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Related Experiment Video

Updated: Jan 29, 2026

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

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Metal Preference Hierarchy in the HDAC8 Active Site: A DFT Study.

Nikolay Toshev¹, Diana Cheshmedzhieva², Yordanka Uzunova^1,3

¹Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vassil Aprilov Blvd, 4002 Plovdiv, Bulgaria.

Molecules (Basel, Switzerland)

|January 28, 2026

Summary

Zinc (Zn²⁺) is the preferred metal cofactor for the histone deacetylase 8 (HDAC8) enzyme. Computational studies reveal its superior binding affinity over other ions like Fe²⁺, Co²⁺, Ni²⁺, and Mg²⁺.

Keywords:

DFT study HDAC8 active site HDACi metal competition metal ion selectivity

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Area of Science:

Biochemistry
Computational Chemistry
Enzymology

Background:

Histone deacetylase 8 (HDAC8) is implicated in various human diseases.
HDAC8 is a Zn²⁺-dependent metalloenzyme, but its interaction with other metal ions is poorly understood.
Understanding metal ion selectivity is crucial for HDAC8 inhibitor design.

Purpose of the Study:

To investigate the binding affinities of biologically relevant metal ions (Fe²⁺, Ni²⁺, Co²⁺, Mg²⁺) for the HDAC8 active site.
To elucidate the mechanism of metal ion competition with Zn²⁺.
To establish the intrinsic metal preference hierarchy of HDAC8.

Main Methods:

Density Functional Theory (DFT) calculations at the B3LYP/6-31+G(d) level.
Polarizable Continuum Model (PCM) computations in aqueous and methanolic solutions.
Thermodynamic analysis of metal ion substitution reactions.

Main Results:

Zn²⁺ is consistently the thermodynamically preferred cofactor for HDAC8.
Fe²⁺ and Co²⁺ show limited stabilization but are outcompeted by Zn²⁺ due to entropic and desolvation penalties.
Ni²⁺ and Mg²⁺ exhibit unfavorable binding, with Mg²⁺ strongly excluded.
Established metal preference hierarchy: Zn²⁺ > Co²⁺ ≈ Fe²⁺ > Ni²⁺ > Mg²⁺.

Conclusions:

HDAC8 exhibits intrinsic selectivity for Zn²⁺ over other tested metal ions.
The findings clarify HDAC8 metallo-regulation mechanisms.
Provides a molecular basis for designing targeted HDAC8 inhibitors.