A review on computer‐aided chemogenomics and drug repositioning for rational<scp>COVID</scp>‐19 drug discovery

Maghsoudi, Saeid; Shahraki, Bahareh Taghavi; Rameh, Fatemeh; Nazarabi, Masoomeh; Fatahi, Yousef; Akhavan, Omid; Rabiee, Mohammad; Mostafavi, Ebrahim; Lima, Éder C.; Saeb, Mohammad Reza; Rabiee, Navid

doi:10.1111/cbdd.14136

Cited by 29 publications

(14 citation statements)

References 163 publications

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“…But molecular docking as well as no dynamic study has been yet reported so far for 25-hydroxy vitamin D against SARS-CoV-2. Since SARS-CoV-1 and SARS-CoV-2 have very similar binding modes to human ACE2, 25-hydroxy vitamin D may have antiviral effects against both of these CoVs as well as any future CoVs that originate from animal reservoirs to infect humans [ 85 ]. Further in-vitro and in-vivo research into this connection is warranted [ 86 , 87 ].…”

Section: Discussionmentioning

confidence: 99%

The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein

Joseph

Suresh

Mahapatra³

et al. 2022

Nutrients

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The environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy vitamin D consumption, even though there is no scientific data to prove that one would not affect the COVID-19 viral infection by 25-hydroxy vitamin D consumption. In this regard, the present study investigates the important literature and the role of 25-hydroxy vitamin D to prevent COVID-19 infection by conducting an in-silico study with SARS-CoV-2 spike protein as a target. Lopinavir, a previously reported drug candidate, served as a reference standard for the study. MD simulations were carried out to improve predictions of receptor-ligand complexes which offer novelty and strength to the current study. MD simulation protocols were explored and subjected to 25-hydroxy vitamin D and a known drug, Lopinavir. Comparison of ligands at refined models to the crystal structure led to promising results. Appropriate timescale simulations have been used to understand the activation mechanism, the role of water networks for receptor function, and the ligand binding process. Furthermore, MD simulations in combination with free energy calculations have also been carried out for lead optimization, evaluation of ligand binding modes, and assessment of ligand selectivity. From the results, 25-hydroxy vitamin D was discovered to have the vital interaction and highest potency in LBE, lower RMSD, and lower inhibition intensity similar to the standard. The findings from the current study suggested that 25-hydroxy vitamin D would be more effective in treating COVID-19. Compared with Lopinavir, 25-hydroxy vitamin D had the most potent interaction with the putative binding sites of the SARS-CoV-2 spike protein of COVID-19.

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Section: Discussionmentioning

confidence: 99%

The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein

Joseph

Suresh

Mahapatra³

et al. 2022

Nutrients

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“…Recently, SARS-CoV-2 and SARS-CoV viruses hidden in various agricultural products have brought irreversible harm to human health [ 42 ], therefore it is an urgent task to find a simple solution to the identification and treatment of such viruses [ [43] , [44] , [45] , [46] ]. However, this pair of viruses belong to β-Coronavirus family with high genetic similarity.…”

Section: Introductionmentioning

confidence: 99%

Hybridization-driven fluorometric platform based on metal-organic frameworks for the identification of the highly homologous viruses

Yang

Liu

Chen

et al. 2023

Microchemical Journal

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“…to discover, among the ENAMINE compounds database, 7,8-diaminopelargonic acid aminotransferase inhibitors that could inhibit the growth of Mycobacterium tuberculosis strain Mtb H37Ra . During the recent pandemic, the use of in silico methods is one of the drug discovery approaches utilized to address an urgent need to find new drugs against COVID-19 and other diseases like HIV-AIDS and cancer. − Our previous study also employed an in silico method as a preliminary tool to screen 14,000 small molecule inhibitors against glycosylation proteins dysregulated in cancer …”

Section: Introductionmentioning

confidence: 99%

Integrating Computational Methods in Network Pharmacology andIn SilicoScreening to Uncover Multi-targeting Phytochemicals against Aberrant Protein Glycosylation in Lung Cancer

et al. 2023

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Glycoproteins are an underexploited drug target for cancer therapeutics. In this work, we integrated computational methods in network pharmacology and in silico docking approaches to identify phytochemical compounds that could potentially interact with several cancer-associated glycoproteins. We first created a database of phytochemicals from selected plant species, Manilkara zapota (sapodilla/chico), Mangifera indica (mango), Annona muricata (soursop/guyabano), Artocarpus heterophyllus (jackfruit/langka), Lansium domesticum (langsat/lanzones), and Antidesma bunius (bignay), and performed pharmacokinetic analysis to determine their drug-likeness properties. We then constructed a phytochemical–glycoprotein interaction network and characterized the degree of interactions between the phytochemical compounds and with cancer-associated glycoproteins and other glycosylation-related proteins. We found a high degree of interactions from α-pinene (Mangifera indica), cyanomaclurin (Artocarpus heterophyllus), genistein (Annona muricata), kaempferol (Annona muricata and Antidesma bunius), norartocarpetin (Artocarpus heterophyllus), quercetin (Annona muricata, Antidesma bunius, Manilkara zapota, Mangifera indica), rutin (Annona muricata, Antidesma bunius, Lansium domesticum), and ellagic acid (Antidesma bunius and Mangifera indica). Subsequent docking analysis confirmed that these compounds could potentially bind to EGFR, AKT1, KDR, MMP2, MMP9, ERBB2, IGF1R, MTOR, and HRAS proteins, which are known cancer biomarkers. In vitro cytotoxicity assays of the plant extracts showed that the n-hexane, ethyl acetate, and methanol leaf extracts from A. muricata, L. domesticum and M. indica gave the highest growth inhibitory activity against A549 lung cancer cells. These may help further explain the reported cytotoxic activities of select compounds from these plant species.

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A review on computer‐aided chemogenomics and drug repositioning for rationalCOVID‐19 drug discovery

Cited by 29 publications

References 163 publications

The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein

The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein

Hybridization-driven fluorometric platform based on metal-organic frameworks for the identification of the highly homologous viruses

Integrating Computational Methods in Network Pharmacology andIn SilicoScreening to Uncover Multi-targeting Phytochemicals against Aberrant Protein Glycosylation in Lung Cancer

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