Unraveling the Catalytic Mechanism and Substrate Selectivity of HDAC10: A Dual-Filter Approach for Polyamine Deacetylation.

Abstract

The histone deacetylase (HDAC) family plays a crucial role in regulating acetylation-dependent cellular processes, with dysregulation linked to diseases ranging from cancer to neurodegeneration. HDAC10, the sole polyamine deacetylase in the HDAC family, uniquely influences pathologies such as tumor immunity, autophagy, inflammation, virus infection, silicosis, etc. Despite its therapeutic potential, the molecular basis of HDAC10's catalytic activity and substrate selectivity remains poorly understood, hindering rational drug design. Here, we address this gap by integrating density functional theory (DFT) and molecular dynamics simulation to systematically investigate HDAC10's catalytic activity and substrate selectivity. Utilizing a 330-atom quantum cluster model, we evaluated five distinct reaction pathways. The double-proton transfer mechanism (D'D) is dominant, featuring a concerted double-proton transfer step and a rate-limiting protonation of the substrate's amide nitrogen (20.4 kcal/mol barrier). Substrate selectivity arises from synergistic effects: N ⁸-acetylspermidine benefits from enhanced binding via active-site hydrogen-bond networks and reduced catalytic barriers compared to N ¹-acetylspermidine, which suffers from electrostatic repulsion and dynamic instability. This study provides the first atomic-resolution framework for HDAC10's catalysis and selectivity, resolving long-standing mechanistic ambiguities. By identifying critical interactions governing substrate recognition and turnover, our work establishes a foundation for designing isoform-specific HDAC10 inhibitors, offering strategic avenues to target its roles in disease.