Docking-based virtual screening and identification of potential COVID-19 main protease inhibitors from brown algae

Rashid, Umer; Khalil, Anees Ahmed; Khan, Shahid Ali; Anwar, Sirajudheen; Alafnan, Ahmed; Alamri, Abdulhakeem S.; Rengasamy, Kannan R.R.

doi:10.1016/j.sajb.2021.06.033

Cited by 11 publications

(3 citation statements)

References 35 publications

(33 reference statements)

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“…The docking results of 7,2′'-Bieckol and SARS-CoV-2 Main protease showed the lowest binding energy (-10.78 kcal/mol) compared with standard drugs Lopinavir (-9.23 kcal/mol) and Remdesivir (-9.00 kcal/mol) using MOE 2016.0802. This protein ligand complex showed four H-bond formations (THR24, THR26, GLY143 AND GLU189), and the drug compound is mainly involved in Domain -I and Domain -II [34]. Similarly, Hymenidin docked complex also displayed the four H-bond interactions in Domain -II and Domain -III.…”

Section: Sars-cov-2 Mainmentioning

confidence: 92%

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Murugesan¹,

Ragavendran²,

Almasi‐Hashiani³

et al. 2022

Preprint

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have triggered a recent pandemic of respiratory disease and affected almost every country all over the world. A large amount of natural bioactive compounds is under clinical investigation for various diseas-es. Especially, marine natural compounds are gaining more attention in the new drug develop-ment process. The present study has aimed to identify potential marine-derived inhibitors against the target proteins of COVID-19 using a computational approach. Currently, 16 marine clinical-level compounds were selected for computational screening against the four SARS-CoV-2 main proteases. Computational screening resulted from the best drug candidates for each target based on the binding affinity scores and amino acid interactions. Among these, five marine-derived compounds namely Chrysophaentin A (-6.6 kcal/mol), Geodisterol sulfates (-6.6 kcal/mol), Hymenidin (-6.4 kcal/mol), Plinabulin (-6.4 kcal/mol) and Tetrodotoxin (-6.3 kcal/mol) expressed the minimized binding energy and molecular interactions such as covalent and hydrophobic interactions to the SARS CoV-2 Main Protease. Using Molecular dynamic stud-ies, the Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (ROG), and Hydrogen bonds (H-Bonds) values were calculated for SARS-CoV-2 Main Protease with Hymenidin docked complex. Additionally, in silico Druglikeness and pharmaco-kinetic property assessments of the compounds demonstrated favorable druggability. These re-sults suggested that marine natural compounds are capable of fighting SARS-CoV-2. Further, in vitro and in vivo studies need to be carried out to confirm their inhibitory potential.

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Section: Sars-cov-2 Mainmentioning

confidence: 92%

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Murugesan¹,

Ragavendran²,

Almasi‐Hashiani³

et al. 2022

Preprint

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“…The interactions between the top seven chemicals (7,2"-bieckol 98, 7hydroxyeckol-hepta-acetate 99, 5-hydroxy-cystofurano-quinol 100, sargaquinoic acid 101, triacetoxy-18-hydroxy-2,7-dolabelladiene 102, fallahydroquinone 103, and methoxybifurcarenone 104 (Figure 8)) and the active site of the M pro were investigated in more detail. Compound 98 displayed the lowest binding energy (high binding affinity) among all the compounds under investigation [96] (Table 2). Out of 10 active compounds found in Aloe vera, ferolide (68) (Figure 7) was demonstrated as the most potent compound against a viral protein, i.e., 3CL pro , an enzyme that plays a key role in post-translational protein regulation, particularly the cleavage of viral polyproteins into functional protein units.…”

Section: Hydrophobic and Other Interactionsmentioning

confidence: 99%

A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

et al. 2023

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The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2—the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins—were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.

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“…In addition, inhibitory action on ACE2 receptor binding of SARS-CoV-2 in the host cells and anti-inflammatory activities of seaweed extracts may also be explored in the treatment of COVID-19, which is marked by a severe hyperinflammatory response that plays a key role in the severity of infection and prognosis of the disease. Both of red algae and brown algae could be potential antiviral therapeutic agents against SARS-CoV-2 and can be used to reduce the deleterious consequences of SARS-CoV-2 infection (Pereira and Critchley 2020 ; Rauf et al 2021 ). Dietary seaweeds and their derivatives can effectively inhibit SARS-CoV-2 entry and may provide protection against COVID-19 through different mechanisms in humans and hypothetically could render protection in animals too, for which purpose further investigation and clinical trials are required to conclude their efficacy (Li et al 2020 ; Tamama 2021 ; Kuznetsova et al 2021 ; Yim et al 2021 ).…”

Section: The Effect Of Seaweed Antioxidants On Animal Health and Prod...mentioning

confidence: 99%

Antioxidant effects of seaweeds and their active compounds on animal health and production – a review

Michalak

Tiwari

Dhawan

et al. 2022

Veterinary Quarterly

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Natural antioxidants applied as feed additives can improve not only animals’ health and overall performance but also increase their resistance to environmental stress such as heat stress, bad housing conditions, diseases, etc. Marine organisms, for example seaweeds – red, brown, and green macroalgae contain a plethora of biologically active substances, including phenolic compounds, polysaccharides, pigments, vitamins, micro- and macroelements, and proteins known for their antioxidant activity, which can help in the maintenance of appropriate redox status in animals and show pleiotropic effects for enhancing good health, and productivity. The dysregulated production of free radicals is a marked characteristic of several clinical conditions, and antioxidant machinery plays a pivotal role in scavenging the excessive free radicals, thereby preventing and treating infections in animals. Supplementation of seaweeds to animal diet can boost antioxidant activity, immunity, and the gut environment. Dietary supplementation of seaweeds can also enhance meat quality due to the deposition of marine-derived antioxidant components in muscles. The use of natural antioxidants in the meat industry is a practical approach to minimize or prevent lipid oxidation. However, overconsumption of seaweeds, especially brown macroalgae, should be avoided because of their high iodine content. An important point to consider when including seaweeds in animal feed is their variable composition which depends on the species, habitat, location, harvest time, growing conditions such as nutrient concentration in water, light intensity, temperature, etc. This review highlights the beneficial applications of seaweeds and their extracted compounds, which have antioxidant properties as feed additives and impact animal health and production.

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Docking-based virtual screening and identification of potential COVID-19 main protease inhibitors from brown algae

Cited by 11 publications

References 35 publications

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

Antioxidant effects of seaweeds and their active compounds on animal health and production – a review

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