Supplementary File S2
Quantitative Structure-Activity Relationship (QSAR) analysis is used to identify anti-viral activities of different approved anti-viral drugs, which are experimentally studied against SARS CoV 2. The experimental validation of the anti-viral activity of chosen five natural compounds and their ability to inhibit the S protein-ACE2 interaction is shown here by QSAR study. In this QSAR study of various antiviral compounds, some descriptor parameters of selected chemical properties with calculated binding energies with ACE2 & spike protein structure, are used to correlate with quantitative structure-activity relationship (QSAR) analysis using multiple linear regression (MLR) model.
In various models developed using MLR technique, the statistical parameters, like cross validated coefficient (CV) defines the goodness of prediction, whereas the non-cross validated conventional correlation coefficient (r 2 ) defines the goodness of fit of the QSAR model.
There are several steps in QSAR model development. First a dataset of similar chemical compounds with same biological activity have been identified. This QSAR study is performed with 43 compounds. First 36 compounds [1] , [2] , [3] , [4] , [5] , [6] and their antiviral activities are compared with chosen five natural compounds and two well-known drugs for treatment of COVID-19 (chloroquine and hydroxychloroquine) [7] , [8] with inhibitory effects against SARS CoV 2 in this study. Then different types of descriptors are calculated and using generic algorithm most suitable descriptors have been identified. With the help of these selected descriptors QSAR model is constructed.
The model is generated using four descriptors in Multiple Linear Regression model in BuildQSAR software [9] . The QSAR Model is represented as QSAR equation, with the correlation coefficients calculated for each descriptor used in the regression model. By plotting the experimental activity (Yobs) vs predicted activity (Ycalc), the built model is evaluated for its predictive powers to determine activity as QSAR model for anti-viral activity of five natural compounds. One linear model is built using four selected descriptors. The plot for correlation analysis between observed binding energy and calculated binding energy, is shown in Figure S2 . This QSAR investigation indicates that the descriptors, namely AWeight, ncocl, diametert and Bertzct, are chosen GA-selected descriptors for the set of anti-viral compounds. These chosen compounds can act as spike protein inhibitors for ACE2 binding in laboratory experimental studies and are found to have a great deal to positively contribute to biological activity -antiviral activity against SARS CoV2.
Molecular dynamics study with the bound structure of ACE2 & spike protein fragment is performed using simulation tool (http://mmb.irbbarcelona.org/MDWeb/index.php) [10] , known as course-grained molecular dynamics (Brownian dynamics: C-alpha) after preparing the molecule with GROMACS molecular simulation and AMBER-99SB* forcefield is carried out. Simulation study is completed for 100 ps (Δt 0.01ps) with force constant 40.0 Kcal/mol*Å 2 . Output frequency is recorded for 10 steps and the distance between alpha carbon atoms is 3.8 Å. The bound structures of ACE2 & spike protein fragment in absence and presence of hesperidin after molecular dynamics simulation study are compared here.
The bound structure of ACE2 & spike protein fragment in absence and presence of hesperidin after molecular dynamics simulation study is presented in Figure S2 .2 (a) and (b). Structure of ACE2 protein molecules with spike protein fragment present in molecular dynamics trajectory is represented by ribbon structure in absence of hesperidin and by liquorice structure in presence of hesperidin. 
In absence of hesperidin, B factor per residue varies from 0.0 to 20.0 and in presence of modulator the same characteristic changes from 0.0 to 700.0 for each residue of bound structure. Due to presence of hesperidin, the degree of thermal mobility and static disorder of atoms around 130 sequence position, are increased abruptly. This position of ACE2 protein is its ligand binding site for spike protein fragment (Figure 6 and 7) . It proves that hesperidin can act as a modulator and decreases the ligand binding affinity of spike protein to its receptor ACE2 protein molecule.
The radius of gyration is a quantitative measurement of the overall size of a protein molecule. The change in the structure of a protein during MD simulations can be quantified by radius of gyration. The radius of gyration of the bound structure of ACE2 & spike protein fragment in absence and presence of hesperidin after molecular dynamics simulations are presented in the following Figure S.2.4 a) and b). The radius of gyration of the bound structure of ACE2 & spike protein fragment decreases up to 7 snapshots of MD simulation and in last three snapshots remains almost unchanged. In presence of hesperidin molecule, the value of the radius of gyration of the bound structure of ACE2 & spike protein fragment fluctuates during MD simulation due to instability in docking structure. From molecular simulation study for various parameters, it can be concluded that hesperidin can act as modulator for the bound structure of ACE2 & spike protein fragment. This analysis confirms the antiviral activity of natural compound hesperidin as non-competitive allosteric modulator of spike protein binding with its human host receptor.