Introduction

Severe Acute Respiratory Syndrome (SARS) Coronavirus, a novel coronavirus (2019-nCoV), also known as SARS-CoV-2, posed a huge threat to the world since 2019. The Centre for Disease Control and Prevention (CDC) tracked the outbreak of SARS-CoV-2 in Wuhan, China. The virus spread across the globe and leads to a pandemic situation with significant mortality rates that differed from country to country. People with heart disease, diabetes, lung disease, HIV, and pregnant women are at an increased risk of developing a serious illness or contracting COVID-19. The virus does not travel through the air, but rather through the respiratory droplets or aerosols of an infected individual (Dwarka et al. 2020). SARS CoV-2 is a member of the Coronaviridae family of the Nidovirales order. It is classified into four genera and SARS CoV-2 is closely related to the Betacoronavirus genus. Genome sequencing revealed higher similarity with the previous SARS CoV (2003 outbreak). Both viruses share the same membrane-bound exopeptidase Angiotensin converting enzymes (ACE2) as the host receptor to enter the cells (Chakraborty and Member 2020; Silva et al. 2020). Different structural proteins such as spike proteins play the main role in attachment to host receptors. Apart from the structural proteins, different proteases also play a major role in viral replication and immune evasion of the host. Different cysteine proteases: chymotrpsin-like proteases or main proteases (3CLpro), papain-like proteases (PLpro) are important non-structural proteins. The 3CL-like protease (3CLpro) hydrolyzes viral polyproteins to create functional proteins, which are required for coronavirus replication.Papain-like protease is essential for the release of NSP 1–16 from open reading frames ORF1a and ORF 1ab, which forms large polyproteins ppa1a and ppa1ab (Li et al. 2020). Papain-like protease (PLpro) is a SARS CoV-2 enzyme that is required for digesting viral polyproteins to generate a functional replicase complex that allows the virus to spread. It negatively regulates the host immune response by its deubiquitinating and deISGylating effect (Shah et al. 2020; Shin et al. 2020; Mohanraj et al. 2018).

Computer aided drug design tools such as molecular docking and molecular dynamic simulation help us to find the potential inhibitors against various viral targets in lesser time (El-hoshoudy 2020; Shawk et al. 2020; Meng et al. 2020). Plant-based immune modulatory compounds could reduce the effect of inflammatory response and cytokine storm (Abdellatiif et al. 2021; Pall et al. 2020; Vardhan and Sahoo 2020). Several antiviral inhibitors have been found to be more effective against the SARS CoV-2 virus (Alfaroa et al. 2020). Phytochemicals boost immunity and protect against illness (Zhu et al. 2020). This study discusses the results of docking studies of various phytochemicals against SARS CoV-2's papain-like protease (PLpro).

Material and methods

Preparation of protein

The crystal structure of papain-like protease of severe acute respiratory virus -2 (SARS-CoV-2) PDB ID 6W9C was retrieved from PDB database https://doi.org/10.2210/pdb6W9C/pdb and it was used in the present study. It has a resolution of 2.70 Å and molecular weight of 107.81 kDa. It has three chains A, B and C with a total sequence length of 317 amino acids. Energy minimization of the retrieved structure was performed using the SWISS PDB viewer. It helps to repair the distorted geometrics by moving atoms to release internal constraints and is used to minimise the protein energy (Kodchakorn et al. 2020; Tripathi et al. 2011; Trott and Olson 2010).

Preparation of ligand

Antiviral compounds derived from plant resources with variety of traditional applications were screened from a variety of phytochemical databases such as IMPPAT https://cb.imsc.res.in/imppat/ (Indian Medicinal Plants, Phytochemicals and Therapeutics) (Ni et al. 2020; Swain et al. 2020). Compounds with anti-viral properties were screened based on ADME and drug-likeliness properties using SWISS ADME server. (http://www.swissadme.ch/) (Meyer-Almes 2020; Garg et al. 2020). Based on the results, forty phytoligands were chosen for the study. As a control, five commonly recommended synthetic antiviral drugs such as Elbasvir, Cefpiramide, Cefpiramide, Daclatasvir and Delamanid were also docked with PLpro (Sharma et al. 2020; Swain et al. 2020). The structure of phytoligands and drugs was obtained from Pubchem database (https://pubchem.ncbi.nlm.nih.gov/) in SDF format. The phytoligands were then converted from SDF to PDB format using the online SMILES converter. (https://cactus.nci.nih.gov/translate/). ChemSketch was used to convert the 2D structure of certain ligands into a 3D format. (https://www.acdlabs.com/resources/free-chemistry-software-apps/chemsketch-freeware/#chemsketch_modal) (Ferreira et al. 2015). Various phytoligands and synthetic drugs were docked with the target protein, Papain-like protease of SARS CoV-2 using Autodock Vina in blind docking mode (Venkateshana et al. 2020).

Molecular dynamic simulation of Tinosponone

The complex of Tinosponone with Papain-like protease was prepared for Molecular Dynamic simulation and run for 50 ns using GROMACS (version 2022.1) through Google Colab pro (Salsbury 2010; Dutt and Roy 2020). Topology generation and energy minimization of ligand were performed and energy minimization of ligand was performed using the Google colab pro GPU server.

Results and discussion

Molecular docking analysis

The binding energies of forty phytoligands against SARS-CoV-2 papain-like protease (6W9C) ranged from − 9.3 kcal/mol (Tinosponone) to − 2.5 kcal/mol (Methyl Rosmarinate), while synthetic anti-viral drugs ranged from − 9.1 kcal/mol (Bictegravir) to − 13.0 kcal/mol (Elbasvir). Tinosponone and Hespiridin had the highest binding affinity for the PLpro. Because the latter's drug-likeliness had some flaws, Tinosponone from Tinospora cordifolia was further subjected to MD simulation to study its binding stability. The list of various phytochemicals, their sources and their docking score were given in Table 1

Table 1 Docking scores of Phytochemicals with source and PUBCHEM ID
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The pharmacokinetic properties of the selected ligands with preferred docking scores is given in Table 2. Out of five ligands and a drug, Nimbin and Rhoifolin did not meet the required properties as Nimbin’s molecular weight was greater than 500 Da and Rhoifolin’s number of hydrogen acceptors was greater than 10. Tinosponone, Berberine, Rosamanol and Elbasvir satisfied all rules of Lipinski.

Table 2 ADME Analysis of selected compounds
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Prediction of the active site of PLpro

The probable active sites or binding pockets of the four viral proteins were identified with PyMOL (Bharadwaj et al. 2020; Yuan et al. 2017). Five phytochemical molecules were analyzed for the identification of the active site of the target molecule which is listed in Table 3. The target protein PLpro contains three chains A, B and C. The binding complex of Tinosponone with the active site of PLpro of SARS CoV-2 is shown in Fig. 1.

Table 3 Active site of selected phytochemicals with A, B and C chain of PLpro
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Fig. 1
figure 1

Active site predicted using PyMOL for the docked structure of Tinosponone with PLpro of SARS CoV-2

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Molecular dynamic simulation of Tinosponone with PLpro

The molecular dynamic simulation was carried out for the docked complex of Tinosponone with papain-like protease using GROMACS (version 2022.1) through Google Colab pro. The conformation of the molecule binding of the compound was found to be stable with a mean RMSD value deviation in the range of 0.2 nm when simulation was done for the period of 50 ns using Google colab pro. RMSD value was plotted as the function of time frame was plotted as shown in Fig. 2. RMSF fluctuation of binding of Tinosponone with PLprowas shown in Fig. 3 (Silva et al. 2020). The number of hydrogen bonds formed during 50 ns Molecular dynamic simulation was shown in Fig. 4

Fig. 2
figure 2

Time dependence RMSD plot of binding of Tinosponone with PLpro using MD simulation

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Fig. 3
figure 3

Time dependence RMS fluctuation plot of binding of Tinosponone with PLpro using MD simulation

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Fig. 4
figure 4

Number of Hydrogen Bonds of Tinosponone binding with PLpro in 50 ns MD simulation

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Discussion

In the current study, Tinosponone derived from the plant Tinospora cordifolia showed better binding activity with the binding energy of − 9.6 kcal/mol using Autodock Vina, Similarly in another study by Krupanidhi et al. (2020), Tinosponone showed a better binding affinity with 3CL pro also with binding activity of − 7.7 kcal/mol (Krupanidhi et al. 2020). Results of molecular dynamic simulation with Papain protease of SARS CoV-2 with Tinosponone also indicates the stable binding when the simulation was performed in the 50 ns range (Table 4).

Table 4 Affinity of docked Tinosponone with SARS CoV-2 PLpro in different docking modes
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Conclusion

Virtual screening of SARS CoV-2 papain-like protease (PDB ID: 6W9C) with various phytoligands demonstrated the five phytoligands, Tinosponone, Rhoifolin, Rosmanol, Berberin, and Nimbin with the best inhibitory potential in terms of higher binding affinities. Tinosponone had a binding affinity of − 9.3 kcal/mol and obeyed all Lipinski rules, making it a potential inhibitor for SARS Cov-2 PLpro. Tinosponone's binding site with the target PLpro was identified as P246 on chain C of SARS CoV-2's papain-like protease (PLpro). Therefore, Tinosponone could be used as a potential inhibitor of papain like protease of SRS CoV-2 based on further in-vitro and in-vivo investigations.