Computational screening of natural compounds from Salvia plebeia R. Br. for inhibition of SARS-CoV-2 main protease

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Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
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Doi: 10.1007/s42535-021-00304-z
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Keywords: Main protease, n Salvia plebeia R. Br., Rutin, Plebeiosides B, ADMET, PASS, Molecular docking, Molecular dynamic simulation


Abstract


The novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has emerged to be the reason behind the COVID-19 pandemic. It was discovered in Wuhan, China and then began spreading around the world, impacting the health of millions. Efforts for treatment have been hampered as there are no antiviral drugs that are effective against this virus. In the present study, we have explored the phytochemical constituents of Salvia plebeia R. Br., in terms of its binding affinity by targeting COVID-19 main protease (Mpro) using computational analysis. Molecular docking analysis was performed using PyRx software. The ADMET and drug-likeness properties of the top 10 compounds showing binding affinity greater than or equal to − 8.0 kcal/mol were analysed using pkCSM and DruLiTo, respectively. Based on the docking studies, it was confirmed that Rutin and Plebeiosides B were the most potent inhibitors of the main protease of SARS-CoV-2 with the best binding affinities of − 9.1 kcal/mol and − 8.9 kcal/mol, respectively. Further, the two compounds were analysed by studying their biological activity using the PASS webserver. Molecular dynamics simulation analysis was performed for the selected protein–ligand complexes to confirm their stability at 300 ns. MM-PBSA provided the basis for analyzing the affinity of the phytochemicals towards Mpro by calculating the binding energy, and secondary structure analysis indicated the stability of protease structure when it is bound to Rutin and Plebeiosides B. Altogether, the study identifies Rutin and Plebeiosides B to be potent Mpro inhibitors of SARS-CoV-2.

Graphic abstract

Introduction

The current coronavirus pandemic, commonly known as COVID-19, is brought about by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) (Gil et al. 2020) and was first reported in Wuhan, China, in December 2019 (Das and Koner 2020). On February 12, 2020, the WHO proceeded to name the disease “coronavirus disease 2019” (COVID-19) and on March 11, 2020, they declared the outbreak a global pandemic. On conducting a whole viral genome evaluation, it was found that 88% of the viral sequence identity was shared with two SARS-like coronaviruses obtained from bats. This led to it being named “SARS coronavirus 2”, primarily based on the taxonomy and phylogeny (Fauci et al. 2020; Ranney et al. 2020). The Coronaviruses (CoVs) are a part of the subfamily Orthocoronavirinae, which belongs to the family Coronaviridae, coming under the order Nidovirales. Orthocoronavirinae has 4 genera within it, that is, Alphacoronavirus (α-CoV), Betacoronavirus (β-CoV), Gammacoronavirus (γ-CoV) and Deltacoronavirus (δ-CoV) (Li et al. 2020). The Coronaviruses are positively stranded RNA, enveloped viruses (Xiu et al. 2020). Mammals have been shown to be affected by α-CoV and β-CoV genera, and on the other hand, birds are known to be affected by γ-CoV and δ-CoV genera (Amin and Jha 2020).

The identification of biochemical events critical to the viral life cycle provides various significant targets to inhibit viral replication. An important process is the breakdown of the multidomain, viral polyprotein into 16 non-structural proteins (nsps). These individual proteins combine to form complexes that carry out the synthesis of viral RNA (Kandeel et al. 2020; Naidoo et al. 2020). Along with these non-structural proteins, the SARS-CoV-2 further possesses four structural proteins, namely the Spike surface glycoprotein, the membrane protein, the envelope protein and the nucleocapsid protein. These are all required for the infection and assembly of the virus (Li et al. 2020). When the virus is inhaled, the spike proteins help it interact with the epithelial cells by binding to the human receptor, ACE2. The virus then proceeds to proliferate and enter into the alveolar epithelial cells. This, in turn, triggers a vigorous immune response leading to cytokine storm syndromes as well as damage to the pulmonary tissue (Li et al. 2020; Mason 2020).

Main protease (Mpro) is an enzyme of great importance to the coronaviruses as it plays a crucial part in the replication of the virus and transcription. This functional significance of Mpro in the life cycle of the virus, along with the lack of any similarly related homologues in humans, has identified it as an attractive target for the development of medication against SARS-CoV-2. The structure of SARS-CoV-2 Mpro complexed with N3 is found in PDB (PDB ID: 6LU7) and it provides a basis to identify potential inhibitors against SARS-CoV-2 Mpro, with the help of virtual screening. From the literature, it can be seen that N3 is a Michael acceptor inhibitor that can inhibit Mpro from a range of coronaviruses like MERS-CoV and SARS-CoV and also displays potent antiviral activity. From the crystal structure of Mpro it was seen that it comprises protomers A and B which associate to form a dimer and each protomer consists of three domains. The residues of the active site of Mpro are conserved and make a catalytic Cys145-His41 dyad. N3 binds in the substrate-binding pocket situated in a cleft in the middle of domain I and domain II. The amino acid residues involved in the specific interactions of N3 with Mpro include Phe140, Cys145, Glu166, Leu4, Val3, Ala2, His172, Leu167, Asn142, His163, Met49, Leu141, His41, Met165, Tyr54, Gln192, Asp187, Phe185, Thr25, Gln189, Thr24 and Pro168 (Jin et al. 2020).

Presently, there is a lack of drugs targeted towards COVID-19 treatment, and effective therapeutic options are scarce (Jin et al. 2020). One of the potential methods of treatment that is currently being looked into by researchers is drug repurposing, which is also referred to as drug reprofiling or drug repositioning, where drugs that were intended as a treatment against other diseases or similar viruses (SARS and MERS) are used as a treatment against COVID-19. While this method substantially decreases the time it would have taken for the development of a new drug, drug repurposing does also pose certain challenges such as the absence of patent protection, establishment of the efficacy, demonstration of its safety and in certain cases the continuous need for risky and expensive trials (Nurton 2020; Pushpakom et al. 2018; Shineman et al. 2014; Talevi and Bellera 2020). Problems faced by synthetic or synthetically derived drugs such as harmful side effects and antibiotic resistance in the case of antibiotics, lead to the shift towards natural remedies. Herbal drug preparations, obtained from biologically active products, have been an important part of traditional medicine. The compounds obtained from natural products are known to be pharmacophores and possess certain properties, such as high stereochemistry and metabolite-likeness that make them ideal as alternative medicines (Marathe and Datey 2012; Harvey et al. 2015; Ngane et al. 2011; Veeresham 2012).

Salvia plebeia R. Br. belongs to the genus Salvia, which is a major genus of the family Lamiaceae (Wang et al. 2019). It is known to be an annual or biennial grass that is generally found in various countries, for example, China, India, Korea and Australia (Liang et al. 2020; Ren et al. 2014). In Traditional Chinese Medicine, it is believed to be used for various home remedies. A folk medicine, Badarangboya, made from S. plebeia, is used extensively in India (Ren et al. 2014). A majority of the traditional and folk medicines prepared from S. plebeia are known to be used for the treatment of the common cold, flu, cough, asthma, hepatitis, diarrhea, haemorrhoids and tumours (Bang et al. 2018; Liang et al. 2020; Ma et al. 2014; Nugroho et al. 2012; Ren et al. 2014; Wang et al. 2019).

The various phytochemical studies performed on S. plebeia unveiled the presence of diterpenoids, sesquiterpenoids, flavonoids, lignans, phenylpropanoids, aliphatic compounds and caffeic acid derivatives (Liang et al. 2020; Ren et al. 2014). All these compounds have shown various pharmacological properties such as anti-inflammatory activity, antioxidant activity, anti-tyrosinase, anti-viral activity against H1N1 and HSV-1, and anti-proliferative activity. Some of the other major activities shown by S. plebeia are inhibitory activity, antimicrobial activity, hypoglycemic activity, hepatoprotective activity, hemostatic activity, skin protective activity, antitumor activity, anti-obesity effects and anti-ageing effects (Liang et al. 2020).

In the present study, the computational screening of the biologically active compounds of Salvia plebeia R. Br. was performed to identify potential lead inhibitors of the Mpro enzyme of SARS-CoV-2. Molecular docking was initially carried out to screen the phytochemicals of S. plebeia and the pharmacokinetic or ADMET properties as well as the drug-likeness parameters of the phytochemicals were also studied to understand the disposition of the compounds and to ensure they possessed pharmacophoric features. The pharmacological activities of the selected compounds were analysed using the PASS webserver. To predict the dynamic behaviour as well as stability, molecular dynamics simulation and secondary structure analysis were executed for the protein–ligand complexes. MM-PBSA (Molecular Mechanics Poisson–Boltzmann Surface Area) supplied the grounds for analyzing the affinity of the phytochemicals towards Mpro by calculating the binding energy.

Main protease, n                     Salvia plebeia R. Br., Rutin, Plebeiosides B, ADMET, PASS, Molecular docking, Molecular dynamic simulation


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References


Amin SA, Jha T (2020) Fight against novel coronavirus: a perspective of medicinal chemists. Eur J Med Chem 201:112559


Araruna MKA et al (2012) Evaluation of antibiotic & antibiotic modifying activity of pilocarpine & rutin. Indian J Med Res 135(2):252


Bang S et al (2016) Antiviral activities of compounds from aerial parts of Salvia plebeia R. Br. J Ethnopharmacol 192:398–405


Bang S et al (2018) Anti-influenza effect of the major flavonoids from Salvia plebeia R.Br. via inhibition of influenza H1N1 virus neuraminidase. Nat Prod Res 32(10):1224–1228


Das S, Koner BC (2020) Pre-analytical, analytical, and post-analytical considerations while processing samples of COVID-19 patients: perspective from a clinical chemistry laboratory in India. Asian J Med Sci 11(5):112–115


Das P, Majumder R, Mandal M, Basak P (2020) In-silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of calendula officinalis. J Biomol Struct Dyn 39:1–16


Fauci AS, Clifford Lane H, Redfield RR (2020) Covid-19—navigating the uncharted. N Engl J Med 382(13):1268–1269


Fereidoonnezhad M et al (2018) Multitarget drug design, molecular docking and PLIF studies of novel tacrine−coumarin hybrids for the treatment of Alzheimer’s disease. Iran J Pharm Res 17(4):1217–1228


Ghasemnezhad A, Ghorbanzadeh A, Sarmast MK, Ghorbanpour M (2020) A review on botanical, phytochemical, and pharmacological characteristics of Iranian Junipers (Juniperus Spp.). Plant-derived bioactives: production, properties and therapeutic applications. Springer, Singapore


Gibaldi M, Levy G (1976) Pharmacokinetics in clinical practice: I. Concepts. JAMA J Am Med Assoc 235(17):1864–1867


Gil C et al (2020) COVID-19: drug targets and potential treatments. J Med Chem. https://doi.org/10.1021/acs.jmedchem.0c00606


Gupta S et al (2020) Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2020.1776157


Han Y et al (2019) In silico ADME and toxicity prediction of ceftazidime and its impurities. Front Pharmacol 10(APR):434


Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discovery 14(2):111–129


Ibrahim MAA, Abdeljawaad KAA, Abdelrahman AHM, Hegazy MEF (2020) Natural-like products as potential SARS-CoV-2 Mpro inhibitors: in-silico drug discovery. J Biomol Struct Dyn 39:1–13


Jacob RB, Andersen T, Mcdougal OM (2012) “Accessible high-throughput virtual screening molecular docking software for students and educators” ed Fran Lewitter. PLoS Comput Biol 8(5):e1002499


Jin Z et al (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582(7811):289–293. https://doi.org/10.1038/s41586-020-2223-y


JP, Lin, et al (2009) Rutin inhibits the proliferation of murine leukemia WEHI-3 cells in vivo and promotes immune response in vivo. Leuk Res 33(6):823–828


Kandeel M, Ibrahim A, Fayez M, Al-Nazawi M (2020) From SARS and MERS CoVs to SARS-CoV-2: moving toward more biased codon usage in viral structural and nonstructural genes. J Med Virol 92(6):660–666


Karami M, Jalali C, Mirzaie S (2017) Combined virtual screening, MMPBSA, molecular docking and dynamics studies against deadly anthrax: an in silico effort to inhibit bacillus anthracis nucleoside hydrolase. J Theor Biol 420:180–189


Krishna S, Kumar SB, Krishna Murthy TP, Murahari M (2021) Structure-based design approach of potential BCL-2 inhibitors for cancer chemotherapy. Comput Biol Med 134:104455


Kumar S, Pandey AK (2013) Chemistry and biological activities of flavonoids: an overview. Sci World J 2013:1–16


Kumar SB et al (2021) Screening of natural compounds from Cyperus Rotundus Linn against SARS-CoV-2 main protease (Mpro): an integrated computational approach. Comput Biol Med 134:104524–104524


Kumar B et al (2021) In silico screening of therapeutic potentials from strychnos nux-vomica against the dimeric main protease (Mpro) structure of SARS-CoV-2. J Biolmol Struct Dyn. https://doi.org/10.1080/07391102.2021.1902394


Kumari R, Kumar R, Lynn A (2014) G-Mmpbsa -A GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951–1962. https://doi.org/10.1021/ci500020m


Li H et al (2020) Coronavirus Disease 2019 (COVID-19): current status and future perspectives. Int J Antimicrobial Agents 55(5):105951


Liang Y et al (2020) Salvia plebeia R. Br.: an overview about its traditional uses, chemical constituents, pharmacology and modern applications. Biomed Pharmacother 121(219):109589


Lindahl, Abraham, Hess, van der Spoel (2019) GROMACS 2019.4 manual


Ma Q et al (2014) Chemistry and Pharmacology of Salvia Plebeia R. Brown (Lamiaceae ). J Chem Pharm Res 6(10):777–783


Mansoor A, Mahabadi N (2021) Volume of Distribution. In: StatPearls [Internet]. StatPearls Publishing, Treasure Island (FL). https://www.ncbi.nlm.nih.gov/books/NBK545280/


Marathe SA, Datey AA (2012) Herbal cocktail as anti-infective: promising therapeutic for the treatment of viral diseases. Recent Pat Anti-Infective Drug Discov 7(2):123–132


Mason RJ (2020) Pathogenesis of COVID-19 from a cell biology perspective. Eur Respir J 55(4):2000607


Murugesan S, Venkateswaran MR, Jayabal S, Periyasamy S (2020) Evaluation of the antioxidant and anti-arthritic potential of zingiber officinale Rosc. by in vitro and in silico analysis. S Afr J Bot 130:45–53


Naidoo D et al (2020) Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis. J Biomol Struct Dyn 39:1–13


Ngane A, Ngono R et al (2011) Ethnobotanical survey of some cameroonian plants used for treatment of viral diseases. Afr J Plant Sci 5(1):15–21


Nisius B, Sha F, Gohlke H (2012) Structure-based computational analysis of protein binding sites for function and druggability prediction. J Biotechnol 159(3):123–134


Nugroho A et al (2012) In vivo sedative and gastroprotective activities of Salvia plebeia extract and its composition of polyphenols. Arch Pharmacal Res 35(8):1403–1411


Nurton J (2020) Drug repurposing and the COVID-19 pandemic, WIPO Magazine. https://www.wipo.int/wipo_magazine/en/2020/02/article_0004.html


Patil R et al (2010) “Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing” ed Sridhar Hannenhalli. PLoS ONE 5(8):e12029


Pires DEV, Blundell TL, Ascher DB (2015) PkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med cinal Chem 58(9):4066–72. http://structure.bioc.cam.ac.uk/. Accessed 28 Jul 2020


Pollastri MP (2010) Overview on the rule of five. Curr Protoc Pharmacol 49(1):9.12.1-9.12.8


Prasanth DSNBK et al (2020) In silico identification of potential inhibitors from cinnamon against main protease and spike glycoprotein of SARS CoV-2. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2020.1779129


Pushpakom S et al (2018) Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discovery 18(1):41–58


Ranney ML, Griffeth V, Jha AK (2020) Critical supply shortages—the need for ventilators and personal protective equipment during the Covid-19 pandemic. N Engl J Med 382(18):E41


Ren DB et al (2014) Separation of nine compounds from Salvia plebeia R.Br. using two-step high-speed counter-current chromatography with different elution modes. J Sep Sci 37(16):2118–2125


Schüttelkopf AW, Van Aalten DMF (2004) “PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr Sect D Biol Crystallogr 60(8):1355–1363. http://scripts.iucr.org/cgi-bin/paper?S0907444904011679. Accessed 29 Jul 2020


Shineman DW et al (2014) Overcoming obstacles to repurposing for neurodegenerative disease. Ann Clin Transl Neurol 1(7):512–518


Talevi A, Bellera CL (2020) Challenges and opportunities with drug repurposing: finding strategies to find alternative uses of therapeutics. Expert Opin Drug Discov 15(4):397–401


Tao J et al (2007) In vitro anti-HIV and -HSV activity and safety of sodium rutin sulfate as a microbicide candidate. Antiviral Res 75(3):227–233


Veeresham C (2012) Natural products derived from plants as a source of drugs. J Adv Pharm Technol Res 3(4):200–201


Wang J et al (2019) Biosynthesis, chemistry, and pharmacology of polyphenols from Chinese salvia species: a review. Molecules 24(1):1–23


Xiu S et al (2020) Inhibitors of SARS-CoV-2 entry: current and future opportunities. J Med Chem. https://doi.org/10.1021/acs.jmedchem.0c00502


Zhang MQ, Wilkinson B (2007) Drug discovery beyond the ‘rule-of-five.’ Curr Opin Biotechnol 18(6):478–488

 


Acknowledgements



Author Information


Zackria Afraa Aqeel
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India

Murthy T. P. Krishna
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India

tpk@live.in
Kumar S. Birendra
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India


Mathew Blessy Baby
Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India

Biju Vinai George
Department of Computer Science and Engineering, Christ (Deemed-to-be University), Bengaluru, India