|Year : 2021 | Volume
| Issue : 1 | Page : 28-39
Computational modeling and analysis of Ayurvedic compounds in fighting against COVID-19
Pramodkumar P Gupta1, Shraddha U Nayak2, Mala M Parab1, Debjani Dasgupta1, Maheshkumar S Harit2
1 School of Biotechnology and Bioinformatics, D Y Patil Deemed to be University, CBD Belapur, India
2 School of Ayurveda, D Y Patil Deemed to be University, Nerul, Navi Mumbai, Maharashtra, India
|Date of Submission||21-Jul-2021|
|Date of Acceptance||16-Aug-2021|
|Date of Web Publication||14-Dec-2021|
Dr. Pramodkumar P Gupta
School of Biotechnology and Bioinformatics, D Y Patil Deemed to be University, Plot 50, Sector 15, CBD Belapur, Navi Mumbai 400614, Maharashtra.
Source of Support: None, Conflict of Interest: None
AIM: To screen the selective Ayurvedic amalgams against severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) main protease in the investigation of antiviral activity using computational-based methods. MATERIALS AND METHODS: The current research study endeavors to gauge the in silico potency of Ayurvedic molecules/drugs, chosen from primeval classical literature and former human medication protocols of Ayurveda for the preemption and treatment of contagion (COVID-19). Overall, 84 Ayurvedic compounds on the basis of antiviral activity were searched from literature and public database sources and canonical smiles format molecular information was retrieved from the PubChem database. All the compounds were sketched using Chemsketch tool and optimized using UFF force field. The selected molecules were then virtually screened against the SARS-CoV-2 main protease available structure. RESULTS: The outcomes were evaluated based on docking scores and pharmacophoric-based interactions; five compounds exhibited an optimum interaction within the binding site of SARS-CoV-2 main protease. CONCLUSION: The current research study lay the foundation of drug repurposing with the amalgamation of knowledge of Ayurveda and computational aided modeling in fighting against COVID-19. Therefore, the pragmatic dogma proposed here will facilitate learning, generate evidence, and pave the way forward.
Keywords: Ayurvedic amalgams, COVID-19, in silico docking, pandemic, SARS-CoV-2
|How to cite this article:|
Gupta PP, Nayak SU, Parab MM, Dasgupta D, Harit MS. Computational modeling and analysis of Ayurvedic compounds in fighting against COVID-19. J Drug Res Ayurvedic Sci 2021;6:28-39
|How to cite this URL:|
Gupta PP, Nayak SU, Parab MM, Dasgupta D, Harit MS. Computational modeling and analysis of Ayurvedic compounds in fighting against COVID-19. J Drug Res Ayurvedic Sci [serial online] 2021 [cited 2022 Jan 17];6:28-39. Available from: http://www.jdrasccras.com/text.asp?2021/6/1/28/332497
| Introduction|| |
Recurrent epidemic and sporadic pandemic outbreaks by viruses among humans, birds, and animals are known since eons. In the past era, different subtypes of influenza virus, through multifarious animal reservoirs, have been reported to instigate respiratory disease pandemic periods. Numerous cases of pneumonia with mysterious etiology among the people of Wuhan were observed toward the end of December, 2019.
This zoonotic disease was named as novel coronavirus, which is also known as SARS-CoV-2, belonging to the family of coronaviruses. The coronaviruses family is extensively studied and well known, is widespread, and is solely responsible for SARS and Middle East respiratory syndrome (MERS) epidemics in the past two decades., These viruses demonstrate a heterogenous assortment of medical traits from a symptomless course to the necessity of hospitalization in the intensive care unit; triggering infirmities in respiratory, gastrointestinal, hepatic, and neurologic systems. As of December 24, 2020, the WHO reports 77,530,799 confirmed cases with a total death toll of 1,724,904 worldwide.
The CoV-2 is a pleomorphic RNA virus, with coronet-shaped peplomers, approximately 80–160 nM in size with a positive polarity of 27–32 kb. The structure of SARS-CoV-2 glycosylated spike (S) protein is reported to have 14 binding residues and consists of eight amino acids specifically conserved for SARS-CoV-2. These S proteins of SARS-CoV and SARS-CoV-2 have been reported to mediate host cell invasion via an angiotensin-converting enzyme 2 (ACE2) receptor positioned on the membranal surface of host cells. The recent study showed that the process of invasion requires S-protein priming promoted by the host cell-produced serine protease TMPRSS211. Besides, the viral genome has also been reported to encrypt several nonstructural proteins such as RNA-dependent RNA polymerase (RdRp), coronavirus main protease (3CLpro), and papain-like protease (PLpro). PLpro has been observed to act as a deubiquitinase that may deubiquitinate certain host cell proteins, including interferon factor 3 and NF-κB, resulting in immune suppression.
Ayurveda, the primogenital medical system, describes fever (Jvara) as a major disease in its classics like Charaka Samhita. The features of Sannipata Jvara described in Ayurvedic classics have been correlated to symptoms of COVID-19. Further, life-threatening cases of COVID-19 have been found to have the best match with symptoms described for Sama Sannipata jvara (due to aggravation of three doshas). It emanates from Janapada dhamsa vikara and can be grouped in Bhutabhishanga agantuja Vikara (external source of microbes, due to spirit possession)., Based on the pathogenesis and the symptoms exhibited in patients with COVID, the disease COVID-19 in Ayurveda can be fairly considered under Agantuja Abhishangaja jvara (exogenous due to curse) caused by krimi (worms or microbes) or bhuta,, which is aupasargika in nature, which means infectious. Some researchers have reported it as sannipatika jvara, because even in Agantuja jvara (exogenous) eventually there is vitiation of all the three doshas or humors.Krimi or bhuta in the up-to-date milieu includes all infectious pathogens, namely bacteria, helminth, protozoa, as well as viruses.
Traditionally in Ayurveda, treatment for epidemics or pandemics; Rasayana or immunomodulators are advocated to boost immunity as well as to combat the krimi or bhuta (pathogen) by breaking the chain and/or constraining proliferation of the pathogens, thus they would have beneficial chattels from the treatment aspect. Among the line of treatment for krimi suggested in Ayurveda, one is prakrtivighata (counteracting the cause of disease), which is developing a nonconductive environment in the body to prevent the growth of krimi by the continuous use of Katu (pungent), Tikta (Bitter), Kashaya (Astringent), Kshara (alkali), and Ushna (hot) dravyas (substances); the measures combating Kapha and Purisha are Apakarshana (removal of cause of disease) and Nidana parivarjana (avoidance of etiological factors).
A popular formulation suggested is shadangapaniya in jvara constituting the drugs Musta-Cyperus rotundus L., Chandana-Santalum album L, parpata-Fumaria parviflora Lam,,ushiraChrysopogon zizanioides (L.) Roberty Syn Vetiveria zizanioides (L.) Nash Udichya-Pavonia odorata Willd and Nagara-Zingiber officinale Roscoe, and Yavagu (medicated gruel) with drugs of a predominantly bitter taste that are antipyretic in action. After the sixth day of JvaraPachanashamana Kashaya, medicated decoctions with digestive and therapeutic effects are recommended, for example, Musta (Cyperus rotundus L.) Parpataka Fumaria parviflora Lam. or with Nagara (Zingiber officinale Roscoe). Also, Shatyadi varga kashaya and Brihatyadi kvatha are especially suggested in sannipata jwara with symptoms of cough, dyspnea, cardiac symptoms, fatigue, and all other resultant complications. Surasadi gana is indiacted in cough and respiratory complications induced by infectious agents. In case of relapse too, drugs such as Guduchi (Tinospora sinensis [Lour.] Merr.), Musta (Cyperus rotundus L.), and Parpata Fumaria parviflora Lam. are suggested in [Table 1].
|Table 1: Phytochemicals screened with the properties and formulations cited in classics of selected potential Ayurvedic drugs|
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Numerous computational-based analyses have supported in the design, development, and screening of the drug regimen in the COVID-19 pandemic. Computational structure-based drug discovery approaches, including molecular docking and virtual screening, has widely supported the screening of the large compound libraries and understanding the binding affinity and molecular interactions between the protein–ligand complexes. The traditional medicine system/Ayurveda is, thus, an opulent compendium of natural leads that are yet to be unveiled. Several studies are being carried out vigorously in this direction to find an apt therapeutic drug. Compounds from Tinospora cordifolia and Ocimum tenuiflorum were screened and reported as inhibitors for SARS-CoV-2 main protease by implementing molecular docking and MD simulations techniques. An in silico study published by Gandhi et al. reported that 6-gingesulfonic acid, a phytoconstituent of Shunthi (Zingiber officinale Roscoe), has a higher binding energy over hydroxychloroquine and quinine and compared with other drugs screened. A single phytoconstituent was selected from each of the drugs chosen. Plants have multiple pharmacologically active phytoconstituents. The present research study implicates an in silico based screening of multiple phytochemicals, with reported antiviral properties from each medicinal plant documented in various Ayurvedic texts for the treatment of infectious diseases/ bhuta/krimi; bearing jvaraghna (antipyretic), krimighna (anthelmintic drugs), vishaghna (antitoxic), kasaghna (anti-tussive), and shwasaghna (anti-dysneic) drugs based on the manifestation of a particular symptom or severity of the disease to understand their potential role in COVID-19, integrating the in silico tools for drug activity predictions.
| Materials and Methods|| |
Target protein preparation
Here, we have considered the crystal structure of SARS-CoV-2 main protease, Pdb-id–6LU7 complex with an inhibitor. The 3D structure was solved using the X-diffraction method, at resolution 2.6 A; before subjecting for further analysis, the structure was cleaned by removing the co-crystallized ligand and water molecules that are present in it. The protein was then subjected for energy minimization, using the Steepest descent method and was solvated under TIP3P based water model with 6 Na+ ions to neutralize the system. The stability of the structure is evaluated by its potential energy, bond angle, bonds, and proper dihedrals [Figure 1]A–D.
|Figure 1: (A) GROMACS potential energy, (B) angle, (C) bond, and (D) proper dihedral|
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Binding site region
The default binding site of the inhibitor from 6LU7.pdb is considered in the study for structure-based screening. The binding site regions consist of the following amino acids: Phe-140, Gly-143, Cys-145, His-164, Glu-166, Glu-189, and Thr-190. Finally, the grid site region with a center value of “X = −10.6616; Y = 12.2195; Z = 68.8699” A with dimension region “X = 25.00; Y = 25.00; Y = 25.00” A [Figure 2] is selected in Autodock PyRx tool.
Here, we have considered 84 selective antiviral Ayurveda compounds [Table 1]. The information on compounds was retrieved from NCBI Pubchem database in the canonical smile format. All the selected antiviral compounds were sketched using the tool ACD Chemsketch version 12.0 saved in 3D form using.mol format. All the ligands were energy-wise optimized using Universal force field in Argus lab tool and saved in.pdb format.,
Virtual screening (molecular docking)
For virtual screening, we have used Autodock-Pyrx tool. The geometric and energy-wise optimized viral protein and selected compounds are loaded into the Vina wizard of Auto dock Pyrx tool, and the pdb format of protein and compounds are converted to pdbqt file format as a required input form for Autodock tools. Pharmacophore-based binding site selection is carried out in the study; from the working panel of Autodock Pyrx, the individual amino acid is selected and the grid box dimension is adjusted to accommodate all the selected amino acids [Figure 2]. AutoDock Vina generated nine poses for each of the compounds and their interaction analysis; the lowest energy form and lowest bound RMSD compounds were selected as our generated output. The protein–ligand docked complex was generated using UCSF Chimera tool, and all the molecular interactions were analyzed using Biovia Discovery Studio version 16.
| Results|| |
The energy-wise optimized SARS-CoV-2 3D structure of the main protease exhibited a stable conformation and potential energy of −1.5155e + 6 kJ/mol [Figure 1A] with a total drift from −149666 kJ/mol. Similarly, the angle, bond, and proper dihedral reported energy of 2376.27, 2376.27, and 156.559 kJ/mol [Figure 1B]–D] with a total drift of energy from initial to final being −122.277, −1137.63, and −44.3801 kJ/mol. The graphical representation depicts the stability in the structure with a linear form of a graph in [Figure 1A]–[D].
All the 84 selected ligands [Table 2] were sketched geometrically and energy-wise optimized to attain the global minima form and further subjected to a structure-based virtual screening study. All the compounds were targeted to the defined binding site region of the viral protein [Figure 2].
|Table 2: Docking result with the binding energy of all 84 compounds with target protein SARS-CoV-2 main protease|
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Out of the 84 selected compounds, the majority were acquired with the binding site region and made a desired binding interaction with H-bond, Pi-interaction, and Vander Waal interactions. The binding energy ranged from −8.8 to −0.8 Kcal/mol [Table 2]. We have considered the topmost high-ranked complexes with the cutoff binding energy of −8.0 Kcal/mol; out of 84 compounds, 16 compounds scored a binding energy between −8.8 and −8.0 Kcal/mol and they are as follows: Mundulinol, Isocolumbin, Tinosporin, Diosgenin, Isopomiferin, Kutkoside, 6-Feruloyl catalpol, Glycyrrhizin, Picroside-II, Sitosterol, Stigmasterol, Melianone, Triterpenoids, Silymarin, Ursolic acid, and Carpesterol [Table 2].
Based on selective amino acid that serves as a pharmacophore and types of interaction, five compounds exhibited an optimum result: Mundulinol −8.8 Kcal/mol and forms one H-bond with GLY-143, two pi-interaction with and three Vanderwaal interactions with HIS-164, GLU-166, THR-190 [Figure 3A]; Isocolumbin with −8.6 Kcal/mol and forms two H-bonds with HIS-164 and GLU-166, one pi-interaction with CYS-145, and three Vanderwaal interactions with PHE-140, GLY-143, and GLN-189 [Figure 3B]; Kutkoside with −8.4 Kcal/mol and forms two H-bonds with PHE-140 and GLY-143, one pi-interaction with CYS-145, and four Vanderwaal interactions with PHE-140, HIS-164, GLU-166, and GLN-189 [Figure 3C]; Isopomiferin −8.4 Kcal/mol and forms one H-bonds with GLY-143, one pi-interaction with CYS-145, and three Vanderwaal interactions with PHE-140, HIS-164, GLU-166, and GLN-189 [Figure 3D]; Ursolic acid −8.0 Kcal/mol and forms one H-bond with GLU-166, one pi-interaction with CYS-145, and three Vanderwaal interactions with GLY-143, HIS-164, and GLN-189 [Figure 3E] and [Table 3].
|Figure 3: (A) Mundulinol, (B) Isocolumbin, (C) Kutkoside, (D) Isopomiferin, (E) Ursolic acid docking result|
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|Table 3: Molecular docking of compounds with pharmacophoric interactions|
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| Discussion|| |
No adverse effects have been yet reported with the plants with the bioconstituents Mundulinol, Isocolumbin, Kutkoside, Isopomerin, and Ursolic acid. However, the classics have documented Tulsi and barbari with the constituents ursolic acid to be Daha (burning sensation) and pittakrit (vitiate pitta) and stated that they need to be used with caution. In addition, liver injury was reported in a few patients with COVID-19; being hepatoprotective, these drugs definitely have an edge over other drugs in terms of treatment.,,,,,,
Ayurveda classics have recommended decoctions or exudates of many medicinal plants; in Jvara (fever), Shvasa (difficulty in breathing), Kasa (cough), which are common symptoms in COVID-19 and Krimi. Furthermore, a few of these drugs; either alone (as mentioned in [Table 2]) or in combination in the form of Paniya, Yavagu, and various Kashaya such as Shadanga paniya, Shatyadi Kashaya, Brihatyadi Kashaya, Surasadi gana, Vishaghna such as Shirisha have been documented to have therapeutic applications in these conditions. Thus, based on any reported or published antiviral activity, a total of 78 phytochemicals from 20 medicinal plants and 6 compounds from 1 Anukta (extra-pharmacopeal) drug were screened to understand their action against the new COVID-19 virus in this research study.
The docking results revealed five phytochemicals, that is, Mundulinol, Isocolumbin, Kutkoside, Isopomiferin, and Ursolic acid, to have high binding affinity properties against the COVID-19 main protease.
Mundulinol is a vital phytometabolite found in plants like Silybum marianum. This plant also known as milk thistle though Anukta or extra-pharmacopeial drug, has been recommended as a good liver tonic and is integral component of a few effective Ayurveda liver syrups. It has also been reported to treat viral hepatitis. Furthermore, phytometabolites Derrisin, Mundulinol, and Isopomiferin are also being used as novel DENV inhibitors.
Isocolumbin is a constituent of Guduchi, that is, Tinospora sinensis (Lour.) Merr. Tinospora sinensis (Lour) Merr is a very popular drug used in around more than 300 formulations, which shows its wide range and potent activity. It is used in many formulations indicated in Jwara, a few of which are Guduchyadi Svarasa, Guduchyadi kavatha, Pippalyadi Kavtha, Drakshadi Kvatha, Vishwadi kvatha, Saptatcchadi kvatha, Triphaladi Kvatha,Krimi and Panchatikta kvatha. It is one of the ingredient of Samshamani vati, a popular combination. It is used in all types of Doshic imbalance. It has Tikta (bitter), Kashaya (astringent), rasa (taste), Ushna virya (hot potency), Guru snigdha guna (attribute), Madhura vipaka (sweet on biotransformation), and Jvaraghna (antipyretic) Bhutaghna properties. As per earlier published works, Tinospora was found to have compounds that reduced the recurring resistance of the HIV virus to antiretroviral therapy (ART).
A diterpenoid, tinosporin, exhibited activity against HIV, HTLV, including numerous viral diseases, and it is reported for its immunomodulatory activity and selective inhibition of the virus to target T helper cells. Therefore, the compounds of Guduchi Berberin, Magnoflorine, Jatrrorhizine, Palmatine, Choline, Tinosporin tetrahydropalmatine, and Isocolumbin were screened. Among all, Isocolumbin was found to be active against COVID-19.
Katukarohini (Picrorhiza kurroa Royle ex Benth), an ingredient in Katurohinyadi Churna Pathyadi Kvatha, Tiktadi kvatha, Drakshadi Kvatha, Duralabhadi Kvatha, Mridvikadi Kavtha, Nagaradi Kvatha, Triphaladi Kvatha, and Mustadi Kvatha, is predominantly suggested in Pitta and Kapha imbalance. It has Tikta rasa, Laghu ruksha guna, Katu vipaka, Sheeta virya, and Vishamajwaranashini (irregular fever) properties. Previous literature found that there are several active ingredients in Picrorhiza kurroa, such as Acetophenone derivatives, Iridioids (Picroside I, II, III, Pikuroside, Kutkoside, and 6-feruloyl catalpol), and Cucurbitacins (extremely bitter glycosides, including apocynin) whose antiviral activity has been reported. Accordingly, the constituents Kutkoside, 6-feruloyl catalpol, Picroside I, Picroside II, Picroside III, and Pikuroside were screened; among them, Kutkoside was found to be have potential activity against the COVID-19 virus. The active component of Kutkin is a concoction of Kutkoside and Picroside whereas its other ingredients are Apocynin, Andorsin, and Cucurbitacin glycosides. Kutkoside is an Iridoid glycoside.
Former studies suggest that Ursolic acid, a constituent of Tulsi (Ocimum tenuiflorum L) and Barbari (Ocimum basilicum L.), can be a potential source for COVID-19 therapy. Ursolic acid was chosen due to an earlier report on the vast range of antiviral activity against DNA viruses such as RNA virus, HSV-1, and adenoviruses., Ursolic acid is a Pentacyclic triterpinoid compound with anti-inflammatory effects.Tulsi has Katu tikta, ushna, Katu, ushna, laghu ruksha, and Barbari-Ocimum basilicum; a variety of Tulsi has Katu Tikta rasa, Laghu ruksha, Tikshana guna, Katu Vipaka, Ushna, VeeryaKrimighna (antihelmentic, antimicrobial), and vishaghna (antitoxic) properties, which substantiate its role as an antiviral agent.
The current study is limited to understanding the molecular interaction between SARS-CoV-2 main protease protein and a few phytochemicals that were reported with antiviral activity. Medicinal plants are a reservoir of phytochemicals and other bioconstituents that could have better efficacy too and need to be identified and screened for their better biological efficacy.
| Conclusion|| |
The current research study demonstrates the activity of several phytochemicals having multifarious medicinal chattels. On the basis of selective amino acid as a pharmacophore and types of interaction with the 3D structure of the SARS-CoV-2 main protease, five phytochemicals, that is, Mundulinol, Isocolumbin, Kutkoside, Isopomiferin, and Ursolic acid, were scored as having a good binding affinity and a good degree of pharmacophoric interactions with the SARS-CoV-2 protein main protease. We propose that these molecules could be further studied under in vitro and in vivo conditions for their effectiveness in COVID-19. In addition, Ayurvedic principles use whole plants where multiple bioconstituents play a diverse role in the pathology of a disease; thus, network pharmacology and further clinical studies are recommended to authenticate the results found in this study.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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[Figure 1], [Figure 2], [Figure 3]
[Table 1], [Table 2], [Table 3]