Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine

Yoshiaki Yasutake,Hiroaki Mitsuya,Shin-Ichiro Hattori,Kenji Maeda,Kouki Matsuda,Noriko Tamura,Satoru Kohgo

doi:10.1038/s41598-020-59775-w

Abstract

Chronic hepatitis B virus (HBV) infection is a major public health problem that affects millions of people worldwide. Nucleoside analogue reverse transcriptase (RT) inhibitors, such as entecavir (ETV) and lamivudine (3TC), serve as crucial anti-HBV drugs. However, structural studies of HBV RT have been hampered due to its unexpectedly poor solubility. Here, we show that human immunodeficiency virus type-1 (HIV-1) with HBV-associated amino acid substitutions Y115F/F116Y/Q151M in its RT (HIVY115F/F116Y/Q151M) is highly susceptible to ETV and 3TC. Additionally, we experimentally simulated previously reported ETV/3TC resistance for HBV using HIVY115F/F116Y/Q151M with F160M/M184V (L180M/M204V in HBV RT) substituted. We determined crystal structures for HIV-1 RTY115F/F116Y/Q151M:DNA complexed with 3TC-triphosphate (3TC-TP)/ETV-triphosphate (ETV-TP)/dCTP/dGTP. These structures revealed an atypically tight binding conformation of 3TC-TP, where the Met184 side-chain is pushed away by the oxathiolane of 3TC-TP and exocyclic methylene of ETV-TP. Structural analysis of RTY115F/F116Y/Q151M/F160M/M184V:DNA:3TC-TP also demonstrated that the loosely bound 3TC-TP is misaligned at the active site to prevent a steric clash with the side chain γ-methyl of Val184. These findings shed light on the common structural mechanism of HBV and HIV-1 resistance to 3TC and ETV and should aid in the design of new agents to overcome drug resistance to 3TC and ETV.

Highlights

Chronic hepatitis B virus (HBV) infection is a major public health problem that affects millions of people worldwide
Previous characterization of HBV reverse transcriptase (RT) mutants suggested that the M204V/I mutation is crucial for both 3TC/ETV resistance. 3TC is approved as an anti-human immunodeficiency virus type-1 (HIV-1) agent, and M184V in HIV-1 RT, which corresponds to M204V in HBV RT, has been reported as an amino acid substitution responsible for 3TC resistance in HIV-119
We recently reported that the HBV-associated Q151M mutation alone in HIV-1 RT renders HIV-1 highly sensitive to ETV, and we determined the crystal structure of HIV-1 RTQ151M:DNA complexed with ETV-triphosphate (ETV-terminal protein (TP))[24]

Summary

Introduction

Chronic hepatitis B virus (HBV) infection is a major public health problem that affects millions of people worldwide. Structural analysis of RTY115F/F116Y/Q151M/F160M/M184V:DNA:3TC-TP demonstrated that the loosely bound 3TC-TP is misaligned at the active site to prevent a steric clash with the side chain γ-methyl of Val[184] These findings shed light on the common structural mechanism of HBV and HIV-1 resistance to 3TC and ETV and should aid in the design of new agents to overcome drug resistance to 3TC and ETV. Both 3TC and ETV are bulkier NRTI compared with tenofovir, their structures are considerably different from each other: 3TC is a l-nucleoside analogue that has an oxathiolane instead of a ribose ring, whereas ETV is a common d-nucleoside guanosine analogue with protruded cyclopentyl methylene. We assumed that crystallographic studies of HIV-1 RT containing HBV-associated amino acids at the N-site should provide important clues for understanding the mechanism of 3TC/ETV resistance caused by common M204V/I in HBV RT (M184V/I in HIV-1 RT)

Methods

Results

Conclusion