Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase (preprint)

An under-explored target for SARS-CoV-2 is non-structural protein 14 (Nsp14), a crucial enzyme for viral replication that catalyzes the methylation of N7-guanosine of the viral RNA at 5-prime-end; this enables the virus to evade the host immune response by mimicking the eukaryotic post-transcriptional modification mechanism. We sought new inhibitors of the S-adenosyl methionine (SAM)-dependent methyltransferase (MTase) activity of Nsp14 with three large library docking strategies. First, up to 1.1 billion make-on-demand (tangible) lead-like molecules were docked against the enzyme SAM site, seeking reversible inhibitors. On de novo synthesis and testing, three inhibitors emerged with IC50 values ranging from 6 to 43 M, each with novel chemotypes. Structure-guided optimization and in vitro characterization supported their non-covalent mechanism. In a second strategy, docking a library of 16 million tangible fragments revealed nine new inhibitors with IC50 values ranging from 12 to 341 M and ligand efficiencies from 0.29 to 0.42. In a third strategy, a newly created library of 25 million tangible, virtual electrophiles were docked to covalently modify Cys387 in the SAM binding site. Seven inhibitors emerged with IC50 values ranging from 3.2 to 39 M, the most potent being a reversible aldehyde. Initial optimization of a second series yielded a 7 M acrylamide inhibitor. Three inhibitors characteristic of the new series were tested for selectivity against 30 human protein and RNA MTases, with one showing partial selectivity and one showing high selectivity. Overall, 32 inhibitors encompassing eleven chemotypes had IC50 values <50 M and 5 inhibitors in four chemotypes had IC50 values <10 M. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing multiple starting points for optimizing towards antiviral activity.

The Genomic Profile Associated with Risk of Severe Forms of COVID-19 in Amazonian Native American Populations.

Genetic factors associated with COVID-19 disease outcomes are poorly understood. This study aimed to associate genetic variants in the SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, and ABO genes with the risk of severe forms of COVID-19 in Amazonian Native Americans, and to compare the frequencies with continental populations. The study population was composed of 64 Amerindians from the Amazon region of northern Brazil. The difference in frequencies between the populations was analyzed using Fisher's exact test, and the results were significant when p ≤ 0.05. We investigated 64 polymorphisms in 7 genes; we studied 47 genetic variants that were new or had impact predictions of high, moderate, or modifier. We identified 15 polymorphisms with moderate impact prediction in 4 genes (ABO, CXCR6, FYCO1, and SLC6A20). Among the variants analyzed, 18 showed significant differences in allele frequency in the NAM population when compared to others. We reported two new genetic variants with modifier impact in the Amazonian population that could be studied to validate the possible associations with COVID-19 outcomes. The genomic profile of Amazonian Native Americans may be associated with protection from severe forms of COVID-19. This work provides genomic data that may help forthcoming studies to improve COVID-19 outcomes.

Comparison of pneumonia features in children caused by SARS-CoV-2 and other viral respiratory pathogens. (preprint)

Pneumonia is a frequent manifestation of COVID-19 in hospitalized children. Methods The study involved 80 hospitals in the SARS-CoV-2 Spanish Pediatric National Cohort. Participants were children <18 years, hospitalized with SARS-CoV-2 community-acquired pneumonia (CAP). We compared the clinical characteristics of SARS-CoV-2-associated CAP with CAP due to other viral etiologies from 2012 to 2019. Results In total, 151 children with SARS-CoV-2-associated CAP and 138 with other viral CAP included. Main clinical features of SARS-CoV-2-associated CAP were cough 117/151(77%), fever 115/151(76%) and dyspnea 63/151(46%); 22/151(15%) patients were admitted to a pediatric intensive care unit (PICU), and 5/151(3%) patients died. Lymphopenia was found in 63/147(43%) patients. Chest X-ray revealed condensation (64/151[42%]) and other infiltrates (87/151[58%]). Compared with CAP from other viral pathogens, COVID-19 patients were older (8 vs.1 year; odds ratio [OR] 1.42 [95% confidence interval, CI 1.23;1.42]), with lower CRP levels (23 vs.48 mg/L; OR 1 [95%CI 0.99;1]), less wheezing (17 vs.53%; OR 0.18 [95%CI 0.11;0.31]) and greater need of mechanical ventilation, MV (7 vs.0.7%, OR 10.8 [95%CI 1.3;85). Patients with non-SARS-CoV-2-associated CAP had a greater need for oxygen therapy (77 vs.44%, OR 0.24 [95%CI 0.14;0.40]). There were no differences in the use of CPAP or HVF or PICU admission between groups. Conclusion SARS-CoV-2-associated CAP in children presents differently to other virus-associated CAP: children are older and rarely have wheezing or high CRP levels; they need less oxygen but more CPAP or MV. However, several features overlap, and differentiating the etiology may be difficult. The overall prognosis is good.