Biology subjects

Lahav, N.

Publications and source records attributed to Lahav, N..

5 recordsLinked to original sources

bioRxiv2026

Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors

Compounds that bind to the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) main protease (MPro) often produce biphasic concentration-response curves (CRCs) in biochemical assays; low concentrations activate the enzyme and high concentrations inhibit it. This biphasic behavior complicates data analysis. Here, we compare three approaches to data analysis: fitting the Hill equation to the activation phase, fitting it to the inhibition phase, and fitting an enzyme kinetics model that incorporates dimerization and ligand binding to the complete CRC. In the latter case, cellular efficacy is predicted by extrapolating the model to high enzyme concentrations. For compounds in our drug lead series, all three procedures yield inhibitory concentrations that are correlated with live-virus antiviral assays. The latter procedure provides the most accurate forecast of cellular efficacy rank. These data analysis procedures may be valuable for antiviral drug discovery against MERS-CoV MPro and other enzymes with similar kinetics.

biochemistry↗

bioRxiv2025

A Structure-Based Computational Pipeline for Broad-Spectrum Antiviral Discovery

The rapid emergence of viruses with pandemic potential continues to pose a threat to public health worldwide. With the typical drug discovery pipeline taking an average of 5-10 years to reach clinical readiness, there is an urgent need for strategies to develop broad-spectrum antivirals that can target multiple viral family members and variants of concern. We present a structure-based computational pipeline designed to identify and evaluate broad-spectrum inhibitors across viral family members for a given target in order to support spectrum breadth assessment and prioritization in lead optimization programs. This pipeline comprises three key steps: (1) an automated search to identify viral sequences related to a specified target construct, (2) pose prediction leveraging any available structural data, and (3) scoring of protein-ligand complexes to estimate antiviral activity breadth. The pipeline is implemented using the drugforge package: an open-source toolkit for structure-based antiviral discovery. To validate this framework, we retrospectively evaluated two overlapping datasets of ligands bound to the SARS-CoV-2 and MERS-CoV main protease (Mpro), observing useful predictive power with respect to experimental binding affinities. Additionally, we screened known SARS-CoV-2 Mpro inhibitors against a panel of human and non-human coronaviruses, demonstrating the potential of this approach to assess broad-spectrum antiviral activity. Our computational strategy aims to accelerate the identification of antiviral therapies for current and emerging viruses with pandemic potential, contributing to global preparedness for future outbreaks.

bioinformatics↗

bioRxiv2025

Discovery of orally bioavailable Zika and West Nile Virus antiviral compounds targeting the NS2B-NS3 protease

Flaviviruses are a class of pathogenic viruses with pandemic potential that are typically transmitted via infected arthropods. In addition, Zika virus is sexually transmissible and causes congenital malformations if infection occurs during pregnancy. Although over 1.5 million people were infected during the 2015-2016 Zika outbreak, to date, there are no clinical-stage vaccines or antivirals. Herein, we report the discovery of potent inhibitors of the Zika virus NS2B-NS3 protease that also show activity against the West Nile virus NS2B-NS3 protease. Starting from a crystallographic fragment screen, we employed a pharmacophore approach coupled with high-throughput library chemistry to elaborate fragments in the active site. Potent, metabolically stable, non-covalent, non-peptidomimetic inhibitors were identified with antiviral activity in vitro. The lead compound was progressed to a three-day Zika virus challenge study in AG129 mice, where it displayed significant viral RNA load reduction in both mouse plasma and spleen.

microbiology↗

bioRxiv2025

Open-science discovery of DNDI-6510, a compound that addresses genotoxic and metabolic liabilities of the COVID Moonshot SARS-CoV-2 Mpro lead inhibitor

The 2020 SARS-CoV-2 coronavirus pandemic highlighted the urgent need for novel small molecule antiviral drugs. (S)-x38 DNDI-6510 is a non-covalent SARS-CoV-2 main protease inhibitor developed by the open science collaboration COVID Moonshot. Here, we report on the metabolic and toxicologic optimization of the lead series previously disclosed by the COVID Moonshot Initiative, leading up to the selection of (S)-x38 DNDI-6510 as the preclinical candidate. We describe the thorough profiling of the series, identifying key risks such as formation of genotoxic metabolites and high clearance, which were successfully addressed during lead optimization. In addition, we disclose the in vitro and in vivo evaluation of (S)-x38 DNDI-6510 in pharmacokinetic and pharmacodynamic models, exploring multiple approaches to ameliorate rodent-specific metabolic clearance, and show that both co-dosing of (S)-x38 DNDI-6510 with an ABT inhibitor and utilizing a metabolically humanized mouse model (8HUM) achieve significant improvements in exposure. Through comparisons of ABT co-dosing and humanized mouse models in efficacy experiments, we demonstrate that continuous exposure over cellular EC90 is required for SARS-CoV-2 antiviral efficacy in vivo in an antiviral model using a mouse-adapted SARS-CoV-2 strain. Finally, (S)-x38 DNDI-6510 was assessed in maximum tolerated dose experiments in two species, demonstrating significant in vivo PXR-linked auto-induction of metabolism, leading to the discontinuation of this compound. In summary, we report the successful effort to overcome series-specific AMES liabilities in a lead development program. Downstream optimization of existing series will require in-depth optimization of rodent-specific liabilities and metabolic induction profile.

pharmacology and toxicology↗

bioRxiv2024

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

microbiology↗