Jumping from Fragment to Drug via Smart Scaffolds.

A focused drug repurposing approach is described where an FDA-approved drug is rationally selected for biological testing based on structural similarities to a fragment compound found to bind a target protein by an NMR screen. The approach is demonstrated by first screening a curated fragment library using 19 F NMR to discover a quality binder to ACE2, the human receptor required for entry and infection by the SARS-CoV-2 virus. Based on this binder, a highly related scaffold was derived and used as a "smart scaffold" or template in a computer-aided finger-print search of a library of FDA-approved or marketed drugs. The most interesting structural match involved the drug vortioxetine which was then experimentally shown by NMR spectroscopy to bind directly to human ACE2. Also, an ELISA assay showed that the drug inhibits the interaction of human ACE2 to the SARS-CoV-2 receptor-binding-domain (RBD). Moreover, our cell-culture infectivity assay confirmed that vortioxetine is active against SARS-CoV-2 and inhibits viral replication. Thus, the use of "smart scaffolds" based on binders from fragment screens may have general utility for identifying candidates of FDA-approved or marketed drugs as a rapid repurposing strategy. Similar approaches can be envisioned for other fields involving small-molecule chemical applications.

Characterization of the antiviral effects of REP 2139 on the HBV lifecycle in vitro.

During hepatitis B virus (HBV) infection, HBV subviral particles (SVP) are produced in large excess in comparison to infectious virions and account for the major source of HBV surface antigen (HBsAg) in the blood. This abundant circulating HBsAg has been postulated to promote HBV chronicity by inducing immune exhaustion against HBsAg. Nucleic acid polymers (NAPs) such as REP 2139 display promising antiviral activity against both HBV and hepatitis Delta virus (HDV) in clinical trials. REP 2139 is accompanied by clearance of HBsAg from blood with concomitant reappearance of anti-HBsAg antibodies. To decipher the mechanism-of-action of NAPs, a recently developed cell-based assay in human HepG2.2.15 cells was used (Blanchet et al., 2019). This assay recapitulates the HBsAg secretion inhibition observed in treated patients. In the present study, we analysed the antiviral effect of REP 2139 on the HBV lifecycle. Importantly, we confirm here the potent inhibitory activity of the compound on HBsAg secretion, and report minor or no effect on other viral markers such as intracellular DNA and RNA, and HBeAg or Dane particle secretion. Notably, intracellular HBsAg accumulation is prevented by proteasomal and lysosomal degradation.

HadD, a novel fatty acid synthase type II protein, is essential for alpha- and epoxy-mycolic acid biosynthesis and mycobacterial fitness.

Mycolic acids (MAs) have a strategic location within the mycobacterial envelope, deeply influencing its architecture and permeability, and play a determinant role in the pathogenicity of mycobacteria. The fatty acid synthase type II (FAS-II) multienzyme system is involved in their biosynthesis. A combination of pull-downs and proteomics analyses led to the discovery of a mycobacterial protein, HadD, displaying highly specific interactions with the dehydratase HadAB of FAS-II. In vitro activity assays and homology modeling showed that HadD is, like HadAB, a hot dog folded (R)-specific hydratase/dehydratase. A hadD knockout mutant of Mycobacterium smegmatis produced only the medium-size alpha'-MAs. Data strongly suggest that HadD is involved in building the third meromycolic segment during the late FAS-II elongation cycles, leading to the synthesis of the full-size alpha- and epoxy-MAs. The change in the envelope composition induced by hadD inactivation strongly altered the bacterial fitness and capacities to aggregate, assemble into colonies or biofilms and spread by sliding motility, and conferred a hypersensitivity to the firstline antimycobacterial drug rifampicin. This showed that the cell surface properties and the envelope integrity were greatly affected. With the alarmingly increasing case number of nontuberculous mycobacterial diseases, HadD appears as an attractive target for drug development.