4A6C

Stereoselective Synthesis, X-ray Analysis, and Biological Evaluation of a New Class of Lactam Based HIV-1 Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis, X-Ray Analysis, and Biological Evaluation of a New Class of Stereopure Lactam-Based HIV-1 Protease Inhibitors.

Wu, X.Ohrngren, P.Joshi, A.A.Trejos, A.Persson, M.Arvela, R.K.Wallberg, H.Vrang, L.Rosenquist, A.Samuelsson, B.B.Unge, J.Larhed, M.

(2012) J.Med.Chem. 55: 2724

  • DOI: 10.1021/jm201620t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In an effort to identify a new class of druglike HIV-1 protease inhibitors, four different stereopure β-hydroxy γ-lactam-containing inhibitors have been synthesized, biologically evaluated, and cocrystallized. The impact of the tether length of the c ...

    In an effort to identify a new class of druglike HIV-1 protease inhibitors, four different stereopure β-hydroxy γ-lactam-containing inhibitors have been synthesized, biologically evaluated, and cocrystallized. The impact of the tether length of the central spacer (two or three carbons) was also investigated. A compound with a shorter tether and (3R,4S) absolute configuration exhibited high activity with a K(i) of 2.1 nM and an EC(50) of 0.64 μM. Further optimization by decoration of the P1' side chain furnished an even more potent HIV-1 protease inhibitor (K(i) = 0.8 nM, EC(50) = 0.04 μM). According to X-ray analysis, the new class of inhibitors did not fully succeed in forming two symmetric hydrogen bonds to the catalytic aspartates. The crystal structures of the complexes further explain the difference in potency between the shorter inhibitors (two-carbon spacer) and the longer inhibitors (three-carbon spacer).


    Organizational Affiliation

    Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL PROTEIN
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P35963 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Go to UniProtKB:  P35963
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QG9
Query on QG9

Download SDF File 
Download CCD File 
B
METHYL ((S)-1-(2-(3-((3S,4S)-3-BENZYL-4-HYDROXY-1-((1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL)-2-OXOPYRROLIDIN-3-YL)PROPYL)-2-(4-(PYRIDIN-4-YL)BENZYL)HYDRAZINYL)-3,3-DIMETHYL-1-OXOBUTAN-2-YL)CARBAMATE
C43 H51 N5 O6
ZKMZXBMNTSRUBW-NPHQGNLKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QG9Ki: 4.2 nM BINDINGMOAD
QG9Ki: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.100α = 90.00
b = 86.500β = 90.00
c = 46.200γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection