<i>O</i>⁶‑Alkylguanine Postlesion DNA Synthesis Is Correct with the Right Complement of Hydrogen Bonding

The ability of a DNA polymerase to replicate DNA beyond a mismatch containing a DNA lesion during postlesion DNA synthesis (PLS) can be a contributing factor to mutagenesis. In this study, we investigate the ability of Dpo4, a Y-family DNA polymerase from <i>Sulfolobus solfataricus</i>, to perform PLS beyond the pro-mutagenic DNA adducts <i>O</i>⁶-benzylguanine (<i>O</i>⁶-BnG) and <i>O</i>⁶-methylguanine (<i>O</i>⁶-MeG). Here, <i>O</i>⁶-BnG and <i>O</i>⁶-MeG were paired opposite artificial nucleosides that were structurally altered to systematically test the influence of hydrogen bonding and base pair size and shape on <i>O</i>⁶-alkylguanine PLS. Dpo4-mediated PLS was more efficient past pairs containing Benzi than pairs containing the other artificial nucleoside probes. Based on steady-state kinetic analysis, frequencies of mismatch extension were 7.4 × 10^–3 and 1.5 × 10^–3 for Benzi:<i>O</i>⁶-MeG and Benzi:<i>O</i>⁶-BnG pairs, respectively. Correct extension was observed when <i>O</i>⁶-BnG and <i>O</i>⁶-MeG were paired opposite the smaller nucleoside probes Benzi and BIM; conversely, Dpo4 did not extend past the larger nucleoside probes, Peri and Per, placed opposite <i>O</i>⁶-BnG and <i>O</i>⁶-MeG. Interestingly, Benzi was extended with high fidelity by Dpo4 when it was paired opposite <i>O</i>⁶-BnG and <i>O</i>⁶-MeG but not opposite G. These results indicate that hydrogen bonding is an important noncovalent interaction that influences the fidelity and efficiency of Dpo4 to perform high-fidelity <i>O</i>⁶-alkylguanine PLS

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property–free knowledge base for future anticoronavirus drug discovery.</p