Lead Identification of Some Anti-Cancer Agents with Prominent Activity Against Non-small Cell Lung Cancer (NSCLC) and Structure-Based Design

Ligand based-design of potential schistosomiasis inhibitors through QSAR, homology modeling, molecular dynamics, pharmacokinetics, and DFT studies

Objectives

Schistosomiasis, a neglected tropical disease, is a leading cause of mortality in affected geographic areas. Currently, because no vaccine for schistosomiasis is available, control measures rely on widespread administration of the drug praziquantel (PZQ). The mass administration of PZQ has prompted concerns regarding the emergence of drug resistance. Therefore, new therapeutic targets and potential compounds are necessary to combat schistosomiasis.

Methods

Twenty-four potent derivatives of PZQ were optimized via density functional theory (DFT) at the B3LYP/6-31G∗ level. Quantitative structureactivity relationship (QSAR) models were generated and statistically validated, and a lead candidate was selected to develop therapeutic options with improved efficacy against schistosomiasis. The biological and binding energies of the designed compounds were evaluated. In addition, molecular dynamics; drug-likeness; absorption, distribution, metabolism, excretion, and toxicity (ADMET); and DFT studies were performed on the newly designed compounds.

Results

Five QSAR models were generated, among which model 1 had favorable validation parameters (R2train: 0.957, R2adj: 0.941, LOF: 0.101, Q2cv: 0.906, and R2test: 0.783) and was chosen to identify a lead candidate. Other statistical parameters for the chosen model included variance inflation factor values ranging from 1.242 to 1.678, and a Y-scrambling coefficient (cRp2) of 0.747. Five new compounds were designed with improved predicted activity (ranging from 5.081 to 7.022) surpassing those of both the lead compound and PZQ (predicted pEC50 of 5.545). Molecular dynamics simulation revealed high binding affinity of the proposed compounds toward the target receptor. ADMET and drug-likeness assessments indicated adherence to Lipinski's rule of five criteria, thereby suggesting pharmacological and oral safety. In addition, DFT analysis indicated resistance to electronic alteration during chemical reactions.

Conclusion

The proposed compounds exhibited potential drug characteristics, thus indicating their suitability for further investigation to enhance schistosomiasis treatment options.

2D-QSAR, molecular docking, drug-likeness, and ADMET/pharmacokinetic predictions of some non-small cell lung cancer therapeutic agents

Objectives

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with nearly 2 million diagnoses and a 17% 5-year survival rate. The aim of this study was to use computer-aided techniques to identify potential therapeutic agents for NSCLC.

Methods

The two dimensional-quantitative structure-activity relationship (2D-QSAR) modeling was employed on some potential NSCLC therapeutic agents to develop a highly predictive model. Molecular docking-based virtual screening were conducted on the same set of compounds to identify potential hit compounds. The pharmacokinetic features of the best hits were evaluated using SWISSADME and pkCSM online web servers, respectively.

Results

The model generated via 2D-QSAR modeling was highly predictive with R2= 0.798, R2adj = 0.754, Q2CV = 0.673, R2 test = 0.531, and cRp2 = 0.627 assessment parameters. Molecular docking-based virtual screening identified compounds 25, 32, 15, 21, and 23 with the highest MolDock scores as the best hits, of which compound 25 had the highest MolDock score of -138.329 kcal/mol. All of the identified hits had higher MolDock scores than the standard drug (osimertinib). The best hit compounds were ascertained to be drug-like in nature following the Lipinski's rule of five. Also, their ADMET features displayed average pharmacokinetic profiles.

Conclusion

After successful preclinical testing, the hit compounds identified in this study may serve as potential NSCLC therapeutic agents due to their safety and efficacy with the exception of compound 23, which was found to be toxic. They can also serve as a template for designing novel NSCLC therapeutic agents.

Computational design, molecular properties, ADME, and toxicological analysis of substituted 2,6-diarylidene cyclohexanone analogs as potent pyridoxal kinase inhibitors

Leishmaniasis is one of the tropical diseases which affects over 12 million people mainly in the tropical regions of the world and is caused by the leishmanial parasites transmitted by the female sand fly. The lack of vaccines to prevent leishmaniasis, as well as limitations of existing therapies necessitated this study which was focused on a combined virtual docking screening and 3-D QSAR modeling approach to design some diarylidene cyclohexanone analogs, while also performing pharmacokinetic analysis and Molecular Dynamic (MD) simulation to ascertain their drug-ability. As a result, the built 3-D QSAR model was found to satisfy the requirement of a good model with R2 = 0.9777, SDEC = 0.0593, F-test = 105.028, and Q2 LOO = 0.6592. The template (compound 9, MolDock score =  - 161.064) and all seven newly designed analogs were found to possess higher docking scores than the reference drug (Pentamidine, Moldock score = - 137.827). The results of the pharmacokinetic analysis suggest 9 and the new molecules (9a, b, c, e, and f) as orally bioavailable with good ADME and safe toxicological profiles. These molecules also showed good binding interactions with the receptor (pyridoxal kinase). Additionally, the MD simulation result confirmed the stability of the tested protein-ligand complexes, with an estimated ∆G binding (MM/GBSA) of - 65.2177 kcal/mol and - 58.433 kcal/mol for 9_6K91 and 9a_6K91 respectively. Hence, the new compounds, especially 9a could be considered potential anti-leishmanial inhibitors.

Molecular docking-based virtual screening, molecular dynamic simulation, and 3-D QSAR modeling of some pyrazolopyrimidine analogs as potent anti-filarial agents

Lymphatic filariasis and onchocerciasis are common filarial diseases caused by filarial worms, which co-habit symbiotically with the Wolbachia organism. One good treatment method seeks Wolbachia as a drug target. Here, a computer-aided molecular docking screening and 3-D QSAR modeling were conducted on a series of Fifty-two (52) pyrazolopyrimidine derivatives against four Wolbachia receptors, including a pharmacokinetics study and Molecular Dynamic (MD) investigation, to find a more potent anti-filarial drug. The DFT approach (B3LYP with 6-31G** option) was used for the structural optimization. Five ligand-protein interaction pairs with the highest binding affinities were identified in the order; 23_7ESX (-10.2 kcal/mol) > 14_6EEZ (- 9.0) > 29_3F4R (- 8.0) > 26_6W9O (- 7.7) ≈ doxycycline_7ESX (- 7.7), with good pharmacological interaction profiles. The built 3-D QSAR model satisfied the requirement of a good model with R2 = 0.9425, Q2 LOO = 0.5019, SDEC = 0.1446, and F test = 98.282. The selected molecules (14, 23, 26, and 29) perfectly obeyed Lipinski's RO5 for oral bio-availability, and showed excellent ADMET properties, except 14 with positive AMES toxicity. The result of the MD simulation showed the great stability associated with the binding of 23 onto 7ESX's binding pocket with an estimated binding free energy (MM/GBSA) of - 60.6552 kcal/mol. Therefore, 23 could be recommended as a potential anti-filarial drug molecule, and/or template for the design of more prominent inhibitors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-022-00136-y.

Theoretical modeling and design of some pyrazolopyrimidine derivatives as Wolbachia inhibitors, targeting lymphatic filariasis and onchocerciasis

Lymphatic filariasis and onchocerciasis are two common filarial diseases caused by a group of parasitic nematodes called filarial worms, which play host to the bacteria organism Wolbachia. One good treatment approach seeks Wolbachia as drug target. Here, a QSAR study was conducted to investigate the anti-wolbachia activities (pEC₅₀) of 52 pyrazolopyrimidine analogues, while using the built model to predict the pEC₅₀ values of the newly designed analogues. Density Functional Theory was used for the structural optimization, while the model building was based on Genetic Function Algorithm approach. The built QSAR model was validated thus: R² = 0.8104, R² _adj = 0.7629, Q² _cv = 0.6981, R² _test = 0.7501 and cRp² = 0.7476. The predicted pEC₅₀ of all newly designed compounds were higher than that of the template (43). The new compounds were; observed to pass the drug-likeness criteria, uniformly distributed to the brain, and found to be non-mutagenic. Also, the new compounds and the reference drug (doxycycline), were docked onto Ovarian Tumor (OTU) deubiquitinase receptor (PDB ID: 6W9O) using iGEMDOCK tool. This protein is known to help Wolbachia subvert host ubiquitin signaling. The resulting binding scores of the newly designed compounds except A5 were higher than that of doxycycline, while the protein-ligand interactions were majorly characterized by Hydrogen-bonding and hydrophobic interaction types. Therefore, the newly designed molecules could be developed as potential drug candidates for the treatment of lymphatic filariasis and onchocerciasis.