Development of antivirals for the treatment of COVID-19

The rapid spread of the COVID-19 pandemic with exponential growth in cases in Brazil and worldwide, there is great concern about the lethality in those infected and the saturation of hospital beds to treat severe cases. Although the search for an effective vaccine is urgent, any development should require one to two years to be approved, so there is no expectation that it can be used even during this global pandemic. In this context, in addition to the necessary mitigating health measures, there is an urgent need for research on drugs with antiviral activity against the SAR-Cov-2 coronavirus, which can assist in the treatment of infected patients. In this project, a primary compound screening assay will be established and standardized, in an HCS (High Content Screening) model, using humans and the SARS-Cov-2 coronavirus isolated from Brazilian patients and grown under conditions of high biological safety (P3) at ICB- USP The forecast is that in this test it will be possible to evaluate up to 4,000 compounds, being able to expand this study according to the availability of compounds and resources for the reagents and consumables of the tests. Next, we will evaluate several collections of compounds: a library of 1500 FDA-approved compounds; all collections of natural and synthetic molecules from CIBFar / CEPID-FAPESP (which include compounds from NuBBE / IQAr / UNESP /, FCFRP / USP, LSPN-DQ-UFSCar and IQ / UNICAMP); the PITE-FAPESP / MMV / DNDi / Unicamp / USP Consortium; NEQUIMED / IQSC / USP. Fluorescent peptide probes and protease inhibitors, produced at EPM / UNIFESP, will be produced and evaluated in phenotypic and enzymatic assays, based on previous studies on the SARS-Cov coronavirus cysteine ​​protease and also the human TMPRSS2 serine protease, involved in the invasion by COVID-19. Compound libraries from the international organization Medicines for Malaria Ventures will be made available for screening against SARS-Cov-2 in this project: they are libraries ranging from 400 compounds (Pathogen Box and Pandemic Box) to 20-40,000 or up to 150,000 compounds with great chemical diversity . All relevant SARS-Cov-2 coronavirus proteins as potential targets for antiviral drugs will be cloned and expressed in recombinant form in E. coli, and biochemical and biophysical assays will be developed to identify inhibitors and ligands. The identification of hits against SARS-Cov-2 will be important not only for their future development as candidates for new antiviral drugs, but knowledge of their chemical structures can immediately assist us in the emergency effort to reposition drugs already in clinical use for other therapeutic indications, by comparing their active pharmacophoric groups and bioisosterism methods. With the possibility of the emergence of immune escape mutants, the sequencing of SARS-CoV-2 genomes and viral isolation will be carried out during the period of the pandemic occurrence in Brazil to identify possible escape mutants in the receptor binding region. On another research front, simple and alternative synthetic routes will be developed for drugs already approved for use in humans and which are being identified as effective, albeit partially, in the treatment of COVID-19.