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Molecular docking, dynamics and in vitro analysis of multi-target inhibitors for Clostridioides difficile



Nikita Chordia Golchha1, Hasanain Abdulhameed Odhar2, Anand Nighojkar3 & Sadhana Nighojkar *,4



1School of Biotechnology, Devi Ahilya University, Takshashila Campus, Khandwa Road, INDORE-452001, India; 2Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq; 3Maharaja Ranjit Singh College of Professional Sciences, Hemkunt Campus, Khandwa Road, Indore, 452001, India; 4Mata Gujri College of Professional Studies, A.B. Road, Indore, 452001, India



Nikita Chordia Golchha - E-mail: nikita.chordia25@gmail.com

Hasanain Abdulhameed Odhar - E-mail: hodhar3@gmail.com

Anand Nighojkar - E-mail: nanandphd@gmail.com

Sadhana Nighojkar - E-mail: sadhana0301@gmail.com


Article Type

Research Article



Received January 1, 2024; Revised January 31, 2024; Accepted January 31, 2024, Published January 31, 2024



The opportunistic pathogen, Clostridioides difficile owes its extreme pathogenicity for its ability to develop antibiotic resistance and recurrent infections. The current antibiotics used for the treatment are showing declining sensitivity and rising antibiotic resistance. Therefore, it is of interest to develop the anti-clostridial drugs to overcome these issues. Hence, we have explored ZINC library to find the suitable lead compounds against five target proteins of C. difficile. Multistep virtual screening is performed to find the suitable compounds that are checked for their stability using molecular dynamics and are validated in vitro against C. difficile. In our study, five compounds viz., ZINC64969876, ZINC13641164, ZINC13691348, ZINC5554596 and ZINC3894278 that inhibit HisC, Spo0A, PdcA, DAHP synthase and cyclic-di GMP proteins, respectively have been identified. Further, these compounds were tested in vitro against four different isolates of C. difficile and all of them were found to inhibit the pathogen. However, to use these compounds as anti-clostridial drugs, further testing needs to be done. The selected compounds from our study are reported for the first time as antimicrobial agents against C. difficile.



Clostridioides difficile, inhibition, pathogen, compounds, in silico, molecular docking, dynamics, in vitro.



Golchha et al. Bioinformation 20(1): 39-48 (2024)


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.