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Castellanos, M. A.

Publications and source records attributed to Castellanos, M. A..

2 recordsLinked to original sources

How many crystal structures do you need to trust your docking results?

Structure-based drug discovery relies on the prediction of protein-bound poses of new molecule designs, the accuracy of which can impact downstream prioritization. While it is expected that crystal structures of similar molecules would provide the best template for predicting the poses of new designs, the time and cost required motivates identifying a point of diminishing returns for collecting new structures. Using 403 crystal structures of SARS-CoV-2 main protease from the open science COVID Moonshot project, we explore the tradeoff between the cost and utility of obtaining crystal structures for accurately predicting poses of designed molecules. We observe that similar reference ligands enable superior pose prediction and show that success plateaus after approximately five crystal structures per generic Bemis-Murcko scaffold, exceeding 95% for the campaign's lead series. This work provides practical recommendations for resource allocation in structure-enabled drug discovery campaigns.

biophysics↗

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↗