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
First Page: 345
Last Page: 359
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Keywords: Main protease, n Salvia plebeia R. Br., Rutin, Plebeiosides B, ADMET, PASS, Molecular docking, Molecular dynamic simulation


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


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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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
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