G-4288

Computational Screening of Inhibitors Targeting BoNT/A, Neurotoxin A in Clostridium botulinum: A Molecular Docking Approach

 Zahra Farhadi Nezhad ¹ ℗, Elnaz Afshari ² ©   

 
Abstract

Introduction: Botulinum neurotoxins (BoNTs) are recognized as the most potent biological toxins, classified as category A bioterror agents by the Centers for Disease Control and Prevention due to their extreme lethality. An effective research approach that combines empirically guided, structure-based modeling with chemoinformatics was employed to identify potent small molecule inhibitors of the light chain of botulinum neurotoxin serotype A. Inhibiting this protein could potentially prevent infection and mitigate the risks associated with this bacterium. Therefore, this study aimed to identify the most effective inhibitory ligand for the BoNTs using a molecular docking analysis. Methods and Materials: First, we downloaded the 3D structure of BoNT/A, Neurotoxin A,Clostridium botulinum in PDB format (PDB ID:2ISE) from the RCSB PDB database. Next, we obtained 3D structure of 2-mercapto-3-phenylpropionyl-RATKML as inhibitory ligand (PubChem CID: 360358), along with 20 its analogs from the PubChem database in the SDF format to evaluate their potential as drugs. Subsequently, after preparing the protein and ligands, molecular docking was conducted using Molegro Virtual Docker version 6.0. The interactions were analyzed to identify the best binding with the lowest energy via the Molegro Molecular Viewer software. Finally, we assessed pharmacokinetic properties such as absorption, distribution, ligand excretion, and metabolism using the SwissADME server. Results: Among all the inhibitory analogs, the most effective analog for BoNT/A was identified as (3R)-3-benzhydryl-N-(4-chlorophenyl)-2,4-dioxo-4-phenylbutanamide with PubChemCID of 98153225. This compound has a molecular weight of 467.94 g/mol and a binding energy of -145.749 kcal/mol. This analog forms five steric interactions consisting of Lys11, Pro140, Pro13, Lys34, Tyr10, along with one hydrogen bonds involving Lys11. However, no electrostatic bonds were observed. Additionally, the ADME analysis revealed that this ligand has a water solubility (logS) score of -6.80, lipophilicity (XLogP3) of 6.56, polarity (TPSA) of 63.24 A2, and one hydrogen bond donors and three hydrogen bond acceptors. Conclusion and Discussion: Our results demonstrated that (3R)-3-benzhydryl-N-(4-chlorophenyl)-2,4-dioxo-4-phenylbutanamide exhibited the lowest binding energy and the most stable interaction among the inhibitory analogs evaluated. Furthermore, its pharmacokinetic profile was consistent with the Lipinski’s Rule of Five, indicating favorable drug-like properties and promising candidate for the inhibition of BoNT/A in Clostridium botulinum. However, further in vitro and in vivo studies are required to confirm its efficacy and potential as a therapeutic agent.

Keywords: Clostridium botulinum, (3R)-3-benzhydryl-N-(4-chlorophenyl)-2,4-dioxo-4-phenylbutanamide, BoNT/A, Neurotoxin A, Molecular Docking