5WLO | pdb_00005wlo

a novel 13-ring macrocyclic HIV-1 protease inhibitors involving the P1'-P2' ligands

• PDB DOI: https://doi.org/10.2210/pdb5WLO/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-27 Released: 2017-10-11 
• Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), Ministry of Education, Culture, Sports, Science and Technology (Japan), Ministry of Health,Labour and Welfare (Japan), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.205 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, X-ray studies, and biological evaluation of novel macrocyclic HIV-1 protease inhibitors involving the P1'-P2' ligands.

Ghosh, A.K., Sean Fyvie, W., Brindisi, M., Steffey, M., Agniswamy, J., Wang, Y.F., Aoki, M., Amano, M., Weber, I.T., Mitsuya, H.

(2017) Bioorg Med Chem Lett 27: 4925-4931

• PubMed: 28958624 
• DOI: https://doi.org/10.1016/j.bmcl.2017.09.003
• Primary Citation Related Structures: 
  5WLO


• PubMed Abstract: 
  

  Design, synthesis, and evaluation of a new class of HIV-1 protease inhibitors containing diverse flexible macrocyclic P1'-P2' tethers are reported. Inhibitor 5a with a pyrrolidinone-derived macrocycle exhibited favorable enzyme inhibitory and antiviral activity (K _i =13.2nM, IC ₅₀ =22nM). Further incorporation of heteroatoms in the macrocyclic skeleton provided macrocyclic inhibitors 5m and 5o. These compounds showed excellent HIV-1 protease inhibitory (K _i =62pM and 14pM, respectively) and antiviral activity (IC ₅₀ =5.3nM and 2.0nM, respectively). Inhibitor 5o also remained highly potent against a DRV-resistant HIV-1 variant.

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Organizational Affiliation: 
• Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA. Electronic address: [e-mail].
Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA.
Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan.
Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.46 kDa 
• Atom Count: 1,940 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol
UniProt
Find proteins for Q72498 (Human immunodeficiency virus type 1) Explore Q72498  Go to UniProtKB:  Q72498

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GR7 (Subject of Investigation/LOI)	F [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[(7E)-13-methoxy-1,1-dioxo-1,4,5,6,9,11-hexahydro-10,1lambda~6~,2-benzoxathiazacyclotridecin-2(3H)-yl]-1-phenylbutan-2-yl}carbamate C32 H42 N2 O9 S QVQZOHIOYHJWJV-RSNMJCISSA-N
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.205 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.475	α = 90
b = 86.034	β = 90
c = 45.877	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
SHELXL	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM62920
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	a Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Health,Labour and Welfare (Japan)	Japan	a Grant for Promotion of AIDS Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	the Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	--

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence
• Version 1.2: 2017-10-25
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description