Reviewing methods of deep learning for diagnosing COVID-19, its variants and synergistic medicine combinations

Computers in Biology and Medicine, Journal Year: 2023, Volume and Issue: 163, P. 107191 - 107191

Published: June 20, 2023

Language: Английский

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Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: June 28, 2023

Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus’s ability to infiltrate and establish itself in increasing numbers of nations has made it persistent threat public health worldwide. Despite widespread occurrence this potentially fatal disease, no effective treatment options currently on market. As result, there is an immediate need research development novel pharmaceuticals. To begin, molecular docking was performed two possible virus target proteins using panel twelve natural chemicals, including Apigenin, Resveratrol, Hesperetin, Fungisterol, Lucidone, Ganoderic acid, Curcumin, Kaempferol, Cholic Chlorogenic Pinocembrin, Sanguinarine. methyltransferase (PDB ID: 2OY0) binding affinities varied from −7.4 −8.3 kcal/mol, whereas envelope glycoprotein ranged −6.2 −8.1 kcal/mol 2I69). Second, substances with larger weights less likely be unhappy Lipinski rule. Hence, additional carried out without regard weight. In addition, compounds 01, 02, 03, 05, 06, 07, 08, 09, 10 11 more soluble water than compound 04 is. Besides, based maximum affinity, best three (Apigenin, Acid) been dynamic simulation (MDs) at 100 ns determine their stability. MDs data also reported that these mentioned molecules highly stable. Finally, advanced principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, free energy cross correlation matrix theoretical study included established phytochemical as potential drug candidate. Research indicated aforementioned may tool battle against dangerous virus. This aims locate bioactive might used pharmaceutical.

Language: Английский

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Cheminformatics Strategies Unlock Marburg Virus VP35 Inhibitors from Natural Compound Library

Viruses, Journal Year: 2023, Volume and Issue: 15(8), P. 1739 - 1739

Published: Aug. 15, 2023

The Ebola virus and its close relative, the Marburg virus, both belong to family Filoviridae are highly hazardous contagious viruses. With a mortality rate ranging from 23% 90%, depending on specific outbreak, development of effective antiviral interventions is crucial for reducing fatalities mitigating impact outbreaks. In this investigation, virtual screening approach was employed evaluate 2042 natural compounds their potential interactions with VP35 protein virus. Average worst binding energies were calculated all 20 poses, that exhibited <−6 kcal/mol in criteria selected further analysis. Based energies, only six (Estradiol benzoate, INVEGA (paliperidone), Isosilybin, Protopanaxadiol, Permethrin, Bufalin) subsequent investigations, focusing interaction Among these compounds, Estradiol Isosilybin showed strong hydrogen bonds, while others did not. study, Myricetin, benzoate subjected molecular dynamics (MD) simulation free energy calculation using MM/GBSA reference component Myricetin served as control. most stable consistent root-mean-square deviation (RMSD) values, whereas significant fluctuations RMSD. compound lowest ΔG (−22.89 kcal/mol), surpassing control compound’s (−9.29 kcal/mol). Overall, investigation suggested possesses favorable indicating inhibitory mechanism against study proposes could serve therapeutic option preventing infection. However, experimental validation required corroborate findings.

Language: Английский

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Berbamine inhibits porcine epidemic diarrhea virus in vitro and in vivo

Veterinary Microbiology, Journal Year: 2024, Volume and Issue: 298, P. 110244 - 110244

Published: Aug. 30, 2024

Language: Английский

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Exploration of potential inhibitors against chikungunya envelope: an in-silico clue

In Silico Pharmacology, Journal Year: 2025, Volume and Issue: 13(1)

Published: April 7, 2025

Language: Английский

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An Updated and Comprehensive Review of the Health Benefits and Pharmacological Activities of Hesperidin

Biochemical and Biophysical Research Communications, Journal Year: 2025, Volume and Issue: 772, P. 151974 - 151974

Published: May 11, 2025

Language: Английский

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Integrative Strategies in Drug Discovery: Harnessing Genomics, Deep Learning, and Computer-Aided Drug Design

Computational Biology and Chemistry, Journal Year: 2025, Volume and Issue: 119, P. 108530 - 108530

Published: May 30, 2025

Language: Английский

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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

Frontiers in Pharmacology, Journal Year: 2023, Volume and Issue: 14

Published: April 19, 2023

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

Language: Английский

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In Silico Discovery of Small-Molecule Inhibitors Targeting SARS-CoV-2 Main Protease

Molecules, Journal Year: 2023, Volume and Issue: 28(14), P. 5320 - 5320

Published: July 10, 2023

The COVID-19 pandemic has caused severe health threat globally, and novel SARS-Cov-2 inhibitors are urgently needed for antiviral treatment. main protease (Mpro) of the virus is one most effective conserved targets anti-SARS-CoV-2 drug development. In this study, we utilized a molecular docking-based virtual screening approach against catalytic site to identify small-molecule SARS-CoV-2 Mpro. Further biological evaluation helped us two compounds, AF-399/40713777 AI-942/42301830, with moderate inhibitory activity. Besides that, in silico data, including dynamics (MD) simulation, binding free energy calculations, AMDET profiles, suggested that these hits could serve as starting point future development intervention treatments.

Language: Английский

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Inhibiting the oligomerization of mycobacterial DNA-directed RNA polymerase (RNAP) using natural compound via in-silico techniques

Medicine in Novel Technology and Devices, Journal Year: 2024, Volume and Issue: 21, P. 100286 - 100286

Published: Jan. 23, 2024

Mycobacterium tuberculosis (Mtb) is responsible for the spread of (TB). The current study employed virtual screening 2569 natural compounds against DNA-directed RNA polymerase (RNAP) Mtb to identify possible binders that can inhibit its function. in-silico methodology included molecular docking compounds, further, stability and flexibility best complexes were studied using dynamics simulation, MM/GBSA binding free energy technique with decomposition, PCA, FEL, steered MD umbrella sampling. Individual screenings conducted five RNAP subunits (chains A, B, C, D, E) a compound capable inhibiting oligomerization. A promising compound, isoestradiol 3-benzoate, exhibited low score (−7.28 kcal/mol −8.21 kcal/mol) showed ability all protein. Thus, 3-benzoate selected simulation analysis. Furthermore, RMSD bound chain E lowest 0.49 nm, while chains B it had most stable consistent conformations 1.75 nm 1.2 respectively. H-bond between C highest occupancy (58.27 %, 45.33 50.80 42.25 11.75 %). Moreover, MMPBSA strong association (ΔGbind = −126.25 ± 2.03 −129.27 2.25). Additionally, FEL-steered sampling also performed validate ligand Isoestradiol binds strongly E; therefore, should be considered as viable candidate formation protein complex, concluded in this study.

Language: Английский

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