# Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

## TL;DR

This study uses computational methods to find new plant-based compounds and drug targets for treating Waddlia chondrophila, a bacterium linked to miscarriages.

## Contribution

The study identifies novel phytocompounds and drug targets against Waddlia chondrophila using virtual screening and molecular dynamics simulations.

## Key findings

- SigA and 3-deoxy-d-manno-octulosonic acid transferase were identified as potential drug targets.
- Phytocompounds showed strong binding affinity and stability at target protein sites through molecular dynamics simulations.
- Binding free energy calculations confirmed significant interactions between phytocompounds and target proteins.

## Abstract

Waddlia chondrophila is a possible cause of fetal death in humans. This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses. Despite the years of efforts, the underlying mechanism behind the pathogenesis of W. chondrophila is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against W. chondrophila. At first, RNA polymerase sigma factor SigA and 3-deoxy-d-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with W. chondrophila; however, further research is required to ensure their safety.