Identification of SARS-CoV-2 Main Protease Inhibitors Using Chemical Similarity Analysis Combined with Machine Learning.

SARS-CoV-2 Main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome, which is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development. Herein, we performed a large-scale virtual screening by comparing multiple structural descriptors of reference molecules with reported anti-coronavirus activity against a library with >17 million compounds. Further filtering, performed by applying two machine learning algorithms, identified eighteen computational hits as anti-SARS-CoV-2 compounds with high structural diversity and drug-like properties. The activities of twelve compounds on Mpro's enzymatic activity were evaluated by fluorescence resonance energy transfer (FRET) assays. Compound 13 (ZINC13878776) significantly inhibited SARS-CoV-2 Mpro activity and was employed as a reference for an experimentally hit expansion. The structural analogues 13a (ZINC4248385), 13b (ZNC13523222), and 13c (ZINC4248365) were tested as Mpro inhibitors, reducing the enzymatic activity of recombinant Mpro with potency as follows: 13c > 13 > 13b > 13a. Then, their anti-SARS-CoV-2 activities were evaluated in plaque reduction assays using Vero CCL81 cells. Subtoxic concentrations of compounds 13a, 13c, and 13b displayed in vitro antiviral activity with IC50 in the mid micromolar range. Compounds 13a-c could become lead compounds for the development of new Mpro inhibitors with improved activity against anti-SARS-CoV-2.

Discovery and Optimization of Neutralizing SARS-CoV-2 Antibodies Using ALTHEA Gold Plus Libraries™.

We recently reported the isolation and characterization of anti-SARS-CoV-2 antibodies from a phage display library built with the VH repertoire of a convalescent COVID-19 patient, paired with four naïve synthetic VL libraries. One of the antibodies, called IgG-A7, neutralized the Wuhan, Delta (B.1.617.2) and Omicron (B.1.1.529) strains in authentic neutralization tests (PRNT). It also protected 100% transgenic mice expressing the human angiotensin-converting enzyme 2 (hACE-2) from SARS-CoV-2 infection. In this study, the four synthetic VL libraries were combined with the semi-synthetic VH repertoire of ALTHEA Gold Libraries™ to generate a set of fully naïve, general-purpose, libraries called ALTHEA Gold Plus Libraries™. Three out of 24 specific clones for the RBD isolated from the libraries, with affinity in the low nanomolar range and sub-optimal in vitro neutralization in PRNT, were affinity optimized via a method called "Rapid Affinity Maturation" (RAM). The final molecules reached sub-nanomolar neutralization potency, slightly superior to IgG-A7, while the developability profile over the parental molecules was improved. These results demonstrate that general-purpose libraries are a valuable source of potent neutralizing antibodies. Importantly, since general-purpose libraries are "ready-to-use", it could expedite isolation of antibodies for rapidly evolving viruses such as SARS-CoV-2.

In Vitro and In Vivo Characterization of a Broadly Neutralizing Anti-SARS-CoV-2 Antibody Isolated from a Semi-Immune Phage Display Library.

Neutralizing antibodies targeting the receptor-binding domain (RBD) of SARS-CoV-2 are among the most promising strategies to prevent and/or treat COVID-19. However, as SARS-CoV-2 has evolved into new variants, most of the neutralizing antibodies authorized by the US FDA and/or EMA to treat COVID-19 have shown reduced efficacy or have failed to neutralize the variants of concern (VOCs), particularly B.1.1.529 (Omicron). Previously, we reported the discovery and characterization of antibodies with high affinity for SARS-CoV-2 RBD Wuhan (WT), B.1.617.2 (Delta), and B.1.1.529 (Omicron) strains. One of the antibodies, called IgG-A7, also blocked the interaction of human angiotensin-converting enzyme 2 (hACE2) with the RBDs of the three strains, suggesting it may be a broadly SARS-CoV-2 neutralizing antibody. Herein, we show that IgG-A7 efficiently neutralizes all the three SARS-CoV-2 strains in plaque reduction neutralization tests (PRNTs). In addition, we demonstrate that IgG-A7 fully protects K18-hACE2 transgenic mice infected with SARS-CoV-2 WT. Taken together, our findings indicate that IgG-A7 could be a suitable candidate for development of antibody-based drugs to treat and/or prevent SARS-CoV-2 VOCs infection.

Full-genome sequencing and phylogenetic analysis of four neurovirulent Mexican isolates of porcine rubulavirus.

We report the complete genome sequences of four neurovirulent isolates of porcine rubulavirus (PorPV) from 2015 and one historical PorPV isolate from 1984 obtained by next-generation sequencing. A phylogenetic tree constructed using the individual sequences of the complete HN genes of the 2015 isolates and other historical sequences deposited in the GenBank database revealed that several recent neurovirulent isolates of PorPV (2008-2015) cluster together in a separate clade. Phylogenetic analysis of the complete genome sequences revealed that the neurovirulent strains of PorPV that circulated in Mexico during 2015 are genetically different from the PorPV strains that circulated during the 1980s.

Peptides Derived from Glycoproteins H and B of Herpes Simplex Virus Type 1 and Herpes Simplex Virus Type 2 Are Capable of Blocking Herpetic Infection in vitro.

AIMS: The aim of this study was to design peptides derived from glycoproteins H (gH) and B (gB) of herpes simplex viruses type 1 (HSV-1) and type 2 (HSV-2) with the potential to block herpetic infection and to evaluate their ability to inhibit HSV-1 and HSV-2 infection in vitro. METHODS: A library of continuous 15-25 residue stretches (CRSs) located at the surface of gH and gB from HSV-1 and HSV-2 was created. These CRSs were analyzed, and only those that were highly flexible and rich in charged residues were selected for the design of the antiviral peptides (AVPs). The toxicity of the AVPs was evaluated by MTT reduction assays. Virucidal activity of the AVPs was determined by a plaque reduction assay, and their antiviral effect was measured by cell viability assays. RESULTS AND CONCLUSION: Four AVPs (CB-1, CB-2, U-1, and U-2) derived from gB and gH were designed and synthetized, none of which showed high levels of toxicity in Vero cells. The U-1 and U-2 gB-derived AVPs showed high virucidal and antiviral activities against both HSV-1 and HSV-2. The gH-derived peptide CB-1 showed high virucidal and antiviral activities against HSV-2, while CB-2 showed similar results against HSV-1. The peptides CB-1 and CB-2 showed higher IC50 values than the U-1 and U-2 peptides.