Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy

Angew Chem Int Ed Engl. 2018 Mar 1;57(10):2687-2691. doi: 10.1002/anie.201713172. Epub 2018 Feb 2.


HIV-1 nucleocapsid (NCp7) is a two Cys2 HisCys zinc knuckle (N-Zn and C-Zn) protein that plays a key role in viral replication. NCp7 conformational dynamics is characterized by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N-Zn knuckle is conformationally stable, the C-Zn knuckle interconverts on the millisecond timescale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1 %) in which one of the coordination bonds (Cys413-Sγ-Zn or His421-Nϵ2-Zn) is hydrolyzed. These findings explain why antiretroviral thioesters specifically disrupt the C-Zn knuckle by initial acylation of Cys413, and show that transient, sparsely-populated ("dark"), excited states of proteins can present effective targets for rational drug design.

Keywords: HIV-1 nucleocapsid; antiretrovirals; conformational exchange; relaxation dispersion; zinc.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Anti-Retroviral Agents / chemistry
  • Anti-Retroviral Agents / pharmacology*
  • Esters / chemistry
  • Esters / pharmacology*
  • Magnetic Resonance Spectroscopy
  • Molecular Structure
  • Structure-Activity Relationship
  • Sulfhydryl Compounds / chemistry
  • Sulfhydryl Compounds / pharmacology*
  • gag Gene Products, Human Immunodeficiency Virus / antagonists & inhibitors*
  • gag Gene Products, Human Immunodeficiency Virus / chemistry


  • Anti-Retroviral Agents
  • Esters
  • NCP7 protein, Human immunodeficiency virus 1
  • Sulfhydryl Compounds
  • gag Gene Products, Human Immunodeficiency Virus