scholarly journals Molecular docking study of copaíba oil interacting with the spike protein of Sars-CoV-2

2021 ◽  
Author(s):  
Willian Oliveira Santos ◽  
José Robson da Costa Venâncio ◽  
Fernanda Carla Lima Ferreira ◽  
Glaura Caroena Azevedo de Oliveira ◽  
Aldimar Machado Rodrigues ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Inorganic Compounds ◽  
Minimum Energy ◽  
Docking Study ◽  
Binding Energies ◽  
Van Der Waals Interactions ◽  
Molecular Docking Study ◽  
Copaiba Oil ◽  
The Stability ◽  
Potential Inhibitors

Abstract COVID-19 triggered by Sars-CoV-2 has caused hundreds of thousands of deaths worldwide. Organic and inorganic compounds have been tested as potential inhibitors of this lethal virus. For these tests, several techniques are use to design molecules of biological interest for drug composition, in which molecular coupling plays an important role. In the present work, the compounds acids kaurenoic, copalic, and beta-caryophyllene that form the copaiba oil were studied as anti-inflammatories and opens the possibility to inhibit Sars-CoV-2. Molecular docking showed alkyl, pi-alkyl, conventional H-bond, unfavorable bump, and Van der Waals interactions. The calculated electrostatic potential maps showed the nucleophilic and electrophilic regions. The negative binding energies obtained for the three acids suggest the stability of the complexes. The minimum energy states for β-caryophyllene are lower than the other compounds analyzed, and it can be predicted that this is the most stable.

Synthesis, Biological Evaluation of ortho-Carboxamidostilbenes as Potential Inhibitors of Hyperglycemic Enzymes, and Molecular Docking Study

2021 ◽  
pp. 131007
Author(s):  
Norhadi Mohamad ◽  
Phua Yoong Hui ◽  
Mohamad Hafizi Abu Bakar ◽  
Mohammad Tasyriq Che Omar ◽  
Habibah A. Wahab ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Biological Evaluation ◽  
Molecular Docking Study ◽  
Potential Inhibitors

scholarly journals Gymnema Sylvestre A- Potential Inhibitor of COVID-19 Main Protease by MD Simulation Study

2020 ◽  
Author(s):  
Senthil Kumar Subramani ◽  
Yash Gupta ◽  
Manish Manish ◽  
GBKS Prasad
Keyword(s):  
Md Simulation ◽  
Docking Study ◽  
Binding Pocket ◽  
Gymnema Sylvestre ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Strong Candidate ◽  
The Stability ◽  
Potential Inhibitors ◽  
Domain I

Gymnema sylvestre (GS) is one of the herbal plant used since in ancient times. The present study aimed to assess bioactive compounds GS mainly gymnemic acids as potential inhibitors for COVID-19 against Mpro enzyme using a molecular docking study. The docking score observed between -53.4 to - 42.4 of all gymnemic acids and its derivatives. Molecular Dynamics (MD) simulation studies carried out at 100ns supported the stability of GS molecules within the binding pocket. RMSD score of less than 3.6. mainly, our results supported that these GS molecules bind to the domain I & II, and domain II-III linker of 3CLpro enzyme, suggesting its suitability as strong candidate for therapeutic against COVID-19. <br>

scholarly journals Identification of potential inhibitors of SARS-CoV-2 main protease from Aloe vera compounds: A molecular docking study

2020 ◽  
Vol 754 ◽  
pp. 137751 ◽  
Author(s):  
Pius T. Mpiana ◽  
Koto-te-Nyiwa Ngbolua ◽  
Damien S.T. Tshibangu ◽  
Jason T. Kilembe ◽  
Benjamin Z. Gbolo ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Aloe Vera ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Potential Inhibitors

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 Naturally Occurring Anthraquinones as Potential Inhibitors of SARS-CoV-2 Main Protease: A Molecular Docking Study

2020 ◽  
Author(s):  
Sourav Das ◽  
Atanu Singha Roy
Keyword(s):  
Molecular Docking ◽  
Drug Targets ◽  
Docking Study ◽  
Docking Studies ◽  
World Health ◽  
Molecular Docking Study ◽  
Inhibitory Potential ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Potential Inhibitors

<i>Background:</i> The novel coronavirus (COVID-19) has quickly spread throughout the globe, affecting millions of people. The World Health Organization (WHO) has recently declared this infectious disease as a pandemic. At present, several clinical trials are going on to identify possible drugs for treating this infection. SARS-CoV-2 M<sup>pro</sup> is one of the most critical drug targets for the blockage of viral replication. <i>Method:</i> The blind molecular docking analyses of natural anthraquinones with SARS-CoV-2 M<sup>pro</sup> were carried out in an online server, SWISSDOCK, which is based on EADock DSS docking software. <i>Results: </i>Blind molecular docking studies indicated that several<i> </i>natural antiviral anthraquinones could prove to be effective inhibitors for SARS-CoV-2 M<sup>pro</sup> of COVID-19 as they bind near the active site having the catalytic dyad, HIS41 and CYS145 through non-covalent forces. The anthraquinones showed less inhibitory potential as compared to the FDA approved drug, remdesivir.<i></i> <p><b><i>Conclusion:</i></b><i> </i>Among the natural anthraquinones<i>, </i>alterporriol Q could be the most potential inhibitor of SARS-CoV-2 M<sup>pro</sup> among the natural anthraquinones studied here, as its ∆<i>G</i> value differed from that of remdesivir only by 0.51 kcal/ mol. The uses of these alternate compounds might be favorable for the treatment of the COVID-19.</p>

scholarly journals A Dispersion Corrected DFT Investigation of the Inclusion Complexation of Dexamethasone with β-Cyclodextrin and Molecular Docking Study of Its Potential Activity against COVID-19

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7622
Author(s):  
Youghourta Belhocine ◽  
Seyfeddine Rahali ◽  
Hamza Allal ◽  
Ibtissem Meriem Assaba ◽  
Monira Galal Ghoniem ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Active Sites ◽  
Density Functional ◽  
Inclusion Complexation ◽  
Docking Study ◽  
Van Der Waals Interactions ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Docking Calculations ◽  
Potential Activity

The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the formed Dex@β-CD complex. The complexation energy significantly decreased from −179.50 kJ/mol in the gas phase to −74.14 kJ/mol in the aqueous phase. A molecular docking study was performed to investigate the inhibitory activity of dexamethasone against the COVID-19 target protein (PDB ID: 6LU7). The dexamethasone showed potential therapeutic activity as a SARS CoV-2 main protease inhibitor due to its strong binding to the active sites of the protein target, with predicted free energy of binding values of −29.97 and −32.19 kJ/mol as calculated from AutoDock4 and AutoDock Vina, respectively. This study was intended to explore the potential use of the Dex@β-CD complex in drug delivery to enhance dexamethasone dissolution, thus improving its bioavailability and reducing its side effects.

scholarly journals Superfast Synthesis of Stabilized Silver Nanoparticles Using Aqueous Allium sativum (Garlic) Extract and Isoniazid Hydrazide Conjugates: Molecular Docking and In-Vitro Characterizations

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 110
Author(s):  
Jamal Moideen Muthu Mohamed ◽  
Ali Alqahtani ◽  
Thankakan Vimala Ajay Kumar ◽  
Adel Al Fatease ◽  
Taha Alqahtani ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Spectral Analysis ◽  
Molecular Docking ◽  
Docking Study ◽  
Garlic Extract ◽  
Molecular Docking Study ◽  
Agno3 Solution ◽  
Sustainable Fashion ◽  
The Stability

Green synthesis of silver nanoparticles (AgNPs) was synthesized from fresh garlic extract coupled with isoniazid hydrazide (INH), a commonly used antibiotic to treat tuberculosis. A molecular docking study conducted with the selected compounds compared with anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis. The aqueous extract of garlic was prepared and mixed with silver nitrate (AgNO3) solution for the superfast synthesis of stable AgNPs. INH was then conjugated with AgNPs at different ratios (v/v) to obtain stable INH-AgNPs conjugates (AgNCs). The resulting AgNCs characterized by FTIR spectra revealed the ultrafast formation of AgNPs (<5 s) and perfectly conjugated with INH. The shifting of λmax to longer wavelength, as found from UV spectral analysis, confirmed the formation of AgNCs, among which ideal formulations (F7, F10, and F13) have been pre-selected. The zeta particle size (PS) and the zeta potential (ZP) of AgNPs were found to be 145.3 ± 2.1 nm and −33.1 mV, respectively. These data were significantly different compared to that of AgNCs (160 ± 2.7 nm and −14.4 mV for F7; 208.9 ± 2.9 nm and −19.8 mV for F10; and 281.3 ± 3.6 nm and −19.5 mV for F13), most probably due to INH conjugation. The results of XRD, SEM and EDX confirmed the formation of AgNCs. From UV spectral analysis, EE of INH as 51.6 ± 5.21, 53.6 ± 6.88, and 70.01 ± 7.11 %, for F7, F10, and F13, respectively. The stability of the three formulations was confirmed in various physiological conditions. Drug was released in a sustainable fashion. Besides, from the preferred 23 compounds, five compounds namely Sativoside R2, Degalactotigonin, Proto-desgalactotigonin, Eruboside B and Sativoside R1 showed a better docking score than trpD, and therefore may help in promoting anti-tubercular activity.

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