scholarly journals Investigation of the anti-TB potential of selected alkaloid constituents using molecular docking approach

2020 ◽  
Author(s):  
Mohammad Kawsar Sharif Siam ◽  
Mohammad Umer Sharif Shohan ◽  
Zaira Zafroon
Keyword(s):  
Free Energy ◽  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Protein Binding ◽  
Binding Free Energy ◽  
Chemical Constituents ◽  
Biological Evaluation ◽  
Natural Sources ◽  
Docking Score ◽  
Docking Approach

AbstractMycobacterium tuberculosis, the leading bacterial killer disease worldwide, causes Human tuberculosis (TB). Due to the growing problem of drug resistant Mycobacterium tuberculosis strains, new anti-TB drugs are urgently needed. Natural sources such as plant extracts have long played an important role in tuberculosis management and can be used as a template to design new drugs. A wide screening of natural sources is time consuming but the process can be significantly sped up using molecular docking. In this study, we used a molecular docking approach to investigate the interactions between selected natural constituents and three proteins MtPanK, MtDprE1 and MtKasA involved in the physiological functions of Mycobacterium tuberculosis which are necessary for the bacteria to survive and cause disease. The molecular docking score, a score that accounts for the binding affinity between a ligand and a target protein, for each protein was calculated against 150 chemical constituents of different classes to estimate the binding free energy. The docking scores represent the binding free energy. The best docking scores indicates the highest ligand protein binding which is indicated by the lowest energy value. Among the natural constituents, Shermilamine B showed a docking score of - 8.5kcal/mol, Brachystamide B showed a docking score of −8.6 kcal/mol with MtPanK, Monoamphilectine A showed a score of −9.8kcal/mol with MtDprE1.These three compounds showed docking scores which were superior to the control inhibitors and represent the opportunity of in vitro biological evaluation and anti-TB drug design. Consequently, all these compounds belonged to the alkaloid class. Specific interactions were studied to further understand the nature of intermolecular bonds between the most active ligands and the protein binding site residues which proved that among the constituents monoamphilectine A and Shermilamine B show more promise as Anti-TB drugs. Furthermore, the ADMET properties of these compounds or ligands showed that they have no corrosive or carcinogenic parameters.Graphical Abstract

scholarly journals The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach

2021 ◽  
Vol 1 (1) ◽  
pp. 32-39
Author(s):  
Baiq Ressa Puspita Rizma ◽  
Agus Dwi Ananto ◽  
Anggit Listyacahyani Sunarwidhi
Keyword(s):  
Molecular Docking ◽  
Medicinal Plants ◽  
Virus Disease ◽  
Molecular Study ◽  
Ant System ◽  
Docking Score ◽  
Docking Approach ◽  
Rapid Transmission ◽  
Potent Drug ◽  
Potential Inhibitors

Corona Virus Disease 2019 (COVID-19) is a new strain of coronavirus called SARS-CoV-2, which was identified in Wuhan, China, in December 2019. The rapid transmission of COVID-19 from human to human forced researchers to find a potent drug by setting aside the time-consuming traditional method in drug development. The molecular docking approach is one a reliable method to screening compound from chemical drug or by finding a compound from Indonesian herbal plants. The present study aimed to assess the potency of compounds from five medicinal plants as potential inhibitors of PLpro and 3CLpro from SARS-CoV-2 using molecular study. The molecular docking was performed using Protein-Ligand Ant System (PLANTS) to analyze the potential compounds by the docking score. Remdesivir triphosphate was used as a standard for the comparison of the test compounds. The docking score obtained from the docking of PLpro with native ligand, remdesivir triphosphate, curcumin, demethoxycurcumin, bisdemethoxycurcumin, luteolin, apigenin, quercetin, kaempferol, formononetin-7-O-glucuronide, andrographolide, and neoandrographolide were -111.441, -103.827, -103.609, -102.363, -100.27, -79.6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452, respectively. Meanwhile, docking score with 3CLpro for the same ligand were -64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345, -70.3368, -71.5539, -68.4321, -72.0154, -75.9777, and -93.7746. The docking score data suggest that curcumin was the most potential as a PLpro inhibitor, while neoandrographolide was the best as a 3CLpro inhibitor.

scholarly journals An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn

2018 ◽  
Vol 11 (3) ◽  
pp. 72 ◽  
Author(s):  
Mayara Teles Fujishima ◽  
Nayara Silva ◽  
Ryan Ramos ◽  
Elenilze Batista Ferreira ◽  
Kelton Santos ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Xanthine Oxidase ◽  
Quantum Chemical ◽  
Binding Free Energy ◽  
Chemical Constituents ◽  
Docking Study ◽  
Antioxidant Potential ◽  
Molecular Docking Study ◽  
Hydroalcoholic Extract ◽  
Curatella Americana

Reactive oxygen species (ROS) are continuously generated in the normal biological systems, primarily by enzymes as xanthine oxidase (XO). The inappropriate scavenging or inhibition of ROS has been considered to be linked with aging, inflammatory disorders, and chronic diseases. Therefore, many plants and their products have been investigated as natural antioxidants for their potential use in preventive medicine. The leaves and bark extracts of Curatella americana Linn. were described in scientific research as anti-inflammatory, vasodilator, anti-ulcerogenic, and hypolipidemic effects. So, the aim of this study was to evaluate the antioxidant potentials of leaf hydroalcoholic extract from C. americana (HECA) through the scavenging DPPH assay and their main chemical constituents, evaluated by the following quantum chemical approaches (DFT B3LYP/6-31G**): Maps of Molecular Electrostatic Potential (MEP), Frontier Orbital’s (HOMO and LUMO) followed by multivariate analysis and molecular docking simulations with the xanthine oxidase enzyme. The hydroalcoholic extract showed significant antioxidant activity by free radical scavenging probably due to the great presence of flavonoids, which were grouped in the PCA and HCA analysis with the standard gallic acid. In the molecular docking study, the compounds studied presented the binding free energy (ΔG) values close each other, due to the similar interactions with amino acids residues at the activity site. The descriptors Gap and softness were important to characterize the molecules with antioxidant potential by capturing oxygen radicals.

Current Trends in Docking Methodologies

Oncology ◽  
2017 ◽  
pp. 829-847
Author(s):  
Shubhandra Tripathi ◽  
Akhil Kumar ◽  
Amandeep Kaur Kahlon ◽  
Ashok Sharma
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Energy Calculation ◽  
Molecular Binding ◽  
New Horizons ◽  
Current Trends ◽  
Complex Scheme ◽  
Dynamics Simulations

Molecular docking was earlier considered to predict the binding affinity of the receptor and ligand molecules. With the progress in computational power and developing approaches, new horizons are now opening for accurate prediction of molecular binding affinity. In the current book chapter, recent strategies for Computer-Aided Drug Designing (CADD) including virtual screening and molecular docking, encompassing molecular dynamics simulations, and binding free energy calculation methods are discussed. Brief overview of different binding free energy methods MMPBSA, MMGBSA, LIE and TI have also been given along with the recent Relaxed Complex Scheme protocol.

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