Coronavirus Disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), that is responsible for respiratory illness and probably many more is yet to be discovered. This novel virus was first identified on 30 ^th December, 2019, with its first infection case infecting a human, which was reported in Wuhan city located in Hubei, China ¹ . Coronaviruses are mainly zoonotic, and are present amongst birds and mammals, causing respiratory, neurological, hepatic and enteric diseases ² as well as comprises of enveloped RNA. The World Health Organization (WHO) declared this disease as a pandemic on 11th March, 2020 and SARS-CoV-2 as the deadliest virus till date on earth claiming 217,896 deaths till 30 ^th April, 2020 ³ .

Then, it is necessary for the rapid development and approval of a vaccine, which is not yet available ⁴ . Nevertheless, Chang et al., ⁵ have suggested that some drugs against same type of viruses approved by the US Food and Drug Administration (FDA) might offer promising results. Hydroxychloroquine is one such drug that is used worldwide whereas Remdesivir and Ivermectin have been reported to work against COVID-19 in silico by others.

The transmission of this coronavirus occurs due to the binding of the CoV spike protein to the angiotensin converting enzyme 2 (ACE2) receptor present on the cell surface of the human host. The ACE2 receptor is present in the respiratory organs, kidneys, gastrointestinal tract (at high levels in the esophagus, colon, and small intestine, but low in the stomach), and testes. Virulence of this novel virus is due to the presence of main protease responsible for virus replication along with many major functions ⁶ . Therefore, we have employed the main protease structure 6m03 as the target protein to identify the best inhibitory drugs in silico for our study.

SARS-CoV-2 (negatively stained) when observed under the electron micrograph was found to be spherical in shape with some pleiomorphic characteristic. The epithelial sections of human airway when observed, viruses were found in membrane bound vesicles in cytoplasm along with inclusion bodies. The virions appear similar to solar corona due to 9- to 12-nm distinctive spikes and the virions are 60 to 140 nm in diameter. Thus, it was established due to these morphological characteristics that this virus belongs to the Coronaviridae family along with its genome having more than 85% identity with a bat SARS-like CoV (bat-SL-CoVZC45, MG772933.1) genome as previously assessed via genome sequencing ⁶ . SARS-Cov-2 initially infects lower airways, binds to ACE2 receptor on cells activating immune cells, thus, inducing the secretion of inflammatory cytokines and chemokines in human pulmonary system ⁴ . Most COVID-19 patients exhibit flu-like symptoms within a span of two weeks from the exposure to the virus whereas there have been a majority rise in the asymptomatic COVID-19 patients.

In this work, we have performed high throughput virtual screening since it is the fastest approach in finding the probable drug against the target. High-throughput virtual screening (HTVS) of two databases was carried out via PyRx (Python prescription) software, which uses dock, Vina and Autodock as the docking tool. Autodock itself uses MGLTools comprising of computer aided drug discovery (CADD) pipeline for high throughput virtual screening of large databases for probable hits as target drugs. HTVS enables docking of multiple ligands on a single protein. PyRx is a freely available HTVS software. Docking results are based on the identification of pose visually and quantitatively using a scoring algorithm. Docking calculates the free binding energy (∆G) between the ligands and the protein. The free binding energy, thus calculated, is fundamental to the formation of complex systems in biochemistry and molecular biology. Lower free binding energy corresponds to a more favorable ligand binding affinity between a receptor and a ligand ⁷ .

HTVS is one of the best methods for identifying molecules acting against drug targets in a very short time period, when compared to traditional drug identification strategies. Remdesivir was detected as COVID-19 inhibitory drug via virtual screening method ⁶ . Therefore, keeping the present scenario in our mind, we undertook this study to provide individuals with COVID-19 with drugs already available. Surprisingly, we have found good hits from the databases with medicinal properties.

Artefenomel is known to treat malaria and other parasitic diseases. Betulinic acid is under trial for the treatment of dysplastic nevus syndrome. Atovaquone is an approved drug for the treatment of Pneumocystis carinii pneumonia and malaria. Tetrandrine is in the experimental stage for anticancer, antimalarial, antiparasitic category. Eprinomectin and doramectin are veterinary antiparasitic drugs.

Many of the natural compounds identified have medicinal properties. Taraxerone has allelopathic and antifungal effect ²⁰ , Morusin has anti-oxidant and anticancer properties ²¹ , RA VII compound is an antitumor agent ²² , and neoruscogenin is used against chronic venous disorders ²³ . Justicidin D exhibits anti-inflammatory properties ²⁴ , Licoricidin is an antimetastatic molecule ²⁵ whereas euphol is used against asthma and cancer along with syphilis, and rheumatism ²⁶ . Schisandrene has anti-oxidant activity ²⁷ , curine is reported as a vasodilator ²⁷ , angoluvarin has antimicrobial activity ²⁸ , baicalin is used to treat cardiovascular diseases, inflammation and hypertension ²⁹ . Glycyrrhetic acid shows anti-inflammatory, anti-ulcer, hepatoprotective, anti-allergic, anti-tumor, antioxidant and anti-diabetic activity ³⁰ . Isomitraphylline has an antioxidant properties ³¹ , bikaverin and rutarensin has anti-tumour activities ^{32, 33} . Jolkinol B has anticancer properties ³⁴ and Ethamidindole exhibits antihistamine properties ³⁵ . Fexofenadine acetate, commonly known as Allegra, is an antihistamine pharmaceutical drug presently used in the treatment of allergy symptoms such as urticaria and hay fever ³⁶ .

When we compared our two datasets, we found that majority of the molecules showed lesser free binding energy as compared to the reference molecules as in Table 1, Table 2, and Table 3. Surprisingly, we obtained good hits from our natural database which is good news since after observing their interaction and biotherapeutic functions, we might have achieved our COVID-19 inhibitory drugs. One such drug from natural database is fexofenadine acetate (Allegra) which is presently in use as anti-allergic medicine. We also have hits from 129 drugs but there is one, atovaquone, which is presently used against pneumonia and malaria and also a very good candidate for COVID-19 treatment.

The best therapeutic drugs inferred from our studies are atovaquone, fexofenadine acetate (Allegra), justicidin D, baicalin, glycyrrhetic acid and ethamidindole based on their docking score, interaction studies and their present applications for probable COVID-19 treatment. The rest of the molecules could also be used as COVID-19 inhibitory drugs after further evaluation. When we compared our data with reference molecules score of currently in use drug against COVID-19, we found that atovaquone showed better binding energy than hydroxychloroquine and remdesivir. It is one of the best drug candidate for COVID-19 treatment since it is already in use for treating Pneumocystis carinii pneumonia and malaria. Fexofenadine acetate is another good target drug for COVID-19 treatment since it is naturally derived and presently used for its anti-histamine properties. Ethamidindole could possibly act as COVID-19 inhibitor since it is reported as anti-histamine and this novel virus activates cytokine secretion in human body. Apart from these, anti-inflammatory natural molecules such as justicidin D, baicalin, and glycyrrhetic acid could work against COVID-19 since SARS-CoV-2 virus induces inflammation. The rest of the top 20 molecules could also be considered since they all have some medicinal properties as explained above.