Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones

Area of Science:

• Biochemistry
• Chemical Biology
• Computational Chemistry

Background:

• Heterocyclic thiones function as reversible covalent warheads due to their electrophilic nature.
• Understanding the mechanism of cysteine labeling by thiones is crucial for drug discovery.
• The main protease of SARS-CoV-2 (Mpro) is a validated target for covalent inhibitors.

Purpose of the Study:

• To elucidate the mechanism of covalent cysteine labeling by thione derivatives.
• To investigate the role of molecular recognition in the binding of covalent inhibitors.
• To benchmark thione inhibitor studies using well-characterized Michael acceptors.

Main Methods:

• Screening of a cysteine-targeting covalent inhibitor library.
• Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations.
• Quantum mechanics (QM) calculations and free energy computations.
• Experimental validation of computational findings.

Main Results:

• Identification of benzoxazole, benzothiazole, and benzimidazole core fragments as covalent inhibitors.
• Discovery of a novel mechanism for covalent cysteine modification by thione derivatives.
• Demonstration of the critical role of molecular recognition in inhibitor binding.
• Experimental data supported the proposed QM/MM simulation findings.

Conclusions:

• Thione derivatives exhibit a unique mechanism for covalent cysteine labeling.
• Molecular recognition is a key factor in the efficacy of covalent inhibitors.
• This study provides valuable insights into the development of novel covalent drugs targeting cysteine residues.