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Molecular docking analysis of Clostridium perfringens beta toxin model with potential inhibitors from the ZINC database



Amit Kumar Solanki, Abhishek Acharya, Himani Kaushik, Bharti Bhatia & Lalit C. Garg*



Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India;



 Dr. Lalit C. Garg - Tel.: +91 11 26703652; Fax: +91 11 26742125. E-mail: lalit@nii.ac.in; Corresponding author:


Article Type

Research Article



Received May 18, 2021; Revised May 21, 2021; Accepted June 3, 2021, Published June 30, 2021



Beta toxin from Clostridium perfringens after being secreted in gut is capable of causing necrotic enteritis in humans and several other animal species and does not respond to routinely used antibiotics. Therefore, there is a need to design an effective inhibitor for the Clostridium perfringens beta toxin (CPB) using cutting edge drug discovery technologies. Hence, potential CPB inhibitors were identified using computer aided screening of compounds from the ZINC database. Further, we document the molecular docking analysis of Clostridium perfringens beta toxin model (that revealed 4 binding pockets, A-D) with the identified potential inhibitors. We show that ZINC291192 [N- [(1-methylindol-3-yl) methyl eneamino]-7,10-dioxabicyclo[4.4.0]deca-2,4,11-triene-8-carboxamide] has optimal binding features with calculated binding energy of -10.38 kcal/mol and inhibition constant of 24.76 nM for further consideration.



Clostridium perfringens, beta-toxin, molecular docking, necrotic enteritis, virtual screening, ZINC database.



Solanki et al. Bioinformation 17(6): 628-636 (2021)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.