Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity

Haydar Bulut,Debananda Das,Manabu Aoki,Prasanth R Nyalapatla,Kalapala Venkateswara Rao,Hiroaki Mitsuya,Hironori Hayashi,Arun K Ghosh,David A Davis,Hiromi Aoki-Ogata,Shin-Ichiro Hattori

doi:10.1038/s41598-020-65993-z

Abstract

HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. However, HIV-1 often acquires resistance to PIs. Here, seven novel PIs were synthesized, by introducing single atom changes such as an exchange of a sulfur to an oxygen, scission of a single bond in P2′-cyclopropylaminobenzothiazole (or -oxazole), and/or P1-benzene ring with fluorine scan of mono- or bis-fluorine atoms around DRV’s scaffold. X-ray structural analyses of the PIs complexed with wild-type Protease (PRWT) and highly-multi-PI-resistance-associated PRDRVRP51 revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2′-subsite. Furthermore, these PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Our work provides the basis for developing novel PIs with high potency against PI-resistant HIV-1 variants with a high genetic barrier.

Highlights

HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy
Four recently reported PIs, designated GRL-142, GRL-121, GRL-001, and GRL-003 have been shown to occupy a larger surface in the binding pockets of PR, forming more extensive van der Waals (vdW) contacts compared to darunavir[1,14]
The eleven PIs examined in the present study exerted significantly greater anti-HIV-1 potency(Figs. 1 and S2 and Table S1) in cell-based assays and some of them including GRL-142, GRL121, GRL-001 and GRL-003 proved to have much higher genetic barriers to the emergence of resistant variants as compared to DRV1

Summary

Introduction

HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. X-ray structural analyses of the PIs complexed with wild-type Protease (PRWT) and highly-multi-PI-resistance-associated PRDRVRP51 revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2′-subsite. These PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Darunavir (DRV) is a second-generation nonpeptidic PI, which is highly potent against wild-type HIV-1 (HIVWT) and has a high genetic barrier to the emergence of DRV-resistant variants, retaining its potent anti-HIV activity over long-term periods in clinical settings[9,10]. Further chemical variations were introduced with a meta- or para-fluoro-substitution on the benzene ring at the P1 site and replacement of cyclopropyl-aminobenzothiazole (Cp-Abt) of GRL-142 with isopropyl-aminobenzothiazole (Ip-Abt) or isopropyl-aminobenzoxazole (Ip-Abo) as a P2′ ligand (Fig. 1)

Methods

Results

Conclusion