Molecular docking identification for the efficacy of some zinc complexes with chloroquine and hydroxychloroquine against main protease of COVID-19

Hussein, Rageh K.; Elkhair, H.M.

doi:10.1016/j.molstruc.2021.129979

Cited by 50 publications

(23 citation statements)

References 32 publications

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“…Furthermore, recent studies have shed a light on molecular docking methodologies as powerful techniques in establishing therapeutic strategies to combat COVID-19 pandemic. In context to the recent demands, molecular docking approach has been applied for screening of organic molecules and coordination complexes as potent inhibitor of COVID-19 virus [ [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] – 35 ]. Metal complexes will eventually lead to the destruction of COVID-19 virus.…”

Section: Introductionmentioning

confidence: 99%

Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline

Mohan

Choudhary

2021

Journal of Molecular Structure

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This work deals with the synthesis, crystal structure, computational study and antiviral potential of mixed ligand copper(II) complex [Cu(L)(phen)]( 1 ), (where, H 2 L = ( Z )- N ’-(( E )-2-hydroxy-3,5-diiodobenzylidene)- N,N- dimethylcarbamohydrazonothioic acid, phen = 1,10-phenanthroline). The Schiff base ligand (H 2 L) is coordinated with Cu(II) ion in O, N, S-tridentate mode. The copper complex ( 1 ) crystallized in the monoclinic system of the space group P21/c with eight molecules in the unit cell and reveals a square pyramidal geometry. Furthermore, we also perform quantum chemical calculations to get insights into the structure-property relationship and functional properties of ligand (H 2 L) and its copper (II) complex [Cu(L)(phen)]( 1 ). Complex [Cu(L)(phen)]( 1 ) was also virtually designed in-silico evaluation by Swiss-ADME. Additionally, inspiring by recent developments to find a potential inhibitor for the COVID-19 virus, we have also performed molecular docking study of ligand and its copper complex ( 1 ) to see if our compounds shows an affinity for the main protease (M pro ) of COVID-19 spike protein (PDB ID: 7C8U ). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant were found to be -7.14 kcal/mol and 5.82 μM for ligand (H 2 L) and -6.18 kcal/mol and 0.76 μM for complex [Cu(L)(phen)]( 1 ) with M pro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of ligand and complex was found to be better than docking results of chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) with M pro protein. The present study may offer the technological solutions and potential inhibition to the COVID-19 virus in the ongoing and future challenges of the global community. In the framework of synthesis and characterization of mixed ligand copper (II) complex; the major conclusions can be drawn as follow:

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Section: Introductionmentioning

confidence: 99%

Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline

Mohan

Choudhary

2021

Journal of Molecular Structure

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“…Similarly, the compounds ADM_13083841, LMG_15521745 and SYN_15517940 with binding energy score − 8.9, −8.7, −8.7 kcal mol −1 , respectively along with 26 FDA-approved drugs revealed a docking score of −7 or higher (Alamri et al 2020 ). On a similar streak, anti-malarial drugs, Chloroquine and Hydroxychloroquine, was recognized as an inhibitor towards SARS-CoV-2 PLpro (Baildya et al 2020 , 2021a , 2021b ; Hussein and Elkhair 2021 ). Negative binding affinity indicated stronger protein-ligand complex (Kodchakorn et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Inhibitory efficacy of 2, 4-diacetylphloroglucinol against SARS-COV-2 proteins: in silico study

2022

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The pandemic of Severe Acute Respiratory Syndrome Coronavirus-2 has affected millions of people worldwide with common symptoms of fever, cough, and respiratory complications. The pandemic has posed a huge challenge to emergency health services due to unavailability of potent therapeutic drugs. The proteins associated with the viral pathogenesis has been identified as suitable targets for drug design and warrants effective drug discovery to abate COVID-19. The papain-like protease (PLpro), nucleocapsid (N), main protease (Mpro) and non-structural protein (nsp12) of SARS-CoV-2, key component of processing of viral polyproteins, transcription, assembly and replication. On this streak, present study evaluated the interaction of ligand 2,4-diacetylphloroglucinol (DAPG) with viral proteins using molecular docking with (i) AutoDock 4.2.6 and (ii) AutoDock Vina followed by molecular dynamic simulation studies of protein-ligand complex configuration. The analysis revealed that PLpro (3E9S) and N (4J3K) protein corresponds to the highest docking score and therefore, selected for molecular dynamics simulation study (100 ns). The study comprised analysis of parameters: (i) RMSD and RMSF, (ii) radius of gyration- which indicated interaction of protein entities with ligand supported steadiness of the complex, (iii) Coulombic and Lennard–Jones interactions, which played a significant role in complex stability. DAPG showed a good number of H-bonds with PLpro and MM-PBSA binding energy when compared to the N protein. This study showed DAPG as a potential bioactive molecule to act as an inhibitor for the PLpro thereby, DAPG can be used as potential inhibitor against SARS-CoV-2 and is potential drug candidate against COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11756-021-00979-4.

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“…The silico method is often used as an initial screening in the discovery of new drugs. The scope of the in silico method used is a docking study (Hussein and Elkhair 2021). The choice of docking study was based on the role of molecular docking, which aims to determine the bond between the ligand and the receptor.…”

Section: Resultsmentioning

confidence: 99%

Potential of Hanjeli (Coix lacryma-jobi) essential oil in preventing SARS-CoV-2 infection via blocking the Angiotensin Converting Enzyme 2 (ACE2) receptor

et al. 2021

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is an ongoing pandemic as we speak in 2022. This infectious disease is caused by the SARS-CoV-2 virus, which infects cells by binding to the angiotensinconverting enzyme 2 (ACE2) receptor on the cell surface. Thus, strategies that inhibit the binding of SARS-CoV-2 to the ACE2 receptor can stop this contagion. Hanjeli (Coix lacryma-jobi) essential oil contains many bioactive compounds, including dodecanoic acid; tetradecanoic acid; 7-Amino-8imino-2-(2-imino-2H-chromen-3-yl); and 1,5,7,10-tetraazaphen-9-one. These compounds suppress viral replication and may prevent Covid-19. Accordingly, this study assessed whether, these four limonoid compounds can block the ACE2 receptor. To this end, their physicochemical properties were predicted using Lipinski's "rule of five" on the SwissADME website, and their toxicity was assessed using the online tools ProTox and pkCSM. Additionally, their interactions with the ACE2 receptor were predicted via molecular docking using Autodock Vina. All the four compounds satisfied the "rule of five" and tetradecanoic acid was predicted to have a higher affinity than the comparison compound remdesivir and the original ligand of ACE2. Molecular docking results suggested that the compounds from hanjeli essential oil interact with the active site of the ACE2 receptor similarly as the original ligand and remdesivir. In conclusion, hanjeli essential oil contains compounds predicted hinder the interaction of SARS-CoV-2 with the ACE2 receptor. Accordingly, our data may facilitate the development of a phytomedical strategy against SARS-CoV-2 infection.

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Molecular docking identification for the efficacy of some zinc complexes with chloroquine and hydroxychloroquine against main protease of COVID-19

Cited by 50 publications

References 32 publications

Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline

Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline

Inhibitory efficacy of 2, 4-diacetylphloroglucinol against SARS-COV-2 proteins: in silico study

Potential of Hanjeli (Coix lacryma-jobi) essential oil in preventing SARS-CoV-2 infection via blocking the Angiotensin Converting Enzyme 2 (ACE2) receptor

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