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Impact of Quercetin on SARS-CoV-2 using DrugX Repurposing Pipeline

Neha Verma, Prashant Singh¹, Robin Sinha¹, Preeti P.¹, Trapti Sharma¹ , Swarsat Kaushik Nath¹, Kamal Rawal^#1

Amity Institute of Biotechnology, Amity University Uttar Pradesh, India. #Corresponding Author Email ID: kamalrawal@gmail.com {Centre for Computational Biology and Bioinformatics}, AIB Amity University, Noida

Abstract

Background-The SARS-CoV-2 is a worldwide pandemic known as COVID-19. The main druggable goals of SARS-CoV-2 consist of 3-chymotrypsin-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase, and spike (S) protein. Quercetin shows anti-blood clotting, anti-inflammatory, and antioxidant properties. The interface of quercetin inhibits the entry of virus spike protein that is SARS-CoV-2 by targeting angiotensin‐converting enzyme 2 (ACE2) expression. Many clinical trials of quercetin are completed and ongoing on COVID-19.

Method- This is done by using CoV- DrugX Pipeline available at http://drugx.kamalrawal.in/drugx/. The first step is to download the SMILE of a drug (Quercetin) from DrugBank (https://go.drugbank.com/) and paste it on the notepad. After input of SMILE, we have selected modules which we want to analyze drug properties. Therefore, the output files need to be extracted and analyzed.

Result- The compiled result of the Average Value shows that Quercetin has a 53.84% probability to consider as drug repurposing against COVID-19.

This method uses the formula for the calculation of the average overall score is-

= No. of module giving score 1/ Total number of modules having data value related to the drug.

Conclusion- DrugX repurposing pipeline is an acceptable and favorable In-Silicon method for detecting the drug repurposing against COVID-19. Quercetin can prevent infection by the interface between ACE2 and SARS-CoV-2. We can use Quercetin for drug repurposable against COVID-19.

Keywords: COVID-19; SARS-CoV-2; infectious diseases; quercetin; drug repurposing.

Availability and implementation COV-DRUGX Software Pipeline: http://drugx.kamalrawal.in/drugx/ and www.kamalrawal.in/tools.html

1. Introduction

COVID-19 (SARS-CoV-2) is a severe acute respiratory syndrome coronavirus that transmits mainly when the individual comes in contact with the breath droplets of infected individuals, like saliva, coughing, sneezing, exposure with the person personally, by touching the mouth, nose, or eyes with contaminated (unwashed) hands [Derosa et al.,2020].

Then SARS-CoV-2 usage the angiotensin-converting enzyme II (ACE2) receptor that is expressed by the human cells and which is used to attach with SARS-CoV-1 [Li et al., 2020]. According to the studies, COVID-19 (SARS-CoV) can survive for several days on different surfaces and remains feasible in aerosols for hours [van Doremalen et al., 2020].

We've previously built several machine learning and bioinformatics platforms. Includes, text mining and network biology-based systems [Jagannadham et al., 2016], vaccine discovery system [Rawal et al. 2021], next-generation sequencing analysis system for cancer and other genomes [Preeti et al., 2021, Rawal et al 2011, Mandal et al 2006],

Quercetin (Figure1) with chemical name 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy chromen-4-one or 3,3′,4′,5,7-pentahydroxyflavone, is a known polyphenolic flavonoid, having a molecular formula of C15H10O7 [Anand et al 2016 ]. Quercetin is found in many foods and herbs and is also used as a regular component of a normal human diet. Quercetin extraction is considered in many diverse conditions that include cardiovascular, rheumatic diseases, hypercholesterolemia, and cancer [Derosa et al.,2020].

Quercetin has been studied and reported to show pharmacological effects like anti-inflammatory, anti-allergy, and anti-atopic that mediated through inhibition of the lipoxygenase and cyclooxygenase pathways, and thus interfere with the production of pro-inflammatory mediators [Derosa et al.,2020].

It has been seen that flavonoids can reduce both transmembrane peptidase serine 2 (TMPRSS2) and Furin, which cleave the SARS‐CoV‐2 Spike protein that enables SARS‐CoV‐2 infection because of their pleiotropic properties and capabilities to synergize with conventional drugs [Russo et al, 2020].

On the outer surface of epithelial cells express enzymes ACE2, ADAM-17, and TMPRSS2 in which the interaction between ACE2 and SARS-CoV-2 leads to infection, while on the other side the interface of Quercetin with ACE2 leads to no infection (Figure 2) [Williamson et al.,2020].

Quercetin inhibits the entry of the SARS-2 virus by targeting angiotensin‐converting enzyme 2 (ACE2) expression (For SARS‐CoV‐2 entry into human cells gene expression of ACE2 is required) (Figure 3) [Glinsky, 2020].

Studies of In-vitro shows the immunomodulatory effects of Quercetin, which is used to prevent the production of tumor necrosis factor‐α (TNF-α) in macrophages [Manjeet & Ghosh, 1999]. Inhibition of interleukin-8 (IL-8) by Quercetin reduces lung inflammation and blood clotting [Geraets et al., 2007]. Quercetin helps in the block of the production of TNF-α and IL-4 that helps in ameliorating inflammation.

The production of interferon‐gamma [IF-ϒ, Th-1-derived cytokine], which enhances the activity of anti-viral and Ag presentation by phagocytosis and expression of MHC-I and II molecules and the inhibition of IL‐4 [Th‐2‐derived cytokine] can be responsible for the good immunostimulatory effects of quercetin as shown in (Figure 3) [Nair et al., 2002].

Moreover, Quercetin activates the zinc ionophore property that inhibits the RNA‐dependent RNA polymerase activity (Viral RdRp) of the SARS-2 virus under in vitro conditions in a dose‐dependent manner (Figure 4) [Read et al. 2019].

Figure 4 numbering shows viral attachment (1), viral entry (2), preparation for viral uncoating (3), viral uncoating, and release viral-genome and viral-protein (4), viral-transcription (5), viral-protein translation (6), viral assembly, and maturation (7) and mature viral particles release (8).

Many clinical studies are going for quercetin in which some have recruited, some completed involve in treatment of SARS-CoV 2, Chronic Obstructive Pulmonary Disease (COPD), Heart Failure and many more (See Table 1).

Implementation-

CoV- DrugX Pipeline can access online(http://drugx.kamalrawal.in/drugx/). The pipeline takes SMILES that download from DrugBank https://go.drugbank.com/ of a particular drug (Quercetin). This pipeline contains 14 modules that are used to analyze drug properties. For the SMILE we have to go to Supplementary File 1 and copy that SMILE on the following Supplementary File 2.

A total of 13 modules named drug-circuit, drug-target, drug_dock_human, drug_dock_viral, drug_dock_KG, drug_phenotype, drug_AI_ranking, drug_condition, drug_side_effet, drug_side_effect_neighbours, drug_gene_expression, drug_dl_11, drug_dl_200 and one compile result output file. Two possible scores are available for these modules: 0 and 1. Zero appears when the particular module is not able to be repurposed and one appears when a particular module has repurposable properties. Flowchart of modules shown in Figure 5.

Dataset Collection-

We extracted drug data from the Drug bank using the keyword ‘Quercetin’ (DB04216). The SMILE was obtained as OC1=CC2=C(C(O)=C1)C(=O)C(O)=C (O2)C1=CC=C(O)C(O) =C1. We used the smile of Quercetin as an input to the Cov-DrugX pipeline (Figure 6). The CoV-DrugX uses 13 different modules( See Table 1) for analysis.

SUPPLEMENTARY FILE OF FIGURES

SUPPLEMENTARY FILE OF TABLES

Result

The first module named Drug_dock_Viral was used to dock quercetin against 23 viral proteins. We obtained binding affinities from the docking experiments. The average binding affinity of Quercetin against 23 viral proteins was -7.09 kcal/mol (see Table 3, figure 7 ). We found Npro, Nsp14, Nsp4, Nsp16, and Mapro as top-ranking binding viral proteins. For instance, Npro had shown the best binding affinity with quercetin (-9.2 Kcal/mol). On the other hand, Nsp1 was found to show the least binding affinity (-3.8 Kcal/mol) (See Table 3, Figure7). Similarly, quercetin when docked against human proteins such as ACE2 and TMPRSS2, the binding energy was -7.4 and -6.9 Kcal/mol respectively(See Table 4).

We used a module termed drug-DL-11, which incorporates important biological properties of drugs such as AlogP, PSA, and Rule of five (See Table 5). The drug-DL-11 binary score was predicted to be 1/0. Drug-DL 200 module produced a binary score predicted as 1/0. Further, the details of 200 different physicochemical properties are shown in (See Table 6).

Compiled results for all the 14 modules are shown in (See Table 2), where we get the final score as 0 and 1 for almost all the modules except docking modules which gives the number in-between the range of 0 and 1, considering the cumulative-score for the docked proteins considered in the docking modules.

Acetyltransferase (PCAT) is used as a target that is similar to COVID-19 associated with Quercetin drug with zero percent similarity(See Table 7). Back pain, throat irritation, cough, blood level decrease, sleep disorder side effects of Quercetin similar to COVID-19 with 42.27% similarity (See Table 8).

Euclidean distance b/w Quercetin & SARS-COV-2 shows the value of 6.38 in all four models, but the highest distance is 11 in model 1 with 1027 rank ( See Table 9). The number of common phenotypes i.e. 103 was found of Quercetin against COVID-19 with 100% similarity (See Table 10).

Quercetin showing response with SARS-CoV-2 pathway circuit having gene protein NFKB1, BAX, HSPB1, NFKB2 and ACTB showing host-virus interaction value 1 or 0 having zero inflammatory response, immune activity, and energetics (See Table 11). Also, Quercetin showed abnormal human gene expression during COVID-19 with 52 DOWN, 30 UP, 1 Unknown, and 83 UP/DOWN gene expression (See Table 12, Figure 8).

Conclusion-

DrugX repurposing pipeline is an acceptable and favorable In-Silicon method for detecting the drug repurposing against COVID-19. Quercetin can prevent infection by the interface between ACE2 and SARS-CoV-2. We can use Quercetin for drug repurposable against COVID-19.

The modules having a score of 1 is 7 that shows that these modules recognize the drug is repurposable against COVID-19. Hence, based upon the average score, we find the probability is 53.84% for the drug to be considered for repurposing against COVID-19.

Acknowledgment-

Dr. Kamal Rawal acknowledges the support provided by SERB, Department of Science and Technology (Grant ID: CVD 2020/000842). The project made use of computational infrastructure (servers, etc.) provided by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India (Grant ID: BT/PRI7252/BID/7/708/2016), as well as the Robert J. Kleberg Jr. and Helen C. Kleberg Foundation and Baylor College of Medicine in Houston, Texas, USA (Grant ID: BT/PRI7252/BID/7/708/2016). We'd like to express our gratitude to Amity University for their assistance with this research.

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