In Silico Screening of Natural Products Isolated from Mexican Herbal Medicines against COVID-19

Rivero-Segura, Nadia Alejandra; Gómez-Verján, Juan Carlos

doi:10.3390/biom11020216

Cited by 28 publications

(17 citation statements)

References 47 publications

(55 reference statements)

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“…The docking of astragalin with M pro was repeated with the COVID-19 Docking Server [52], a user-friendly platform realized by Kong et al for docking peptides and antibodies, but also small organic compounds, against some of the main COVID-19-related proteins investigated by implementation of Autodock Vina and CoDockPP [45,[52][53][54][55]. The ligand file in mol2 format was obtained, starting from informative details on astragalin found in Pubchem (https://pubchem.ncbi.nlm.nih.gov, PubChem CID 5282102) and using the online tool available at the link: http://pasilla.health.unm.edu/tomcat/ biocomp/convert.…”

Section: Covid-19 Docking Server Studiesmentioning

confidence: 99%

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

Vicidomini

Roviello

2021

Symmetry

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Opuntia ficus-indica is a cactaceous plant native to America but, nowadays, widely found worldwide, having been the most common domesticated species of cactus grown as a crop plant in semiarid and arid parts of the globe, including several Mediterranean basin countries. Opuntia ficus-indica can be regarded as a medicinal plant, being source of numerous bioactive phytochemicals such as vitamins, polyphenols, and amino acids. The urgent need for therapeutic treatments for the COronaVIrus Disease 19 (COVID-19), caused by the Severe Acute Respiratory Syndrome (SARS)-Coronavirus (CoV)-2, justifies the great attention currently being paid not only to repurposed antiviral drugs, but also to natural products and herbal medications. In this context, the anti-COVID-19 utility of Opuntia ficus-indica as source of potential antiviral drugs was investigated in this work on the basis of the activity of some of its phytochemical constituents. The antiviral potential was evaluated in silico in docking experiments with Mpro, i.e., the main protease of SARS-CoV-2, that is one of the most investigated protein targets of therapeutic strategies for COVID-19. By using two web-based molecular docking programs (1-Click Mcule and COVID-19 Docking Server), we found, for several flavonols and flavonol glucosides isolated from Opuntia ficus-indica, good binding affinities for Mpro, and in particular, binding energies lower than −7.0 kcal/mol were predicted for astragalin, isorhamnetin, isorhamnetin 3-O-glucoside, 3-O-caffeoyl quinic acid, and quercetin 5,4′-dimethyl ether. Among these compounds, the chiral compound astragalin showed in our in silico studies the highest affinity for Mpro (−8.7 kcal/mol) and also a low toxicity profile, emerging, thus, as an interesting protease inhibitor candidate for anti-COVID-19 strategies.

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Section: Covid-19 Docking Server Studiesmentioning

confidence: 99%

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

Vicidomini

Roviello

2021

Symmetry

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“…Another study aiming to identify selective antiviral agents for the management of COVID-19 pathologies has demonstrated a capacity of coumarin-24 to be effectively used against COVID-19 infection [155]. Most importantly, in silico screening of natural products isolated from Mexican Herbal Medicines reveals the ability of coumarin cichoriin to reach an acceptable level in plasma and high lung levels, while these results suggest its potential as a novel therapeutic tool against COVID-19 [156]. Due to the significant potential of coumarins against SARS-CoV-2, Chidambaram et al have recently evaluated the possibility of synthesis of novel coumarin analogues to identify drugs against COVID-19 [157].…”

Section: Coumarinsmentioning

confidence: 99%

“…Notably, traditional herbal medicine such as traditional Chinese medicine, with its main active constituents including to a large extent phenolic compounds, could also exert significant activity against lung damage and associated inflammatory and immunomodulatory deregulations observed in COVID-19 [156,158]. Immune dysfunction is essential for COVID-19 progression; therefore, the administration of phytochemicals or herbal medicines containing certain compounds with antimicrobial, antiviral, anti-inflammatory, and immune-modulatory effects have great potential as effective prophylactic and therapeutic agents against SARS-CoV-2 [159].…”

Section: Traditional Herbal Medicine Rich In Phenolics Protecting Against Sars-cov-2-induced Lung Damagementioning

confidence: 99%

Targeting phytoprotection in the COVID-19-induced lung damage and associated systemic effects—the evidence-based 3PM proposition to mitigate individual risks

et al. 2021

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The risks related to the COVID-19 are multi-faceted including but by far not restricted to the following: direct health risks by poorly understood effects of COVID-19 infection, overloaded capacities of healthcare units, restricted and slowed down care of patients with non-communicable disorders such as cancer, neurologic and cardiovascular pathologies, among others; social risks—restricted and broken social contacts, isolation, professional disruption, explosion of aggression in the society, violence in the familial environment; mental risks—loneliness, helplessness, defenceless, depressions; and economic risks—slowed down industrial productivity, broken delivery chains, unemployment, bankrupted SMEs, inflation, decreased capacity of the state to perform socially important programs and to support socio-economically weak subgroups in the population. Directly or indirectly, the above listed risks will get reflected in a healthcare occupation and workload which is a tremendous long-term challenge for the healthcare capacity and robustness. The article does not pretend to provide solutions for all kind of health risks. However, it aims to present the scientific evidence of great clinical utility for primary, secondary, and tertiary care to protect affected individuals in a cost-effective manner. To this end, due to pronounced antimicrobial, antioxidant, anti-inflammatory, and antiviral properties, naturally occurring plant substances are capable to protect affected individuals against COVID-19-associated life-threatening complications such as lung damage. Furthermore, they can be highly effective, if being applied to secondary and tertiary care of noncommunicable diseases under pandemic condition. Thus, the stratification of patients evaluating specific health conditions such as sleep quality, periodontitis, smoking, chronic inflammation and diseases, metabolic disorders and obesity, vascular dysfunction, and cancers would enable effective managemenet of COVID-19-associated complications in primary, secondary, and tertiary care in the context of predictive, preventive, and personalized medicine (3PM).

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“…Some vaccines, such as those by Pfizer and Moderna, and some drugs, such as remdesivir, have been approved for use in therapy. The efforts by governments, health organizations, and other sectors to stem the alarmingly increasing numbers of deaths and cases were unprecedented [1][2][3][4][5][6]. However, SARS-CoV-2 continues to threaten the world, with over four million deaths and 227 million cases as of 16 September 2021 (https://www.worldometers.info/coronavirus/ accessed on 27 November 2021).…”

Section: Introductionmentioning

confidence: 99%

Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment

Elzupir

2021

Molecules

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This study demonstrates the inhibitory effect of 42 pyrimidonic pharmaceuticals (PPs) on the 3-chymotrypsin-like protease of SARS-CoV-2 (3CLpro) through molecular docking, molecular dynamics simulations, and free binding energies by means of molecular mechanics–Poisson Boltzmann surface area (MM-PBSA) and molecular mechanics–generalized Born surface area (MM-GBSA). Of these tested PPs, 11 drugs approved by the US Food and Drug Administration showed an excellent binding affinity to the catalytic residues of 3CLpro of His41 and Cys145: uracil mustard, cytarabine, floxuridine, trifluridine, stavudine, lamivudine, zalcitabine, telbivudine, tipiracil, citicoline, and uridine triacetate. Their percentage of residues involved in binding at the active sites ranged from 56 to 100, and their binding affinities were in the range from −4.6 ± 0.14 to −7.0 ± 0.19 kcal/mol. The molecular dynamics as determined by a 200 ns simulation run of solvated docked complexes confirmed the stability of PP conformations that bound to the catalytic dyad and the active sites of 3CLpro. The free energy of binding also demonstrates the stability of the PP–3CLpro complexes. Citicoline and uridine triacetate showed free binding energies of −25.53 and −7.07 kcal/mol, respectively. Therefore, I recommend that they be repurposed for the fight against COVID-19, following proper experimental and clinical validation.

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In Silico Screening of Natural Products Isolated from Mexican Herbal Medicines against COVID-19

Cited by 28 publications

References 47 publications

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

Targeting phytoprotection in the COVID-19-induced lung damage and associated systemic effects—the evidence-based 3PM proposition to mitigate individual risks

Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment

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