Effects of Saikosaponin‐d on CYP3A4 in HepaRG Cell and Protein‐ligand Docking Study

2020 ◽  
Author(s):  
Hongfang Li ◽  
Yunyan Tang ◽  
Weipeng Wei ◽  
Chengchen Yin ◽  
Fushan Tang
Keyword(s):  
Docking Study ◽  
Ligand Docking ◽  
Heparg Cell

IN VITRO AND IN SILICO ALPHA-AMYLASE INHIBITION POTENTIAL (ANTI-DIABETIC ACTIVITY) OF PSEUDERANTHEMUM BICOLOR (SIMS) RADIK

2020 ◽  
pp. 157-161
Author(s):  
RAMESH BS ◽  
LOKESH RAVI
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Ethyl Acetate ◽  
Bioactive Compounds ◽  
Methyl Ether ◽  
Docking Study ◽  
Alpha Amylase ◽  
Ligand Docking ◽  
Standard Drug ◽  
Reference Drug

Objective: Aim of this study is to evaluate theanti-diabetic activity of Pseuderanthemum bicolor commonly called limang-sugat by inhibiting alpha-amylase protein. Methods: Leaves of P. bicolor were extracted with methanol, chloroform, and ethyl acetate. The extracts were subjected for alpha-amylase inhibition assay and gas chromatography–mass spectrometry (GC–MS) analysis. Phytochemical compounds identified by GC-MS were subjected for protein-ligand docking study against alpha-amylase protein. Acarbose was used as a positive standard drug. Results: The major bioactive compounds obtained from methanol, chloroform, and ethyl acetate extracts were 1,6;2,3-Dianhydro-4-Deoxy-Beta-D-Ribo-Hexopyranose, Pseduosarsasapogenin-5,20-Dien, methyl ether/Hexatriacontane, Di-N-decylsulfone/Octadecanal, and squalene, respectively. A total of 19 secondary metabolites were subjected for protein–ligand docking study against the alpha-amylase protein. The reference drug acarbose demonstrated binding energy of −7.8 Kcal/mol and formed 20 hydrogen bonds with the enzyme. Acarbose signified high polar interaction with the amylase enzyme. Among the 19 test ligands, “2,2-Dibromocholestanone” from ethyl acetate extract exemplified the highest binding energy of −9.3 Kcal/mol. The next highest remarkable inhibition was showed by “Pseduosarsasapogenin-5,20-Dien Methyl Ether” present in the methanol extract, with a binding energy of -9.3 Kcal/mol with the formation of 2 hydrogen bonds. Conclusion: From the result, it could be concluded that the P. bicolor leaves contain various bioactive compounds which are considered as a good anti-diabetic drug.

In silico design of a dual TPR/TxS inhibitor for venous thromboembolism and related cardiovascular diseases

2014 ◽  
Vol 92 (4) ◽  
pp. 284-292
Author(s):  
Arpita Yadav ◽  
Abhay Krishna
Keyword(s):  
Venous Thromboembolism ◽  
Cardiovascular Diseases ◽  
Clinical Efficacy ◽  
Synergistic Effects ◽  
Docking Study ◽  
Docking Studies ◽  
Ligand Docking ◽  
Molecular Orbital Calculations ◽  
Starting Point ◽  
Drug Receptor

In recent years, many research efforts have been directed towards preventing vasoconstrictor and platelet aggregatory properties of TxA2 related to the prostaglandin cycle, as TxA2 has been implicated directly or indirectly in pathologies such as cardiovascular diseases, venous thromboembolism, and pulmonary embolism. The TxA2 antagonists and TxS inhibitors undergoing clinical trials have not shown the expected clinical efficacy. This molecular modeling and docking study explains how efficacy may be enhanced by a careful design of multitarget drugs producing synergistic effects simultaneously at different targets. A dual TPR/TxS inhibition strategy is expected to give better clinical efficacy. This study also emphasizes the importance of designing efforts based on detailed analysis of drug−receptor interactions at both targets. Ab initio HF/6-31G(d) and B3LYP/6-31G(d) molecular orbital calculations coupled with flexible ligand docking studies have led to the design of a dual TPR/TxS inhibitor starting from a naturally occurring compound bromelain, derived from pineapple extract with some known pharmacological advantages. A designed lead compound may prove to be a fruitful starting point for the development of clinically efficient drugs for venous thromboembolism and related cardiovascular diseases.

scholarly journals ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

2020 ◽  
pp. 152-155
Author(s):  
RACHAEL EVANGELINE ◽  
NIHAL AHMED
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Water Extract ◽  
Docking Study ◽  
Persea Americana ◽  
Ligand Docking ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Free Binding Energy

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study. Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results. Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active. Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

scholarly journals ANTI-METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS POTENTIAL OF PHYTOCHEMICALS IN TERMINALIA CATAPPA AND THEIR PROPOSED IN SILICO MECHANISM OF ACTION

2019 ◽  
pp. 133-137
Author(s):  
LOKESH RAVI ◽  
DIVYA JINDAM ◽  
SUGANYA KUMARESAN ◽  
VENKATESH SELVARAJ ◽  
JAYARAMA REDDY
Keyword(s):  
Staphylococcus Aureus ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Mechanism Of Action ◽  
In Silico ◽  
Ethanol Extract ◽  
Docking Study ◽  
Ligand Docking ◽  
Methicillin Resistant ◽  
Antibacterial Potential

Objective: The objective of this study was to investigate the antibacterial potential of leaves of this Terminalia catappa and identify the mechanism of action for those phytochemicals present in this leaves. Methods: Phytochemicals were extracted using maceration and the extracts were analyzed using gas chromatography–mass spectrometry (GC-MS) to identify the chemical structure. Antibacterial potential was evaluated using agar well diffusion. The phytochemicals were subjected to in silico protein–ligand docking study to identify the mechanism of action. Results: In vitro antibacterial study demonstrated that the ethanol extract of the leaves has significant antibacterial activity against Staphylococcus aureus (SA) and methicillin-resistant SA (MRSA) with a zone of inhibition of 16 mm and 18 mm, respectively, at a concentration of 2 mg/ml. The chloroform and hexane extracts of the leaves did not demonstrate any significant activity. Based on GC-MS analysis and literature review, 12 phytochemicals were identified to be present in the ethanol extract of the T. catappa leaves. These molecules were subjected to in silico protein–ligand docking study against common drug target proteins of SA and MRSA. Among the studied ligands, granatin A demonstrated the highest significance to inhibit topoisomerase IV with a binding energy of −11.3 kcal/mol and produced 7 hydrogen bonds, followed by punicalin with −10.7 kcal/mol binding energy toward penicillin-binding protein 2a with 6 hydrogen bonds. Conclusion: Phytochemicals of T. catappa demonstrates significant drug ability potential against drug-resistant MRSA pathogen and demands further investigation on their individual activity and mechanism.

Inhibition of PGSH-1 (COX-1) by flavonoids isolated from a neotropical Lauraceae: A docking study

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
I Valdés ◽  
E Coy-Barrera
Keyword(s):  
Docking Study ◽  
Cox 1

Isolation of tetramer stilbenoids from Shorea leprosula Miq., acetylcholinesterase inhibitory activity and molecular docking study

2019 ◽  
Author(s):  
AS Kamarozaman ◽  
N Ahmat ◽  
MSM Johari ◽  
ZZ Hafiz ◽  
MI Adenan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Inhibitory Activity ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Acetylcholinesterase Inhibitory Activity ◽  
Shorea Leprosula

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study

Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking

2020 ◽  
Author(s):  
Kin Meng Wong ◽  
Shirley Siu
Keyword(s):  
Scoring Function ◽  
Ligand Docking ◽  
Receptor Protein ◽  
Pose Prediction ◽  
Grey Wolf ◽  
Success Rates ◽  
Autodock Vina ◽  
Grey Wolf Optimization ◽  
Structure Based Drug Design ◽  
Docking Program

Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein in current structure-based drug design. In this paper, we evaluate the performance of grey wolf optimization (GWO) in protein-ligand docking. Two versions of the GWO docking program – the original GWO and the modified one with random walk – were implemented based on AutoDock Vina. Our rigid docking experiments show that the GWO programs have enhanced exploration capability leading to significant speedup in the search while maintaining comparable binding pose prediction accuracy to AutoDock Vina. For flexible receptor docking, the GWO methods are competitive in pose ranking but lower in success rates than AutoDockFR. Successful redocking of all the flexible cases to their holo structures reveals that inaccurate scoring function and lack of proper treatment of backbone are the major causes of docking failures.

Myricetin Preferentially Binds to Interfacial Regions in Domains 1 – 3 to Inhibit Cholesterol-Dependent Cytolysins: A Molecular Docking Study

2020 ◽  
Author(s):  
Rafael Espiritu
Keyword(s):  
Molecular Docking ◽  
Structural Changes ◽  
Docking Study ◽  
Listeriolysin O ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Streptolysin O ◽  
Molecule Inhibitor ◽  
Human Cd59 ◽  
Anthrolysin O

<p>Cholesterol-dependent cytolysins (CDCs) are proteinaceous toxins secreted as monomers by some Gram-positive and Gram-negative bacteria that contribute to their pathogenicity. These toxins bind to either cholesterol or human CD59, leading to massive structural changes, toxin oligomerization, formation of very large pores, and ultimately cell death, making these proteins promising targets for inhibition. Myricetin, and its related flavonoids, have been previously identified as a candidate small molecule inhibitor of specific CDCs such as listeriolysin O (LLO) and suilysin (SLY), interfering with their oligomerization. In this work, molecular docking was performed to assess the interaction of myricetin with other CDCs whose crystal structures are already known. Results indicated that although myricetin bound to the hitherto identified cavity in domain 4 (D4), much more efficient and stable binding was obtained in sites along the interfacial regions of domains 1 – 3 (D1 – D3). This was common among the tested CDCs, which was primarily due to much more extensive stabilizing intermolecular interactions, as indicated by post-docking analysis. Specifically, myricetin bound to (1) the interface of the three domains in anthrolysin O (ALO), perfringolysin O (PFO), pneumolysin (PLY), SLY, and vaginolysin (VLY), (2) at/near the D1/D3 interface in LLO and streptolysin O (SLO), and (3) along the D2/D3 interface in intermedilysin (ILY). These findings provide theoretical basis on the possibility of using myricetin and its related compounds as a broad-spectrum inhibitor of CDCs to potentially address the diseases associated with these pathogens.</p>

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