De novo Design of SARS-CoV-2 Main Protease Inhibitors

Sulfur-Promoted Oxidative Condensation of Chalcones with Unsubstituted Cyanoacetamide in DMSO: Access to 3-Cyanopyrid-2-ones

Elemental sulfur and DABCO were found to be an excellent combination to promote a one-pot cascade of condensation-oxidative cyclization of chalcones and unsubstituted cyanoacetamide in DMSO to provide 3-cyanopyrid-2-ones.

Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

With the continual evolution of new strains of SARS-CoV-2 that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs SARS-CoV-2 main protease (M^pro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting M^pro appear promising but will elicit selection pressure for resistance. To understand resistance potential in M^pro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high-throughput assays of M^pro function in yeast, based on either the ability of M^pro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to M^pro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the M^pro dimer. The clinical variants of M^pro were predominantly functional in our screens, indicating that M^pro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to M^pro evolution and that are likely to contribute to drug resistance. This complete mutational guide of M^pro can be used in the design of inhibitors with reduced potential of evolving viral resistance.

Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions

Protein-ligand scoring functions are widely used in structure-based drug design for fast evaluation of protein-ligand interactions, and it is of strong interest to develop scoring functions with machine-learning approaches. In this work, by expanding the training set, developing physically meaningful features, employing our recently developed linear empirical scoring function Lin_F9 (Yang, C. J. Chem. Inf. Model. 2021, 61, 4630-4644) as the baseline, and applying extreme gradient boosting (XGBoost) with Δ-machine learning, we have further improved the robustness and applicability of machine-learning scoring functions. Besides the top performances for scoring-ranking-screening power tests of the CASF-2016 benchmark, the new scoring function Δ_{Lin_F9}XGB also achieves superior scoring and ranking performances in different structure types that mimic real docking applications. The scoring powers of Δ_{Lin_F9}XGB for locally optimized poses, flexible redocked poses, and ensemble docked poses of the CASF-2016 core set achieve Pearson's correlation coefficient (R) values of 0.853, 0.839, and 0.813, respectively. In addition, the large-scale docking-based virtual screening test on the LIT-PCBA data set demonstrates the reliability and robustness of Δ_{Lin_F9}XGB in virtual screening application. The Δ_{Lin_F9}XGB scoring function and its code are freely available on the web at (https://yzhang.hpc.nyu.edu/Delta_LinF9_XGB).

Effect of a Substituent in the Fourth Position on the Optical Properties of 2-Oxonicotinonitriles

Based on six representatives of 2-oxonicotinonitriles, the effect of the nature of the substituent in the fourth position of the pyridine system on the photophysical characteristics was studied. The role of the donor/acceptor nature of the substituent and the solvent nature in the absorbing and fluorescent properties of the compounds was shown.