1D4K

HIV-1 PROTEASE COMPLEXED WITH A MACROCYCLIC PEPTIDOMIMETIC INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.

Tyndall, J.D.Reid, R.C.Tyssen, D.P.Jardine, D.K.Todd, B.Passmore, M.March, D.R.Pattenden, L.K.Bergman, D.A.Alewood, D.Hu, S.H.Alewood, P.F.Birch, C.J.Martin, J.L.Fairlie, D.P.

(2000) J.Med.Chem. 43: 3495-3504

  • Primary Citation of Related Structures:  1D4L

  • PubMed Abstract: 
  • Three new peptidomimetics (1-3) have been developed with highly stable and conformationally constrained macrocyclic components that replace tripeptide segments of protease substrates. Each compound inhibits both HIV-1 protease and viral replication ( ...

    Three new peptidomimetics (1-3) have been developed with highly stable and conformationally constrained macrocyclic components that replace tripeptide segments of protease substrates. Each compound inhibits both HIV-1 protease and viral replication (HIV-1, HIV-2) at nanomolar concentrations without cytotoxicity to uninfected cells below 10 microM. Their activities against HIV-1 protease (K(i) 1.7 nM (1), 0.6 nM (2), 0.3 nM (3)) are 1-2 orders of magnitude greater than their antiviral potencies against HIV-1-infected primary peripheral blood mononuclear cells (IC(50) 45 nM (1), 56 nM (2), 95 nM (3)) or HIV-1-infected MT2 cells (IC(50) 90 nM (1), 60 nM (2)), suggesting suboptimal cellular uptake. However their antiviral potencies are similar to those of indinavir and amprenavir under identical conditions. There were significant differences in their capacities to inhibit the replication of HIV-1 and HIV-2 in infected MT2 cells, 1 being ineffective against HIV-2 while 2 was equally effective against both virus types. Evidence is presented that 1 and 2 inhibit cleavage of the HIV-1 structural protein precursor Pr55(gag) to p24 in virions derived from chronically infected cells, consistent with inhibition of the viral protease in cells. Crystal structures refined to 1.75 A (1) and 1.85 A (2) for two of the macrocyclic inhibitors bound to HIV-1 protease establish structural mimicry of the tripeptides that the cycles were designed to imitate. Structural comparisons between protease-bound macrocyclic inhibitors, VX478 (amprenavir), and L-735,524 (indinavir) show that their common acyclic components share the same space in the active site of the enzyme and make identical interactions with enzyme residues. This substrate-mimicking minimalist approach to drug design could have benefits in the context of viral resistance, since mutations which induce inhibitor resistance may also be those which prevent substrate processing.


    Related Citations: 
    • Substrate-Based Cyclic Peptidomimetics Of Phe Ile Val That Inhibit HIV-1 Protease Using a Novel Enzyme Binding Mode
      March, D.R.,Abbenante, G.,Bergman, D.,Brinkworth, R.I.,Wickramasinghe, W.,Begun, J.,Martin, J.L.,Fairlie, D.P.
      (1996) J.Am.Chem.Soc. 118: 3375
    • Regioselective Structural and Functional Mimicry Of Peptides: Design Of Hydrolytically Stable Cyclic Peptidomimetic Inhibitors Of HIV-1 Protease.
      Abbenante, G.,March, D.,Bergman, D.,Hunt, P.A.,Garnham, B.,Dancer, R.J.,Martin, J.L.,Fairlie, D.P.
      (1995) J.Am.Chem.Soc. 117: 10220
    • Molecular Recognition of Macrocyclic Peptidomimetic Inhibitors by HIV-1 Protease.
      Martin, J.L.,Begun, J.,Schindeler, A.,Wickramasinghe, W.A.,Alewood, D.,Alewood, P.F.,Bergman, D.A.,Brinkworth, R.I.,Abbenante, G.,March, D.R.,Reid, R.C.,Fairlie, D.P.
      (1999) Biochemistry 38: 7978


    Organizational Affiliation

    Centre for Drug Design and Development, The University of Queensland, Brisbane, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PI8
Query on PI8

Download SDF File 
Download CCD File 
A
N-13-[(10S,13S)-9,12-DIOXO-10-(2-BUTYL)-2-OXA-8,11-DIAZABICYCLO [13.2.2] NONADECA-15,17,18-TRIENE] (2R)-BENZYL-(4S)-HYDROXY-5-AMINOPENTANOIC (1R)-HYDROXY-(2S)-INDANEAMIDE
MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 8
C41 H54 N4 O6
ZXUOAWXMXWTRGE-ZKQACQBYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PI8Ki: 0.6 nM BINDINGMOAD
PI8Ki: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.820α = 90.00
b = 58.920β = 90.00
c = 61.860γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description