Leishmaniasis affects more than 12 million humans globally and a further 1 billion people are at risk in leishmaniasis endemic areas. The lack of a vaccine for leishmaniasis coupled with the limitations of existing anti-leishmanial therapies prompted this study. Cheminformatic techniques are widely used in screening large libraries of compounds, studying protein-ligand interactions, analysing pharmacokinetic properties, and designing new drug molecules with great speed, accuracy, and precision. This study was undertaken to evaluate the anti-leishmanial potential of some organoselenium compounds by quantitative structure-activity relationship (QSAR) modeling, molecular docking, pharmacokinetic analysis, and molecular dynamic (MD) simulation. The built QSAR model was validated (R²_train = 0.8646, R²_test = 0.8864, Q² = 0.5773) and the predicted inhibitory activity (pIC₅₀) values of the newly designed compounds were higher than that of the template (Compound 6). The new analogues (6a, 6b, and 6c) showed good binding interactions with the target protein (Pyridoxal kinase, PdxK) while also presenting excellent drug-likeness and pharmacokinetic profiles. The results of density functional theory, MD simulation, and molecular mechanics generalized Born surface area (MM/GBSA) analyses suggest the favourability and stability of protein-ligand interactions of the new analogues with PdxK, comparing favourably well with the reference drug (Pentamidine). Conclusively, the newly designed compounds could be synthesized and tested experimentally as potential anti-leishmanial drug molecules.Communicated by Ramaswamy H. Sarma.

Background: Leishmaniasis is one of the neglected tropical diseases which is prevalent in the tropical regions of the world most especially in Africa. It is caused by the Leishmania species and transmitted to humans majorly through the bite of the female sandfly. This study was carried out in support of the continuous search for new drug molecules effective enough for the treatment of leishmaniasis, and which have very limited side effects. This study was focused on a combined 2-D and 3-D QSAR modeling of thirty-six arylimidamide-azole hybrids, molecular docking study, design, and pharmacokinetic analysis of some selected and newly designed arylimidamide-azole analogs. The density functional theory (DFT) with B3LYP and 6-31G** basis set was employed for the geometry optimization of the various compounds. Genetic function approximation (GFA) and multi-linear regression (MLR) approaches were used for the 2-D QSAR model building, while the fractional factorial design (FFD) and uninformative variable elimination-partial least square (UVEPLS) were employed for building the 3-D QSAR model. Pyridoxal kinase (PdxK) receptor (PDB: 6K91) was the target protein of interest in this study. Results: The built 2-D and 3-D QSAR models were found to satisfy the requirement of both internal and external validation tests as follows: 2-D QSAR; R² = 0.9614, R²_adj = 0.9513, Q²_cv = 0.9350, R²_test = 0.6766 and cRp² = 0.8779, and for 3-D QSAR (UVEPLS at PC = 5); R² = 0.9839, Q²_LOO = 0.7539 and Q²_LTO = 0.7367. The CoMFA steric and electrostatic field contributions were 68.96% and 31.04%, respectively. All the designed analogs showed higher predicted activities than that of the template (36). Also, the new compounds showed higher binding affinities (MolDock scores) than that of the reference drug pentamidine (− 141.793 kcal/mol), with 36e showing the highest negative MolDock score of − 208.595 kcal/mol. Additionally, these newly designed compounds were said to be orally bioavailable (excluding 36f and 36g that violated 2 of the Lipinski’s provisions), with perfect intestinal absorption, less difficult to synthesize, AMES toxicity free, and showed strong interactions with the target. Conclusions: The newly designed compounds especially 36e have shown a marked pharmacological improvement over the template molecule and are therefore recommended for further practical evaluation as superior pyridoxal kinase inhibitors.

Background: Leishmaniasis is a neglected tropical disease caused by a group of protozoan of the genus Leishmania and transmitted to humans majorly through the bite of the female sand fly. It is prevalent in the tropical regions of the world especially in Africa and estimated to affect a population of about 12 million people annually. This theoretical study was therefore conducted in support of the search for more effective drug candidates for the treatment of leishmaniasis. This study focuses on the in silico activity prediction of twenty-eight (28) maleimides, structure-based design, molecular docking study and pharmacokinetics analysis of the newly designed maleimides. All the studied compounds were drawn using ChemDraw Ultra and optimized by the density functional theory (DFT) approach using B3LYP with 6-31G⁄ basis set. Results: The built QSAR model was found to satisfy the requirement of both internal and external validation tests for an acceptable QSAR model with R² = 0.801, R²_adj = 0.748, Q²_cv = 0.710, R²_test = 0.892 and cR_p² = 0.664 and has shown excellent prediction of the studied compounds. Among the five (5) protein receptors utilized for the virtual docking screening, pyridoxal kinase (PdxK) receptor (Pdb id = 6k91) showed the strongest binding interactions with compounds 14, 21 and 24 with the highest binding affinities of − 7.7, − 7.7 and − 7.8 kcal/mol, respectively. The selected templates (14, 21 and 24) were used to design twelve (12) new compounds (N1–N12) with higher docking scores than the templates. N7 (affinity = − 8.9 kcal/mol) and N12 (− 8.5 kcal/mol) showed higher binding scores than the reference drug pentamidine (− 8.10 kcal/mol), while N3 and N7–N12 showed higher predicted pIC₅₀ than the templates. Also, the pharmacokinetics properties prediction revealed that the newly designed compounds, obeyed the Lipinski’s rule for oral bio-availability, showed high human intestinal absorption (HIA), low synthetic accessibility score, CNS and BBB permeability and were pharmacologically active. Conclusions: The activities of the various maleimides were predicted excellently by the built QSAR model. Based on the pharmacokinetics and molecular docking studies therefore, the newly designed compounds are suggested for further practical evaluation and/or validation as potential drug candidates for the treatment of leishmaniasis.

Over twelve million individuals worldwide suffer from leishmaniasis, and an additional billion people are at risk in places where the disease is prevalent. This work was motivated by the lack of vaccination against leishmaniasis and the shortcomings of current anti-leishmanial treatments. Large compound libraries can be screened using computational methods, which can also be used to analyze pharmacokinetic features, explore protein–ligand interactions, and quickly, accurately, and precisely create novel pharmacological entities. Virtual docking screening was performed to assess the multi-protein targeting capability of certain diselenides using four Leishmania protein targets—2XOX, 3SPX, 5ZWY, and 6K91. Following the Lipinski filter's screening of a subset of analogues, density functional theory (DFT), molecular dynamics (MD) simulation analysis, and ADMET profiles were used to profile the lead compounds. The overall average binding affinity of ligands to target proteins is as follows: 3SPX (− 184.998 kcal/mol) > 6K91 (− 180.114 kcal/mol) > 2XOX (− 176.581 kcal/mol) > 5ZWY (− 157.198 kcal/mol). The focus is on ligands that target all investigated proteins with binding scores greater than the average binding scores for the proteins as a whole for which seven compounds were identified that also showed higher MolDock scores than both reference drugs (Miltefosine and Pentamidine). Further screening showed four compounds (4, 7, 25, and 26) passed Lipinski’s test, making them orally bioavailable with excellent ADMET properties that compared well to both reference medications. The DFT analysis and MD simulation results indicate these compounds' favorability, stability, and reactivity in binding to the studied targets, 3SPX and 6K91 with 25_3SPX and 4_6K91 showing the highest binding free energy (MM-GBSA) of − 88.35 kcal/mol and − 90.29 kcal/mol respectively. Conclusively, the chosen diselenides could be developed as prospective anti-leishmanial pharmacological compounds or as useful scaffolds for creating more potent anti-leishmanial drugs.

Onchocerciasis is one of the major neglected tropical diseases caused by the filarial worm (Onchocerca volvulus), affecting an estimated population of about 37 million people living predominantly in tropical Africa. The major treatment approach has been based on the use of Ivermectin, which kills the microfilariae or the less effective Doxycycline targeting Wolbachia, endosymbiont of filarial nematodes. Flubendazole (FBZ) has proved effective in treating adult worms but with threatening adverse effects. Against this backdrop, therefore, a combined molecular docking study and pharmacokinetic screening were conducted on a series of benzimidazole-benzoxaborole hybrids to find more potent analogs with attributes that address the limitations of existing therapies. All the nineteen analogs were found to possess better docking scores than the reference drug (FBZ, Moldock scores = -120.466 and -125.359). The results of pharmacokinetic testing suggest that four molecules (14, 16, 19, and 20) are orally bioavailable and showed better ADMET properties than FBZ. These molecules and FBZ showed good binding interactions with the receptors’ active sites. Also, the molecular dynamic simulation performed on the docked complexes of 20 and FBZ confirmed the rigidity and stability of their interactions. Based on the results of this study, the selected molecules (especially 20) could be considered superior drug candidates for the treatment of Onchocerciasis.