nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone ofMoringa oleiferaand hydroxychloroquine

Abstract

An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with Moringa oleifera, phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/ mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.

Withanone from Withania somnifera Attenuates SARS-CoV-2 RBD and Host ACE2 Interactions to Rescue Spike Protein Induced Pathologies in Humanized Zebrafish Model

“…Using an in silico peptide binding approach, Hamza et al attempted identifying the SARS-CoV-2 peptides which could be potential targets for the phytochemicals, hydroxychloroquine, kaempferol and anthraquinone from Moringa oleifera . 61 The authors translated the SARS-CoV-2 genome in silico (using EMBOSS TRANSEQ server) into peptides which were then used for binding studies with the above mentioned phytochemicals. The maximum binding energies obtained from AutoDock Vina for hydroxychloroquine is −5.1 kcal/mol, kaempferol is −6.2 kcal/mol, and anthraquinone is −6 kcal/mol, 61 which are again less than those observed in the case of withanone and the ACE2-RBD complex (−9.4 kcal/mol) in this study.…”

“… 61 The authors translated the SARS-CoV-2 genome in silico (using EMBOSS TRANSEQ server) into peptides which were then used for binding studies with the above mentioned phytochemicals. The maximum binding energies obtained from AutoDock Vina for hydroxychloroquine is −5.1 kcal/mol, kaempferol is −6.2 kcal/mol, and anthraquinone is −6 kcal/mol, 61 which are again less than those observed in the case of withanone and the ACE2-RBD complex (−9.4 kcal/mol) in this study. Thus, it is possible that withanone might act specifically during viral–host interaction and not target the host factors, sparing the body from side effects.…”

In silico analysis of quranic and prophetic medicinals plants for the treatment of infectious viral diseases including corona virus

“…A threshold value of binding affinity –8 kcal/mol was set for the screening of the best docked phytochemicals, and best orientations for docking confirmation of ligand-receptor complexes. Docked scors were analyzed for the distinction of good or bad docked conformation ( Hamza et al, 2020 , Chopade et al, 2015 ; Qaddir et al, 2017). The Quranic plants are the best source of beneficent phytochemicals.…”

Medicinal Plants, Phytochemicals, and Herbs to Combat Viral Pathogens Including SARS-CoV-2

“…Ethanolic and aqueous leaf extracts of M. oleiferai have kaempferol and anthraquione. Molecular peptide docking of these compounds in comparison with hydroxychloroquine was done and both the compounds revealed important effects regarding the binding of peptides of SARS-CoV-2 [ 78 ]. An aqueous extract of the Phyllanthus species showed antiviral properties against HSV-1 and HSV-2 [ 38 ].…”