Evaluation of potential bacterial protease inhibitor properties of selected hydroxyquinoline derivatives: an in silico docking and molecular dynamics simulation approach

Investigating the Molecular Interactions of Quinoline Derivatives for Antibacterial Activity Against Bacillus subtilis: Computational Biology and In Vitro Study Interpretations

Bacterial infections are evolving and one of the chief problems is emergence and prevalence of antibacterial resistance. Moreover, certain strains of Bacillus subtilis have become resistant to several antibiotics. To counteract this menace, the present work aimed to comprehend the antibacterial activity of synthesized two quinoline derivatives against Bacillus subtilis. Toxicity predictions via Protox II, SwissADME and T.E.S.T (Toxicity Estimation Software Tool) revealed that these derivatives were non-toxic and had little to no adverse effects. Molecular docking studies carried out in Schrodinger with two quinoline derivatives (referred Q1 and Q2) docked against selected target proteins (PDB IDs: 2VAM and1FSE) of B. subtilis demonstrated ideal binding energies (2VAM-Q1: - 4.63 kcal/mol and 2VAM-Q2: - 4.46 kcal/mol, and 1FSE-Q1: - 3.51 kcal/mol, 1FSE-Q2: - 6.34 kcal/mol). These complexes were simulated at 100 ns and the outcomes revealed their stability with slight conformational changes. Anti-microbial assay via disc diffusion method revealed zones of inhibition showing that B. subtilis was inhibited by both Q1 and Q2, with Q2 performing slightly better than Q1, pointing towards its effectiveness against this organism and necessitating further study on other bacteria in prospective studies. Thus, this study demonstrates that our novel quinoline derivatives exhibit antibacterial properties against Bacillus subtilis and can act as potent anti-bacterials.

Virtual screening, molecular docking, molecular dynamics, and MM-GBSA approaches identify prospective fructose-1,6-bisphosphatase inhibitors from pineapple for diabetes management

Diabetes affects millions globally and poses treatment challenges. Targeting the enzyme fructose-1,6-bisphosphatase (FBPase) in gluconeogenesis and exploring plant-based therapies offer potential solutions for improving diabetes management while supporting sustainability and medicinal advancements. Utilizing pineapple (Ananas comosus L. Merr.) waste as a source of drug precursors could be valuable for health and environmental care due to its medicinal benefits and abundant yearly biomass production. Therefore, this study conducted a virtual screening to identify potential natural compounds from pineapple that could inhibit FBPase activity. A total of 112 compounds were screened for drug-likeness and ADMET properties, and molecular docking simulations were performed on 20 selected compounds using blind docking. The lead compound, butane-2,3-diyl diacetate, was subjected to 100 ns MD simulations, revealing a binding energy of -5.4 kcal/mol comparable to metformin (-5.6 kcal/mol). The MD simulation also confirmed stable complexes with crucial hydrogen bonds. Glu20, Ala24, Thr27, Gly28, Glu29, Leu30, Val160, Met177, Asp178, and Cys179 were identified as key amino acids that stabilized the human liver FBPase-butane-2,3-diyl diacetate complex, while Tyr215 and Asp218 played a crucial role in the human liver FBPase-Metformin complex. Our study indicates that the lead compound has high intestinal solubility. Therefore, it would show rapid bloodstream distribution and effective action on the target protein, making butane-2,3-diyl diacetate a potential antidiabetic drug candidate. However, further investigations in vitro, preclinical, and clinical trials are required to thoroughly assess its efficacy and safety.Communicated by Ramaswamy H. Sarma.

Computer-aided anti-cancer drug discovery of EGFR protein based on virtual screening of drug bank, ADMET, docking, DFT and molecular dynamic simulation studies

Numerous malignancies, including breast cancer, non-small cell lung cancer, and chronic myeloid leukemia, are brought on by aberrant tyrosine kinase signaling. Since the current chemotherapeutic medicines are toxic, there is a great need and demand from cancer patients to find novel chemicals that are toxic-free or have low toxicity and that can kill tumor cells and stop their growth. This work describes the in-silico examination of substances from the drug bank as EGFR inhibitors. Firstly, drug-bank was screened using the pharmacophore technique to select the ligands and Erlotinib (DB00530) was used as matrix compound. The selected ligands were screened using ADMET and the hit compounds were subjected to docking. The lead compound from the docking was subjected to DFT and MD simulation study. Using the pharmacophore technique, 23 compounds were found through virtual drug bank screening. One hit molecule from the ADMET prediction was the subject of docking study. According to the findings, DB03365 molecule fits to the EGFR active site by several hydrogen bonding interactions with amino acids. Furthermore, DFT analysis revealed high reactivity for DB03365 compound in the binding pocket of the target protein, based on ELUMO, EHOMO and band energy gap. Furthermore, MD simulations for 100 ns revealed that the ligand interactions with the residues of EGFR protein were part of the essential residues for structural stability and functionality. However, DB03365 was a promising lead molecule that outperformed the reference compound in terms of performance and in-vitro and in-vivo experiments needs to validate the study.Communicated by Ramaswamy H. Sarma.

Computational evaluation of quinones of Nigella sativa L. as potential inhibitor of dengue virus NS5 methyltransferase

Aedes aegypti is the primary vector for the transmission of the dengue virus, which causes dengue fever, dengue hemorrhagic illness and dengue shock syndrome. There is now no antiviral medication available to treat DENV, which kills thousands of people each year and infects millions of individuals. A possible target for the creation of fresh and efficient dengue treatments is the DENV-3 NS5 MTase. So, Nigella sativa quinones were examined using in silico methods to find natural anti-DENV compounds. The in silico docking was conducted utilising the Discovery Studio software on the quinones of N. sativa and the active site of the target protein DENV-3 NS5 MTase. In addition, the druggability and pharmacokinetics of the lead compound were assessed. Dithymoquinone was comparable to the reference compound in terms of its ability to bind to the active site of target protein. Dithymoquinone met the requirements for drug likeness and Lipinski's principles, as demonstrated by the ADMET analysis and drug likeness results. The current study indicated that the dithymoquinone from N. sativa had anti-DENV activity, suggesting further drug development and dengue treatment optimisation.Communicated by Ramaswamy H. Sarma.

In silico evaluation of usnic acid derivatives to discover potential antibacterial drugs against DNA gyrase B and DNA topoisomerase IV

Due to the rising increase in infectious diseases brought on by bacteria and anti-bacterial drug resistance, antibacterial therapy has become difficult. The majority of first-line antibiotics are no longer effective against numerous germs, posing a new hazard to global human health in the 21st century. Through the drug-likeness screening, 184 usnic acid derivatives were selected from an in-house database of 340 usnic acid compounds. The pharmacokinetics (ADMET) prediction produced fifteen hit compounds, of which the lead molecule was subsequently obtained through a molecular docking investigation. The lead compounds, labelled compound-277 and compound-276, respectively, with the substantial binding affinity towards the enzymes were obtained through further docking simulation on the DNA gyrase and DNA topoisomerase proteins. Additionally, molecular dynamic (MD) simulation was performed for 300 ns on the lead compounds in order to confirm the stability of the docked complexes and the binding pose discovered during docking tests. Due to their intriguing pharmacological characteristics, these substances may be promising therapeutic candidate for anti-bacterial medication.Communicated by Ramaswamy H. Sarma.

Usnic acid as potential inhibitors of BCL2 and P13K protein through network pharmacology-based analysis, molecular docking and molecular dynamic simulation

Usnic acid (UA) lately piqued the interest of researchers for its extraordinary biological characteristics, including anticancer activity. Here, the mechanism was clarified through network pharmacology,molecular docking and molecular dynamic simulation. Sixteen proteins were selected through network pharmacology study as they are probable to interact with UA. Out of these proteins, 13 were filtered from PPI network analysis based on their significance of interactions (p < 0.05). KEGG pathway analysis has also aided us in determining the three most significant protein targets for UA, which are BCL2, PI3KCA and PI3KCG. Therefore molecular docking and molecular dynamic (MD) simulations throughout 100 ns were performed for usnic acid onto the three proteins mentioned. However, UA's docking score in all proteins is lower than their co-crystalised ligand, especially for BCL2 (-36.5158 kcal/mol) and PI3KCA (-44.5995 kcal/mol) proteins. The only exception is PI3KCG which has comparable results with the co-crystallised ligand with (-41.9351 kcal/mol). Furthermore, MD simulation has also revealed that usnic acid does not stay fit in the protein throughout the simulation trajectory for PI3KCA protein evident from RMSF and RMSD plots. Nevertheless, it still poses good ability in inhibiting BCL2 and PI3KCG protein in MD simulation. In the end, usnic acid has exhibited good potential in the inhibition of PI3KCG proteins, rather than the other proteins mentioned. Thus further study on structural modification of usnic acid could enhance the ability of usnic acid in the inhibition of PI3KCG as anti-colorectal and anti-small cell lung cancer drug candidate.Communicated by Ramaswamy H. Sarma.