Structure-based identification of pan-arenavirus sites of vulnerability

The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. received a $536,871 Project Grant award from the National Institute of Allergy and Infectious Diseases (NIAID) under the Allergy and Infectious Diseases Research program (CFDA 93.855), effective August 1, 2025, through July 31, 2027. This award supports research to identify structure-based sites of vulnerability in arenaviruses—enveloped RNA viruses that cause hemorrhagic fevers with limited treatment options globally. The foundation will conduct machine learning and artificial neural network-based molecular screening to identify small molecule inhibitors targeting the arenavirus surface glycoprotein complex and RNA polymerase, two critical viral components conserved across diverse arenavirus strains.

The research deliverables include in silico screening of small molecules against structurally conserved, cross-reactive regions of arenavirus proteins (Aim 1 and Aim 2), followed by characterization through in vitro structural, biochemical, and viral neutralization analyses. This work aims to identify and optimize inhibitor candidates for future animal challenge studies and combinatorial therapeutic development, advancing the foundation's effort to develop pan-arenavirus countermeasures applicable across the broad family of Old World and New World arenavirus serogroups.

Abstract

Arenaviruses are enveloped RNA viruses with remarkably diverse old world (OW) and new world (NW) serogroups that cause hemorrhagic fevers, for which there are currently limited treatment options. At present, ribavirin is the only off-label antiviral medication with efficacy against lassa virus. The global prevalence, pandemic potential, probability for zoonotic transfer, and diversity of arenaviruses therefore justifies a sustained effort to identify and develop therapeutic countermeasures. Accelerated small molecule discovery, in addition to distinguishing novel inhibitors, may also provide essential mechanistic details of viral pathogenesis, revealing the molecular determinants of pan-reactivity of a diverse viral family. The arenavirus surface pre-glycoprotein polyprotein complex (GPC) and RNA polymerase (rnap) complexes are two critical components of the viral cell entry and replication cycle. Given the overall similarity in molecular architecture and specific localized sequence conservation for each of these molecules across the large arenavirus family, they represent attractive targets for small molecule inhibitor identification. Recent structural information for prototypic OW and NW arenavirus gpcs and rnaps has provided a foundation for identifying molecules that target structurally conserved, cross-reactive regions of these vital viral proteins. The proposed studies aim to fill a critical void in our understanding of pan- arenavirus sites of vulnerability through machine learning, artificial neural network molecular screening of small molecules against arenavirus gpcs (aim 1) and rnaps (aim 2). Further characterization by in vitro structural, biochemical, and viral neutralization analysis of small molecule candidate inhibitors identified by the in silico screen will allow for inhibitor optimization for future animal challenge studies and combinatorial therapeutic development. By identifying GPC or polymerase-targeting molecules with broad, pan-arenavirus activity, we will define molecular specificities and commonalities of disparate arenavirus gpcs and polymerase complexes to guide immunogen design.