Docking Molecular analysis of potential Aldosterone antagonists

Background: Aldosterone antagonists (spironolactone, eplerenone) inhibit the action of aldosterone in the collecting duct; as such, these agents cause modest diuresis but inhibit potassium and hydrogen ion secretion. We report first time Potential Aldosterone antagonists by in Silico approach, using AutoDock Vina and AutoDock 4 (or MGL Tool), estimated with Pyrx and AM Dock Software, calculating three different important parameters: Binding Affinity ( kcal/mol), estimated Ki ( in nM units) and Ligand Efficiency ( L.E. in kcal/mol). After a selective analysis of over 1000 drugs, processed with Pyrx (a Virtual Screening software for Computational Drug Discovery) in the Ligand Binding site pocket of the protein ( ID PDB 2OAX Chain A:), we noticed high values of Binding Energy , about -13.55 kcal/mol estimated by AutoDock 4 with AM Dock Software, concluding that it could be an excellent candidate drug, compared to everyone else Aldosterone antagonists. Indeed, from the results of AutoDock Vina and AutoDock 4 ( or AutoDock 4.2 ), implemented with Lamarckian genetic algorithm, LGA, trough AMDock Software, our results of Binding Energy are very similar to the crystallized Spironolactone in PDB 2OAX Chain A protein.

Studi Penambatan Molekuler Senyawa Bioaktif Biji Habbatussauda (Nigella sativa) terhadap ERα sebagai Alternatif Pengobatan Kanker Payudara dalam Upaya Pemberian Data Ilmiah Thibbun Nabawi

Pendahuluan: Reseptor Estrogen α (ERα) merupakan salah satu target reseptor utama dari pengobatan kanker payudara, sehingga penghambat ERα adalah salah satu obat yang paling potensial dalam pengobatan kanker payudara. Pencarian terhadap molekul penghambat ERα dapat ditemukan pada senyawa dari tanaman tradisional, seperti misalnya habbatussauda (Nigella sativa). Habbatussauda telah dijelaskan pada Thibbun Nabawi sebagai tumbuhan yang dapat mengobati segala penyakit, namun masih belum ada penelitian yang menjelaskan senyawa dalam habbatussauda sebagai penghambat ERα. Habbatussauda diketahui memiliki beberapa kandungan senyawa yang memiliki aktivitas farmakologis, seperti antioksidan dan antikanker. Penelitian ini bertujuan untuk mengetahui potensi dan interaksi dari senyawa yang terkandung dalam habbatussauda sebagai pengobatan baru kanker payudara dengan target ERα. Metode: Penelitian ini menggunakan metode penambatan molekuler dengan peranti lunak AutoDock 4.2 dengan metode pencarian Lamarckian Genetic Algorithm (LGA). Penambatan molekuler dikenal ilmuwan sebagai metode yang cepat dan hemat biaya. Hasil: Hasil penelitian ini menunjukan bahwa senyawa stigmasterol dalam habbatussauda berpotensi sebagai inhibitor ERα dengan nilai ΔG sebesar -10,14 kkal/mol dan Ki sebesar 36,99 nM. Kesimpulan: Penelitian ini menunjukkan bahwa stigmasterol merupakan kandidat potensial sebagai inhibitor ERα yang baru. Selain itu, penelitian ini mendapatkan beberapa residu asam amino yang diduga penting dalam aktivitas penghambatan ERα, yaitu Leu346, Glu353, Leu387, dan Arg394, serta memberikan bukti ilmiah bahwa senyawa kimia dalam Nigella sativa memiliki potensi sebagai obat kanker payudara.

MOLECULAR DOCKING STUDIES OF ISOLATED COMPOUNDS ANDROGRAPHOLIDE AND BETULIN FROM METHANOLIC LEAVES EXTRACT OF ANDROGRAPHIS ECHIOIDES AS ALPHA-AMYLASE AND ALPHA-GLUCOSIDASE ACTIVATORS

Objective: The purpose of this study is to isolate and characterize the andrographolide and betulin from methanolic leaves extract of Andrographis echioides and also used to evaluate the alpha-amylase and alpha-glucosidase inhibitory activity of isolated compounds using in silico docking studies. Methods: The isolation was done using column chromatography using gradient mobile phase. Structural elucidation was carried out on the basis of spectral analysis. In this view, andrographolide and betulin were prepared for the docking evaluation. In silico docking studies were carried out using a recent version of Auto Dock 4.2, which has the basic principle of Lamarckian genetic algorithm. Results: On the basis of the spectral data, the compounds have been established as andrographolide and betulin are being reported from this plant for the first time. The result showed that the andrographolide showed a binding affinity for amylase: (-7.9 kcal/mol) and for glucosidase (-7.2 kcal/mol) while betulin showed (-8.6 kcal/mol) and (-5.2 kcal/mol), respectively. Conclusion: Therefore, it is suggested that isolated compounds andrographolide and betulin contributed excellent α-amylase and α-glucosidase inhibitory activity because of its structural parameters. Thus, these isolated compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores.

Synthesis, Characterization and Molecular Docking Studies of Substituted Benzofuran and Pyrazole Derivatives

A series of 5-(5-bromobenzofuran-2-yl)-substituted 1,3,4-oxadiazole- 2-thiol derivatives (4a-d) and substituted benzylidene-3-methyl-1- (5-bromobenzofuran-2-carbonyl)-1H-pyrazol-5(4H)-one derivatives (6a-d) have been synthesized in good yields and characterized by IR and NMR analyses. Auto Dock 4.0/ADT program was used to investigate binding interaction of oxadiazole and pyrazole derivatives to DNA GyrB. DNA gyrase of Mycobacterium tuberculosis (MTB) is a type II topoisomerase and well-established and validated target for the development of novel therapeutics. The search was based on the Lamarckian genetic algorithm and the results were analyzed using binding energy. Analysis was based on lowest docked energy and inhibition constant values. Among the tested compounds 4b, 6b and 6c derivatives of oxadiazole and pyrazole showed highest binding energy with the lowest inhibition constant. From the observed results, it is concluded that compounds 4b, 6b and 6c showed more affinity to DNA GyrB protein.

A Series of New Hydrazone Derivatives: Synthesis, Molecular Docking and Anticholinesterase Activity Studies

Background: Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are known to be serine hydrolase enzymes responsible for the hydrolysis of acetylcholine (ACh), which is a significant neurotransmitter for regulation of cognition in animals. Inhibition of cholinesterases is an effective method to curb Alzheimer’s disease, a progressive and fatal neurological disorder. Objective: In this study, 30 new hydrazone derivatives were synthesized. Then we evaluated their anticholinesterase activity of compounds. We also tried to get insights into binding interactions of the synthesized compounds in the active site of both enzymes by using molecular docking approach. Methods: The compounds were synthesized by the reaction of various substituted/nonsubstituted benzaldehydes with 6-(substitute/nonsubstituephenyl)-3(2H)-pyridazinone-2-yl propiyohydrazide. Anticholinesterase activity of the compounds was determined using Ellman’s method. Molecular docking studies were done by using the ADT package version 1.5.6rc3 and showed by Maestro. RMSD values were obtained using Lamarckian Genetic Algorithm and scoring function of AutoDock 4.2 release 4.2.5.1 software. Results: The activities of the compounds were compared with galantamine as cholinesterase enzyme inhibitor, where some of the compounds showed higher BChE inhibitory activity than galantamine. Compound F111 was shown to be the best BChE inhibitor effective in 50 μM dose, providing 89.43% inhibition of BChE (IC50=4.27±0.36 μM). Conclusion: This study supports that novel hydrazone derivates may be used for the development of new BChE inhibitory agents.

Comparative Docking Analysis of Rational Drugs Against COVID-19 Main Protease

COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available, and investigations regarding COVID-19 treatment are lacking. Crystallised COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess drugs found in literature as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. The docking was cross-validated using Swiss Dock. COVID-19 Mpro was docked with several compounds, and docking was analysed by Biovia Discovery Studio 2020. Quinine and hydroxychloroquine were used as standards for comparison. The binding energies obtained from the docking of 6LU7, 2GTB with screened drugs viz., Quinine, Artesunate, Clotrimazol, Artemether, Quercetin, Mefloquine, ciprofloxacin, clindamycin, cipargamin, SJ-733 were in between -7.0 to -9.6 kcal/mol. On consideration of similar binding energy obtained from Autodock vina and SWISSDock and interaction residue pattern specifically (GLU 166,CYS 145, CYS44 and MET 49 residue) for SJ-733 & JPC-3210 may represent potential treatment options, and appeared to have the best potential to act as COVID-19 Mpro inhibitors. However, further research is necessary to investigate their potential medicinal use against CoV.

Comparative Docking Analysis of Rational Drugs Against COVID-19 Main Protease

COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available, and investigations regarding COVID-19 treatment are lacking. Crystallised COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess drugs found in literature as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. The docking was cross-validated using Swiss Dock. COVID-19 Mpro was docked with several compounds, and docking was analysed by Biovia Discovery Studio 2020. Quinine and hydroxychloroquine were used as standards for comparison. The binding energies obtained from the docking of 6LU7, 2GTB with screened drugs viz., Quinine, Artesunate, Clotrimazol, Artemether, Quercetin, Mefloquine, ciprofloxacin, clindamycin, cipargamin, SJ-733 were in between -7.0 to -9.6 kcal/mol. On consideration of similar binding energy obtained from Autodock vina and SWISSDock and interaction residue pattern specifically (GLU 166,CYS 145, CYS44 and MET 49 residue) for SJ-733 & JPC-3210 may represent potential treatment options, and appeared to have the best potential to act as COVID-19 Mpro inhibitors. However, further research is necessary to investigate their potential medicinal use against CoV.

Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study

COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available and investigations regarding COVID-19 treatment are lacking. Liu et al. (2020) successfully crystallised the COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess bioactive compounds found in medicinal plants as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. COVID-19 Mpro was docked with several compounds, and docking was analysed by Autodock 4.2, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Nelfinavir and lopinavir were used as standards for comparison. The binding energies obtained from the docking of 6LU7 with native ligand, nelfinavir, lopinavir, kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, epicatechin-gallate, zingerol, gingerol, and allicin were -8.37, -10.72, -9.41, -8.58, -8.47, -8.17, -7.99, -7.89, -7.83, -7.31, -7.05, -7.24, -6.67, -5.40, -5.38, and -4.03 kcal/mol, respectively. Therefore, nelfinavir and lopinavir may represent potential treatment options, and kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, and epicatechin-gallate appeared to have the best potential to act as COVID-19 Mpro inhibitors. However, further research is necessary to investigate their potential medicinal use.

A Hybrid DELGA Algorithm for Protein Ligand Docking

Protein-ligand docking is a computational molecular modeling method that is used in drug design to predict the optimal binding pose between the ligand and receptor. AutoDock is an open-source freeware program used to predict docking poses. It uses LGA) Lamarckian genetic algorithm to enumerate the binding energy. In this research work, we proposed an approach of hybrid Differential evolution base Lamarckian genetic (DELGA) algorithm to calculate the lowest binding energy. The experiment conducted to compute the 65 molecular instances, the results exposed that our approach predicts lowest docking energy with minimum root mean square deviation (RMSD) in comparison to the LGA, SA and PSO algorithms.

In silico evaluation of antidiabetic molecules of the seeds of Swietenia mahagoni Jacq

Diabetes is a chronic metabolic disorder. WHO has projected that India will have around 57 million persons with diabetes by 2025. Swietenia mahagoni Jacq. (Meliaceae) is a large, deciduous tree whose seeds and bark were used for diabetes traditionally. The in silico hyperglycemic activity of the seeds of Swietenia mahagoni Jacq was studied by using AUTODOCK version 4.2 which reveals the putative binding sites of the compound to target protein. Homology modeling was done using MODELLER for the crystal structure of sodium/glucose co-transporter 2(SGLT2). The putative binding modes of compounds were identified using the search method of Lamarckian Genetic Algorithm (LGA).Atomic affinity and electrostatic potential grid maps were calculated using Auto Grid 4.2. From the fallout, we may scrutinize that for successful docking, intermolecular hydrogen bonding and lipophilic interactions between the ligand and the receptor are very essential. The results evolved with the least binding energy ensures that the Oleanolic showed good inhibitory activity and further work may help to develop the compound as an active therapeutic agent for the treatment of hyperglycemia. Keywords: Diabetes mellitus, Swietenia mahagoni Jacq, Docking, Oleanolic acid.