Computation screening of narcissoside a glycosyloxyflavone for potential novel coronavirus 2019 (COVID-19) inhibitor

Dubey, Kushagra; Dubey, Raghvendra

doi:10.1016/j.bj.2020.05.002

Cited by 49 publications

(35 citation statements)

References 18 publications

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“…The existence of a hydrogen bond is crucial to the inhibition mechanism between drug candidates and Mpro receptors. This nding by the authors is compromised by a previous study 56 . Almost all molecular docking calculations between ligands and Mpro receptor always react with the amino acid residues of GLY143, next CYS145, GLU166, and HIS163, so the amino acid residues are hypothesized as a priority in inhibiting Mpro receptor 57 .…”

Section: Discussioncontrasting

confidence: 59%

Molecular Docking Studies of SARS-Cov-2 Mainprotease Potential Inhibitors

Utami¹,

Fitriani

Aziz

et al. 2020

Preprint

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BACKGROUND : SARS-Cov-2 causes an coronavirus disease 2019 (COVID-19), and the vaccines or drugs of this disease have not been found to inhibit this replication of the virus. Researchers are engaged in all fields of study to discover new potential inhibitors. This study aimed to compute the binding energy (BE) and interactions between the new potential inhibitors and the SARS-Cov-2 Mainprotease (Mpro).METHODS: In this study, we docked between twenty-seven patented drugs and the Mpro receptor (PDB ID: 6W63). The molecular docking calculation was performed using AutoDock Tools 1.5.6. software. Moreover, the information about the biological activity of ligands was calculated using the PASS online server. The result of the calculation was then analyzed and visualized using Biovia Discovery Studio Visualizer. Further calculation, such as the ligand-protein interaction using STITCH database and Lipinski’s rule five were employed in this research.RESULTS: The molecular docking calculation results showed that nelfinavir was strongly bound to Mpro with BE of -9,51 kcal/mol, followed by lopinavir, vitamin D, ritonavir, and dexamethasone. From these ligands, we considered dexamethasone because this ligand works as an anti-inflammatory agent. CONCLUSIONS: Following the calculation, nelfinavir, lopinavir, and dexamethasone are proposed as a potential inhibitor of the Mpro receptor, but there is a need for further investigation.

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Section: Discussioncontrasting

confidence: 59%

Molecular Docking Studies of SARS-Cov-2 Mainprotease Potential Inhibitors

Utami¹,

Fitriani

Aziz

et al. 2020

Preprint

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“…The flavonoid narcissoside is reported to have a high affinity towards the protease protein (PDB 6W63 ) according to molecular docking studies. Thus these three protease proteins (PDB 6LU7 , PDB 6M03 , and PDB 6W63 ) can be included in the category of non-structural proteins in the structure of SARS-CoV-2 [ 58 , 59 ].…”

Section: Resultsmentioning

confidence: 99%

Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins

Al‐Zaqri

Pooventhiran²,

Alsalme

et al. 2020

Journal of Molecular Liquids

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Melatonin is a natural hormone from the pineal gland that regulates the sleep-wake cycle. We examined the structure and physico-chemical properties of melatonin using electronic structure methods and molecular-mechanics tools. Density functional theory (DFT) was used to optimise the ground-state geometry of the molecule from frontier molecular orbitals, which were analysed using the B3LYP functional. As its electrons interacted with electromagnetic radiation, electronic excitations between different energy levels were analysed in detail using time-dependent DFT with CAM-B3LYP orbitals. The results provide a wealth of information about melatonin's electronic properties, which will enable the prediction of its bioactivity. Molecular docking studies predict the biological activity of the molecules against the coronavirus2 protein. Excellent docking scores of −7.28, −7.20, and −7.06 kcal/mol indicate that melatonin can help to defend against the viral load in vulnerable populations. Hence it can be investigated as a candidate drug for the management of COVID.

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“…The two inhibitors shared the same complex, but narcissoside interacted with three amino acids (Leu167, Pro52 and Pro168) different than those interacting with X77 (His172, Leu27 and Thr26). Finally, the better fit of the glycosyloxyflavone into the active site of the 6W63 was also reinforced by thirteen hydrogen bonds compared to the four established by X77 [ 67 ].…”

Section: Flavonoids Against Coronavirusesmentioning

confidence: 99%

Roles of flavonoids against coronavirus infection

Russo

Moccia

Spagnuolo

et al. 2020

Chemico-Biological Interactions

282

223

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In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of “savage” protocols, based on “old” anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenol family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL pro , 3CL pro , NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections.

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Computation screening of narcissoside a glycosyloxyflavone for potential novel coronavirus 2019 (COVID-19) inhibitor

Cited by 49 publications

References 18 publications

Molecular Docking Studies of SARS-Cov-2 Mainprotease Potential Inhibitors

Molecular Docking Studies of SARS-Cov-2 Mainprotease Potential Inhibitors

Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins

Roles of flavonoids against coronavirus infection

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