2. Academic Validation
  3. Structural Insights into the Mechanisms of Action of Functionally Distinct Classes of Chikungunya Virus Nonstructural Protein 1 Inhibitors

Structural Insights into the Mechanisms of Action of Functionally Distinct Classes of Chikungunya Virus Nonstructural Protein 1 Inhibitors

  • Antimicrob Agents Chemother. 2021 Jun 17;65(7):e0256620. doi: 10.1128/AAC.02566-20.
Kristina Kovacikova 1,  Marina Gorostiola González 2 3,  Rhian Jones 4,  Juan Reguera 4,  Alba Gigante 5,  María-Jesús Pérez-Pérez 5,  Gerhard Pürstinger 6,  Julia Moesslacher 7,  Thierry Langer 8,  Lak Shin Jeong 9,  Leen Delang 10,  Johan Neyts 10,  Eric J Snijder 1,  Gerard J P van Westen 2,  Martijn J van Hemert 1
Affiliations

Affiliations

  • 1 Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
  • 2 Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands.
  • 3 Oncode Institute, Leiden, the Netherlands.
  • 4 Aix-Marseille Université, INSERM, CNRS, AFMB UMR 7257, Marseille, France.
  • 5 Instituto de Química Médica (IQM-CSIC), Madrid, Spain.
  • 6 Department of Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria.
  • 7 Department of Pharmacy, University of Innsbruck, Innsbruck, Austria.
  • 8 Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.
  • 9 College of Pharmacy, Seoul National University, Seoul, South Korea.
  • 10 KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
PMID: 33875421 DOI: 10.1128/AAC.02566-20
Abstract

Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) harbors the methyltransferase (MTase) and guanylyltransferase (GTase) activities needed for viral RNA capping and represents a promising Antiviral drug target. We compared the Antiviral efficacies of nsP1 inhibitors belonging to the MADTP, CHVB, and FHNA series (6'-fluoro-homoneplanocin A [FHNA], its 3'-keto form, and 6'-β-fluoro-homoaristeromycin). Cell-based phenotypic cross-resistance assays revealed that the CHVB and MADTP series had similar modes of action that differed from that of the FHNA series. In biochemical assays with purified Semliki Forest virus and CHIKV nsP1, CHVB compounds strongly inhibited MTase and GTase activities, while MADTP-372 had a moderate inhibitory effect. FHNA did not directly inhibit the enzymatic activity of CHIKV nsP1. The first-of-their-kind molecular-docking studies with the cryo-electron microscopy (cryo-EM) structure of CHIKV nsP1, which is assembled into a dodecameric ring, revealed that the MADTP and CHVB series bind at the S-adenosylmethionine (SAM)-binding site in the capping domain, where they would function as competitive or noncompetitive inhibitors. The FHNA series was predicted to bind at the secondary binding pocket in the ring-aperture membrane-binding and oligomerization (RAMBO) domain, potentially interfering with the membrane binding and oligomerization of nsP1. Our cell-based and enzymatic assays, in combination with molecular docking and mapping of compound resistance mutations to the nsP1 structure, allowed us to group nsP1 inhibitors into functionally distinct classes. This study identified druggable pockets in the nsP1 dodecameric structure and provides a basis for the rational design, optimization, and combination of inhibitors of this unique and promising Antiviral drug target.

Keywords

Chikungunya virus; GTP; SAM; antivirals; binding pocket; capping; inhibitors; molecular docking; nsP1; resistance.

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