Exploration on Ononin and Corylin molecule Against Anti-Influenza H1N1 A Virus via Molecular Docking, Molecular dynamics simulation and Binding free energy calculations

doi:10.21203/rs.3.rs-2431868/v1

Ononin and Corylin drug molecules exhibit antiviral effects against the H1N1 influenza A virus, with IC₅₀ values of30%at 200 µM and > 115 µM, respectively.The drug molecules Ononin and Corylin obey the Lipinski’s rule of five. Ononin and Corylin's ADMET properties indicate that the molecules can be exploited as an oral drug due to high solubility nature. The combined approach of computational methods such as molecular docking, molecular dynamics simulation and binding free calculations was used as a tool to achieve the drug-receptor intermolecular interactions, molecular electrostatic potential, conformational and energetic stability for Ononin and Corylin with H1N1 NA enzyme. The NBO, global and local reactivity descriptors were computed to find the stabilization energy, chemical reactivity, kinetic stability and toxicity nature for Ononin and Corylin molecules. As a consequence, the Ononin and Corylin molecules has good biological activity and could be used as a probable treatment against the H1N1 influenza A virus.

Druglikeness

Molecular Docking

Dipole moment

Molecular Dynamics

Binding Free Energy

Influenza A virus is a highly infectious virus that causes acute to chronic respiratory disease in humans and has caused multiple global outbreaks[1]. The virus isa zoonotic pathogen that infects swine, avian, horse, and other species. Because they are vulnerable to infection by both human and avian influenza viruses, swine have been identified as a key influenza virus mixing vessel, promoting re-assortment among distinct influenza virus strains[2–4]. Influenza A virus is divided into subgroups based on the presence of two glycoproteins: Hemagglutinin (HA)[5, 6] and Neuraminidase (NA)[7, 8]. As a consequence, there are 18 subdivisions of HA and 11 subdivisions of NA, with H1N1 and H3N2 being endemic in humans[9, 10]. HA was a cell-anchoring viral glycoprotein that mediates virus entry and fusion by connecting monosaccharide sialic acid with receptors on host cells and causing viral infection[11, 12]. NA (sialidase) is a hydrolytic viral glycoprotein that may cleave sialic acid off the cell surface as well as release progeny virus particles from host cells[13, 14]. As a result of the expulsion of virus particles from host cells, the viral NA enzyme has been a functioning exploration territory action against anti-influenza drugs. The vast majority of influenza illnesses resolve on their own, although complications can be dangerous in some circumstances[15, 16]. In this regard, there is an urgent need for new anti-influenza drugs to be developed. Most researchers are currently working on fewer generic impactsplant derivative antiviral drug molecules to treat the influenza A virus.Ononin (found in a variety of plants and herbs like soybean and glycyrrhiza uralensis) and Corylin(that is isolated from Psoralea corylifolia L and glycyrrhiza uralensis) is a major isoflavones which belongs to the family Fabaceae. Ononin and Corylinhave various biological effects like anti-viral, anti-bacterial etc. Ononin and Corylin molecules have antiviral activities against the H1N1 influenza A virus, and have been reported to inhibit the H1N1 NA enzyme with IC₅₀ values of 30 percent at 200 µM and > 115 µM, respectively[17].

According to recent literature, there is no extensive study for Ononin and Corylin drug molecules on quantum chemistry calculations utilizing DFT (density functional theory), molecular docking, and molecular dynamics. So far, we investigate the, structural features, HOMO-LUMO,NBO, druglikeness, and ADMET predictions for Corylin and Ononin.The drug-receptor intermolecular interactions, electrostatic potential, conformational and energetic stability of the selected antiviral drugs were also investigated to determine their inhibitory mechanism via molecular docking, molecular dynamics simulation and binding free energy calculations. The goal of this research is to understand how antiviral drugs that target the influenza A virus's replication machinery work.

The structure of Ononin and Corylin molecules was drawn via ChemDraw Ultra 8.0[18]program package. Utilizing Gaussian 09W[19]software program the molecules Ononin and Corylin was optimized to its minimum energy level through density functional theory (DFT)methodwith the basis set 6-311G(d,p).Furthermore, the geometrical parameters, HOMO (Highest Occupied Molecular Orbitals)– LUMO (Lowest Unoccupied Molecular Orbitals) plot, MEP map with Mulliken charges were analysed via Gauss view 5.0.8 [20]software for Ononin and Corylin molecules. Using NBO3.1[21]program the second order Fock matrix which regulates donor-acceptor interactionsfor Ononin and Corylin molecules was computed.The dipole moment structure was drawn via Chemcraft 1.8 software. The molecular docking analysis wasexecuted with AutoDock4.2[22]software program package and their intermolecular interactions amid Ononin and Corylin molecules with H1N1 NA enzyme were performed through PyMOL[23], Discovery Studio[24] and UCSF Chimera[25]software programmes.Molecular dynamics simulation has been implemented through AmberTools14[26] software.

Drug likeness and Bioactivity

Drug likeness prediction (Lipinski’s rule of five)[27, 28]is the most essential parameter in the drug discovery process to appraise the bioavailabilityof the bulk materials.Drug likeness descriptors for Ononin and Corylin are predicted via Molinspiration cheminformaticsonline program (https://www.molinspiration.com) and listed in Table 1.Generally, the molecule active means have to obey the subsequent rules, ≤ 5 hydrogen bond donors (Ononin holds 4 and Corylin holds 1), ≤ 10 hydrogen bond acceptors (Ononin holds 9 and Corylin holds 4), molecular mass ≤ 500 Dalton (Ononin holds 430.41 and Corylin holds 320.34), high lipophilicity (expressed as LogP less than 5) (Ononin holds 1.31 and Corylin holds 4.24), molar refractivity should be among 40–140 (Ononin holds 138.82 and Corylin holds 59.67).Therefore, the molecule Ononin and Corylin obeys the rule of five.

Table 1

Drug likeness descriptor of Ononin and Corylin molecules predicted from Molinspiration
Descriptors	Ononin	Corylin
Hydrogen Bond Donor (nOHNH)	4	1
Hydrogen Bond Acceptor (nON)	9	4
Partition coefficient, Mi logP	1.31	4.24
Molecular Weight (MW)	430.41	320.34
Topological Polar Surface Area (TPSA)(Å²)	138.82	59.67
Number of atoms (natoms)	31	24
Number of rotatable bonds (nrotb)	5	1
Number of violations (nviolations)	0	0
Volume	365.68	283.20

The bioactivity score of Ononin and Corylin molecule is predicted from Molinspiration cheminformatics online tool and listed in Table 2. The probability of bioactive score for biological molecule values under − 0.50 to 0.00 reveals that the molecule moderately active, > -0.50 reveals that the molecule biologically inactive and < 0.00 reveals that the molecule active. Bioactive score for Ononin and Corylin were analysed for GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor, enzyme inhibitor. Thenuclear receptor ligand score value for Ononin (0.03) and Corylin (0.55) is active, expect this nuclear receptor ligand all the score values for Ononin and Corylin falls under − 0.50 to 0.00, thus it is moderately active. Consequently, the molecules Ononin and Corylin are probable candidate for bioactive applications and further applied for docking process.

Table 2

Bioactivity score of Ononin and Corylin molecules predicted from Molinspiration
Compound	GPCR ligand	Ion channel modulator	Kinase inhibitor	Nuclear receptor ligand	Protease inhibitor	Enzyme inhibitor
Ononin	-0.07	-0.42	-0.12	0.03	-0.34	0.22
Corylin	-0.03	-0.54	-0.06	0.55	-0.39	0.24

ADMET Predictions

Today’s generation all the peoples are affected by new unknown diseases easily, so there is a need of new drugs to cure or prevent from diseases. Inventing new drugs faces lot of risk for investment and also has some technical failures at different stages of the drug discovery owing to lengthy process and cost effective. Therefore, before experimental we compute theoretical pharmacokinetic and toxicity properties (absorption, distribution, metabolism, excretion and toxicity [29](ADMET)) via ADMETLAB 2.0 (https://admetmesh.scbdd.com) online platform. The predicted ADMET profiles are elucidate in Table 3.

Table 3

Prediction of ADMET profiles for Ononin and Corylin molecules
ADMET	Ononin	Corylin
Absorption
Caco-2 cell permeability (nm/s)	-5.359^♥	-4.78^•
MDCK cell permeability (nm/s)	6.1e-05^•	1.9e-05^•
P-glycoprotein inhibitor	0.003^•	0.35^♦
P-glycoprotein substrate	0.103^•	0.054^•
Human Intestinal Absorption (HIA+, %)	0.467^♦	0.005^•
Distribution
Plasma Protein Binding (PPB, %)	78.30^•	99.58^♥
Volume Distribution (VD)	1.052^•	0.539^•
Blood Brain Barrier (BBB+)	0.597^♦	0.032^•
Fraction unbound (Fu) in plasms	10.19^•	1.122^♥
Metabolism
CYP 1A2 inhibitor	0.071^•	0.972^♥
CYP 1A2 substrate	0.101^•	0.344^♦
CYP 2C19 inhibitor	0.058^•	0.947^♥
CYP 2C19 substrate	0.077^•	0.066^•
CYP 2C9 inhibitor	0.026^•	0.795^♥
CYP 2C9 substrate	0.732^♥	0.939^♥
CYP 2D6 inhibitor	0.182^•	0.96^♥
CYP 2D6 substrate	0.888^♥	0.893^♥
CYP 3A4 inhibitor	0.051^•	0.886^♥
CYP 3A4 substrate	0.09^•	0.245^•
Excretion
Clearance (CL)	2.491^♥	3.646^♥
T_1/2 (half-life)	0.172^•	0.303^•
Toxicity
Human Ether-a-go-go-Related Gene (HERG) Inhibition	0.128^•	0.432^♦
Human Hepatotoxicity (H-HT)	0.075^•	0.653^♦
Drug Induced Liver Injury (DILI)	0.725^♥	0.563^♦
Ames Toxicity	0.332^♦	0.014^•
Rat Oral Acute Toxicity	0.179^•	0.309^♦
Maximum Recommended Daily Dose (FDAMDD)	0.024^•	0.772^♥
Skin Sensitization	0.062^•	0.532^♦
Carcinogenicity	0.887^♥	0.816^♥
Eye Corrosion	0.003^•	0.003^•
Eye Irritation	0.013^•	0.499^♦
Respiratory Toxicity	0.038^•	0.894^♥
^•for excellent bioactivity, ^♦for medium bioactivity and ^♥for poor bioactivity.

The Caco-2 and MDCK cell permeability are the two significant paraments to reveal the oral absorption of drug molecules. The Caco-2 cell permeability values for Ononin holds poor bioactivity and Corylin holds optimal bioactivity.MDCK cell permeability values for Ononin and Corylin are found to be very low, therefore the drug moleculesboth are very less absorption capacity.The human intestinal absorption (HIA) value for Ononin shows moderate effect and Corylin holds excellent bioactivity.Plasma Protein Binding (PPB) has been used to assess metabolism-related drug-drug interactions and the computed PPB % for Ononin and Corylin is 78.30 and 99.58, respectively; the higher significance indicates that the two drugs interact at the same time. The Corylin exhibits good volume distribution when compare with Ononin. Ononin (0.597) and Corylin (0.032) have exceptionally low Blood Brain Barrier (BBB) values. Therefore, BBB penetration potential in the central nervous system suggests that it has less capacity to cross the BBB. Ames test is a mutagenicity characterization that determines the mutagenicity of a pharmacological molecule. Ames toxicity for Corylin drug molecule has less toxicity and Ononin has high toxicity.On comparing all the ADMET properties for Ononin and Corylin molecule, Corylin hold good bioactivity resultswhen compare to Ononin molecule.

Molecular Docking Analysis

The Ononin and Corylin molecule is a proved inhibitor of H1N1 NA enzyme activity with 30% at 200and ˃115 µM[17]respectively. The PDB structure of H1N1 NA enzyme (PDB ID: 4B7Q with 2.73 Å resolution) wereacquired from RCSB protein data bank. After removing the ions, water and ligand molecules from the protein using UCSF chimera[25]software, it can be taken as a target. Using ChemDraw Ultra 8.0[18]software the Ononin and Corylin 2D structure was drawn andthe structures converted into 3D format through Chem3D Ultra 8.0 [18] program. The drawn converted structures Ononin and Corylin were optimized to its minimum energy conformation through Gaussian 09W [19]software then the optimized structures were converted into PDB format, it can be taken as a ligand.Furthermore, the molecular docking analysis was performed by Autodock4.2 [22]software program based onthe steps followed in the literature[30].

From the docking results, the predicted 10 conformers and their corresponding binding energy values are listed in Table 4. Among these 10 conformers 6th conformer is the best conformer for Ononin and 9th conformer is the best conformer for Corylin. The docking analysis predicts the lowest docked energy for Ononin and Corylin molecule are-4.98 and − 7.53 kcal/mol (with 224.92 and 3.02 ki uM (micromol) inhibition constant) respectively. The intermolecular interactions and surface view formed by Ononin and Corylin molecule in the active site of NA enzyme are shown in Figs. 1 and 2 respectively. The binding of these molecules to the NA enzyme leads to a structural change in the NA enzyme. The investigation of the structural change is responsible for the inhibition of the NA enzyme.

Table 4

The docking score value of 10 possible conformers of Ononin and Corylin molecules in the active site of NA enzyme
Conformers	Ononin		Corylin
Conformers	Binding energy (kcal mol^− 1)	Inhibition constant, ki uM (micromol)	Binding energy (kcal mol^− 1)	Inhibition constant, ki uM (micromol)
1	-3.87	1450.00	-7.5	3.2
2	-4.97	228.36	-6.04	37.08
3	-3.98	1210.00	-6.76	11.05
4	-4.50	506.32	-6.82	10.1
5	-4.31	943.00	-6.73	11.76
6	-4.98	224.92	-6.88	9.01
7	-4.57	444.70	-7.38	3.88
8	-4.15	913.30	-6.77	10.85
9	-4.18	869.84	-7.53	3.02
10	-4.31	698.08	-7.37	3.99

Ononin - H1N1 NA enzyme complex

The amino acid residues involved in the intermolecular interactions with Ononin molecule in the active site of NA enzyme are Arg 220, Asn 221, Pro 246, Ala 251, Glu 268, Met 269, Asn 270 and Ala 271. Among these residues the amino acids Glu 268, Met 269, Asn 270 and Ala 271 are involved in the strong conventional hydrogen bonding interactions with the Ononin molecule at the distances of 2.23, 1.96, 2.73 and 1.68 Å respectively. These strongly suggest that the Ononin molecule is stabilized by forming hydrogen bonding interactions with these important amino acid residues.The amino acids Arg 220, Pro 246 and Ala 251 form Pi-Alkyl interactions with Ononin molecule. The Arg 220 forms Pi-cation interaction with Ononin molecule at a distance of 3.22 and 3.29 Å.

Corylin - H1N1 NA enzyme complex

The active site amino acid residues for Corylin molecule interact with NA enzyme are Ile 118, Phe 174, Glu 175, Trp 190, Lys 207, Asn 209 and Gly 210. Among these residues Trp 190 forms two strong Pi-Pi T-shaped interactions with Corylin molecule at a distance of 4.69 and 4.55 Å and also forms one Amide-Pi stacked interaction with Asn 209 at a distance of 3.90 Å. The Corylin molecule forms strong conventional hydrogen bonding interaction with Ile 118 and Trp 190 with a distance of 2.01 and 1.93Å respectively. The amino acid residues Lys 207 and Phe 174 forms Pi-Alkyl interactions with Corylin molecule at a distance of 5.38 and 4.52 Å respectively.

On comparing these two moleculesinteract with NA enzyme, Corylin exhibits good binding score and interactions. Consequently, Corylin is a potential candidate for H1N1 NA enzyme.

Structural Aspects

Ononin - H1N1 NA enzyme complex

Figure 3(a) exposes the ball and stick model of Ononin molecule in gasphase and active site of H1N1 NA enzyme with atom numbering scheme. The selected geometrical parameters ofOnonin molecule in both phases (gas phase and active site) are represented in Table 5. Bond angles and bond lengths for the Ononin molecule have not shown much variation. The docking analysis reveals that the compound adopts a new confirmation in the active site, which is due to an intermolecular interaction between Ononin and the H1N1 NA enzyme. The torsional angles for Ononin molecule have much variation in active site.The bond value for C7 − O12 − C14 − H36, H36 − C14 − C15 − H37 and C14 − C15 − O23 − H46 are-38.3/-35.9, 77.4/74.9 and − 78.5/59.9 respectively. The torsional angle of H36 − C14 − C15 − O23, C16 − C15 − O23 − H46 and O22 − C16 − C17 − H39 bonds also have deviation because it fits very well in the active site cavity and the values are − 39.1/-42.1, 46.3/65.0 and − 48.8/-50.1 respectively.

Table 5

Selected geometrical parameters of Ononin and Corylin molecules in gas phase and active sites
Parameters	Ononin		Parameters	Corylin
Torsion angles(°)	Gas phase	Active site	Torsion angles(°)	Gas phase	Active site
C4 − C5 − C6 − H34	-178.9	-179.4	C1 − C2 − C18 − C17	140.1	-137.9
H34 − C6 − C7 − H12	-1.2	-0.6	C1 − C2 − C18 − C19	-38.8	43.1
C7 − C8 − C9 − C4	0.4	0.4	C3 − C2 − C18 − C17	-39.9	42.1
C7 − O12 − C14 − H36	-38.3	-35.9	C3 − C2 − C18 − C19	141.1	-137.0
C18 − O13 − C14 − H36	168.0	168.7	H28 − C8 − C9 − O10	0.2	0.3
C14 − O13 − C18 − H40	-166.9	-165.8	C23 − C13 − C14 − H30	81.6	84.3
O12 − C14 − C15 − C16	76.0	76.1	C14 − C13 − C23 − H36	59.8	64.0
H36 − C14 − C15 − C16	-162.8	-165.8	C14 − C13 − C23 − H37	-59.8	-56.0
H36 − C14 − C15 − O23	-39.1	-42.1	O22 − C13 − C23 − H35	58.6	63.8
H36 − C14 − C15 − H37	77.4	74.9	O22 − C13 − C23 − H36	-61.7	-56.2
C14 − C15 − C16 − H38	164.0	165.9	C24 − C13 − C23 − H35	-55.5	-60.0
H37 − C15 − C16 − C17	167.1	166.1	C24 − C13 − C23 − H36	-175.7	180.0
H37 − C15 − C16 − O22	44.1	43.1	C24 − C13 − C23 − H37	64.7	60.0
H37 − C15 − C16 − H38	-75.8	-74.8	H30 − C14 − C15 − H31	0.4	-3.0
C14 − C15 − O23 − H46	-78.5	-59.9	C2 − C18 − C19 − O11	-3.8	-1.9
C16 − C15 − O23 − H46	46.3	65.0	H33 − C19 − C20 − O11	1.7	0.8
H37 − C15 − O23 − H46	163.9	-177.0
C15 − C16 − C17 − H39	-169.9	-171.2
O22 − C16 − C17 − H39	-48.8	-50.1
H38 − C16 − C17 − C18	-165.7	-168.4
H38 − C16 − C17 − O21	-44.9	-47.6
H38 − C16 − C17 − H39	73.7	69.7
H39 − C17 − O21 − H44	68.9	70.0
C17 − C18 − C19 − H42	57.2	55.5
H40 − C18 − C19 − O20	54.4	52.1
C2 − C24 − C25 − H47	3.7	2.0
C29 − C24 − 25 − H47	-176.9	-178.5
H49 − C28 − C29 − H50	0.9	0.3

Corylin - H1N1 NA enzyme complex

The ball and stick model of Corylin molecule (gas phase and active site of H1N1 NA enzyme) is exposed in Fig. 3(b). Table 5 depicts the selected geometrical parameters of Corylin molecule in gas phase and active site. As per the docking analysis, the drug molecule Corylin accepts a new confirmation in the active site as a result of an intermolecular interaction between Corylin and the H1N1 NA enzyme. Bond angles and bond lengths for the Corylin molecule have not varied significantly.The torsional angles of C1 − C2 − C18 − C17, C3 − C2 − C18 − C19 and C24 − C13 − C23 − H37 are high in gas phase and the values are 140.1/-137.9, 141.1/-137.0 and 64.7/60.0 respectively. The angles have large difference in active site for torsional angles C1 − C2 − C18 − C19, C3 − C2 − C18 − C17 and C24 − C13 − C23 − H36 and high in gas phase for torsional angles C3 − C2 − C18 − C19 and C24 − C13 − C23 − H37. The Corylin molecule when enters in the active site the molecule twisted and fits very well in active site.

Global Reactivity Descriptors

In quantum chemistry, the HOMO and LUMO are the crucial electronic parameters (global reactivity descriptors) to explore the chemical reactivity, kinetic stability and toxicity nature of Ononin and Corylin molecules.The global reactivity descriptors such as HOMO energy (E_HOMO), LUMO energy (E_LUMO), energy gap (E_g= E_HOMO -E_LUMO), ionization potential (I = -E_HOMO), electron affinity (A = -E_LUMO), global hardness (η = (I-A)/2), electronegativity (χ = (I + A)/2), chemical potential (µ = -χ), electrophilicity (ω = µ²/2η), and chemical softness (s = 1/2η) are the parameters listed in Table 6. The HOMO and LUMO orbitals of Ononin and Corylin molecules in gas phase and active site are exposed in Fig. 4. The energy gap is the difference in energy between the HOMO and LUMO orbitals, softmolecules have smaller band gap energy, while hard molecules have greater band gap energy[31–36]. The Ononin (4.239eV for gas phase and 4.227eV for active site) and Corylin (4.009eV for gas phase and 4.005eV for active site) molecules have small energy gap, therefore the molecules fall under soft molecule category. The concept of electrophilicity index initially proposed by Parr et al[37]. to determine the energy lowering owing to maximal electron flow between acceptor and donor to expose the material's toxicity. The electrophilicity value for Ononin (3.130eV for gas phase and 3.178eV for active site) and Corylin (3.232eV for gas phase and 3.252eV for active site) molecules is found to be very low; therefore the molecule has less toxicity.

Table 6

Calculated global reactivity descriptors for Ononin and Corylin molecules
Molecular descriptors Energy(eV)	Ononin		Corylin
Molecular descriptors Energy(eV)	Gas phase	Active site	Gas phase	Active site
HOMO energy (E_HOMO)	-5.761	-5.779	-5.603	-5.611
LUMO energy (E_LUMO)	-1.523	-1.552	-1.595	-1.606
Energy gap (E_g)	4.239	4.227	4.009	4.005
Ionization potential (I)	5.761	5.779	5.603	5.611
Electron affinity (A)	1.523	1.552	1.595	1.606
Global hardness (η)	2.119	2.113	2.004	2.002
Electronegativity (χ)	3.642	3.665	3.599	3.609
Chemical potential (µ)	-3.642	-3.665	-3.599	-3.609
Electrophilicity (ω)	3.130	3.178	3.232	3.252
Chemical softness (s)	0.236	0.237	0.249	0.250

Molecular Electrostatic Potential

Molecular electrostatic potential (MEP) map is to reveal thedetails about electron density throughout the drug molecule in biological environment. In MEP map the electron rich area tends to electrophilic sites and electron poor area tends to nucleophilic sites.The MEP map canalso beused to locate the reactive sites of ligand molecules attached to biological receptors[38, 39].The colour code for MEP map is in the increasing electron density order ofred < orange < yellow < green < skyblue < blue, respectively.Furthermore, the Mulliken sketch was given similar to the MEP in Fig. 5, and the MEP map is coloured based on Mulliken atomic charges to conclude the appropriate indication of unique atoms. The MEP map colour code is in the ranges from − 6.299e-2 to 6.299e-2 (for Ononin gas phase),-7.506e-2 to 7.506e-2 (for Ononin active site), -7.375e-2 to 7.375e-2 (for Corylin gas phase), and − 7.277e-2 to 7.277e-2 (for Corylin active site).The positive electrostatic potential is indicated by orange to darkest red colour, negative electrostatic potential is denoted by the sky blue to deepest blue colour, and neutral charge is represented by the green colour for the Ononin and Corylin molecules.TheMEP map values are modified in active sites for Ononin and Corylin molecules, because it fits very well in the active site cavity.

Natural Bond Orbital Analysis

The NBO analysis was used to reveal the intermolecular orbital interactions in the complex, particularly charge transfer, as well as intra and intermolecular interactions at both the filled and virtual levels.Utilizing second order perturbation theory analysis through Fock matrix with hyperconjugative interactions, the donor-acceptor interactions can be quantized based on stabilization energy (E2)[40].

F_ij, q_i, and ε_i,jare the Fock matrix elements between i and j NBO orbitals, donor orbital occupancy, and diagonal element orbital energies.Table 7 expose the natural bond energies of Ononin and Corylin molecules.The possible interactions for Ononin and Corylin molecules areπ → π*, LP → σ* and LP → π*. The electron density transfer from lone pair LP(2) of oxygen atoms O(10), O(10), O(12) and O(22) interact with π* areπ*(C1 − C2), π*(C4 − C9), π*(C7 − C8) and π*(C20 − C21) with high stabilization energies of 29.41, 28.15, 31.34, and 26.63 kJ/mol respectively, has resulted in a strong hyper conjugative interaction for Corylin molecule. In Ononin molecule, the LP(2) of oxygen atoms O(10), O(10),O(12) and O(30) interacts with 29.95, 27.46, 29.38 and 30.74 kJ/mol respectively. This value clearly declares that the molecules Ononin and Corylin possess strong stabilization energy with lone pair of oxygen atoms.

Table 7

Second order perturbation theory analysis of Fock matrix in NBO basis for Ononin and Corylin molecules at 6-311G(d,p) level of theory
Corylin							Ononin
Donor (i)	ED (e)	Acceptor (j)	ED (e)	E(2)^a (kJ mol^− 1)	E(j) − E(i)^b (a.u)	F(i, j)^c (a.u)	Donor (i)	ED (e)	Acceptor (j)	ED (e)	E(2)^a (kJ mol^− 1)	E(j) − E(i)^b (a.u)	F(i, j)^c (a.u)
π(C1 − C2)	1.835	π*(C3 − O11)	0.262	19.70	0.32	0.072	π(C1 − C2)	1.835	π*(C3 − O11)	0.259	19.79	0.32	0.072
π(C4 − C9)	1.641	π*(C3 − O11)	0.262	21.80	0.30	0.074	π(C4 − C9)	1.625	π*(C3 − O11)	0.259	21.61	0.30	0.073
π(C4 − C9)	1.641	π*(C5 − C6)	0.259	20.22	0.30	0.072	π(C4 − C9)	1.625	π*(C5 − C6)	0.292	22.05	0.30	0.074
π(C4 − C9)	1.641	π*(C7 − C8)	0.370	14.95	0.28	0.058	π(C4 − C9)	1.625	π*(C7 − C8)	0.373	16.13	0.28	0.060
π(C5 − C6)	1.723	π*(C4 − C9)	0.427	15.29	0.28	0.061	π(C5 − C6)	1.718	π*(C4 − C9)	0.444	14.97	0.28	0.060
π(C5 − C6)	1.723	π*(C7 − C8)	0.370	24.05	0.27	0.074	π(C5 − C6)	1.718	π*(C7 − C8)	0.373	23.83	0.28	0.074
π(C7 − C8)	1.692	π*(C4 − C9)	0.427	24.14	0.30	0.078	π(C7 − C8)	1.658	π*(C4 − C9)	0.444	25.39	0.29	0.078
π(C7 − C8)	1.692	π*(C5 − C6)	0.259	13.03	0.31	0.057	π(C7 − C8)	1.658	π*(C5 − C6)	0.292	14.45	0.30	0.059
π(C14 − C15)	1.919	π*(C16 − C17)	0.367	11.59	0.32	0.058	π(C24 − C25)	1.677	π*(C26 − C27)	0.393	17.49	0.27	0.063
π(C16 − C17)	1.654	π*(C14 − C15)	0.091	15.15	0.29	0.064	π(C24 − C25)	1.677	π*(C28 − C29)	0.294	20.37	0.29	0.069
π(C16 − C17)	1.654	π*(C18 − C19)	0.397	18.43	0.28	0.065	π(C26 − C27)	1.663	π*(C24 − C25)	0.372	22.22	0.30	0.073
π(C16 − C17)	1.654	π*(C20 − C21)	0.369	23.36	0.28	0.072	π(C26 − C27)	1.663	π*(C28 − C29)	0.294	15.59	0.30	0.062
π(C18 − C19)	1.656	π*(C16 − C17)	0.367	21.43	0.29	0.071	π(C28 − C29)	1.975	π*(C24 − C25)	0.372	17.56	0.28	0.064
π(C18 − C19)	1.656	π*(C20 − C21)	0.369	18.28	0.28	0.064	π(C28 − C29)	1.975	π*(C26 − C27)	0.393	22.90	0.27	0.072
π(C20 − C21)	1.638	π*(C16 − C17)	0.367	17.70	0.30	0.065	LP(2)O10	1.747	π*(C1 − C2)	0.195	29.95	0.38	0.096
π(C20 − C21)	1.638	π*(C18 − C19)	0.397	23.10	0.29	0.074	LP(2)O10	1.747	π*(C4 − C9)	0.444	27.46	0.37	0.094
LP(2)O10	1.746	π*(C1 − C2)	0.195	29.41	0.38	0.096	LP(2)O11	1.883	σ*(C2 − C3)	0.070	19.57	0.70	0.106
LP(2)O10	1.746	π*(C4 − C9)	0.427	28.15	0.37	0.095	LP(2)O11	1.883	σ*(C3 − C4)	0.066	19.03	0.71	0.105
LP(2)O11	1.883	σ*(C2 − C3)	0.070	19.53	0.70	0.105	LP(2)O12	1.833	π*(C7 − C8)	0.373	29.38	0.34	0.094
LP(2)O11	1.883	σ*(C3 − C4)	0.066	18.98	0.71	0.105	LP(2)O13	1.894	σ*(O12 − C14)	0.074	15.69	0.58	0.086
LP(2)O12	1.861	π*(C7 − C8)	0.370	31.34	0.35	0.099	LP(2)O30	1.839	π*(C26 − C27)	0.393	30.74	0.34	0.097
LP(2)O22	1.842	π*(C20 − C21)	0.369	26.63	0.35	0.091

Dipole Moment

The dipole moment is simply the measure of net polarity in a drug molecule. If a molecule contains the polar bonds that are unevenly distributed about the centre, there will be an uneven charge distribution across the entire molecule, making it a polar molecule. Dipole moments tell us about the charge separation in a molecule. Larger the electro-negativities of bonded atoms, larger the dipole moment. The dipole moment signifies the change inpolarity of a molecule due to the intermolecular interaction with environment and also reveals the information about charge redistribution.

The dipole moment values were calculated for Ononin and Corylin molecules in gas phase and active site forms are presented in Table 8.The dipole moment value of Ononin molecule ingas phase is7.0943 Debye, this value is decreased to 6.2193 Debye when the molecule present in the active site of influenza H1N1 NA enzyme. This can be observed from the high alteration in the orientation of the dipole moment vectors, shown by the superimposed view in Fig. 6(a). This difference is due to the charge redistribution taking place in the active site when the molecule forms intermolecular interactions with the active site residues.The dipole moment values of Corylin molecule ingas phase and the active site forms are 2.6709 Debye and 3.7780 Debye respectively. The value of dipole moment is significantly increased in the active site, this enhancement is due to the strong intermolecular interaction present in the active site. This variation can be well understood when compare the dipole moment vectors of gas phase and active site forms of Corylin molecule shown in Fig. 6(b).

Table 8

The dipole moment values of ononin and Corylin molecules in gas phase and active site forms
Descriptors (Debye)	Ononin		Corylin
Descriptors (Debye)	Gas phase	Active site	Gas phase	Active site
µ_x	-3.2826	-3.0731	1.2613	-0.9073
µ_y	6.1572	4.9961	2.2236	-2.2217
µ_z	1.2822	2.0676	-0.7737	2.9179
µ	7.0943	6.2193	2.6709	3.7780

Molecular Dynamics (MD) Simulation

On comparing all the above studies with Ononin molecule the Corylin molecule holds good results, therefore the further MD simulation is only computed for Corylin molecule. In order to understand the binding stability ofCorylin molecule-influenza H1N1 NA enzyme complex duringthe MDsimulation has been performed using AmberTools14[26]software up to 100ns. Figure 7(a)shows the root mean square deviation (RMSD) contours for Corylin-influenza H1N1 NA enzyme complex.During the MD simulation there is a continuous fluctuation was observed, this expose that the complex is less stable.In the initial period, the RMSD is found to be increased up to 37 ns, further there are many fluctuations found up to 40 ns. After 44 ns, the RMSD was stabilized until 58 ns, this can be understood from the figure. Beyond58 ns, the RMSD again decreased and reached the maximum value at ~ 66 ns followed by the gradual decreased; further the RMSD was stabilized and remains the same at the end of the MD simulation. Figure 7(b) displays the root mean square fluctuation (RMSF) of 380 amino acid residues of the influenza H1N1 NA enzyme bound to Corylin molecule.From the figure, the influenza H1N1 NA enzyme residues 60–70 are showing high fluctuation; this is due to the impact of Corylin binding with the active site. This study reveals some vital ideas about the development of anti-influenza agents against H1N1 influenza A virus.

Binding Free Energy Calculation

The MM/GBSA(Molecular Mechanics/Generalized Born Surface Area)binding free energy calculation of Corylin complexed with influenza H1N1 NA enzyme is represented in Table 9.The Van der Waals free energy contribution for Corylin molecule is found to be -20.4681 kcal/mol, this value confirms the molecule has strong contribution with influenza H1N1 NA enzyme. The Electrostatic binding free energy contribution for Corylin molecule is found to be -25.5907 kcal/mol. The total binding energy values of Corylin bound withinfluenza H1N1 NA enzyme is-20.9481kcal/mol and this value is well agreement with theIC₅₀ values of > 115 µM.These values show that the molecule Corylin has strong influence withinfluenza H1N1 NA enzyme.

Table 9

Binding Free Energy and its components based on MM/GBSA method (kcal/mol) for Corylin molecule
Binding Free energy/ BFE components	Corylin
MM energy components
∆E_ele	-25.5907 ± 0.1749
∆E_vdw	-20.4681 ± 0.1183
∆E_MM	-46.0588 ± 0.2932
GBSA energy components
∆G_GB	28.0771 ± 0.1035
∆G_SA	-2.9664 ± 0.0083
∆E_ele+∆G_GB(∆G_polar)	2.4864 ± 0.2784
∆E_vdw+∆G_SA(∆G_nonpolar)	-23.4345 ± 0.1266
Total binding free energy
∆G_bind	-20.9481 ± 0.405
∆E_ele – Electrostatic contribution in the binding free energy.
∆E_vdw – Van der Waals contribution in the binding free energy.
∆E_MM – Molecular mechanics contribution in the binding free energy.
∆G_GB – Polar solvation contribution in the binding free energy.
∆G_SA – Non-polar solvation contribution in the binding free energy.
∆G_bind – Binding free energy without entropic contribution.
∆G_total – Total binding free energy.

In the present study, the selected anti-viral agents Ononin and Corylin molecules obeys the Lipinski’s rule of five and the Corylin molecule holds good bioactivity score when compare to Ononin. In ADMET prediction the Corylin drug molecule holds the good values when compare with Ononin molecule. The docking results revealed that Corylin molecule holds good binding energy and forms strong inter molecular interactions with influenza H1N1 NA enzyme compare with Ononin molecule.The Ononin and Corylin molecules fall under soft molecule category. The electrophilicity value for Ononin and Corylin has less values therefore both the molecules hold less toxicity. The molecules Ononin and Corylin possess strong stabilization energy with lone pair of oxygen atoms. The dipole moment value for Corylin molecule holds good values when present in active site form due to strong intermolecular interactions present in active site. On comparing all the studies Corylin molecule holds good results when compare with Ononin molecule, therefore the molecular dynamics and binding free energy calculation only done for Corylin molecule.On the whole, the findings of these studies provide some keyideas for further development of anti-influenza agents against H1N1 Influenza A virus.

Ethics approval

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Competing Interest

There are no conflicts of interest to declare for each contributing author.

Authors’ contribution

Sathya Bangaru - Software, Conceptualization, Formal analysis, Investigation, Data Curation,

Methodology, Validation, Writing - Original Draft, Writing - Review & Editing.

KeerthivasanThamotharan - Software, Validation, Investigation.

Srinivasan Manickam - Software, Validation, Investigation.

Anandha Krishna Ramasamy - Software, Validation, Investigation.

Ramasamy Perumalsamy - Supervision, Correction.

Funding - The authors did not receive funds, grants, or other support from any organization for the submitted work.

Availability of data and materials

Not applicable.

Z. Wang, L. P. Cheng, X. H. Zhang, W. Pang, L. Li, and J. L. Zhao, Bioorg. Med. Chem. Lett. 27, 5429 (2017).
J. S. Griffith and L. E. Orgel, Q. Rev. Chem. Soc. 11, 381 (1957).
D. Kobasa, A. Takada, K. Shinya, M. Hatta, P. Halfmann, S. Theriault, H. Suzuki, H. Nishimura, K. Mitamura, N. Sugaya, T. Usui, T. Murata, Y. Maeda, S. Watanabe, M. Suresh, T. Suzuki, Y. Suzuki, H. Feldmann, and Y. Kawaoka, Nature 431, 703 (2004).
T. M. Tumpey, A. García-Sastre, J. K. Taubenberger, P. Palese, D. E. Swayne, and C. F. Basler, Proc. Natl. Acad. Sci. 101, 3166 (2004).
Z. Zhu, R. Li, G. Xiao, Z. Chen, J. Yang, Q. Zhu, and S. Liu, Eur. J. Med. Chem. 57, 211 (2012).
X. Xu, X. Zhu, R. A. Dwek, J. Stevens, and I. A. Wilson, J. Virol. 82, 10493 (2008).
R. P. Verma and C. Hansch, Bioorg. Med. Chem. 14, 982 (2006).
S. J. Gamblin, L. F. Haire, R. J. Russell, D. J. Stevens, B. Xiao, Y. Ha, N. Vasisht, D. A. Steinhauer, R. S. Daniels, A. Elliot, D. C. Wiley, and J. J. Skehel, Science (80-. ). 303, 1838 (2004).
A. Sakudo, K. Baba, M. Tsukamoto, A. Sugimoto, T. Okada, T. Kobayashi, N. Kawashita, T. Takagi, and K. Ikuta, Bioorg. Med. Chem. 17, 752 (2009).
J. L. McKimm-Breschkin, S. Barrett, P. A. Pilling, S. Hader, A. G. Watts, and V. A. Streltsov, J. Med. Chem. 61, 1921 (2018).
Y. Li, Z. Lin, M. Zhao, T. Xu, C. Wang, L. Hua, H. Wang, H. Xia, and B. Zhu, ACS Appl. Mater. Interfaces 8, 24385 (2016).
M. N. Matrosovich, T. Y. Matrosovich, T. Gray, N. A. Roberts, and H.-D. Klenk, J. Virol. 78, 12665 (2004).
P. Palese, K. Tobita, M. Ueda, and R. W. Compans, Virology 61, 397 (1974).
P. C. Nair and M. E. Sobhia, Eur. J. Med. Chem. 43, 293 (2008).
P. M. Colman, P. A. Hoyne, and M. C. Lawrence, J. Virol. 67, 2972 (1993).
H. Goto and Y. Kawaoka, Proc. Natl. Acad. Sci. 95, 10224 (1998).
U. Grienke, M. Schmidtke, S. von Grafenstein, J. Kirchmair, K. R. Liedl, and J. M. Rollinger, Nat. Prod. Rep. 29, 11 (2012).
L. D. Mendelsohn, J. Chem. Inf. Comput. Sci. 44, 2225 (2004).
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb,J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson,H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino,G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda,J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd,E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski,G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels,O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision B.01, Gaussian, Gaussian, Inc., Wallingford CT, Gaussian, Inc., Wallingford CT. (2010).
E. Frisch, H.P. Hratchian, R.D. Dennington II. et al., Gaussview Version 5.0.8, 235 (Gaussian Inc,Wallingford, 2009).
F. Weinhold, C.R. Landis, Weinhold, valency and bonding: a natural bond orbital donor acceptorperspective (Cambridge University Press, Cambridge, 2005).
G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, and A. J. Olson, J. Comput. Chem. 30, 2785 (2009).
W. L. DeLano, The PyMOL Molecular Graphics System, Schrödinger LLC, Wwwpymolorg, Version 1.8, 2002, http://www.pymol.org., https://doi.org/citeulike-article-id:240061.
Dassault Syst_emes BIOVIA, Discovery Studio, 2016. DS2016Client32, SanDiego: Dassault Syst_emes (2016).
E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, J. Comput. Chem. 25, 1605 (2004).
D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods, J. Comput. Chem. 26, 1668 (2005).
C. A. Lipinski, F. Lombardo, B. W. Dominy, and P. J. Feeney, Adv. Drug Deliv. Rev. 46, 3 (2001).
E. A. Alodeani, M. Arshad, and M. A. Izhari, Asian Pac. J. Trop. Biomed. 5, 676 (2015).
C. Kramer, A. Ting, H. Zheng, J. Hert, T. Schindler, M. Stahl, G. Robb, J. J. Crawford, J. Blaney, S. Montague, A. G. Leach, A. G. Dossetter, and E. J. Griffen, J. Med. Chem. 61, 3277 (2018).
M. H. Syed Mohd. Danish Rizvi, Shazi. Shakil, EXCLI J. 12, 831 (2013).
B. Sathya and M. Prasath, Res. Chem. Intermed. 45, 2135 (2019).
S. Bangaru, M. Saravanan, S. Manickam, P. Manivannan, and R. Perumalsamy, Res. Chem. Intermed. 48, 2745 (2022).
B. Sathya, M. Prasath, M. Selvapandiyan, and K. Prabha, J. Clust. Sci. 30, 1025 (2019).
S. Bangaru and P. Manivannan, Res. Chem. Intermed. 47, 2775 (2021).
S. Bangaru, P. Manivannan, and S. Muthu, Chem. Data Collect. 30, 100580 (2020).
B. Sathya, S. Karthi, K. Ajaijawahar, and M. Prasath, Res. Chem. Intermed. 46, 4475 (2020).
R. G. Parr and R. G. Pearson, J. Am. Chem. Soc. 105, 7512 (1983).
E. Scrocco and J. Tomasi, in (1978), pp. 115–193.
P. Politzer and J. S. Murray, Theor. Chem. Accounts Theory, Comput. Model. (Theoretica Chim. Acta) 108, 134 (2002).
F. Weinhold, C.R. Landis, Weinhold, valency and bonding: a natural bond orbital donor acceptorperspective (Cambridge University Press, Cambridge, 2005).

No competing interests reported.

Exploration on Ononin and Corylin molecule Against Anti-Influenza H1N1 A Virus via Molecular Docking, Molecular dynamics simulation and Binding free energy calculations

Status:

Journal Publication

Version 1

Abstract

Figures

Introduction

Computational Details

Drug likeness and Bioactivity

ADMET Predictions

Molecular Docking Analysis

Ononin - H1N1 NA enzyme complex

Corylin - H1N1 NA enzyme complex

Structural Aspects

Ononin - H1N1 NA enzyme complex

Corylin - H1N1 NA enzyme complex

Global Reactivity Descriptors

Molecular Electrostatic Potential

Natural Bond Orbital Analysis

Dipole Moment

Molecular Dynamics (MD) Simulation

Binding Free Energy Calculation

Conclusion

Declarations

References

Additional Declarations

Status:

Journal Publication

Version 1