Molecular Docking as a Potential Approach in Repurposing Drugs Against COVID-19: a Systematic Review and Novel Pharmacophore Models

Fadlalla, Mohamed; Ahmed, Mazin; Ali, Musab A. M.; Elshiekh, Abdulrhman A.; Yousef, Bashir A.

doi:10.1007/s40495-022-00285-w

Cited by 20 publications

(16 citation statements)

References 108 publications

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“…It is also thought to have properties that help break up and expel mucus. Many pathological microbial diseases are connected to the involvement of protease in infection of organs such as the mouth, skin, lungs, ears, eyes, nose, and other soft tissues and cavities [ 10 , 11 ]. A virus uses protease to facilitate entry into the host cell and break promising proteins used to pack the new virus particle.…”

Section: Resultsmentioning

confidence: 99%

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Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

et al. 2022

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Natural resources, particularly plants and microbes, are an excellent source of bioactive molecules. Bromelain, a complex enzyme mixture found in pineapples, has numerous pharmacological applications. In a search for therapeutic molecules, we conducted an in silico study on natural phyto-constituent bromelain, targeting pathogenic bacteria and viral proteases. Docking studies revealed that bromelain strongly bound to food-borne bacterial pathogens and SARS-CoV-2 virus targets, with a high binding energy of −9.37 kcal/mol. The binding interaction was mediated by the involvement of hydrogen bonds, and some hydrophobic interactions stabilized the complex and molecular dynamics. Simulation studies also indicated the stable binding between bromelain and SARS-CoV-2 protease as well as with bacterial targets which are essential for DNA and protein synthesis and are required to maintain the integrity of membranous proteins. From this in silico study, it is also concluded that bromelain could be an effective molecule to control foodborne pathogen toxicity and COVID-19. So, eating pineapple during an infection could help to interfere with the pathogen attaching and help prevent the virus from getting into the host cell. Further, research on the bromelain molecule could be helpful for the management of COVID-19 disease as well as other bacterial-mediated diseases. Thus, the antibacterial and anti-SARS-CoV-2 virus inhibitory potentials of bromelain could be helpful in the management of viral infections and subsequent bacterial infections in COVID-19 patients.

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Section: Resultsmentioning

confidence: 99%

“…Docking is a quick and economical method for prioritising or choosing possible drug-like compounds for experimental trials. Thus, docking and simulation studies were conducted to find a preventive and potential therapeutic antiviral and antibacterial agent as soon as possible [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

et al. 2022

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“…Recently, several reviews have focused on drug repurposing strategies applied to the evaluation of existing drugs for treatment of COVID-19 [32,33,[111][112][113][114][115][116][117]. Most of these reviews give an overview of potential molecular drug targets of SARS-CoV-2, the currently available therapeutic approaches for the disease, and drug repurposing as a strategy to identify new drugs.…”

Section: Discussionmentioning

confidence: 99%

“…Computer-aided approaches applied to drug discovery against COVID-19 have mostly employed docking screen, molecular simulation, pharmacophore models, or machine learning-based virtual screens [110]. There are several reviews that summarize the use of machine learning and AI approaches in COVID-19 drug discovery [32,33,[111][112][113][114][115][116][117]. Machine learning-aided molecular docking has been frequently used for virtual screening, involving the following steps: dataset of druglike or approved molecules; crystal structure or homology model of the target; molecular docking programs; compute resources [112,118,119].…”

Section: In Silico Repurposing Strategies To Identify Potential Drugs...mentioning

confidence: 99%

“…Machine learning-aided molecular docking has been frequently used for virtual screening, involving the following steps: dataset of druglike or approved molecules; crystal structure or homology model of the target; molecular docking programs; compute resources [112,118,119]. Several molecules have been identified by docking to fit the binding site of various SARS-CoV-2 proteins essential for viral replication [116].…”

Section: In Silico Repurposing Strategies To Identify Potential Drugs...mentioning

confidence: 99%

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Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates

et al. 2022

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In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) was first identified in the province of Wuhan, China. Since then, there have been over 400 million confirmed cases and 5.8 million deaths by COVID-19 reported worldwide. The urgent need for therapies against SARS-CoV-2 led researchers to use drug repurposing approaches. This strategy allows the reduction in risks, time, and costs associated with drug development. In many cases, a repurposed drug can enter directly to preclinical testing and clinical trials, thus accelerating the whole drug discovery process. In this work, we will give a general overview of the main developments in COVID-19 treatment, focusing on the contribution of the drug repurposing paradigm to find effective drugs against this disease. Finally, we will present our findings using a new drug repurposing strategy that identified 11 compounds that may be potentially effective against COVID-19. To our knowledge, seven of these drugs have never been tested against SARS-CoV-2 and are potential candidates for in vitro and in vivo studies to evaluate their effectiveness in COVID-19 treatment.

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Gut microbial considerations and feasibility of phytochemicals as anti‐COVID prophylaxis: Critical role of bioavailability

Dey

2023

Phytotherapy Research

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Molecular Docking as a Potential Approach in Repurposing Drugs Against COVID-19: a Systematic Review and Novel Pharmacophore Models

Cited by 20 publications

References 108 publications

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates

Gut microbial considerations and feasibility of phytochemicals as anti‐COVID prophylaxis: Critical role of bioavailability

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