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A Phytochemical-Based Medication Search for the SARS-Cov-2

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A Phytochemical-Based Medication Search for the SARS-Cov-2 RSC Advances View Article Online PAPER View Journal | View Issue A phytochemical-based medication search for the SARS-CoV-2 infection by molecular docking Cite this: RSC Adv.,2021,11, 12003 models towards spike glycoproteins and main proteases† Anju Choorakottayil Pushkaran,a Prajeesh Nath EN,b Anu R. Melge,a Rammanohar Puthiyedath b and C. Gopi Mohan *a Identifying best bioactive phytochemicals from different medicinal plants using molecular docking techniques demonstrates a potential pre-clinical compound discovery against SARS-CoV-2 viral infection. The in silico screening of bioactive phytochemicals with the two druggable targets of SARS- CoV-2 by simple precision/extra precision molecular docking methods was used to compute binding affinity at its active sites. phyllaemblicin and cinnamtannin class of phytocompounds showed a better binding affinity range (À9.0 to À8.0 kcal molÀ1) towards both these SARS-CoV-2 targets; the Creative Commons Attribution-NonCommercial 3.0 Unported Licence. corresponding active site residues in the spike protein were predicted as: Y453, Q496, Q498, N501, Y449, Q493, G496, T500, Y505, L455, Q493, and K417; and Mpro: Q189, H164, H163, P168, H41, L167, Q192, M165, C145, Y54, M49, and Q189. Molecular dynamics simulation further established the structural and energetic stability of protein–phytocompound complexes and their interactions with their key residues supporting the molecular docking analysis. Protein–protein docking using ZDOCK and Prodigy server predicted the binding pose and affinity (À13.8 kcal molÀ1) of the spike glycoprotein towards the human ACE2 enzyme and also showed significant structural variations in the ACE2 recognition site upon Received 12th December 2020 the binding of phyllaemblicin C compound at their binding interface. The phyllaemblicin and Accepted 6th March 2021 pro This article is licensed under a cinnamtannin class of phytochemicals can be potential inhibitors of both the spike and M proteins of DOI: 10.1039/d0ra10458b SARS-CoV-2; furthermore, its pharmacology and clinical optimization would lead towards novel COVID- rsc.li/rsc-advances 19 small-molecule therapy. Open Access Article. Published on 24 March 2021. Downloaded 9/25/2021 11:42:33 PM. Introduction than 43 million people were infected globally with a mortality rate of 4%. Different neurological symptoms and respiratory The severe acute respiratory syndrome coronavirus 2 (SARS- manifestations associated with COVID-19 patients were CoV-2) infection commonly referred to as novel coronavirus revealed. The most prevalent symptom is the severe acute disease 2019 (COVID-19) has been declared pandemic by the respiratory complication leading to ventilator support; other World Health Organization. This contagious viral infection neurological signs include headache, fever, nausea, pneu- around the world reminds us the vulnerability of the human monia, loss of smell, unconsciousness, ataxia, epilepsy, race towards this invisible enemy. Different zoonotic viral neuralgia, and cerebrovascular and musculoskeletal disease.2,3 diseases that emerged earlier including SARS, Ebola, and In some patients, this viral infection causes acute encephalop- Middle East respiratory syndrome were highly infectious and athy and acute hemorrhagic necrotizing encephalopathy, which resulted in millions of death.1 However, these viruses are might lead to blood–brain barrier breakdown.4 successfully contained without causing a global pandemic. In The bioactive phytochemical compounds are well known in contrast, the present COVID-19 is highly contagious and more pharmaceutical industries for developing treatment towards different health conditions such as inammation, cancer, and infectious diseases. Phytochemicals isolated from various a Computational Biology and Bioinformatics Lab, Center for Nanosciences and natural sources have gained great interest in the development of Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi 682041, Kerala, India. E-mail: [email protected]; [email protected]; [email protected]; anti-viral treatment for chikungunya, HIV, in uenza, dengue, 5 [email protected]; Tel: +91-484-4001234 ext. 8769 and SARS. Since the outbreak of SARS-CoV-1 in 2003, several bAmrita School of Ayurveda, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, phytochemicals from ora and fauna were tested for their anti- India. E-mail: [email protected]; [email protected] viral activity, which include alkaloids, avones, avonols, fatty † Electronic supplementary information (ESI) available. See DOI: acids, tannins and terpenes. Jo et al.6 reported key 10.1039/d0ra10458b © 2021 The Author(s). Published by the Royal Society of Chemistry RSC Adv.,2021,11,12003–12014 | 12003 View Article Online RSC Advances Paper pharmacophoric chemical features such as hydrophobic inhibiting the two key SARS-CoV-2 druggable targets and to groups, electron donors (hydroxyl) and carbohydrate moieties further understand its molecular mechanism of inhibition. for anti-SARS-CoV-1 infection apart from lipophilic and hydro- These include (i) Phyllanthus emblica (Amalaki), (ii) Cinnamo- philic groups seen in other anti-viral drugs. Furthermore, mum zeylanica (Tvak), (iii) Embelia ribes (Vidanga), (iv) Curcuma different computational and in vitro studies have been recently longa (Haridra) and (v) Justicia adhatoda (Vasa) herbs which are reported, which demonstrated the anti-viral properties of well documented in classical Ayurvedic texts. Out of these ve bioactive phytochemicals from medicinally important plant herbs, P. emblica is ascribed with immunomodulatory sources such as green tea, turmeric, gooseberry, and basil (rasayana) and anti-ageing (vayasthapana) properties,32 C. zey- against SARS-CoV-2.7–9 It is to be noted at this juncture that the lanica is indicated for the management of oropharyngeal development of bioactive natural products is more desirable (kantharuk) and respiratory afflictions (kasa).33 E. ribes34 and C. than specic vaccine design for this new virus despite heavy Longa35 are attributed with microbicidal activity (krimighna). J. experimental measurements involving extraction, chemical adhatoda is specically indicated in the management of respi- complexity and diversity of natural compounds. ratory illnesses (kasa and svasa).36 In addition, the present Different studies are in progress with the aim of developing computational modeling revealed for the rst time the struc- an effective therapeutic for the treatment of COVID-19 and its ture–function relationships of key phytochemicals in blocking spike receptor binding domain (RBD) mutants and other target the human ACE-2 receptor recognition site towards the binding mutants.10,11 Among them, structure-based drug design is of the SARS-CoV-2 spike protein. playing an important role to understand the molecular mech- anism of interaction at the atomic level of SARS-CoV-2 drug- gable proteins with the host cell receptor for the discovery of Materials and methods clinically efficacious drugs.12–17 Furthermore, a computational COVID-19 protein target selection strategy can be employed to identify bioactive compounds from The two important molecular targets of novel SARS-CoV-2 pro Creative Commons Attribution-NonCommercial 3.0 Unported Licence. natural sources by a virtual screening technique in order to contributing to its virulence are the spike protein and M . shorten the time period required for anti-viral drug The X-ray crystallographic coordinate of the RBD domain of the 6,18,19 discovery. Therefore, this technique has become the main spike protein in complex with human cell receptor ACE2 with strategy for the scienti c community for developing novel a resolution of 2.45 A was retrieved from PDB having an 20,21 inhibitors. For example, Ngo et al., used a database of accession code ‘6M0J’.26 Initially, the crystal structure was natural products to identify putative drug candidates targeting optimized using the Protein Preparation Wizard module of the SARS-CoV-2. Moreover, in silico drug repurposing techniques for Schrodinger¨ soware. The ACE2 protein and the water mole- the identi cation of SARS-CoV-2 inhibitors have been re- cules were removed from this complex structure. Furthermore, 22,23 ported. This is possible due to the powerful atomic scale the RBD of the SARS-CoV-2 spike protein structure was pre- This article is licensed under a ff view of the three-dimensional (3D) structure of di erent drug- processed by adding hydrogen atoms, removing the alternate gable proteins solved for SARS-CoV-2 by X-ray crystallography, conformations of the amino acids and also adding the missing NMR and cryo-EM techniques. At present, 330 structures atoms. The geometry of the pre-processed structure is opti- Open Access Article. Published on 24 March 2021. Downloaded 9/25/2021 11:42:33 PM. account for SARS-CoV-2 druggable targets in protein data bank mized followed by energy minimization by employing (PDB), which includes non-structural and structural OPLS2005 force eld. Similarly, the X-ray crystal structure of 24–29 proteins, and all are freely available to the scienti c Mpro of SARS-CoV-2 (PDB code – 6LU7)24 was optimized with the community. same protocol as mentioned above. Finally, these two key Recently, many types of SARS-CoV-2 vaccine candidates have druggable targets of SARS-CoV-2 were used for molecular ff been reported, some of which are reported to be highly e ective docking studies to understand the molecular mechanism of 30,31 for the management of COVID-19. However, the long-term
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