Cooperative molecular interaction networks govern PARP1 inhibitor selectivity and binding affinity

Abstract

Selective inhibition of PARP1 represents a promising strategy to improve the therapeutic index of PARP inhibitors, a class of anticancer agents that exploit defects in DNA repair pathways. While PARP inhibitors have shown remarkable clinical benefit, particularly in BRCA-mutated tumors, the lack of discrimination between PARP1 and its close homolog PARP2, often leads to hematological toxicity and limits treatment efficacy. Thus, achieving molecular selectivity for PARP1 remains a central challenge in the rational design of safer and more potent inhibitors. To explore the molecular determinants of ligand selectivity, we focus on four clinically relevant PARP inhibitors--two PARP1-selective (saruparib and NMS-P118) and two non-selective (veliparib and olaparib) inhibitors--and perform atomistic potential-of-mean-force calculations of the PARP1 catalytic binding domain in the presence of these molecules. Our simulations near-quantitatively capture the experimental relative binding preferences, demonstrating that our approach reliably reflects selectivity patterns. Based on these findings, we analyze protein-ligand contact frequencies to identify the stabilizing interaction network and contact connectivity inducing protein selectivity. The most frequent protein-inhibitor contacts are primarily mediated by tyrosine triads and electrostatic interactions, showing a cooperative complex network of intermolecular contacts which strongly relies on protein multivalency. To dissect the decisive role of individual residues across the binding site, we also perform targeted mutagenesis of the PARP1 catalytic pocket in complex with saruparib, replacing several active-site amino acids by glycines. Progressively increasing the number of mutations markedly reduces binding stability, with distinct residue combinations exerting two primary effects: destabilization of the final bound state and the emergence of energetic barriers along the ligand association pathway. Together, our results provide a coherent mechanistic framework for understanding PARP1 selectivity and informs the rational design of next-generation inhibitors with improved efficacy and safety.