Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations

• Published in: Scientific reports Vol. 14; no. 1; pp. 15742 - 13
• Main Authors: Yasutake, Yoshiaki, Hattori, Shin-ichiro, Kumamoto, Hiroki, Tamura, Noriko, Maeda, Kenji, Mitsuya, Hiroaki
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08-07-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326/22/1295; 631/326/22/1434; 631/326/596/1550; 631/45/535/1266; Amino acids; Antiviral activity; Antiviral agents; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding Sites; Catalytic Domain; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; Drug delivery; Drug development; Drug resistance; Drug Resistance, Viral - genetics; Global health; Health risks; Hepatitis B; Hepatitis B virus - drug effects; Hepatitis B virus - genetics; HIV; HIV Reverse Transcriptase - antagonists & inhibitors; HIV Reverse Transcriptase - chemistry; HIV Reverse Transcriptase - genetics; HIV Reverse Transcriptase - metabolism; HIV-1 - drug effects; HIV-1 - genetics; Human immunodeficiency virus; Humanities and Social Sciences; Humans; Hydrophobicity; Models, Molecular; multidisciplinary; Mutants; Mutation; Nucleoside analogs; Nucleosides - chemistry; Nucleosides - metabolism; Nucleosides - pharmacology; Protein Binding; Public health; Reverse Transcriptase Inhibitors - chemistry; Reverse Transcriptase Inhibitors - metabolism; Reverse Transcriptase Inhibitors - pharmacology; RNA-directed DNA polymerase; RNA-Directed DNA Polymerase - chemistry; RNA-Directed DNA Polymerase - genetics; RNA-Directed DNA Polymerase - metabolism; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-66505-z

While certain human hepatitis B virus-targeting nucleoside analogs (NAs) serve as crucial anti-HBV drugs, HBV yet remains to be a major global health threat.
E
-CFCP is a 4′-modified and fluoromethylenated NA that exhibits potent antiviral activity against both wild-type and drug-resistant HBVs but less potent against human immunodeficiency virus type-1 (HIV-1). Here, we show that HIV-1 with HBV-associated amino acid substitutions introduced into the RT’s dNTP-binding site (N-site) is highly susceptible to
E
-CFCP. We determined the X-ray structures of HBV-associated HIV-1 RT mutants complexed with DNA:
E
-CFCP-triphosphate (
E
-CFCP-TP). The structures revealed that exocyclic fluoromethylene pushes the Met184 sidechain backward, and the resultant enlarged hydrophobic pocket accommodates both the fluoromethylene and 4′-cyano moiety of
E
-CFCP. Structural comparison with the DNA:dGTP/entecavir-triphosphate complex also indicated that the cyclopentene moiety of the bound
E
-CFCP-TP is slightly skewed and deviated. This positioning partly corresponds to that of the bound dNTP observed in the HIV-1 RT mutant with drug-resistant mutations F160M/M184V, resulting in the attenuation of the structural effects of F160M/M184V substitutions. These results expand our knowledge of the interactions between NAs and the RT N-site and should help further design antiviral NAs against both HIV-1 and HBV.