SwissADME and pkCSM Webservers Predictors: an integrated Online Platform for Accurate and Comprehensive Predictions for In Silico ADME/T Properties of Artemisinin and its Derivatives

Azzam, Khaldun AL

doi:10.31643/2023/6445.13

Cited by 52 publications

(34 citation statements)

References 25 publications

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“…Following a virtual screening using the PyRx program 42,43 , ve compounds were selected due to having the lowest binding energy (about -10 kcal/mol) and the hydrogen binding number to the active site compared to the standard ligand (empagli ozin). The pharmacokinetic properties of the six desired compounds were investigated along with the standard drug empagli ozin and three approved drugs (canagli ozin, dapagli ozin, and ertugli ozin) using programs the Schrödinger (Schrodinger Release 2021.2: QikProp, Schrodinger, LLC, New York, NY, 2021) and SwissADME [44][45][46][47] , that only two compounds (306 and 580) were in range for 95% known drugs. After examining the docking studies of the two selected compounds of the previous stage and the approved drugs utilizing Moe 2019 48,49 , a proper conformer of the standard drug and compounds 306, and 580 was entered into a molecular simulation study via GROMACS 2018 50,51 .…”

Section: Methodsmentioning

confidence: 99%

“…These approaches are very effective, applicable to a wide range of compounds, and elicit a link between structure and activity from high-quality data. Early detection of poor candidates can greatly decrease the amount of time and money spent, as well as speeds up the entire development process [44][45][46][47] . In this study, SwissADME (http://www.swissadme.ch/index.php), a free online program, and the QikProp module from the Schrodinger Suite 56-58 were used to predict ADME properties for the standard drug Empagli ozin, four chosen natural compounds containing ZINC000096032072 (580), ZINC000253499253 (1131), ZINC000012658504 (212), ZINC000049782048 (357), and three approved drugs as SGLT2i (Ertagli ozin, Dapagli ozin, Canagli ozin).…”

Section: Accurate Adme Property Predictionmentioning

confidence: 99%

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In silico discovery of potential sodium–glucose cotransporter-2 inhibitors from natural products for Prevent Kidney Failure in Patients with Type 2 Diabetes

Shakour

Hoseinpoor

Iranshahi

et al. 2023

Preprint

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Associated with Type 2 diabetes (T2DM), renal dysfunction contributes to an increased death rate. Consequently, it would appear that preventing the advancement of renal disease is crucial in the treatment of diabetic patients. SGLT2 inhibitors have been linked to reduced renal mortality, decreased hospitalization, and slowed the progression of renal impairment and albuminuria. The objective of this study was aimed to identify natural SGLT2 inhibitors using an in silico evaluation of the compounds of zinc database using structure-based virtual screening. Using pharmacophore modelling of the standard drug, a total of 1,1336 natural compounds that have the potential to act as SGLT2 inhibitors were identified; six of these compounds, 580, 1131, 212, 357, 822, and 306, had a similar docking affinity to the four known SGLT2 inhibitors. The top two finds, 580 and 306, were chosen due to the convenience of the pharmacokinetic characteristics from the absorption, distribution, metabolism and excretion (ADME), oral bioavailability, and parameters from molecular dynamics simulation (MD). Compound 580 was discovered as a potential treatment candidate after estimations of the metabolic processes and cardiotoxicity. This study may assist in the advancement of both in vitro and in vivo validation, as well as the development of new SGLT2 inhibitors.

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Section: Methodsmentioning

confidence: 99%

Section: Accurate Adme Property Predictionmentioning

confidence: 99%

In silico discovery of potential sodium–glucose cotransporter-2 inhibitors from natural products for Prevent Kidney Failure in Patients with Type 2 Diabetes

Shakour

Hoseinpoor

Iranshahi

et al. 2023

Preprint

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show abstract

“…(Hydrogen bond acceptor, Hydrogen bond donor, TPSA, Bioavailability Index) The key emphasis of the Lipinski five Rule has been generated using Swiss ADME "(http://www. swissadme.ch/index.php)" (Azzam, 2023). Frontiers in Pharmacology frontiersin.org…”

Section: Determination Of the Data Of Lipinski Rulementioning

confidence: 99%

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach

et al. 2023

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During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.

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“…pkCSM is one the latest methodology that is used extensively for predicting and optimizing toxicity and pharmaco-kinetic perspectives relying on distance based graphical signatures [38,39]. SwissADME is a freely available online tool, which is being employed for prediction of ADME parameters and drug-likeness [37,40].…”

Section: Pharmacokinetic Properties Analysismentioning

confidence: 99%

Amentoflavone derivatives against SARS-CoV-2 main protease (MPRO): An in silico study

Hossain

Mahmud

Khalipha

et al. 2023

MGC

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Globally, novel coronavirus (nCoV19) outbreak is a great concern to humanity owing to the unavailability of effective medication or vaccine to date. Therefore, the development of drugs having anti-COVID-19 potential is a need of time. In this milieu, in-silico studies have proven to be rapid, inexpensive and effective as compared to other experimental studies. Evidently, natural products have shown significant potential in drug development to curtail different ailments, which have opened a new horizon in the screening of anti-COVID-19 agents. In this study, in-silico analysis were performed on derivatives of amentoflavone (4′, 4′′′-Dimethylamentoflavone, 4′′′, 7-Di-O-Methylamentoflavone, 4′′′′′′-methylamentoflavone, 4′-Monomethylamentoflavone, 7,4′-Dimethylamentoflavone, 7′-O-Methylamentoflavone, 7-O-methylamentoflavone, Heveaflavone, kayaflavone, and Sciadopitysin) and FDA approved anti-viral drug (camostatmesylate). All the derivatives of amentoflavone and FDA-approved anti-viral drugs were docked against SARS-CoV2 main protease (MPRO). The ten derivatives of amentoflavone showed strong interactions with the MPRO protein. In all cases, derivatives of amentoflavone showed good interaction with the targeted protein and better binding/docking score (–9.0351, –8.8566, –8.8509, –8.7746, –8.6192, –8.2537, –8.0876, –7.9501, –7.6429, and –7.6248 respectively) than FDA approved anti-viral drug. Therefore, derivatives of amentoflavone may be potent leads in drug discovery to combat HCoVs, such as SARS-CoV2. Moreover, to support the outcomes of this study further in-vivo investigations are required.

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SwissADME and pkCSM Webservers Predictors: an integrated Online Platform for Accurate and Comprehensive Predictions for In Silico ADME/T Properties of Artemisinin and its Derivatives

Cited by 52 publications

References 25 publications

In silico discovery of potential sodium–glucose cotransporter-2 inhibitors from natural products for Prevent Kidney Failure in Patients with Type 2 Diabetes

In silico discovery of potential sodium–glucose cotransporter-2 inhibitors from natural products for Prevent Kidney Failure in Patients with Type 2 Diabetes

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach

Amentoflavone derivatives against SARS-CoV-2 main protease (MPRO): An in silico study

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