QSAR and molecular docking studies of lethal factor protease inhibitors against Bacillus anthracis

ABSTRACT

Bacillus anthracis is considered as a biological warfare agent because it is the causative agent of the serious infectious anthrax disease. Delay in treatment leads to lethal factor-mediated toxaemia which is very critical due to lack of therapeutic options. Consequently, attempts have been made to discover potent lethal factor (LF) protease inhibitors such as small-molecule synthetic 2-thio-1,3-thiazolidine-4-one (rhodanine) compounds. But computed descriptor-based quantitative structure–activity relationship (QSAR) and drug design studies on such aspect are poorly represented. Therefore, an attempt was made for developing QSAR models using structural descriptors for 1,3-thiazolidine-4-one compounds. The models were developed on a series of 49 LF protease inhibitors using the combination of constitutional, functional group, atom-centred fragment and molecular property descriptors. The best QSAR model included four variables, namely, C-040, nR05, GVWAI-80 and ALOGP that correlated well with the anti-LF protease activity with a good correlation coefficient (r = 0.870) of good statistical significance (F_{4, 29} = 14.09 (α = 0.001) F_{4, 29} = 6.19). This model was also validated and explained 58.1% of variances of the Bacillus anthracis inhibitory activities of the studied compounds with r²_pred = 0.710 which denotes external predictability. Finally, molecular docking was carried out to predict the mode of binding of some highly active congeneric compounds. It was shown that VAL 1403 is an important residue for phenyl ring. TYR 1456 and HIS 1418 are responsible for interaction with the rhodanine nucleus. Therefore, these residues are considered responsible for the inhibition of LF protease anthrax and can predict significant dimension of essential structural features of these inhibitors to evaluate, screen and help priorities of the synthesis of the candidates against anthrax bioterrorism.

KEYWORDS:

• Anthrax lethal factor (LF)
• protease inhibitors
• rhodanine compounds
• computed structural descriptors
• QSAR
• molecular docking

Acknowledgements

The author is sincerely thankful to Professor Kunal Roy, Drug Theoretics and Chemoinformatics Lab, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India for providing ‘NanoBridges’ software.

Disclosure statement

No potential conflict of interest was reported by the authors. CSIR-CDRI communication no. 9886.

Supplementary material

Supplemental data for this article can be accessed at: https://doi.org/10.1080/1062936X.2019.1658219.