Genomics approaches to synthesize plant-based biomolecules for therapeutic applications to combat SARS-CoV-2

Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Manoj; Prasad, Manoj

doi:10.1016/j.ygeno.2020.07.033

Cited by 17 publications

(11 citation statements)

References 108 publications

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“…To date, several bioactive phytocomponents such as tannins, biflavonoids, and phenols from different parts of R. succedanea have been extracted, characterized and analyzed for anti-viral activity (Chen & Lin, 1975 , 1976 ; Fa-Ching et al., 1974 ; Khan et al., 2020 ). Information on the molecular structure of biflavonoids offers a chance to explore and identify promising pharmacological activity against SARS-CoV-2 (Sharma et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach

Lokhande

Nawani

Venkateswara

et al. 2020

Journal of Biomolecular Structure and Dynamics

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The recent outbreak of SARS-CoV-2 has quickly become a worldwide pandemic and generated panic threats for both the human population and the global economy. The unavailability of effective vaccines or drugs has enforced researchers to hunt for a potential drug to combat this virus. Plant-derived phytocompounds are of applicable interest in the search for novel drugs. Bioflavonoids from Rhus succedanea are already reported to exert antiviral activity against RNA viruses. SARS-CoV-2 Mpro protease plays a vital role in viral replication and therefore can be considered as a promising target for drug development. A computational approach has been employed to search for promising potent bioflavonoids from Rhus succedanea against SARS-CoV-2 Mpro protease. Binding affinities and binding modes between the biflavonoids and Mpro enzyme suggest that all six biflavonoids exhibit possible interaction with the Mpro catalytic site (−19.47 to −27.04 kcal/mol). However, Amentoflavone (−27.04 kcal/mol) and Agathisflavone (−25.87 kcal/mol) interact strongly with the catalytic residues. Molecular dynamic simulations (100 ns) further revealed that these two biflavonoids complexes with the Mpro enzyme are highly stable and are of less conformational fluctuations. Also, the hydrophobic and hydrophilic surface mapping on the Mpro structure as well as biflavonoids were utilized for the further lead optimization process. Altogether, our findings showed that these natural biflavonoids can be utilized as promising SARS-CoV-2 Mpro inhibitors and thus, the computational approach provides an initial footstep towards experimental studies in in vitro and in vivo , which is necessary for the therapeutic development of novel and safe drugs to control SARS-CoV-2. Communicated by Ramaswamy H. Sarma Research highlights Rhus succedanea biflavonoids have antiviral activity. The molecular interactions and molecular dynamics displayed that all six biflavonoids bound with a good affinity to the same catalytic site of Mpro. The compound Amentoflavone has a strong binding affinity (−27.0441 kcal/mol) towards Mpro. The binding site properties of SARS-CoV-2-Mpro can be utilized in a novel discovery and lead optimization of the SARS-CoV-2-Mpro inhibitor.

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Section: Introductionmentioning

confidence: 99%

Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach

Lokhande

Nawani

Venkateswara

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…In the form of a Quadruple Helix innovation system [25][26][27], the ongoing development pathway for an effective COVID-19 vaccine is seeing the full collaboration of not only industry, government and academia, but also a synergy between biotechnology and pharmaceutical companies, to bring forward a variety of innovative vaccine technology platforms [28]. The current global COVID-19 R&D landscape include hundredth of vaccine candidates that rely on a wide range of vaccine technology platforms, including recombinant protein, virus-like particle, nucleic acid, viral vector, peptide, live attenuated and inactivated virus approaches [29][30][31][32][33]. Many vaccine candidates have now moved into clinical trials, including the mRNA-1273 from Moderna, the Ad5-nCoV from CanSino Biologicals, the INO-4800 from Inovio and the pathogen-specific aAPC from the Geno-Immune Medical Institute of Shenzhen [34].…”

Section: Introductionmentioning

confidence: 99%

COVID-19 Vaccine Development in a Quadruple Helix Innovation System: Uncovering the Preferences of the Fourth Helix in the UAE

Niankara

Muqattash

Niankara³

et al. 2020

Journal of Open Innovation: Technology, Market, and Complexity

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Successful development and uptake of vaccine technology in a Quadruple Helix Innovative health or economic system requires a clear understanding of society’s preferences as the fourth helix. With significant financial commitments to find a safe and effective COVID-19 vaccine still ongoing, this study introduces a random utility theoretic behavioral health model to analyze individuals’ prospective demand for the vaccine in the United Arab Emirates (UAE). To this end, we use a cross-sectional sample of stated vaccine preferences data collected online using the snowball method, between 4 July and 4 August 2020, gathering 1109 responses across all seven Emirates of the UAE. We found that in addition to socio-economic and demographic influences, the factors affecting individuals’ preferences for the prospective COVID-19 vaccine in the UAE include those put forth by the WHO’s SAGE group on immunization. Though the estimated indirect cost, in the form of expected marginal utility of time spent to get the vaccine is not statistically significant, the expected marginal utility of every dirham spent to get the vaccine is −1.76 AED and significant, suggesting a significant expected dis-utility from COVID-19 vaccine seeking/payment by the average person. Our findings also highlight significant perceived financial, temporal and spatial barriers to COVID-19 vaccine uptake in the UAE. Therefore, a set of measures are suggested to help mitigate the adverse effects of these three constraints. Our study thus contributes methodologically to the literature on vaccine demand, hesitancy and development. It also contributes to the nascent empirical evidence on the novel coronavirus disease, by providing significant insights for evidence based policy making that should increase the effectiveness of any prospective COVID-19 vaccination program in the UAE.

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“…Herbal plants are supplemented with various phytochemicals like alkaloids, flavonoids, phenolic acids, lignins, and terpenoids. (Sharma N. et al, 2020;Xian et al, 2020).…”

Section: Potential Of Plant-derived Biomolecules For Covid-19mentioning

confidence: 99%

“…(A) Structure of SARS-CoV-2 and available biomolecules. (B) Rich resources of Chinese herbal medicines targeting SARS-CoV-2 ( Sharma N. et al, 2020 ; Xian et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…As the identification of plant-based moieties with anti–SARS-CoV-2 action is in a devolving phase, it will take a long time to explore their full potential using the traditional drug development method. The omics techniques used in plant molecular biology could accelerate this procedure using a strategically planned study design and provide a platform to researchers and the bio-manufacturer of these biomolecules to manage the COVID-19 pandemic ( Sharma N. et al, 2020 ; Chojnacka et al, 2020 ). This article has explored the plant-based compounds that contain antiviral activities to assess the impact of the multi-omics approach for plant biomolecular research and its potential application against SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

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Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

Singh

Kumar

et al. 2021

Front. Pharmacol.

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COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.

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Genomics approaches to synthesize plant-based biomolecules for therapeutic applications to combat SARS-CoV-2

Cited by 17 publications

References 108 publications

Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach

Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach

COVID-19 Vaccine Development in a Quadruple Helix Innovation System: Uncovering the Preferences of the Fourth Helix in the UAE

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

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