scholarly journals Molecular Docking and Simulation Studies of Antidiabetic Agents Devised from Hypoglycemic Polypeptide-P of Momordica charantia

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Rawaba Arif ◽  
Sajjad Ahmad ◽  
Ghulam Mustafa ◽  
Hafiza Salaha Mahrosh ◽  
Muhammad Ali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Glucose Transporter ◽  
Momordica Charantia ◽  
Interaction Patterns ◽  
Receptor Proteins ◽  
Lipinski’S Rule ◽  
Glucose Transporter 2 ◽  
Sodium Glucose Cotransporter ◽  
Docking Approach ◽  
Dynamics Simulations

Diabetes mellitus termed as metabolic disorder is a collection of interlinked diseases and mainly body’s inability to manage glucose level which leads to cardiovascular diseases, renal failure, neurological disorders, and many others. The drugs contemporarily used for diabetes have many inevitable side effects, and many of them have become less responsive to this multifactorial disorder. Momordica charantia commonly known as bitter gourd has many bioactive compounds with antidiabetic properties. The current study was designed to use computational methods to discover the best antidiabetic peptides devised from hypoglycemic polypeptide-P of M. charantia. The binding affinity and interaction patterns of peptides were evaluated against four receptor proteins (i.e., as agonists of insulin receptor and inhibitors of sodium-glucose cotransporter 1, dipeptidyl peptidase-IV, and glucose transporter 2) using molecular docking approach. A total of thirty-seven peptides were docked against these receptors. Out of which, top five peptides against each receptor were shortlisted based on their S-scores and binding affinities. Finally, the eight best ligands (i.e., LIVA, TSEP, EKAI, LKHA, EALF, VAEK, DFGAS, and EPGGGG) were selected as these ligands strictly followed Lipinski’s rule of five and exhibited good ADMET profiling. One peptide EPGGGG showed activity towards insulin and SGLT1 receptor proteins. The top complex for both these targets was subjected to 50 ns of molecular dynamics simulations and MM-GBSA binding energy test that concluded both complexes as highly stable, and the intermolecular interactions were dominated by van der Waals and electrostatic energies. Overall, the selected ligands strongly fulfilled the drug-like evaluation criterion and proved to have good antidiabetic properties.

scholarly journals Interactions of Alkyl Gallates with SARS-CoV-2 Main Protease: A Molecular Docking Approach

2020 ◽  
Vol 3 (1) ◽  
pp. 9
Author(s):  
Amalia Stefaniu ◽  
Lucia Pintilie ◽  
Bujor Albu ◽  
Lucia Pirvu
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Synthetic Compounds ◽  
X Ray ◽  
Lipinski’S Rule ◽  
Alkyl Gallates ◽  
Main Protease ◽  
Docking Approach ◽  
Lipinski’S Rule Of Five ◽  
In Silico Methods

Ten natural and semi-synthetic compounds (gallic acid and alkyl gallates) were investigated by in silico methods in order to evaluate their potential inhibitory activity against SAR-CoV-2 using the X-ray structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 Å (PDB ID: 6WNP). The evaluation of drug-likeness in terms of Lipinski’s Rule of Five and docking results in terms of docking score and interactions with the amino acids residues from the active binding site of the target protein were reported.

scholarly journals Natural xanthone compounds as promising drug candidates against COVID-19 - An integrated molecular docking and dynamics simulation study

2020 ◽  
Author(s):  
Shravan Kumar Gunda ◽  
Hima Kumari P ◽  
Gourav Choudhir ◽  
Anuj Kumar ◽  
P B. Kavi Kishor ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Agents ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Lipinski’S Rule ◽  
Drug Candidates ◽  
Main Protease ◽  
Lipinski’S Rule Of Five ◽  
Dynamics Simulations ◽  
Potential Inhibitors

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease2019 (COVID-19). SARS-CoV-2 is known for its high pathogenicity and transmission due to thepresence of polybasic cleavage sites. No specific drug is available for the treatment. To identifythe potential inhibitors, we have performed molecular docking against the SARS-CoV-2 mainprotease (6Y84) with fifteen important natural xanthone compounds. The docking results showedall the compounds exhibited good binding energies and interactions with the main protease. Thevalidation of representative docking complexes through molecular dynamics simulations showedthat xanthones binds with a higher binding affinity and lower free energy than the standardligand with Brasixanthone C and Brasixanthone B on 50 ns. Natural xanthone compounds havealso passed the Absorption, Distribution, Metabolism, and Excretion (ADME) property criteriaas well as Lipinski’s rule of five. The present integrated molecular docking and dynamicssimulations study unveil the use of xanthones as potential antiviral agents against SARS-CoV-2.

scholarly journals Mechanistic Validation of an Ergogenic T. arjuna Standardized Extract (Oxyjun®) Using a Molecular Docking Approach

2021 ◽  
pp. 54-63
Author(s):  
Kavita Pandey ◽  
Gursimran Kaur Uppal ◽  
Ratna Upadhyay
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Terminalia Arjuna ◽  
Lipinski’S Rule ◽  
Protein Ligand Interactions ◽  
Potential Efficacy ◽  
Ligand Interactions ◽  
Docking Approach ◽  
Cardio Vascular ◽  
Botanical Extract

The bark of the tree Terminalia arjuna commonly referred as Arjuna is widely used in Ayurveda as a therapeutic agent for heart disease. More recently, a proprietary botanical extract of T. arjuna with tradename, Oxyjun®, demonstrated cardiotonic and ergogenic benefits for the first time in a younger and healthier population. However, the mechanism of action and biological actives of this novel sports ingredient were not clear. A molecular docking approach was adopted to understand the protein-ligand interactions and establish the most probable mechanism(s) of cardio vascular actions of the phytoconstituents of the T. arjuna standardized extract (TASE). Twenty-one phytochemicals (ligands) were chosen from Arjuna and their binding affinities against eight proteins serving cardiovascular functions (target proteins) were investigated. Autodock Vina was used to carry out the molecular docking studies. Potential efficacy in humans was assessed on the basis of ADMET properties and Lipinski’s Rule of 5. We found that arjunic acid, arjungenin, arjunetin, arjunglucoside1, chrysin, kaempferol, luteolin, rhamnetin and taxifolin demonstrated good docking scores and bioactivity.

scholarly journals Exploring the Potency of Nigella sativa Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations

2021 ◽  
Vol 21 (5) ◽  
pp. 1252
Author(s):  
Ari Hardianto ◽  
Muhammad Yusuf ◽  
Ika Wiani Hidayat ◽  
Safri Ishmayana ◽  
Ukun Mochammad Syukur Soedjanaatmadja
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Global Economy ◽  
Nigella Sativa ◽  
Scientific Information ◽  
Dynamics Simulation ◽  
Lipinski’S Rule ◽  
Main Protease ◽  
Dynamics Simulations

Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening campaigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments.

scholarly journals A Molecular Docking Approach to Evaluate the Pharmacological Properties of Natural and Synthetic Treatment Candidates for Use against Hypertension

2019 ◽  
Vol 16 (6) ◽  
pp. 923 ◽  
Author(s):  
Syed Attique ◽  
Muhammad Hassan ◽  
Muhammad Usman ◽  
Rana Atif ◽  
Shahid Mahboob ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Angiotensin Ii ◽  
Renin Angiotensin System ◽  
Angiotensin I ◽  
Middle Income ◽  
Lipinski’S Rule ◽  
Docking Approach ◽  
Physicochemical Features ◽  
Wnk Kinases ◽  
Potential Inhibitors

Cardiovascular diseases (CVDs) have become the leading cause of disability and death worldwide, particularly in low- and middle-income countries. Hypertension, a major cause of CVD progression, is widely attributable to genetic, behavioral, and environmental risk factors. Among the genetic reasons, angiotensin II enzyme, produced as a result of abnormal functioning of the renin–angiotensin system, is reported as the foremost cause of hypertension. A cascade of genes, including those encoding for WNK kinases (WNK1 and WNK4), Bp1, Bp2, angiotensinogen, and other enzymes, is involved in the conversion of angiotensin I to angiotensin II. However, the angiotensin-converting enzyme (ACE) plays a crucial role in this pathway. Therefore, ACE could be a potential therapeutic target in regulating the conversion of angiotensin I to angiotensin II and eventually controlling hypertension. In this study, a molecular docking-based approach was utilized for identifying and evaluating potential inhibitors of ACE present in herbs, other natural sources, and synthetic sources, on the basis of these compounds’ binding affinities and other physicochemical features. In addition, the suitability of these inhibitors as drugs for biological systems, considering their adsorption, distribution, metabolism, and excretion (ADME), was predicted using Lipinski’s rule. In conclusion, our study provides a novel and clearer insight into the interaction properties of known putative inhibitors of ACE.

scholarly journals Duodenal Sodium/Glucose Cotransporter 1 Expression Under Fasting Conditions Is Associated With Postload Hyperglycemia

2017 ◽  
Vol 102 (11) ◽  
pp. 3979-3989 ◽  
Author(s):  
Teresa Vanessa Fiorentino ◽  
Evelina Suraci ◽  
Gaetano Paride Arcidiacono ◽  
Antonio Cimellaro ◽  
Chiara Mignogna ◽  
...  
Keyword(s):  
Glucose Tolerance ◽  
Messenger Rna ◽  
Glucose Transporter ◽  
Normal Glucose Tolerance ◽  
Upper Gastrointestinal Endoscopy ◽  
Cross Sectional ◽  
Glucose Levels ◽  
Glucose Transporter 2 ◽  
Sodium Glucose Cotransporter ◽  
Rna Levels

Abstract Context Type 2 diabetes (T2DM) is associated with a higher intestinal expression of the glucose transporters sodium/glucose cotransporter 1 (SGLT-1) and glucose transporter 2 (GLUT-2). It is currently unsettled whether prediabetes conditions characterized by postprandial hyperglycemia, such as impaired glucose tolerance (IGT) and normal glucose tolerance (NGT) with 1-hour postload glucose ≥155 mg/dL (8.6 mmol/L) (NGT-1h-high) are associated with increased expression of these glucose carriers in the intestine. Objective We evaluated whether duodenal abundance of SGLT-1 and GLUT-2 is augmented in subjects with IGT and NGT-1h-high, in comparison with subjects with NGT and 1-hour postload glucose ˂155 mg/dL (NGT-1h-low). Design Cross-sectional. Patients A total of 54 individuals underwent an upper gastrointestinal endoscopy. Main Outcome Measures Duodenal SGLT-1 and GLUT-2 protein and messenger RNA levels were assessed by Western blot and reverse transcription polymerase chain reaction, respectively. Results Of the 54 subjects examined, 18 had NGT-1h-low, 12 had NGT-1h-high, 12 had IGT, and 12 had T2DM. Duodenal SGLT-1 protein and messenger RNA levels were significantly higher in individuals with NGT-1h-high, IGT, or T2DM in comparison with NGT-1h-low subjects. GLUT-2 abundance was higher in individuals with T2DM in comparison with NGT-1h-low subjects; no substantial increase in GLUT-2 expression was observed in NGT-1h-high or IGT individuals. Univariate correlations showed that duodenal SGLT-1 abundance was positively correlated with 1-hour postload plasma glucose levels (r = 0.44; P = 0.003) but not with fasting or 2-hour postload glucose levels. Conclusions Duodenal SGLT-1 expression is increased in individuals with 1-hour postload hyperglycemia or IGT, as well as in subjects with T2DM, and it positively correlates with early postload glucose excursion.

scholarly journals Computer-Aided Drug Discovery Identifies Alkaloid Inhibitors of Parkinson’s Disease Associated Protein, Prolyl Oligopeptidase

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Apoorva M. Kulkarni ◽  
Shailima Rampogu ◽  
Keun Woo Lee
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Docking ◽  
Level Set ◽  
Neurodegenerative Disorder ◽  
Alpha Synuclein ◽  
Interaction Patterns ◽  
Prolyl Oligopeptidase ◽  
Lipinski’S Rule

Parkinson’s disease is a common neurodegenerative disorder marked by the accumulation of the protein alpha synuclein. Studies have indicated the role of prolyl oligopeptidase (POP), a serine protease, in alpha synuclein accumulation. Therefore, POP emerges as an attractive medicinal target. Traditionally, most of the early medicines have been plant-based owing to their ready availability and negligible side effects. Alkaloids owing to their neurotransmitter modulatory, anti-amyloid, anti-oxidant, and anti-inflammatory activities have shown potential in neurodegenerative disease. In this work, we computationally evaluated alkaloid class of phytochemicals for their therapeutic efficacy against POP. Alkaloids were retrieved from the publically available database, Chemical Entities of Biological Interest (ChEBI), and screened for their drug likeness (Lipinski’s rule of 5) and absorption, distribution, metabolism, and excretion, and toxicity (ADMET) in Discovery Studio by ensuring parameters suitable for a central nervous system disease such as blood-brain barrier (BBB) level set to ≤2, absorption level set to 0 and solubility level permitted set to 2, 3, or 4. Next, molecular docking was performed to learn about the affinity of the filtered alkaloids with the POP. Subsequently, molecular dynamic simulations were conducted to assess the reliability and stability of the alkaloid-protein complex. Our study identified metergoline, pipercallosine, celacinnine, lobeline, cystodytin G, lycoperine A, hookerianamide J, and martefragin A as putative lead compounds against POP. Among these, metergoline, pipercallosine, hookerianamide J, and lobeline showed the most promising results. These compounds demonstrated better or equivalent molecular docking scores in comparison to three POP inhibitors that had reached clinical trials, i.e., Z-321, S-17092, and JTP-4819. MD simulations indicated that these compounds remained intact at the active site while adhering to the binding mode and interaction patterns as that of the reported inhibitors. The research conducted here, therefore, provides evidence for conducting in vitro POP inhibitory studies of these newly identified plant-based POP inhibitors.

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