Mechanistic Insights into Binding of Ligands with Thiazolidinedione Warhead to Human Histone Deacetylase 4.

Markus Schweipert,Neha Upadhyay,Ewelina Wozny,Franz-Josef Meyer-Almes,Niklas Jänsch,Marlene Müller,Kalpana Tilekar,Ramaa C S,Sidra Basheer,Eva Wurster

doi:10.3390/ph14101032

Markus Schweipert, Neha Upadhyay + Show 8 more

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https://doi.org/10.3390/ph14101032

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Abstract

Recently, we have reported that non-hydroxamate thiazolidinedione (TZD) analogs are capable of inhibiting human deacetylase 4 (HDAC4). This study aims at the dissection of the molecular determinants and kinetics of the molecular recognition of TZD ligands by HDAC4. For this purpose, a structure activity relationship analysis of 225 analogs was combined with a comprehensive study of the enzyme and binding kinetics of a variety of HDAC4 mutant variants. The experimental data were rationalized by docking to the two major conformations of HDAC4. TZD ligands are competitive inhibitors and bind via a two-step mechanism involving principal molecular recognition and induced fit. The residence time of 24 g is (34 ± 3) min and thus much larger than that of the canonical pan-HDAC inhibitor SAHA ((5 ± 2) min). Importantly, the binding kinetics can be tuned by varying the structure of the CAP group.

Highlights

human deacetylase 4 (HDAC4) is a class IIa zinc-dependent histone deacetylase (HDAC) which is highly expressed in the brain, heart, and skeletal muscle and plays a major role in tissue growth and physiological development [1]
We reported TZD ligands as inhibitors of HDAC4 lacking the problematic zinc binding group hydroxamic acid
TZD compounds bind to the active site of cdHDAC4wt, and are competitive and reversible inhibitors, which bind via a two-step or one-step binding mechanism depending on the CAP group

Summary

Introduction

HDAC4 is a class IIa zinc-dependent histone deacetylase (HDAC) which is highly expressed in the brain, heart, and skeletal muscle and plays a major role in tissue growth and physiological development [1]. With a length of 972 to 1084 amino acids and a molecular weight of ca. The catalytic domain of HDAC4 (cdHDAC4) was used, which consists of 410 amino acids (human HDAC4 T648-T1057) and has a molecular weight of 44.2 kDa. In vivo as well as in vitro HDAC4 shows an exceptionally low to nonexistent deacetylation activity towards natural acetylated substrates due to tyrosine to histidine mutation located in the active site. Like all members of class IIa HDACs, HDAC4 has a highly flexible structural zinc binding domain (sZBD) with a second zinc atom in addition to the catalytic zinc in the enzyme’s active site. Because of the sZBD HDAC4 can adopt two distinct conformations with different types of inhibitors (open and closed) in x-ray crystal structures [3,4]

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