Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus DOI
Ali A. Rabaan, Zainab H. Almansour,

Ali Al Bshabshe

и другие.

Journal of Biomolecular Structure and Dynamics, Год журнала: 2024, Номер unknown, С. 1 - 20

Опубликована: Янв. 17, 2024

Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement design and develop efficient therapeutic molecules. Here, comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented identify the potential molecule from anti-dengue compound library that can inhibit function VP24 protein Marburg. Virtual high throughput screening identified five effective binders after 484 compounds. These compounds were treated in MD at four different temperatures: 300, 340, 380, 420 K. Higher temperatures showed dissociation hit protein. Further, triplicates 100 ns conducted which ID = 118717693, 5361 strong stability molecule. further validated using ΔG binding free energies they showed: −30.38 kcal/mol, −67.83 kcal/mol energies, respectively. Later, these two used steered detect its dissociation. Compound maximum pulling force 199.02 kcal/mol/nm dissociate protein-ligand complex while 118717693 had 101.11 kcal/mol/nm, This ligand highest number hydrogen bonds varying occupancies 89.93%, 69.80%, 57.93%, 52.33%, 50.63%. study bind strongly has be in-vitro experiment.

Язык: Английский

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

Qandeel Rafique,

Ali Rehman,

Muhammad Sher Afghan

и другие.

Computers in Biology and Medicine, Год журнала: 2023, Номер 163, С. 107191 - 107191

Опубликована: Июнь 20, 2023

Язык: Английский

Процитировано

25
Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation DOI Creative Commons

Shopnil Akash,

İmren Bayıl, Md. Anisur Rahman

и другие.

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Июнь 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.

Язык: Английский

Процитировано

17
Cheminformatics Strategies Unlock Marburg Virus VP35 Inhibitors from Natural Compound Library DOI Creative Commons
Isra Alsaady, Leena H. Bajrai, Thamir A. Alandijany

и другие.

Viruses, Год журнала: 2023, Номер 15(8), С. 1739 - 1739

Опубликована: Авг. 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.

Язык: Английский

Процитировано

15
Berbamine inhibits porcine epidemic diarrhea virus in vitro and in vivo DOI
Hongwei Xiang,

Jixue Qiao,

H Lin

и другие.

Veterinary Microbiology, Год журнала: 2024, Номер 298, С. 110244 - 110244

Опубликована: Авг. 30, 2024

Язык: Английский

Процитировано

5
Exploration of potential inhibitors against chikungunya envelope: an in-silico clue DOI

Aparna Chaudhuri,

Bidyut Bandyopadhyay,

Buddhadev Mondal

и другие.

In Silico Pharmacology, Год журнала: 2025, Номер 13(1)

Опубликована: Апрель 7, 2025

Язык: Английский

Процитировано

0
An Updated and Comprehensive Review of the Health Benefits and Pharmacological Activities of Hesperidin DOI
Olalekan Bukunmi Ogunro

Biochemical and Biophysical Research Communications, Год журнала: 2025, Номер 772, С. 151974 - 151974

Опубликована: Май 11, 2025

Язык: Английский

Процитировано

0
Integrative Strategies in Drug Discovery: Harnessing Genomics, Deep Learning, and Computer-Aided Drug Design DOI

Nizakat Ali,

Urooj Qureshi,

Asaad Khalid

и другие.

Computational Biology and Chemistry, Год журнала: 2025, Номер 119, С. 108530 - 108530

Опубликована: Май 30, 2025

Язык: Английский

Процитировано

0
Inhibiting the oligomerization of mycobacterial DNA-directed RNA polymerase (RNAP) using natural compound via in-silico techniques DOI Creative Commons
Ehssan Moglad

Medicine in Novel Technology and Devices, Год журнала: 2024, Номер 21, С. 100286 - 100286

Опубликована: Янв. 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.

Язык: Английский

Процитировано

3
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 DOI Creative Commons

Shopnil Akash,

Arafat Hossain, Nobendu Mukerjee

и другие.

Frontiers in Pharmacology, Год журнала: 2023, Номер 14

Опубликована: Апрель 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.

Язык: Английский

Процитировано

7
In Silico Discovery of Small-Molecule Inhibitors Targeting SARS-CoV-2 Main Protease DOI Creative Commons

Menghan Gao,

Dongwei Kang, Na Liu

и другие.

Molecules, Год журнала: 2023, Номер 28(14), С. 5320 - 5320

Опубликована: Июль 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.

Язык: Английский

Процитировано

7