scholarly journals Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 554
Author(s):  
Faisal Ahmad ◽  
Aqel Albutti ◽  
Muhammad Hamza Tariq ◽  
Ghufranud Din ◽  
Muhammad Tahir ul Qamar ◽  
...  

Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson–Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds (S)-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study.

2019 ◽  
Vol 16 (6) ◽  
pp. 696-710
Author(s):  
Mahmoud Balbaa ◽  
Doaa Awad ◽  
Ahmad Abd Elaal ◽  
Shimaa Mahsoub ◽  
Mayssaa Moharram ◽  
...  

Background: ,2,3-Triazoles and imidazoles are important five-membered heterocyclic scaffolds due to their extensive biological activities. These products have been an area of growing interest to many researchers around the world because of their enormous pharmaceutical scope. Methods: The in vivo and in vitro enzyme inhibition of some thioglycosides encompassing 1,2,4- triazole N1, N2, and N3 and/or imidazole moieties N4, N5, and N6. The effect on the antioxidant enzymes (superoxide dismutase, glutathione S-transferase, glutathione peroxidase and catalase) was investigated as well as their effect on α-glucosidase and β-glucuronidase. Molecular docking studies were carried out to investigate the mode of the binding interaction of the compounds with α- glucosidase and β -glucuronidase. In addition, quantitative structure-activity relationship (QSAR) investigation was applied to find out the correlation between toxicity and physicochemical properties. Results: The decrease of the antioxidant status was revealed by the in vivo effect of the tested compounds. Furthermore, the in vivo and in vitro inhibitory effects of the tested compounds were clearly pronounced on α-glucosidase, but not β-glucuronidase. The IC50 and Ki values revealed that the thioglycoside - based 1,2,4-triazole N3 possesses a high inhibitory action. In addition, the in vitro studies demonstrated that the whole tested 1,2,4-triazole are potent inhibitors with a Ki magnitude of 10-6 and exhibited a competitive type inhibition. On the other hand, the thioglycosides - based imidazole ring showed an antioxidant activity and exerted a slight in vivo stimulation of α-glucosidase and β- glucuronidase. Molecular docking proved that the compounds exhibited binding affinity with the active sites of α -glucosidase and β-glucuronidase (docking score ranged from -2.320 to -4.370 kcal/mol). Furthermore, QSAR study revealed that the HBD and RB were found to have an overall significant correlation with the toxicity. Conclusion: These data suggest that the inhibition of α-glucosidase is accompanied by an oxidative stress action.


Author(s):  
Jéssica Nogueira ◽  
Flávia Verza ◽  
Felipe Nishimura ◽  
Umashankar Das ◽  
Ícaro Caruso ◽  
...  

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the etiologic agent of the current pandemic of corona virus disease 2019 (COVID-19) that has inflicted the loss of thousands of lives worldwide. The coronavirus surface spike (S) glycoprotein is a class I fusion with a S1 domain which is attached to the human angiotensin converting enzyme 2 (ACE2) receptor, and a S2 domain which enables fusion with the host cell membrane and internalization of the virus. Curcumin has been suggested as a potential drug to control inflammation and as a potential inhibitor of S protein, but its therapeutic effects are hampered by poor bioavailability. We performed a molecular docking and dynamic study using 94 curcumin analogues designed to have improved metabolic stability against the SARS-CoV-2 spike protein and compared their affinity with curcumin and other potential inhibitors. The docking analysis suggested that the S2 domain is the main target of these compounds and compound 2606 displayed a higher binding affinity (-9.6 kcal mol-1) than curcumin (-6.8 kcal mol-1) and the Food and Drug Administration (FDA) approved drug hydroxychloroquine (-6.3 kcal mol-1). Further additional validation in vitro and in vivo of these compounds against SARS-CoV-2 may provide insights into the development of a drug that prevents virus entry into host cells.


2021 ◽  
Author(s):  
Shalini Saxena ◽  
Kranti Meher ◽  
Madhuri Rotella ◽  
Subhramanyam Vangala ◽  
Satish Chandran ◽  
...  

Since 2019 the world has seen severe onslaught of SARS-CoV-2 viral pandemic. There is an urgent need for drugs that can be used to either prevent or treat the potentially fatal disease COVD-19. To this end, we screened FDA approved antiviral drugs which could be repurposed for COVID-19 through molecular docking approach in the various active sites of receptor binding domain (RBD). The RBD domain of SARS-CoV-2 spike protein is a promising drug target due to its pivotal role in viral-host attachment. Specifically, we focussed on identifying antiviral drugs which could a) block the entry of virus into host cells, b) demonstrate anti-inflammatory and/or anti-thrombogenic properties. Drugs which poses both properties could be useful for prevention and treatment of the disease. While we prioritized a few antiviral drugs based on molecular docking, corroboration with in vitro studies including a new 3D human vascular lung model strongly supported the potential of Homoharringtonine, a drug approved for chronic myeloid leukaemia to be repurposed for COVID-19. This natural product drug not only antagonized the biding of SARS-CoV-2 spike protein RBD binding to human angiotensin receptor 2 (ACE-2) protein but also demonstrated for the first time anti-thrombogenic and anti-leukocyte adhesive properties in a human cell model system. Overall, this work provides an important lead for development of rapid treatment of COVID-19 and also establishes a screening paradigm using molecular modelling and 3D human vascular lung model of disease to identify drugs with multiple desirable properties for prevention and treatment of COVID-19.


2019 ◽  
Vol 9 (4) ◽  
pp. 674-684 ◽  
Author(s):  
Nail Salavatovich Akhmadiev ◽  
Albina Midkhatovna Galimova ◽  
Vnira Rakhimovna Akhmetova ◽  
Veronika Radievna Khairullina ◽  
Rozaliia Akramovna Galimova ◽  
...  

Purpose: In order to investigate mechanisms underlying the hepatoprotective action of S,Spalladaheterocycle,inhibition of cytochromes P450 has been modeled by molecular dockingof four palladaheterocycle stereoisomers to the active sites of an enzymatic oxidase system. Toobtain a deeper insight into biochemical aspects providing a basis for the therapeutic effects offive-membered palladacycles (as mixture of stereoisomers), a number of preclinical trials hasbeen conductedMethods: 2D and 3D structures of palladaheterocycle stereoisomers were obtained viaconverting into SDF files by means of software MarvinSketch. Binding of palladaheterocycle atthe active sites of cytochromes P450 2E1 and P450 2C9 has been studied by molecular dockingusing LeadIT 2.3.2. Hepatoprotective activity of palladaheterocycle at 2.5, 25 and 250 mg/kgdoses has been studied based on a model of acute intoxication by CCl4 using in vivo methods.Results: By molecular docking it was identify amino acid fragments responsible for bindingwith palladacyclic isomers. The tested compound is comparable, in terms of its activity tothe hepatoprotective drug SAM according to the in vivo and in vitro experiments such asanimal survival data, the efficiency of correction of the cytolytic syndrome, the liver excretoryfunction, carbohydrate, protein and lipid metabolism, and the correction efficiency of the liverantitoxic function (the latter has been determined based on the results of a hexobarbital controlexperiment).Conclusion: Taking into account results obtained in vivo, in vitro and in silico, it can be concludedthat the five-membered S,S-palladaheterocycle effectively protect the liver against acute damagecaused by CCl4, via activation of catalase and glucuronyltransferase, as well as via inhibition ofthe oxidative stress enzymes.<br />


2021 ◽  
Vol 49 (9) ◽  
pp. 030006052110443
Author(s):  
İrem İnanç ◽  
Esra Erdemli

Coronavirus disease 2019 (COVID-19) following infection by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global pandemic that is still having serious effects worldwide. This virus, which targets the lungs in particular, can also damage other tissues. Angiotensin converting enzyme 2 (ACE-2) plays a key role in viral entry into host cells. The presence of ACE-2 in various tissues may permit viral infection. Studies of COVID-19 often make use of postmortem tissues. Although this information provides various useful results, it is also necessary to conduct in vitro studies to understand optimal treatment approaches. Because the virus may show species-specific differences, in vitro technologies using human cells are particularly important. Organoid technologies, three-dimensional structures that can be obtained from human cells, are playing increasingly important roles in studies of SARS-CoV-2. This technology offers a significant advantage in terms of mimicking in vivo tissue structures and testing antiviral compounds. In this mini-review, we summarize studies of SARS-CoV-2 using both histopathological and organoid technology approaches.


Molecules ◽  
2020 ◽  
Vol 25 (10) ◽  
pp. 2271 ◽  
Author(s):  
Noor Rahman ◽  
Zarrin Basharat ◽  
Muhammad Yousuf ◽  
Giuseppe Castaldo ◽  
Luca Rastrelli ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused about 2 million infections and is responsible for more than 100,000 deaths worldwide. To date, there is no specific drug registered to combat the disease it causes, named coronavirus disease 2019 (COVID-19). In the current study, we used an in silico approach to screen natural compounds to find potent inhibitors of the host enzyme transmembrane protease serine 2 (TMPRSS2). This enzyme facilitates viral particle entry into host cells, and its inhibition blocks virus fusion with angiotensin-converting enzyme 2 (ACE2). This, in turn, restricts SARS-CoV-2 pathogenesis. A three-dimensional structure of TMPRSS2 was built using SWISS-MODEL and validated by RAMPAGE. The natural compounds library Natural Product Activity and Species Source (NPASS), containing 30,927 compounds, was screened against the target protein. Two techniques were used in the Molecular Operating Environment (MOE) for this purpose, i.e., a ligand-based pharmacophore approach and a molecular docking-based screening. In total, 2140 compounds with pharmacophoric features were retained using the first approach. Using the second approach, 85 compounds with molecular docking comparable to or greater than that of the standard inhibitor (camostat mesylate) were identified. The top 12 compounds with the most favorable structural features were studied for physicochemical and ADMET (absorption, distribution, metabolism, excretion, toxicity) properties. The low-molecular-weight compound NPC306344 showed significant interaction with the active site residues of TMPRSS2, with a binding energy score of −14.69. Further in vitro and in vivo validation is needed to study and develop an anti-COVID-19 drug based on the structures of the most promising compounds identified in this study.


2020 ◽  
Vol 8 ◽  
Author(s):  
Abdul Sadiq ◽  
Umer Rashid ◽  
Sadiq Ahmad ◽  
Mohammad Zahoor ◽  
Mohamed F. AlAjmi ◽  
...  

Natural-based drugs are believed to be safe, effective and economical. Based on the medicinal importance of the genus Eryngium and unexplored nature of Eryngium caeruleum, we have evaluated its antidiabetic and antioxidant potentials. Both in-vitro and in-vivo assays have been carried out for antidiabetic assays. The antioxidant activity was determined by using different free radicals [i.e., 1,1-diphenyl,2-picrylhydrazyl (DPPH), 2,2-azinobis[3-ethylbenzthiazoline]-6-sulfonic acid (ABTS), and hydrogen peroxide (H2O2)]. Moreover, different phytoconstituents were identified in the most active solvent fraction by GC-MS analysis. Furthermore, comparative fingerprints of methanolic extract and chloroform fraction were also analyzed via High Performance Liquid Chromatography coupled with Diode Array Detector (HPLC-DAD). The crude methanolic extract of E. caeruleum (Ec.Cr) and its sub-fractions [i.e., n-hexane (Ec.Hex), chloroform (Ec.Chf), ethyl acetate (Ec.EtAc), and aqueous (Ec.Aq) were employed in this study]. In the α-glucosidase inhibition assay, a concentration-dependent inhibitory response was observed against the enzyme. The most active sample was Ec.Chf which revealed an IC50 of 437 μg/ml in comparison to the standard acarbose (IC50 25 μg/ml). The rest of the samples showed moderate inhibition of α-glucosidase. In antioxidant assays, Ec.Chf and Ec.Cr exhibited a considerable scavenging effect against all the free radicals. The IC50 values recorded for Ec.Chf were 112, 109, and 150 μg/ml against DPPH, ABTS, and H2O2 respectively. Based on the in-vitro potential of Ec.Chf, this was subjected to the in-vivo model experiment. The Ec.Chf lowered the blood glucose level up to 10.3 mmol/L at 500 μg/Kg. The Ec.Chf was also subjected to GC-MS analysis. The GC-MS analysis confirmed the presence of 60 compounds. The identified phytoconstituents consist of some essential compounds previously reported with antidiabetic and antioxidant studies, which include thymol, tocopherol, phytol, nerolidol, (I)-neophytadiene, linolenic acid, and falcarinol. Similarly, the HPLC-DAD chromatograms of Ec.Cr and Ec.Chf exhibited a variety of peaks, which further demonstrates the possibility of important phytochemicals. In a nutshell, we can conclude that Eryngium caeruleum is a potential source of bioactive compounds which may be beneficial for the management of ailments like diabetes and free radicals mediated disorders. Molecular docking was performed to explore the possible role of all the identified bioactive compounds in the chloroform fraction of Eryngium caeruleum into active sites of the homology model of α-glucosidase.


2021 ◽  
Vol 11 (2) ◽  
pp. 145-152
Author(s):  
G Suresh Kumar ◽  
R. Manivannan ◽  
B. Nivetha

Molecular docking analysis is routinely used in modern drug research to understand and predict the relationship between a drug molecule and a target protein from a microbe. The entry and replication of pathogens in host cells can be prevented by drugs identified in this way. The coronavirus disease associated with SARS-CoV-2, COVID-19, has become today's most infectious and lethal pandemic disease in the world. Burgeoning in the absence of any particular vaccine or therapeutic agent against SARS-CoV-2.The situation urges the need for appropriate medications to treat patients infected with the virus. Consequently, the study focus on evaluate the therapeutic potential of flavonoids present in Corriandrum sativum seeds that could serve as suitable remedies for COVID19.We analyzed the binding affinity of four flavonoids were screened against Mpro protein of SARS-CoV-2 by PyRx Virtual Screening tool and also results are validated with Lig-Plot Plus. Lopinavir shows binding affinity of -8.3 Kcal/mol and exhibit stable, strong interaction with active site of COVID19 main protease. Besides flavonoids, Rutin found to have the highest binding affinity compared to Lopinavir with the Mpro protease, followed by Chlorogenic acid, Quercetin and Caffeic acid. The present study concludes that Rutin present in the integrant of seeds shows the highest potentiality for acting as in inhibitor of main protease enzyme. Further, characterization of the amino acid residues comprising the viral binding site and the nature of the hydrogen bonding involved in the ligand receptor interaction shows significant findings with Rutin binding to the MPro protein at  amino acid. The amino acid acid present in active sites of Mpro protease responsible for virus pathogenicity. The findings of the present study need in vivo experiments to prove the utility of Rutin compounds and further use in making Corriandrum sativum seeds as anti-SARS-CoV-2 product in near future. Keywords: Corriandrum sativum seeds,Novel Coronavirus, SARS-CoV2, COVID-19, Protease, Molecular Docking.


2021 ◽  
Vol 10 (16) ◽  
pp. e69101623220
Author(s):  
Marcos Túlio da Silva ◽  
Matheus Gabriel de Oliveira ◽  
José Realino de Paula ◽  
Vinicius Barreto da Silva ◽  
Kidney de Oliveira Gomes Neves ◽  
...  

Objective: To quantify the quassinoids of P. sprucei, a medicinal plant that is native to the Amazon region, using qNMR and investigate the inhibitory potential of isobrucein B and neosergeolide on the 3CLpro and RdRp targets of SARS-CoV-2 through in silico approaches. Methods: the quantification was performed in a fraction (F2-F3) enriched with the quassinoids isobrucein B and neosergeolide using the PULCON method. In silico assays were performed using molecular docking to assess interactions and binding affinity between neosergeolide and isobrucein B ligands with SARS-CoV-2 3CLpro and RdRp targets, and online servers were used to estimate pharmacokinetic and toxicity. Results: It was possible to determine the quantity of the two quassinoids isobrucein B and neosergeolide in the F2-F3 fraction (769.6 mg), which were present in significant amounts in the PsMeOH extract (5.46%). The results of the docking analysis, based on the crystallized structures of RdRp and 3CLpro, indicated that isobrucein B and neosergeolide are potential inhibitors of the two proteins evaluated, as well as showing the importance of hydrogen bonding and pi (π) interactions for the active sites foreseen for each target. Conclusion: The results suggest that P. sprucei quassinoids may interact with 3CLpro and RdRp targets. In vitro and in vivo experiments are needed to confirm the results of molecular docking and investigate the risks of using P. sprucei as a medicinal plant against COVID-19.


Author(s):  
Junjian Li ◽  
Lianbao Ye ◽  
Yuanyuan Wang ◽  
Ying Liu ◽  
Xiaobao Jin ◽  
...  

Background: Spirocyclic indoline compounds widely exist in numerous natural products with good biological activities and some drug molecules in many aspects. In recent years, it has attracted extensive attention as potent anti-tumor agents in the fields of pharmacology and chemistry. Objective: In this study, we focused on designing and synthesizing a set of novel 1'-H-spiro[indole-3,4'-piperidine] derivatives, which were evaluated by preliminary bioactivity experiment in vitro and molecular docking. Method: The key intermediate 1'-methylspiro[indoline-3,4'-piperidine] (B4) reacted with benzenesulfonyl chloride with different substituents under alkaline condition to obtain its sulfonyl derivatives (B5-B10). We evaluated their antiproliferative activities against A549, BEL-7402 and HeLa cells by MTT assay. We performed the CDOCKER module in Discovery Studio 2.5.5 software for molecular modeling of compound B5, and investigated the binding of compound B5 with the target proteins from PDB database. Results: The results indicated that compounds B4-B10 exhibited good antiproliferative activities against the above three types of cells, in which compound B5 with chloride atom as electron-withdrawing substituent on a phenyl ring showed the highest potency against BEL-7402 cells (IC50=30.03±0.43 μg/mL). By binging of the prominent bioactive compound B5 to CDK, c-Met, EGFR protein crystals, The binding energy of B5 with these three types receptors are -44.3583 kcal/mol, - 38.3292 kcal/mol, -33.3653 kcal/mol respectively. Conclusion: Six 1'-methylspiro[indoline-3,4'-piperidine] derivatives were synthesized and evaluated against BEL-7402, A- 549, HeLa cell lines. Compound B5 showed significant inhibition on BEL-7402 cell lines. Molecular docking revealed that B5 showed good affinity by the good fitting between B5 and these three targets with amino acid residues in active sites which encourage us to conduct further evaluation such as the kinase experiment.


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