A polyomavirus peptide binds to the capsid VP1 pore and has potent antiviral activity against BK and JC polyomaviruses

Abstract

In pursuit of therapeutics for human polyomaviruses, we identified a peptide derived from the BK polyomavirus (BKV) minor structural proteins VP2/3 that is a potent inhibitor of BKV infection with no observable cellular toxicity. The thirteen-residue peptide binds to major structural protein VP1 with single-digit nanomolar affinity. Alanine-scanning of the peptide identified three key residues, substitution of each of which results in ~1000 fold loss of binding affinity with a concomitant reduction in antiviral activity. Structural studies demonstrate specific binding of the peptide to the pore of pentameric VP1. Cell-based assays demonstrate nanomolar inhibition (EC50) of BKV infection and suggest that the peptide acts early in the viral entry pathway. Homologous peptide exhibits similar binding to JC polyomavirus VP1 and inhibits infection with similar potency to BKV in a model cell line. Lastly, these studies validate targeting the VP1 pore as a novel strategy for the development of anti-polyomavirus agents.

The Inhibition of DNA Viruses by the Amphibian Antimicrobial Peptide Temporin G: A Virological Study Addressing HSV-1 and JPCyV

“…According to the obtained model, TG was able to bind VP1 within the upper part of the five-fold symmetry pore (Figure 4C) formed by the pentameric arrangement of VP1 monomers [23,37]. Notably, these predictions are in line with recent research showing that peptides derived from the two minor capsid proteins VP2 and VP3 of polyomaviruses can bind to the same region of VP1 [38].…”

“…These data suggest that the peptide can bind to the upper region of the 5-fold pore formed by the major capsid component VP1 [23]. Interestingly, recently developed peptides, endowed with effective anti-polyomaviruses properties, were found to bind to the same site on VP1 [38]. In line with this evidence, it has been reported that ligand-induced structural perturbations occurring at the VP1 pore can significantly impair the JCPyV entry process [37], thus explaining the efficacy of TG against this virus.…”

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors

“…Remarkably, these pockets correspond to the interaction interface with the minor capsid protein VP2, as observed in the cryo-EM structure of BKV virions 9 and in the X-ray structures of both murine polyomavirus VP1 complexed with truncated VP2 50 and BKPyV VP1 complexed with a thirteen-residue long VP2 derived peptide. 26 Hence the three pockets in the pentamer pore are also likely to be relevant for capsid assembly and function, and should be explored towards rational drug design. A detailed analysis of these pockets and fragments binding therein will be presented elsewhere.…”

Antivirals against human polyomaviruses: Leaving no stone unturned

“…The EC 50 was 0.03 µM for BKPyV and 0.35 µM for JCPyV, and no cytotoxicity was observed in the concentration range tested (Tables 2 and 4). 162 This study demonstrates the principle of direct targeting polyomavirus capsid proteins, but peptide delivery to the relevant sites of replicative disease in the kidney and the brain is unresolved. Also, peptide immunogenicity eliciting neutralizing antibodies and serum sickness after repeated exposure might be problematic.…”