Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S Proteasome

Abstract

The COVID-19 pandemic has been a public health emergency with continuously evolving deadly variants around the globe. Among many preventive and therapeutic strategies, the design of covalent inhibitors targeting the main protease (M^pro) of SARS-CoV-2 that causes COVID-19 has been one of the hotly pursued areas. Currently, about 30% of marketed drugs that target enzymes are covalent inhibitors. Such inhibitors have been shown in recent years to have many advantages that counteract past reservation of their potential off-target activities, which can be minimized by modulation of the electrophilic warhead and simultaneous optimization of nearby noncovalent interactions. This process can be greatly accelerated by exploration of binding affinities using computational models, which are not well-established yet due to the requirement of capturing the chemical nature of covalent bond formation. Here, we present a robust computational method for effective prediction of absolute binding free energies (ABFEs) of covalent inhibitors. This is done by integrating the protein dipoles Langevin dipoles method (in the PDLD/S-LRA/β version) with quantum mechanical calculations of the energetics of the reaction of the warhead and its amino acid target, in water. This approach evaluates the combined effects of the covalent and noncovalent contributions. The applicability of the method is illustrated by predicting the ABFEs of covalent inhibitors of SARS-CoV-2 M^pro and the 20S proteasome. Our results are found to be reliable in predicting ABFEs for cases where the warheads are significantly different. This computational protocol might be a powerful tool for designing effective covalent inhibitors especially for SARS-CoV-2 M^pro and for targeted protein degradation.

Figure 1.

Thermodynamic cycle for calculating the absolute binding free energy of a covalent inhibitor. α is the bond energy which is canceled in the cycle.

Figure 2.

Covalent binding scheme of inhibitors involving (a) an α-ketoamide and (b) an aldehyde warhead with Cys145 of the main protease of SARS-CoV-2.

Figure 3.

Upper panel shows structures of Bsc2189 and MG132. The lower panel shows, on the left side, the cylinder structure of 20S proteasome, while the right-hand depicts the interactions between Bsc2189 and the β5 subunit of the 20S proteasome (PDB code: 4NO8).

Figure 4.

The left-hand panel shows the structure of M^pro. The right-hand panel shows the interactions between PF07321332 (orange) and the active site of M^pro (PDB code: 7VH8).

Figure 5.

Structures of the seven inhibitors targeting the M^pro.