scholarly journals MOLECULAR DOCKING SENYAWA POTENSIAL ANTICOVID-19 SECARA IN SILICO

2021 ◽  
Vol 5 (2) ◽  
pp. 159
Author(s):  
Analekta Tiara Perdana ◽  
Angga Aditya Permana
Keyword(s):  
Molecular Docking ◽  
Mycophenolic Acid ◽  
In Silico ◽  
Autodock Vina

Pandemi COVID-19 memacu peneliti menginvestigasi beberapa senyawa potensial yang dapat menghambat SARS-CoV-2. Tujuan dari penelitian ini adalah mengevaluasi senyawa menggunakan pendekatan molecular docking untuk menghambat domain makro SARS-CoV-2 (PDB: 7CZ4). Evaluasi dilakukan berdasarkan skor docking menggunakan AutoDock Vina. Konformasi terbaik dari kompleks reseptor ligan diindikasikan oleh afinitas tertinggi atau energi bebas Gibbs’/ΔG paling negatif. Hasil penelitian menunjukkan bahwa curcumin, rhamnetin, mycophenolic acid dan quercetin memiliki afinitas tertinggi. Selain itu, penelitian ini juga menunjukkan jumlah ikatan hidrogen dengan residu asam amino tertinggi sebagai indikator stabilitas secara berturut-turut: 4S0765P9W8, curcumin, rhamnetin dan mycophenolic acid. Hasil ini merupakan screening awal potensi senyawa tersebut sebagai anticovid-19 sehingga perlu dilengkapi dengan uji in vitro dan in vivo.

scholarly journals In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

2020 ◽  
Vol 3 (4) ◽  
pp. 989-1000
Author(s):  
Mustapha Abdullahi ◽  
Shola Elijah Adeniji
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Docking Simulation ◽  
Basis Set ◽  
Hybrid Functional ◽  
Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

scholarly journals Antiurolithiatic Evaluation of α- Mangostin Fraction Isolated from Garcinia mangostana Pericarp through Computational, in vitro and in vivo Approach

2021 ◽  
pp. 63-78
Author(s):  
Akash Kumaran ◽  
Prabhu Sukumaran
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Animal Studies ◽  
Oxalate Oxidase ◽  
Garcinia Mangostana ◽  
Molecular Docking Study ◽  
Group I ◽  
Fruit Pericarp

Background: The aqueous crude extract of Garcinia mangostana fruit pericarp was already proven to contain antiurolithiatic property. Based on this previous study the current study was focused on analysing the anti-urolithiatic property of α- mangostin, a xanthone polyphenol isolated from the fruit pericarp of G. manostana, which has not been tested for its anti-urolithiatic property till now. Objective: The aim of this present study is to evaluate the anti-urolithiatic property of the isolated α- mangostin from G. mangostana fruit pericarp using in silico, in vitro and in vivo analysis. Study Design: Antiurolithiatic activity of α- mangostin through Molecular docking study à In vitro S.S.M model study à Animal studies. Place and Duration: Department of Biotechnology, Sri Venkateswara College of Engineering, Post Bag No.1, Pennalur, Sriperumbudur Tk, Kancheepuram Dt, TN-602117, India. Materials and Methods: In silico Molecular docking of α- mangostin with Kidney stone forming proteins- Xanthine dehydrogenase (Xdh), Oxalate oxidase and Tamm-Horesefall Protein (THP) were performed using AutoDock 4.0 and was visualised in Discovery studio software. In vitro Simultaneous Static flow Model (S.S.M) was performed to investigate its Antiurolithiatic property against Calcium Oxalate (CaOx) and Calcium Phosphate (CaP) crystals. Based on the in silico and in vitro analysis, the study was extrapolated to Ethylene Glycol (EG) induced urolithiasis rat models. The animal study was performed with 36 Albino Wistar rats which were divided into 6 groups. All group except group I received EG (0.75% in drinking water) for the induction of Urolithiasis for 28 days under curative regimen. Group III was administered orally with Cystone (750 mg/kg) from 15th to 28thday. Group IV to VI was administered orally with GMPE (300 mg/kg, 500 mg/kg and 750 mg/kg) from 15thto 28th day. Results: Molecular Docking studies showed an inhibitory interaction of α- mangostin with oxalate oxidase, Xdh and THP with binding affinity of -4.47, -4.00 and -3.41 Kcal/mol respectively. S.S.M showed 54.71% inhibition for CaOx crystals and 62.21% inhibition of CaP crystals. The animal studies showed significant results in reduction of serum calcium (P<0.01), serum phosphate (P<0.01), urine calcium(P<0.001) and urine phosphate(P<0.01). Conclusion: Thus, α- mangostin proved to be potent Anti-urolithiatic agent by reducing and disintegrating the urinary crystals.

scholarly journals Investigation of biological activities of Colocasia gigantea Hook.f. leaves and PASS prediction, in silico molecular docking with ADME/T analysis of its isolated bioactive compounds

2020 ◽  
Author(s):  
Safaet Alam ◽  
Nazim Uddin Emon ◽  
Mohammad A. Rashid ◽  
Mohammad Arman ◽  
Mohammad Rashedul Haque
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Castor Oil ◽  
Biological Activities ◽  
Kappa Opioid Receptor ◽  
Soluble Extract ◽  
Docking Score

AbstractBackgroundColocasia gigantea is locally named as kochu and also better known due to its various healing power. This research is to investigate the antidiarrheal, antimicrobial, and antioxidant possibilities of the methanol soluble extract of Colocasia gigantea.MethodsAntidiarrheal investigation was performed by using in vivo castor oil induced diarrheal method where as in vitro antimicrobial and antioxidant investigation have been implemented by disc diffusion and DPPH scavenging method respectively. Moreover, in silico studies were followed by molecular docking analysis of several secondary metabolites were appraised with Schrödinger-Maestro v 11.1.ResultsThe induction of plant extract (200 and 400 mg/kg, b.w, p.o), the castor oil mediated diarrhea has been minimized 19.05 % (p < 0.05) and 42.86 % (p < 0.001) respectively. The methanolic extract of C. gigantea showed mild sensitivity against almost all the tested strains but it shows high consistency of phenolic content and furthermore yielded 67.68 μg/mL of IC50 value in the DPPH test. The higher and lower binding affinity was shown in beta-amyrin and monoglyceryl stearic acid against the kappa-opioid receptor (PDB ID: 4DJH) with a docking score of -3.28 kcal/mol and -6.64 kcal/mol respectively. In the antimicrobial investigation, Penduletin and Beta-Amyrin showed the highest and lowest binding affinity against the selected receptors with the docking score of -8.27 kcal/mol and -1.66 kcal/mol respectively.ConclusionThe results of our scientific research reflect that the methanol soluble extract of C. gigantea is safe which may provide possibilities of alleviation of diarrhea and as a potential wellspring of antioxidants which can be considered as an alternate source for exploration of new medicinal products.

scholarly journals Comparative Study of Piper sylvaticum Roxb. Leaves and Stems for Anxiolytic and Antioxidant Properties Through In Vivo, In Vitro, and In Silico Approaches

Biomedicines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 68 ◽  
Author(s):  
Md. Adnan ◽  
Md. Nazim Uddin Chy ◽  
A.T.M. Mostafa Kamal ◽  
Md Obyedul Kalam Azad ◽  
Kazi Asfak Ahmed Chowdhury ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Antioxidant Activities ◽  
Antioxidant Properties ◽  
Reducing Power ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Dose Dependent

Piper sylvaticum Roxb. is traditionally used by the indigenous people of tropical and subtropical countries like Bangladesh, India, and China for relieving the common cold or a variety of chronic diseases, such as asthma, chronic coughing, piles, rheumatic pain, headaches, wounds, tuberculosis, indigestion, and dyspepsia. This study tested anxiolytic and antioxidant activities by in vivo, in vitro, and in silico experiments for the metabolites extracted (methanol) from the leaves and stems of P. sylvaticum (MEPSL and MEPSS). During the anxiolytic evaluation analyzed by elevated plus maze and hole board tests, MEPSL and MEPSS (200 and 400 mg/kg, body weight) exhibited a significant and dose-dependent reduction of anxiety-like behavior in mice. Similarly, mice treated with MEPSL and MEPSS demonstrated dose-dependent increases in locomotion and CNS simulative effects in open field test. In addition, both extracts (MEPSL and MEPSS) also showed moderate antioxidant activities in DPPH scavenging and ferric reducing power assays compared to the standard, ascorbic acid. In parallel, previously isolated bioactive compounds from this plant were documented and subjected to a molecular docking study to correlate them with the pharmacological outcomes. The selected four major phytocompounds displayed favorable binding affinities to potassium channel and xanthine oxidoreductase enzyme targets in molecular docking experiments. Overall, P. sylvaticum is bioactive, as is evident through experimental and computational analysis. Further experiments are necessary to evaluate purified novel compounds for the clinical evaluation.

scholarly journals Anti-Arthritic and Anti-Inflammatory Potential of Spondias mangifera Extract Fractions: An In Silico, In Vitro and In Vivo Approach

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 825
Author(s):  
Mohammad Khalid ◽  
Mohammed H. Alqarni ◽  
Ambreen Shoaib ◽  
Muhammad Arif ◽  
Ahmed I. Foudah ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Arthritis Score ◽  
Beneficial Effects ◽  
Tnf Α ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 1

The fruits of Spondias mangifera (S. mangifera) have traditionally been used for the management of rheumatism in the northeast region of India. The present study explores the probable anti-arthritis and anti-inflammatory potential of S. mangifera fruit extract’s ethanolic fraction (EtoH-F). To support this study, we first approached the parameters in silico by means of the active constituents of the plant (beta amyrin, beta sitosterol, oleonolic acid and co-crystallised ligands, i.e., SPD-304) via molecular docking on COX-1, COX-2 and TNF-α. Thereafter, the absorption, distribution, metabolism, excretion and toxicity properties were also determined, and finally experimental activity was performed in vitro and in vivo. The in vitro activities of the plant extract fractions were evaluated by means of parameters like 1,1-Diphenyl-2- picrylhydrazyl (DPPH), free radical-reducing potential, albumin denaturation, and protease inhibitory activity. The in vivo activity was evaluated using parameters like COX, TNF-α and IL-6 inhibition assay and arthritis score in Freund Adjuvant (CFA) models at a dose of 400 mg/kg b.w. per day of different fractions (hexane, chloroform, alcoholic). The molecular docking assay was performed on COX-1, COX-2 and TNF-α. The results of in vitro studies showed concentration-dependent reduction in albumin denaturation, protease inhibitors and scavenging activity at 500 µg/mL. Administration of the S. mangifera alcoholic fraction at the abovementioned dose resulted in a significant reduction (p < 0.01) in arthritis score, paw diameters, TNF-α, IL-6 as compared to diseased animals. The docking results showed that residues show a critical binding affinity with TNF-α and act as the TNF-α antagonist. The alcoholic fraction of S. mangifera extract possesses beneficial effects on rheumatoid arthritis as well as anti-inflammatory potential, and can further can be used as a possible agent for novel target-based therapies for the management of arthritis.

scholarly journals Cascade Transformations of 1-R-Ethynyl-9,10-anthraquinones with Amidines: Expanding Access to Isoaporphinoid Alkaloids

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6883
Author(s):  
Sergey Francevich Vasilevsky ◽  
Ol’ga Leonidovna Krivenko ◽  
Irina Vasilievna Sorokina ◽  
Dmitry Sergeevich Baev ◽  
Tatyana Genrikhovna Tolstikova ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Concanavalin A ◽  
In Silico ◽  
Intraperitoneal Injection ◽  
Antitumor Drug ◽  
Inflammatory Activity ◽  
Antitumor Properties ◽  
Anti Inflammatory

The interaction of acetamidine and phenylamidine with peri-R-ethynyl-9,10-anthraquinones in refluxing n-butanol leads to the formation of cascade transformations products: addition/elimination/cyclization―2-R-7H-dibenzo[de,h]quinolin-7-ones and(or) 2-R-3-aroyl-7H-dibenzo[de,h]quinolin-7-ones. The anti-inflammatory and antitumor properties of the new 2-R-7H-dibenzo[de,h]quinolin-7-ones were investigated in vivo, in vitro, and in silico. The synthesized compounds exhibit high anti-inflammatory activity at dose 20 mg/kg (intraperitoneal injection) in the models of exudative (histamine-induced) and immunogenic (concanavalin A-induced) inflammation. Molecular docking data demonstrate that quinolinones can potentially intercalate into DNA similarly to the antitumor drug doxorubicin.

scholarly journals In vitro and in vivo antidiabetic activity, isolation of flavonoids, and in silico molecular docking of stem extract of Merremia tridentata (L.)

2022 ◽  
Vol 146 ◽  
pp. 112611
Author(s):  
Lenh Vo Van ◽  
Em Canh Pham ◽  
Cuong Viet Nguyen ◽  
Ngoc Thoi Nguyen Duong ◽  
Tuong Vi Le Thi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Antidiabetic Activity ◽  
Stem Extract ◽  
In Silico Molecular Docking

scholarly journals An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Pankaj Jain ◽  
Amit Joshi ◽  
Nahid Akhtar ◽  
Sunil Krishnan ◽  
Vikas Kaushik
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Docking ◽  
In Silico ◽  
Cell Epitope ◽  
Cost Effective ◽  
Dynamics Simulation ◽  
Cloning And Expression

Abstract Background Canine circovirus is a deadly pathogen of dogs and causes vasculitis and hemorrhagic enteritis. It causes lethal gastroenteritis in pigs, fox, and dogs. Canine circovirus genome contains two main (and opposite) transcription units which encode two open reading frames (ORFs), a replicase-associated protein (Rep) and the capsid (Cap) protein. The replicase protein and capsid protein consist of 303 amino acids and 270 amino acids respectively. Several immuno-informatics methods such as epitope screening, molecular docking, and molecular-dynamics simulations were used to craft peptide-based vaccine construct against canine circovirus. Results The vaccine construct was designed by joining the selected epitopes with adjuvants by suitable linker. The cloning and expression of the vaccine construct was also performed using in silico methods. Screening of epitopes was conducted by NetMHC server that uses ANN (Artificial neural networking) algorithm. These methods are fast and cost-effective for screening epitopes that can interact with dog leukocyte antigens (DLA) and initiate an immune response. Overall, 5 epitopes, YQHLPPFRF, YIRAKWINW, ALYRRLTLI, HLQGFVNLK, and GTMNFVARR, were selected and used to design a vaccine construct. The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. Conclusion The results suggest that the vaccine construct can be useful in preventing the dogs from canine circovirus infections. However, the results need further validation by performing other in vitro and in vivo experiments.

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