Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

Abstract

Cysteine proteases are an important target for the development of inhibitors that could be used as drugs to regulate the activity of these kinds of enzymes involved in many diseases, including COVID-19. For this reason, it is important to have methodological tools that allow a detailed study of their activity and inhibition, combining computational efficiency and accuracy. We here explore the performance of different quantum mechanics/molecular mechanics methods to explore the inhibition reaction mechanism of the SARS-CoV-2 3CL protease with a hydroxymethyl ketone derivative. We selected two density functional theory (DFT) functionals (B3LYP and M06-2X), two semiempirical Hamiltonians (AM1d and PM6), and two tight-binding DFT methods (DFTB3 and GFN2-xTB) to explore the free energy landscape associated with this reaction. We show that it is possible to obtain an accurate description combining molecular dynamics simulations performed using tight-binding DFT methods and single-point energy corrections at a higher QM description. The use of a computational strategy that provides reliable results at a reasonable computational cost could assist the in silico screening of possible candidates during the design of new drugs directed against cysteine proteases.

Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism

“…In this sense, the empirical valence bond, tight binding, and semiempirical methods are computationally affordable options for obtaining free-energy surfaces. A recent study has suggested that DFTB3, GFN2-xTB, AM1, and PM6 methods underestimated, with respect to the density functional theory (DFT) values, the activation free energies of the inhibition reaction mechanism of SARS-CoV-2 M pro protease with a hydroxymethyl ketone derivative . DFTB3 was also applied to study nitrile and vinyl sulfone inhibitors of cruzain and underestimated the reaction barrier .…”

“…A recent study has suggested that DFTB3, GFN2-xTB, AM1, and PM6 methods underestimated, with respect to the density functional theory (DFT) values, the activation free energies of the inhibition reaction mechanism of SARS-CoV-2 M pro protease with a hydroxymethyl ketone derivative. 89 DFTB3 was also applied to study nitrile and vinyl sulfone inhibitors of cruzain and underestimated the reaction barrier. 46 Recently, it was suggested that the reaction-free energy computed with the PM6/MM potential is in agreement with the experimental data.…”

Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces

“…Note also that the inclusion of dispersion corrections in B3LYP has been recommended in QM calculations when modeling cysteine reactivity . Other recent contributions have used the B3LYP-D3 potential to describe the QM region in hybrid QM/MM free-energy calculations involving the study of the formation of the covalent enzyme–inhibitor complex. − Although the B3LYP functional presents limitations for predicting a stable enolate and carbanion intermediates, , a recent study has demonstrated that B3LYP correctly describes the nucleophilic attack of a thiolate to a Michael acceptor if this attack takes place together with the proton transfer …”

Unravelling interactions between active site residues and DMAP in the initial steps of prenylated flavin mononucleotide biosynthesis catalyzed by PaUbiX

“…For those calculations, we resorted to the GFN2-xTB method [21]. This DFT tight-binding method was developed with a focus on systems comprising a few thousand atoms including biological ones and it has been recently shown to provide a very good geometrical description of an enzymatic reaction [22]. At the enzyme-substrate state, no proton exchange was observed between neither Lys129 and DMAP, and Lys129 and Glu140 (Figure S1, A).…”