Tyrosyl-DNA phosphodiesterase 1, TDP1, is a molecular target for the sensitization of cancer cells to the FDA-approved topoisomerase inhibitors topotecan and irinotecan. However, current TDP1 inhibitors have low binding affinity or are substrate mimics with low specificity. Through high-throughput screening of natural products and extracts library in the search for novel TDP1 inhibitors, we identified a new class of complex knotted peptides with a unique disulfide-bond topology from the marine sponge Axinella sp.¹

The active component was a 42-residue peptide named recifin A. Unlike previously described TDP1 inhibitors which bind to the C-terminal catalytic domain of TDP1, recifin A acts as an allosteric inhibitor and binds to the N-terminal regulatory domain. The three-dimensional NMR structure revealed a novel fold comprising a four-strand antiparallel }-sheet and two helical turns stabilized by a complex disulfide-bond network that creates an embedded ring around one of the strands. The structure is locked in place by a centrally located tyrosine residue, resulting in the Tyr-lock family name.

Recifin A represents both the first of a unique structural class of knotted disulfide-rich peptides and defines a previously unseen mechanism of TDP1 inhibition that could lead to the development of a new class of TDP1 inhibitors with improved specificity that could be exploited for potential anticancer applications.

Reference

1. Lauren R. H. Krumpe, Brice A. P. Wilson, Christophe Marchand, Suthananda N. Sunassee, Alun Bermingham, Wenjie Wang, Edmund Price, Tad Guszczynski, James A. Kelley, Kirk R. Gustafson, Yves Pommier, K. Johan Rosengren, Christina I. Schroeder, and Barry R. O'Keefe. Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I. JACS, 2020, 142, 21178-21188.