor type 4 (CXCR4) receptors. However, such interactions, which should be critical for rational structure-based discovery of new CXCR4 inhibitors, remain poorly understood. Here we first determined the effects of amino acid substitutions in CXCR4 on HIV-1NL 4 - 3 glycoprotein-elicited fusion events using site-directed mutagenesis-based fusion assays and identified 11 potentially key amino acid substitutions, including D97A and E288A, which caused >30% reductions in fusion. We subsequently carried out a computational search of a screening library containing ∼604,000 compounds, in order to identify potential CXCR4 inhibitors. The computational search used the shape of IT1t, a known CXCR4 inhibitor, as a reference and employed various algorithms, including shape similarity, isomer generation, and docking against a CXCR4 crystal structure. Sixteen small molecules were identified for biological assays based on their high shape similarity to IT1t, and their putative binding modes formed hydrogen bond interactions with the amino acids identified above. Three compounds with piperidinylethanamine cores showed activity and were resynthesized. One molecule, designated CX6, was shown to significantly inhibit fusion elicited by X4 HIV-1NL 4 - 3 glycoprotein (50% inhibitory concentration [IC50], 1.9 μM), to inhibit Ca(2+) flux elicited by stromal cell-derived factor 1α (SDF-1α) (IC50, 92 nM), and to exert anti-HIV-1 activity (IC50, 1.5 μM). Structural modeling demonstrated that CX6 bound to CXCR4 through hydrogen bond interactions with Asp97 and Glu288. Our study suggests that targeting CXCR4 residues important for fusion elicited by HIV-1 envelope glycoprotein should be a useful and feasible approach to identifying novel CXCR4 inhibitors, and it provides important insights into the mechanism by which small-molecule CXCR4 inhibitors exert their anti-HIV-1 activities.