In Silico Approach of Potential Phytochemical Inhibitor from Moringa oleifera, Cocos nucifera, Allium cepa, Psidium guajava, and Eucalyptus globulus for the treatment of COVID-19 by Molecular Docking

Coronavirus disease 2019 (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2. COVID-19 has devastating effects on people in all countries and getting worse. We aim to investigate an in-silico docking analysis of phytochemical compounds from medicinal plants that used to combat inhibition of the COVID-19 pathway. There are several phytochemicals in medicinal plants, however, the mechanism of bioactive compounds remains unclear. These results are obtained from in silico research provide further information to support the inhibition of several phytochemicals. Molecular docking used to determine the best potential COVID-19 M pro inhibitor from several bioactive compounds in Moringa oleifera, Allium cepa, nucifera, Psidium guajava, and Eucalyptus globulus. Molecular docking was conducted and scored by comparison with standard drugs remdesivir. ADME properties of selected ligands were evaluated using the Lipinski Rule. The interaction mechanism of the most recommended compound predicted using the STITCH database.


Results
There was no recommended compound in Moringa oleifera as a potential inhibitor for COVID-19. Oleanolic acid in Allium cepa, α-tocotrienol in Cocos nucifera, asiatic acid in Psidium guajava and culinoside in Eucalyptus globulus were the most recommended compound in each medicinal plant. Oleanolic acid was reported to exhibit anti-COVID-19 activity with binding energy was − 9.20 kcal/mol. This score was better than remdesivir as standard drug. Oleanolic acid interacted through the hydrogen bond with HIS41, THR25, CYS44, GLU166. Oleanolic acid binding with CASP-3, CASP-9, and XIAP signaling pathway.

Conclusions
Oleanolic acid in Allium cepa found as a potential inhibitor of COVID-19 M-pro that should be examined in future studies. These results suggest that oleanolic acid may be useful in COVID-19 treatment.
Background COVID-19 rst found in Wuhan China and become the pandemic in the world declared by theWorld Health Organization on 11 March 2020 1

. Coronavirus disease 2019 (COVID-19) is caused by infection with
Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). COVID-19 has devastating effects on people in all countries. Since 2019 n-CoV disrupts and damages the human immune system, causing varying degrees of damage to organs throughout the body 2 . By comparing coronavirus hosts infection trends in other vertebrates, SARS-CoV-2 was found to be identical SARS-CoV and MERS-CoV. SARS-CoV-2 may also be transmitted between humans. It can infect human cells by using human angiotensinconverting enzyme 2 (ACE2) as a receptor 3 .
The number of con rmed cases of COVID-19 has already exceeded 12.847.288 and 567.734 deaths worldwide on 12 July 2020 04:59 GMT, according to WHO, while estimates global mortality at 7%. In condition, things are getting worse. Unfortunately, there is no speci c antiviral treatment for the current pandemic. There is an urgent need to treat the infected patient and reduce mortality 4 .
Currently, there are no authorized vaccinations available for the prevention of SARS-CoV-2. Drug researchers and clinicians are working hard against COVID-19 to discover potential drugs. In the United States, remdesivir has been reported in improving the clinical condition for COVID-19 patients and has obtained emergency usage permission for the treatment of COVID-19. Therefore, potential chemotheraupetic agents are urgently needed to treat this disease 5 . However, there is much clinical research in China, but no drug has been approved for the treatment of COVID-19 6 .
Medicinal plants have been used as pharmaceuticals because of the signi cant role in health care.
Medicinal plants have antiviral activity, however its mechanism for the treatment of COVID- 19 has not yet been explained. 7 . Bioactive compounds from phytochemicals become the source of therapeutic potential. Phytochemical has many spectra of chemical compounds with various function. Plants are believed to possess medicinal properties and have better compatibility than drugs in the human body 8 .
Traditional medicine and the conventional method can turn into modern medicine after chemical and pharmaceutical screening 7 .
Studies of traditional medicinal plants have increased recently because the natural resources and variety of such plants enable them to complement modern pharmacological. As computer technology has developed, in silico approaches was widely used in efforts to elucidate the pharmacological basis of the functions of conventional medicinal plants. The application of virtual screening in drug discovery will enrich active compounds among the candidates and accurately indicate the mechanism of medicinal plants action, lowering costs, and increasing the effectiveness of the entire procedure. Several FDA approved drugs were developed by in silico approaches from natural herbs or animals 9 . Study of the molecular docking can be a simple gateway to the quest for successful natural drugs against these conditions 10 .
Guava (Psidium guajava) helps the body improve immunity. Flavonoids in guava fruit are responsible for antibacterial action by inhibiting bacterial replication in the body and also preventing bacterial adhesion to healthy body cells. Moringa olifera is a rich source of bioactive compounds that have many nutritional and pharmacological properties. Many of the works reveal that M. oleifera derived gist inhibits the initiation of the viral replication cycle. Moringa also used for anti-in ammatory 11 . Cocos nucifera has anti-oxidants, antidiabetic, bactericidal, and antiviral activities. Extracts of kopyor coconut were hypothesized and indicated for anti-itching, anti-bacterial, antioxidant, anti-viral, analgesic, and antiin ammatory drugs 12 . Onion (Allium cepa) contains quercetin, which has antiviral properties 13 .
COVID-19 is a highly contagious disease with high mortality, and there are no licensed drugs or vaccines yet. Computational methods used to design and manufacture drugs. Low time criteria for in silico approaches enable high throughput sampling of existing medicines to classify new drugs, and to forecast the adverse effects of novel drugs. However, clinical research is required. Computational chemistry has a signi cant role in investigating new medicines by molecular docking study in this work. The identi cation of speci c targets now has grown through the use of computational tools to design new drugs 15 . We can nd that the molecular docking experiment was carried out between several ligands and target for SARS-CoV-2 under speci c method.
Computational methods can inform the design of experimental research. Recent work has demonstrated the usefulness of computational methods to nd potential antiviral drugs of SARS-CoV-2. Protease in these viruses is crucial to hosting infection and is necessary for cell replication 16 . Molecular docking used to study the a nity between the ligands and the binding site. The purpose of this research is to conduct an in-silico docking analysis of phytochemical compounds from medicinal plants namely: Moringa oleifera, Allium cepa, Cocos nucifera, Psidium guajava, and Eucalyptus globulus that used to combat inhibition of COVID-19 pathway, with the hope will be a potential drug which has better activity.

Method Molecular Docking
Binding mode of the phytoconstituents into the target of main protease (M-pro) was investigated using molecular docking study. The analysis was carried out in silico docking using AutoDock Tools 4. Auto We performed docking simulation from several medicinal plants into 3CLpro-X77 as a protein receptor. The structure of 3CLpro-X77 was obtained from PDB using PBD ID in the database (PDB entry 6W63; www.rscb.org/pdb) 19 . Redocking of the co-crystal ligand X77 at SARS-CoV-2 Mpro active site was performed to optimize the molecular docking methods correctly 20 . Chimera 1.13.1 used to prepare the ligands and the receptor protein 21 . All molecules of water were removed, and hydrogen atoms were added. The maximum numbers of generation and evaluation were set at 27000 and 250000, respectively 22 . The ligand was docked in the active site of SARS-CoV-2 M-pro. (PDB ID: 6W63).
Autodock requires pre-calculated grid maps present in the docked ligand, one for each type of atom. The grid stores the potential energy resulting from the macromolecule interaction. The parameters for the Grid box were set using ADT. The Lamarckian Genetic can be validated by the ligand's best conformational with 50 docking runs for each ligand. The parameter was set as default. Ten ligand conformations in complex with the receptor were obtained after complete execution of AutoDock, which were ranked from binding energy 23 .
The lowest binding energy was calculated. Interaction of molecular such as hydrogen bonding, electrostatic, and hydrophobic interaction results was analyzed for structure-activity relationships 24 . Dock Score function was used to scoring all the dock ligands. Analyses from the best pose have been identi ed. In the current study, a docking score indicates the binding e ciency between the phytochemical constituents and the corresponding candidate targets for the treatment of COVID-19 inhibitor 25 .

Lipinski Rule
The restriction of ADME properties by Lipinski rule: a molecular weight less than 500 Daltons, hydrogen bond donors not more than 5, hydrogen bond acceptors not more than 10, and an octanol-water partition coe cient log P not greater than 5. Using DruLiTo software, selected ligands were tested for their Lipinski rule. DruLiTo aims to evaluate the ligand's pharmacokinetics and pharmacodynamic by checking the drug property. Important ADME properties (log P, H bond donor, H-bond acceptor, and molecular weight) are predicted. Based on Lipinski's rule in DruLiTo, the molecular properties and drug similarity of the phytochemical compounds were examined. 26 .

STITCH Database
An interface network between oleanolic acid-target was de ned and established using the Search Tool for Interacting Chemicals (STITCH) database version 5.0 (http://stitch.embl.de/) 27 . The STITCH is a database of predicted interaction between protein and compound to explore the interaction between ligand and protein receptor 28 . Oleanolic acid was inserted in the STITCH database and set as default 29 . The species was set to Homo sapiens, and the molecular network interaction details could be collected.

Results
Several bioactive compounds from medicinal plants have been reported to exhibit antiviral bioactive. Several phytochemical inhibitors from Moringa oleifera, Allium cepa, Cocos nucifera, Psidium guajava, and Eucalyptus globulus have been investigated as potential COVID-19 inhibitors. The compounds pharmachopore compared to remdesivir as a standard drug from in-silico study. Previous studies have investigated the existence of Page 6/25 abundant medicinal plants in nature. The binding energy obtained from docking of 6W63 protein with the native ligand was respectively -9.24 kcal/mol (see Table1). The M-pro was used to build a model for the SARS-CoV-2 M-pro structure. The complex structure (6W63.pdb) determined from Xray crystallographic data, the inhibitor X77 was bonded to SARS-CoV-2 M-pro. AutoDock Tools has calculated the binding energy and binding mode of ligand X77 30 . showed detailed information and the visual evidence of the ligand-inhibitor binding position.

Discussion
In this work, the most effective drugs were chosen to suggest possible treatment of COVID-19 based on molecular docking compared with the ligand X77 and standard drug.  Viruses need host protein to replicate themselves before hijack the host cell.
Therefore, viral replication can be blocked using the host protein inhibitor. The host protein inhibitor will be antiviral drug 35 . Several drugs are predicted to be used in the treatment of COVID-19 but still debated 36  proteins CASP-3, CASP-9, and XIAP, which supported the clinical treatment of COVID-19.
Interaction network can be seen in Figure 2.
Oleanolic acid has antiviral effects. Based on the STITCH database, XIAP (X-linked apoptosis inhibitor) is multifunctional protein that regulates caspase and apoptosis, and modulates inflammatory signal and immunity, cell proliferation, cell invasion, and metastasis. XIAP act as a direct inhibitor of caspase. Caspase 3, apoptosis-related cycteine peptidase, active in triggering of caspases responsible for the execution of apoptosis.
Caspase 9, apoptosis-related peptidase cysteine. Oleanolic acid has KEGG pathways viral myocarditis with pathway ID 05416. Based on the previous study, oleanolic acid mediated apoptosis requiring the release of mitochondria cytochrome C into the cytosol and triggered the activation of caspase-9 and caspase-3 accompanied by polymerase (ADPribose) polymerase (PARP cleavage) 38 .
Oleanolic acid was the most recommended compound in medicinal plants, which can be a potential inhibitor for COVID-19. This research rationalize the limited data on drug efficacy for COVID-19 treatment and give information to select drug candidate for in-vitro trials and in-vivo test. The predicted drug binding and ranking will also be useful in interpreting the results of clinical experiments against COVID-19.

Conclusion
In silico approach of herbal medicine for COVID-19 reported as well. Allium cepa is potent herbal medicine for the development of new therapeutics for COVID-19. Oleanolic acid was the most recommended compound in medicinal plants, which can be a potential inhibitor for COVID-19. Further research is required to examine the potential uses of medicinal plants. These results suggest that antiviral and anti-in ammatory activities from oleanolic acid may be useful in COVID-19 treatment.