scholarly journals Molecular docking study of oligonucleotides with D-mannitol

2017 ◽  
Vol 15 (1) ◽  
pp. 64-68
Author(s):  
V. Shchodryi ◽  
D. Lozhko ◽  
Z. Tkachuk
Keyword(s):  
Molecular Docking ◽  
Molecular Modeling ◽  
Antiviral Activity ◽  
Software Package ◽  
Virus Entry ◽  
Docking Study ◽  
Binding Energies ◽  
Important Task ◽  
Molecular Docking Study ◽  
Hyperchem Software

Aim. Complex of yeast RNA and D-mannitol has a specific antiviral activity. This complex inhibits the neuraminidase and hemagglutinin activity of viruses such as influenza, parainfluenza and thus it blocks virus entry into the cell and his replication. So, nowadays, study of the interaction of this compound is an important task. Study interaction of the oligoribonucleotides and oligodesoxynucleotides with D mannitol molecule. Methods. Molecular modeling structure of oligoribonucleotides and oligodesoxynucleotides were done by using «Hyperchem» software package. The AutoDock program was used to perform accuracy molecular docking. Results. Were obtained binding energies of D-mannitol molecule with oligoribonucleotides and oligodesoxynucleotides. We have shown the possible connections between atoms of oligonucleotides and D-mannitol molecule. Conclusions. The modeling results should give more detailed information about nature of the oligonucleotides binding with a shugar alcohol D-mannitol.Keywords: molecular docking, oligonucleotides, D-mannitol, binding energies.

Synthesis, antiviral activity, and molecular docking study of trans-ferulic acid derivatives containing acylhydrazone moiety

2017 ◽  
Vol 27 (17) ◽  
pp. 4096-4100 ◽  
Author(s):  
Zhenzhen Wang ◽  
Dandan Xie ◽  
Xiuhai Gan ◽  
Song Zeng ◽  
Awei Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Activity ◽  
Ferulic Acid ◽  
Docking Study ◽  
Molecular Docking Study

Chemoenzymatic synthesis of new derivatives of glycyrrhetinic acid with antiviral activity. Molecular docking study

2018 ◽  
Vol 78 ◽  
pp. 210-219 ◽  
Author(s):  
M. Antonela Zígolo ◽  
Maximiliano Salinas ◽  
Laura Alché ◽  
Alicia Baldessari ◽  
Guadalupe García Liñares
Keyword(s):  
Molecular Docking ◽  
Antiviral Activity ◽  
Docking Study ◽  
Glycyrrhetinic Acid ◽  
Chemoenzymatic Synthesis ◽  
Molecular Docking Study ◽  
Derivatives Of

In silico investigation of Alliin as potential activator for AMPA receptor

2021 ◽  
Author(s):  
Hilal Ozturk ◽  
N. Yorulmaz ◽  
Mustafa Durgun ◽  
Harun Basoglu
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ampa Receptor ◽  
Docking Study ◽  
Binding Energies ◽  
Molecular Docking Study ◽  
Gaba A ◽  
Docking Method ◽  
Ampa And Nmda Receptors ◽  
The Central Nervous System

Abstract Natural products from plants, such as flavonoids, arouse immense interest in medicine because of the therapeutic and many other bioactive properties. The molecular docking is a very useful method to screen the molecules based on their free binding energies and give important structural suggestions about how molecules might activate or inhibit the target receptor by comparing reference molecules. Alliin and Allicin differ from many other flavonoids because of containing no benzene rings and having nitrogen and sulfur atoms in their structure. In this study Alliin and Allicin affinity on AMPA, NMDA and GABA-A receptors were evaluated in the central nervous system by using the molecular docking method. Both Alliin and Allicin indicated no inhibitory effects. However Alliin showed significant selectivity to human AMPA receptor (3RN8) as an excitatory. The binding energy of glutamate to 3RN8 was -6.61 kcal/mol, while the binding energy of Allin was -8.08 kcal/mol. Furthermore Alliin’s affinity to the other AMPA and NMDA receptors is quite satisfactory compared to the reference molecule glutamate. In conclusion based on the molecular docking study, Alliin can be useful for synaptic plasticity studies whereas might be enhance seizure activity because of the increased permeability to cations. It also can be beneficial to improve learning and memory and can be used as a supportive product to the hypofunction of NMDA associated problems.

scholarly journals Identification of Potent COVID-19 Main Protease (Mpro) Inhibitors from Natural Polyphenols: An in Silico Strategy Unveils a Hope against CORONA

2020 ◽  
Author(s):  
Sevki Adem ◽  
Volkan Eyupoglu ◽  
Iqra Sarfraz ◽  
Azhar Rasul ◽  
Muhammad Ali
Keyword(s):  
Molecular Docking ◽  
Drug Target ◽  
Docking Study ◽  
Binding Energies ◽  
Therapeutic Drug ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
Main Protease ◽  
Chinese Researcher ◽  
Native Ligand

COVID-19, a rapidly spreading new strain of coronavirus, has affected more than 150 countries and received worldwide attention. The lack of efficacious drugs or vaccines against SARS-CoV-2 has further worsened the situation. Thus, there is an urgent need to boost up research for the development of effective therapeutics and affordable diagnostic against COVID-19. The crystallized form of SARS-CoV-2 main protease (Mpro) was demonstrated by a Chinese researcher Liu et al. (2020) which is a novel therapeutic drug target. This study was conducted to evaluate the efficacy of medicinal plant-based bioactive compounds against COVID-19 Mpro by molecular docking study. Molecular docking investigations were performed by using Molegro Virtual Docker 7 to analyze the inhibition probability of these compounds against COVID-19. COVID-19 Mpro was docked with 80 flavonoid compounds and the binding energies were obtained from the docking of (PDB ID: 6LU7: Resolution 2.16 Å) with the native ligand. According to obtained results, hesperidin, rutin, diosmin, apiin, diacetylcurcumin, (E)-1-(2-Hydroxy-4-methoxyphenyl)-3-[3-[(E)-3-(2-hydroxy-4- methoxyphenyl)-3-oxoprop-1-enyl]phenyl]prop-2-en-1-one, and beta,beta'-(4-Methoxy-1,3- phenylene)bis(2'-hydroxy-4',6'-dimethoxyacrylophenone have been found as more effective on COVID-19 than nelfinavir. So, this study will pave a way for doing advanced experimental research to evaluate the real medicinal potential of these compounds to cure COVID-19.

scholarly journals Some Compounds from Neem leaves extract exhibit binding affinity as high as -14.3 kcal/mol against COVID-19 Main Protease (Mpro): A Molecular Docking Study

2020 ◽  
Author(s):  
Shanmuga Subramanian S
Keyword(s):  
Molecular Docking ◽  
Treatment Option ◽  
Vitamin B1 ◽  
Antiviral Agent ◽  
Docking Study ◽  
Binding Energies ◽  
Potential Treatment ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Neem Leaves

Abstract Currently the new Coronavirus "COVID-19", also known as SARS-CoV-2, has infected nearly 3 million patients and nearly 200,000+ people have lost their lives due to this pandemic. There is an urgent need to find an antiviral agent that may slow down the spread of the virus. The aim of this study is to assess and evaluate compounds present in leaves of Neem tree (Azadirachta Indica) as potential inhibitors for COVID-19 Main Protease (Mpro) (PDB code: 6LU7). This will be done by blind molecular docking using PyRx and Auto Vina software. The compounds Hydroxychloroquine and Remdesivir were used for comparative study. The binding energies obtained from the docking of 6LU7 with meliacinanhydride, nimocinol, isomeldenin, nimbolide, zafaral, nimbandiol, nimbin, nimbinene, desacetylnimbin were -14.3, -12.4, -12.3, -12.2, -11.9, -11.8, -11.7, -11.7, -11.4 kcal/mol respectively. Therefore Meliacinanhydride (Ki=33.36 pM) and the compounds from Neem leaves may be a potential treatment option against COVID-19. In addition to that the leaves contain others compounds like Quercetin, Zinc,Vitamin A,Vitamin B1,B2,B6, Vitamin C,Vitamin E etc., which may boost immunity also (Garba, 2019) .Further investigation is needed to evaluate the results of this study to consider Neem leaves as potential treatment option as it might inhibit the virus and boost immunity also

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

2020 ◽  
Author(s):  
LALIT SAMANT ◽  
Vyomesh Javle
Keyword(s):  
Molecular Docking ◽  
Treatment Options ◽  
Docking Study ◽  
Binding Energies ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Discovery Studio ◽  
Main Protease ◽  
Medicinal Use ◽  
Lamarckian Genetic Algorithm

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.

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

2020 ◽  
Author(s):  
Siti Khaerunnisa ◽  
Hendra Kurniawan ◽  
Rizki Awaluddin ◽  
Suhartati Suhartati ◽  
Soetjipto Soetjipto
Keyword(s):  
Molecular Docking ◽  
Treatment Options ◽  
Docking Study ◽  
Binding Energies ◽  
Molecular Docking Study ◽  
Epicatechin Gallate ◽  
Discovery Studio ◽  
Main Protease ◽  
Lamarckian Genetic Algorithm ◽  
Autodock 4.2

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.

Molecular Docking Study of Active Diazenyl Scaffolds as Inhibitors of Essential Targets Towards Antimicrobial Drug Discovery

2019 ◽  
Vol 20 (15) ◽  
pp. 1587-1602 ◽  
Author(s):  
Harmeet Kaur ◽  
Sudhir Gahlawat ◽  
Jasbir Singh ◽  
Balasubramanian Narasimhan
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Schiff Bases ◽  
Docking Study ◽  
Docking Studies ◽  
Binding Energies ◽  
Antifungal Drugs ◽  
Molecular Docking Study ◽  
Dna Topoisomerase ◽  
Standard Drug

Background: The diazenyl compounds (-N=N- linkage) have been reported to have antimicrobial activity. In modern drug discovery, the drug-receptor interactions are generally explored by the molecular docking studies. Materials and Methods: Three categories of diazenyl scaffolds were screened for the docking studies to explore the binding mechanism of interaction with various microbial targets. The diazenyl Schiff bases (SBN-20, SBN-21, SBN-25, SBN-33, SBN-39, SBN-40 and SBN-42), naphthol pharmacophore based diazenyl Schiff bases (NS-2, NS-8, NS-12, NS-15, NS-21, and NS-23), morpholine based diazenyl chalcones (MD-6, MD-9, MD-14, MD-16, MD-20, and MD-21) were docked against various bacterial and fungal proteins in comparison with different standard drugs. Further, the drug likeliness and ADME properties of these molecules were predicted by QikProp module of the Schrodinger software. Results: Most of the derivatives had shown less docking scores and binding energies towards bacterial proteins, such as dihydropteroate synthase (PDB:2VEG), glucosamine-6-phosphate synthase (PDB:2VF5), dihydrofolate reductase (PDB:3SRW) in comparison with the standard drugs. The naphthol based diazenyl Schiff bases NS-21 and NS-23 were predicted to act on the cytochrome P450 sterol 14-alpha-demethylase (CYP51) (PDB:5FSA) involved in sterol biosynthesis, an essential target for antifungal drugs. The derivative MD-6, NS-2, NS-21, and NS-23 had shown high docking scores against bacterial DNA topoisomerase (PDB:3TTZ) in comparison with the standard drug ciprofloxacin. Further, most of the synthesized derivatives had shown drug like characters. Conclusion: Hence, these compounds can be developed as novel antibacterial agents as potent DNA topoisomerase inhibitors and antifungal agents as CYP51 inhibitors.

scholarly journals Azole-acridine hybrids as potential enzymatic inhibitors of coronavirus-2 main protease and RNA polymerase by molecular modeling strategy

2020 ◽  
Author(s):  
Charles K. Rono ◽  
Banothile C.E. Makhubela
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Study ◽  
Living Cells ◽  
Binding Energies ◽  
Binding Affinities ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Current Outbreak ◽  
Modeling Strategy

Abstract SARS-CoV-2 has been identified as the cause of the current outbreak of coronavirus disease (COVID-19). As part of the efforts to develop potential drugs with promise for clinical use, a molecular docking study on azole (triazole and pyrazole) based molecules on the main protease Mpro and RNA polymerase as possible inhibitors that could be elected for further experimental bioassays. Autodock has been employed to identify azole derivatives 1-6 preferred conformations in the active site of the enzyme and to estimate their binding affinities to the protease and RNA polymerase targets. From the molecular docking strategy, these new azole compounds though nonpeptides in nature display possible inhibition of Mpro activity with comparable affinities (-4.7 kcal/mol to -6.5 kcal/mol) to the recently reported peptide-like inhibitors such as α-ketoamide inhibitor 13b (-5.0 k/cal/mol). They also exhibit improved binding affinities to RNA polymerase (-6.3 to -7.1 kcal/mol) comparable to remdesivir (-6.6 kcal/mol). Based on the observed binding energies, these compounds may possess anti-coronavirus bioactivity through inhibition of the virus main protease as well as RNA polymerase activities in living cells.

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