6OPU

HIV-1 Protease NL4-3 K45I, M46I, V82F, I84V Mutant in complex with darunavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.

Henes, M.Lockbaum, G.J.Kosovrasti, K.Leidner, F.Nachum, G.S.Nalivaika, E.A.Lee, S.K.Spielvogel, E.Zhou, S.Swanstrom, R.Bolon, D.N.A.Kurt Yilmaz, N.Schiffer, C.A.

(2019) Acs Chem.Biol. 14: 2441-2452

  • DOI: 10.1021/acschembio.9b00370
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drug resistance continues to be a growing global problem. The efficacy of small molecule inhibitors is threatened by pools of genetic diversity in all systems, including antibacterials, antifungals, cancer therapeutics, and antivirals. Resistant vari ...

    Drug resistance continues to be a growing global problem. The efficacy of small molecule inhibitors is threatened by pools of genetic diversity in all systems, including antibacterials, antifungals, cancer therapeutics, and antivirals. Resistant variants often include combinations of active site mutations and distal "secondary" mutations, which are thought to compensate for losses in enzymatic activity. HIV-1 protease is the ideal model system to investigate these combinations and underlying molecular mechanisms of resistance. Darunavir (DRV) binds wild-type (WT) HIV-1 protease with a potency of <5 pM, but we have identified a protease variant that loses potency to DRV 150 000-fold, with 11 mutations in and outside the active site. To elucidate the roles of these mutations in DRV resistance, we used a multidisciplinary approach, combining enzymatic assays, crystallography, and molecular dynamics simulations. Analysis of protease variants with 1, 2, 4, 8, 9, 10, and 11 mutations showed that the primary active site mutations caused ∼50-fold loss in potency (2 mutations), while distal mutations outside the active site further decreased DRV potency from 13 nM (8 mutations) to 0.76 μM (11 mutations). Crystal structures and simulations revealed that distal mutations induce subtle changes that are dynamically propagated through the protease. Our results reveal that changes remote from the active site directly and dramatically impact the potency of the inhibitor. Moreover, we find interdependent effects of mutations in conferring high levels of resistance. These mechanisms of resistance are likely applicable to many other quickly evolving drug targets, and the insights may have implications for the design of more robust inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Department of Biochemistry and Biophysics and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease NL4-3
B, A
99Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: pol
Find proteins for Q7ZCI0 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q7ZCI0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download SDF File 
Download CCD File 
B
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
Darunavir, TMC114, UIC-94017
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 61.497α = 90.00
b = 61.497β = 90.00
c = 81.319γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01-GM109767

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-11-27
    Type: Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence