Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

ABSTRACT

In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), N-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.

KEYWORDS:

• Cancer
• HDAC8 inhibitor
• QSAR
• naïve Bayes classification model
• molecular fingerprints
• ECFP_6

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Acknowledgements

Sk. Abdul Amin sincerely acknowledges Council of Scientific and Industrial Research (CSIR), New Delhi, India for awarding the Senior Research Fellowship [FILE NO.: 09/096(0967)/2019-EMR-I, Dated: 01-04-2019]. Suvankar Banerjee and Tarun Jha are grateful to the RUSA 2.0 of University Grants Commission (UGC), New Delhi to Jadavpur University, Kolkata, India for awarding fellowship [REF. NO: R-11/1030/19, Dated: 30-07-2019] and for awarding a project, respectively. Nilanjan Adhikari is thankful to CSIR, New Delhi for providing research associateship (RA) [FILE NO.: 09/096(0966)/2019-EMR-I, Dated: 28-03-2019]. We also thank the support from the Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary material

Supplemental data for this article can be accessed at: https://doi.org/10.1080/1062936X.2020.1723136.

Additional information

Funding

This work was supported by the Council of Scientific and Industrial Research (CSIR), New Delhi [09/096(0967)/2019-EMR-I, Dated: 01-04-2019].