Document Type : Original Research Article

Authors

Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria

10.22034/pcbr.2022.366493.1234

Abstract

The current research was conducted as part of the anti-leishmanial drug discovery effort towards new drug molecules with attributes that overcome the limitations of existing therapies. This work utilizes a combined approach of Quantitative Structure-Activity Relationship (QSAR), virtual docking screening, and pharmacokinetics analysis to design some novel 2,6-diarylidene cyclohexanone analogs using ligand-based drug design methods, while also performing docking investigation, drug-likeness analysis, and Molecular Dynamic (MD) simulation to evaluate their anti-leishmanial potential. Some crucial parameters were calculated for the built QSAR model, including R2 = 0.7827, R2adj = 0.7206, Q2cv = 0.6414, and R2test = 0.8539, which indicate an acceptable QSAR model. The combined results of QSAR, docking, and pharmacokinetics analysis suggested compound 1 as the template. The Six (6) newly designed analogs possessed higher binding scores than the reference drug Pentamidine in the order; 1a (-10.2 kcal/mol) > 1e (-9.6) > 1d (-9.4) > 1c (-9.2) > Template (-9.1) > 1f (-9) > 1b (-8.5) > Pentamidine (-6.9 kcal/mol), while their predicted pIC50 followed the order; 1e (8.7321) > 1c (7.6772) > 1f (7.1602) > 1a (6.8289) > 1d (6.7738) > 1b (6.5772) > Template (5.3824). The results of the drug-likeness testing suggest 1 and the new analogs (especially 1a) as being orally bioavailable with excellent pharmacokinetic profiles. These molecules equally showed good pharmacological interactions with the receptor, Pyridoxal kinase (PDB: 6K91).  In addition, the MD simulation results confirmed the stability and rigidity of 1_6K91 and 1a_6K91. Therefore, the new analogs could be considered as potent anti-leishmanial inhibitors.

Graphical Abstract

Combined QSAR Modeling, Molecular Docking Screening, and Pharmacokinetics Analyses for the Design of Novel 2, 6-Diarylidene Cyclohexanone Analogs as Potent Anti-Leishmanial Agents

Highlights

  • The high limitations of existing therapies resulting in pending cases of leishmanial diseases necessitated the study.

 

  • A computer-aided design of novel 2, 6-diarylidene cyclohexanone analogs as anti-leishmanial agents; 2-D QSAR, molecular docking, pharmacokinetics, and MD simulation were conducted to investigate the anti-leishmanial activities, binding interaction pattern, drug-likeness properties, and the stability of protein-ligand complexes of the newly designed analogs.

 

  • The resulting docking scores were used to identify the best protein-ligand interaction pairs, while the docked poses were post-screened and analyzed for helpful information on binding/pharmacological interactions.

 

  • The generated 2-D QSAR data were subjected to some relevant validation tests in order to qualify the model.

 

  • Also, the newly designed analogs were subjected to pharmacokinetic analysis in order to ascertain their drug-likeness properties, while the protein-ligand complexes of 1 and 1a were analyzed for binding stability using the result of MD simulation.

 

  • The combined results of the study lead to the identification of compound 1a as a potential drug candidate for the treatment of leishmanial infections.

Keywords

Main Subjects

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