Research Article - (2024) Volume 15, Issue 2

Molecular Docking Study of the Benzylidene-bis- (4-Hydroxycoumarin) Derivatives as Antiviral to Coronavirus COVID-19

Cengiz Ipek1* and Hacer Gumus2
*Correspondence: Cengiz Ipek, Department of Civil Engineering, Istanbul Medeniyet University, Istanbul, Turkey, Email:

Author info »


In this study, the geometric structure determination of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule and its parameters (bond length and angles), Nuclear Magnetic Resonance (NMR) spectroscopes, electrical (HOMO, HOMO-1, LUMO and LUMO+1) properties, Mulliken, NBO and Atomic Polar Tensor (APT) charges and Molecular Electrostatic Potential (MEP) surfaces have been theoretically calculated utilizing the Gaussian 09 software. All theoretical calculations were calculated by using B3LYP (Becke’s 3-parameter hybrid functional using B exchange and LYP correlation) and HSEH1PBE (The exchange part of the screened Coulomb potential of Heyd, Scuseria, and Ernzerhof) levels of Density Functional Theory (DFT) method with 6-311++G(d,p) basis set. Moreover, DNA interactions have been viewed employing the molecular docking method of 3,3’-(2-Methoxybenzylidene) bis(4-hydroxycoumarin) molecule with the COVID-19 main protease (PDB 6LU7) responsible for the replication of corona virus.


COVID-19, Molecular docking, DFT, NMR spectra


The coronavirus emerged as a rapidly spreading epidemic in the city of Wuhan, China, in late 2019. An effective antiviral drug has not yet been developed against the SARS-CoV-2 virus, which was named as a global epidemic on March 11, 2020 by the World Health Organization. Rapid and detailed research is ongoing as there is an urgent need to search for effective antiviral agents to combat the COVID-19 virus. Today, many researches go on in drug design using Molecular Docking (MD) studies. Protein-ligand interaction studies by Molecular Docking (MD) play an important role in the knowledge of mechanisms in the discovery, design and development of drugs. Ligand selection in molecular docking is based on their antiviral activity.

The natural coumarins play an important role in plant biochemistry and physiology. They act as antioxidants, enzyme inhibitors and precursors of toxic substances. They are also involved in the actions of plant growth hormones and growth regulators, the control over the respiration and photosynthesis, as well as in the defense against various infections (Weinmann I, 1997). Although most of the existing natural coumarins have been isolated from higher plants, some of them have been discovered in microorganisms, e.g., aminocoumarin antibiotics: Novobiocin, coumermycin A1 and chlorobiocin (produced by the actinomycete Streptomyces niveus) (Marcu MG, 2000).

Synthetic coumarin derivatives have been obtained by chemical modification of the coumarin ring. As a substitution can conceptually occur at any of the six available sites of the basic molecule, these compounds are widely variable in structure and activity. The biological activities of coumarin derivatives, in particular their therapeutic application as anticoagulant and antibacterial agents (Borges F, 2005), has stimulated further interest for the synthesis of this class of compounds. A variety of synthesized coumarin derivatives have been experimentally shown to exert pharmacological activities including inhibition of platelet aggregation, cytochrome P450, and steroid 5-α-reductase. They have also been shown to exert efficient anti-proliferative, antifungal, anti-psoriasis, anti-inflammatory, as well as antiviral activities (Chiang CC, 2008; Cavar S, 2009; Jung JC, 2009; Symeonidis T, 2009; Kostova I, 2007). The interest in coumarins has recently increased significantly because it was found that they inhibit HIV (Human Immunodeficiency Virus), by affecting integrase and reverse transcriptase, which play a critical role in the replicative cycle of HIV (Nolan AK, 2009; Mahajan DH, 2009; Zhao H, et al., 1997). The present study is focused on the antiviral activity evaluation of the 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin). In the light of this information, 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule, one of the compounds containing thiophene with antiviral activity, may be among the drugs tested for the treatment of COVID-19 diseases. In order to better understand the molecular definition of the 3,3’-(2-Methoxybenzylidene) bis(4-hydroxycoumarin) molecule, first of all, the optimized structures of the molecules were determined using the Density Functional Theory (DFT) method in the Gaussian 09W program. Using optimized constructs in molecular docking calculations is more precise, making the program more reliable for use in construct-based drug design.

Materials and Methods

DFT calculations

The theoretical modeling was calculated for the 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule by Gaussian 09 software (Frisch MJ, et al., 2009) in the ground state. The molecular structure of the optimized molecule was drawn by Gaussian View 5 program (Dennington R, 2009). Theoretical calculations of the 3,3’-(2-Methoxybenzylidene) bis(4-hydroxycoumarin) molecule performed with B3LYP (Becke AD, 1997; Lee C, 1988) and HSEh1PBE (Heyd J, 2004; Heyd J, 2004; Heyd J, 2005, Heyd J, 2003) with 6-311++G(d,p) (Frisch MJ, 1984). UV-vis was performed with TD-HSEh1PBE and TDB3LYP approach in ground-state.

Molecular docking calculations (ligand and target protein preparation)

Before starting the molecular docking calculations, the 3D molecular structure of COVID-19 (PDB 6LU7) were downloaded from the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB) (Protein Data Bank, 2023). Thus, the ligand (3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)) and target (PDB 6LU7) were determined for molecular docking calculations. Molecular Docking calculations were performed by using the AutoDock Tools (ADT) version 1.5.6 (Sanner MF, 1999) to find the ligand-protein docking interactions. The PyMOL software package (Delano WL, 2002) has analyzed the output of the AutoDock (version 4.0) program (Morris GM, 2009). In addition, discovery studio visualizer 3.5 software (BIOVIA discovery studio, 2024) was used to visualize the docked active sites in the protein and its H-bond interactions.

Results and Discussion

Geometric structure

The experimental (Završnik D, et al., 2011) structure of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)molecule was shown in Figure 1.


Figure 1: The experimental structure of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)

Obtained geometric data listed in Table 1. In the study, Theoretical bond lengths (for C-C) were found in the range 1.36614-1.45154 Å and 1.35761-1.44606 (in Å) at B3LYP and HSEh1PBE, respectively. Experimental bond lengths (C-C) are seen in the range of 1.33508 and 1.45125 (in Å) (Završnik D, et al., 2011). Experimental O1-C2 bond lengths are 1.34557 Å, respectively (Završnik D, et al., 2011). Calculated bond lengths were observed as 1.37087 Å for the B3LYP and 1.36011 Å for the HSEh1PBE. THE experimental C9-O1-C2 bond angle is 121.07733˚ (Završnik D, et al., 2011), and this angle has been seen at 121.69770˚ for the B3LYP and 121.59628˚ for the HSEh1PBE.

Parameters Experimental Theoretical
Bond length (Å) X-ray DFT/B3LYP DFT/HSEh1PBE
O1-C2 1.34557 1.37087 1.36011
C2-C3 1.45125 1.44294 1.43642
C3-C4 1.33508 1.37396 1.37114
C4-C10 1.47082 1.45154 1.44606
C10-C9 1.36542 1.39896 1.39526
C9-O1 1.38919 1.36614 1.35761
C9-C8 1.37677 1.39363 1.39014
C8-C7 1.35041 1.38775 1.38430
C7-C6 1.40660 1.40157 1.39788
C6-C5 1.40437 1.38528 1.38178
C5-C10 1.37807 1.40554 1.40090
C1’-C2 1.38504 1.41467 1.40987
C2’-C3 1.38100 1.39516 1.39157
C3’-C4 1.37617 1.39462 1.39115
C4’-C5 1.35959 1.38698 1.38384
C5’-C6 1.36939 1.39648 1.39272
C6’-C1’ 1.38859 1.39272 1.38867
C2’’-C3’’ 1.42824 1.44131 1.43580
Bond angles ( ̊)
O1-C2-C3 119.31544 119.21389 119.38489
C2-C3-C4 119.45233 119.52552 119.69162
C3-C-C3’’ 112.52285 112.11446 111.90222
C-C3’’-C2’’ 117.54075 119.76933 119.50576
C3-C4-C10 120.30707 119.80790 119.40176
C4-C10-C5 123.64224 123.24460 123.05636
C4-C10-C9 117.46040 118.12013 118.13498
C10-C9-O1 121.58466 121.18358 121.36507
C9-O1-C2 121.07733 121.69770 121.59628
C10-C9-C8 123.04578 121.55848 121.40624
C9-C8-C7 118.44013 118.88060 118.89863
C8-C7-C6 121.11161 120.57748 120.64294
C7-C6-C5 118.82608 120.10227 120.03365
C6-C5-C10 119.66419 120.24284 120.20647
C5-C10-C9 118.89693 118.63427 118.80772
C1’-C2’-C3 121.34067 120.95104 120.86899
C2’-C3’-C4 119.88476 119.97973 119.94189
C3’-C4’-C5 119.30764 119.97013 120.04320
C4’-C5’-C6 121.13338 119.65885 119.59612
C5’-C6’-C1’ 120.97280 121.94429 121.87009
C6’-C1’-C2 117.33317 117.43165 117.60051

Table 1: Selected theoretical and experimental geometrical parameters

NMR spectroscopy

The combined use of NMR and computer simulation methods offers a powerful way to predict and interpret the structure of large biomolecules. In this study, The 13C and 1H NMR chemical shifts calculations have been carried out using the B3LYP and HSEH1PBE methods with 6-311++G(d,p) basis set for the optimized geometry. In Table 2, the experimental and the theoretical 1H and 13C isotropic chemical shifts (with respect to TMS, all values in ppm) for the 3,3’-(2-Methoxybenzylidene)bis (4-hydroxycoumarin)molecule has been given.

Atom Exp B3LYP /6-311++G(d,p) HSEh1PBE/6-311++G(d,p)
OCH3 3.57 3.33 3.40
OCH3 3.57 3.40 3.49
OCH3 3.57 3.78 3.86
H* 6.25 5.89 6.08
H5' 6.84 6.61 6.85
H3' 6.89 7.04 7.25
H6 7.16 7.30 7.52
H4' 7.17 7.33 7.57
H6 7.32 7.41 7.62
H6" 7.32 7.41 7.63
H8 7.36 7.48 7.69
H8" 7.36 7.48 7.72
H7 7.58 7.53 7.77
H7" 7.58 7.53 7.77
H5 7.90 7.54 7.86
H5" 7.90 7.65 7.86
C* 32.93 38.12 31.45
OCH3 55.51 54.19 48.50
C3 104.80 111.44 104.13
C3" 104.80 111.44 104.13
C3' 110.94 114.60 107.76
C8 115.91 120.58 115.65
C8" 115.91 120.58 115.65
C10 117.54 122.58 116.26
C10" 117.54 123.29 116.92
C5' 119.85 123.91 118.65
C5 123.60 127.85 122.69
C5" 123.60 127.85 122.92
C4' 127.29 128.14 127.96
C6' 128.22 129.43 129.54
C1' 128.29 129.73 130.96
C7 131.63 131.33 131.90
C7" 131.63 132.87 131.90

Table 2: The calculated and experimental 13C and 1H isotropic NMR chemical shifts (with respect to TMS, all values in ppm

Electronic properties

The transition of an electron from HOMO (Highest Occupied Molecular Orbit) to LUMO (Lowest Unoccupied Molecular Orbit) is defined as electronic absorption. Total energies of the frontier molecular orbital of the 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule were investigated at the B3LYP method and shown in Figure 2. The energy gap is important in definition electrical transport properties of the molecule. Quantum chemical parameters (as chemical activity, HOMO-LUMO energies and their energy gap (ΔE), hardness (h), electronegativity (c), and electronic transition energies) were performed with B3LYP and HSEh1PBE methods and calculated values listed in Table 3.

  B3LYP /6-311++G(d,p) HSEh1PBE /6-311++G(d,p)
EHOMO(eV) -6.27091 -6.07336
ELUMO(eV) -2.06727 -2.22727
ΔE=ELUMO-EHOMO(eV) 4.20364 3.84609
I(eV) 6.27091 6.07336
A(eV) 2.06727 2.22727
c(eV) 4.16909 4.150315
h(eV) 2.10182 1.923045
S(eV-1) 0.079733 0.082327
ETOTAL(a.u) -1528.61818533 -1527.02554268

Table 3: FMOs, energies and calculated physico-chemical properties


Figure 2: Molecular orbital pictures for 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) at B3LYP/6-311++G(d,p)

The frontier orbital picture was depicted in Figure 2 with the 3D plots for the gas phase, and the positive and negative phases are represented in red and green color, respectively.

Charge analysis and Molecular Electrostatic Potential (MEP)

Mulliken charge distribution is an old method and common method (Mulliken RS, 1955). This method is a linear combination of atomic orbital results based on the method of obtaining molecular orbital (Figure 3). In case making the distribution to atoms of wave functions, it is based on the principle of equally distributing two overlapping orbits. Mulliken, Atomic Polar Tensor (APT), Natural Bond Orbital (NBO) charges of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)molecule were calculated and results were given in Table 4.

Atom Mulliken APT NBO
O1 -0,107848 -0,058742 -0,766021 -0,768945 -0,49626 -0,48797
C2 -0,131133 -0,173918 1,266719 1,276791 0,76155 0,76267
C3 0,456219  0,457077 -0,456636 -0,461664 -0,10582 -0,12234
C4 0,212323  0,286715 0,831514 0,838380 0,38771 0,36568
C10 0,742426  0,837575 -0,173008 -0,172090 -0,16172 -0,07139
C9 -0,222743  -0,275699 0,377594 0,380751 0,34496 0,31644
C8 -0,205367  -0,256948 -0,085227 -0,020181 -0,23394 -0,24274
C7 -0,045384  -0,087940 -0,012467 0,026362 -0,18352 -0,19008
C6 -0,251935  -0,303304 -0,111337 -0,078859 -0,19785 -0,20865
C5 -0,177932  -0,211178 0,057813 0,141433 -0,14427 -0,17758
C* 0,233055  0,163381 0,244713 0,243784 -0,33443 -0,34663
C3’’ 0,605173  0,700666 -0,458572 -0,464806 -0,15495 -0,16694
C2’’ -0,246357  -0,351988 1,275489 1,285970 0,75083 0,75242
C5’’ -0,101701  -0,128310 0,076376 0,161992 -0,06177 -0,06853
C8’’ -0,304592  -0,419762 -0,094019 -0,027355 -0,23380 -0,24170
C1 0,491858  0,594870 -0,064988 -0,065842 -0,06620 -0,07061
C2 0,159090  0,122966 0,489079 0,492519 0,33357 0,33342
C3 -0,306666  -0,305691 -0,151932 -0,110941 -0,28596 -0,29567
C4 -0,267882  -0,331063 0,032537 0,058516 -0,18147 -0,18669
C5 -0,480995  -0,538916 -0,124592 -0,101670 -0,22474 -0,23266
C6 -0,372054  -0,411745 0,025263 0,081983 -0,18092 -0,18601

Table 4: The mulliken, APT and NBO charge distribution calculated (with 6-311++G(d,p)) for 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule


Figure 3: The mulliken, APT and NBO plots of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)Equation

MEP surface map is very important for the investigation of molecular structure. MEP surface map shows the molecule’s color, shape, charge, size, and electrostatic potential regions at the same time. The color chart of MEP is red for (-) charge, blue for (+) charge, yellow for the slightly electron-rich region, green for neutral. 3D MEPs of the 3,3’-(2-Methoxybenzylidene) bis(4-hydroxycoumarin) molecule were simulated by using the B3LYP and shown in Figure 4.


Figure 4: MEPs maps of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) at B3LYP/6-311G(d,p) level

Molecular docking analysis

Molecular interactions play important roles in the basic biological processes. These molecular interactions lead to the formation of stable ligand-protein complexes that are necessary for their biological functions. Molecular docking was performed by AutoDock (version 4.0) program. The program receives a semi empirical free energy force in docking simulation processes. The PDB 5R7Y target protease exhibits the minimum binding energy of -4.2 kcal/mol, intermolecular energy of -4.27 kcal/mol and an inhibition constant of 836.1 uM. The deviation between the ligand-protease was analyzed, where the Root Mean Square Deviation (RMSD) value was calculated as 21.53 for 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin). 3D molecular interaction diagrams of target (PDB 6LU7) and ligand (3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin)) are shown in Figure 5. Detailed 2D interaction diagrams are shown in Figure 6.


Figure 5: 3D interaction diagrams of the 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) in into the active sites PDB 6LU7


Figure 6: The binding orientation and 2D molecular interaction diagram of the 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) in into the active sites of PDB 6LU7 main proteaseEquation


The geometry of 3,3’-(2-Methoxybenzylidene)bis(4-hydroxycoumarin) molecule was optimized in different levels with DFT/B3LYP and DFT/ HSEH1PBE method using 6-311G(d,p) basis set. The calculated structural parameters (bond distances, bond angles and dihedral angles) compares well with the experimental values. 3,3’-(2-Methoxybenzylidene) bis(4-hydroxycoumarin) molecule and its electrical (HOMO, HOMO-1, LUMO and LUMO+1) properties, Mulliken, NBO and Atomic Polar Tensor (APT) charges and Molecular Electrostatic Potential (MEP) surfaces have been theoretically calculated by using B3LYP (Becke’s 3-parameter hybrid functional using B exchange and LYP correlation) and HSEH1PBE (The exchange part of the screened Coulomb potential of Heyd, Scuseria, and Ernzerhof) levels of Density Functional Theory (DFT) method with 6-311++G(d,p) basis set. The active site binding properties and binding conformations were shown visually with molecular docking study.


Author Info

Cengiz Ipek1* and Hacer Gumus2
1Department of Civil Engineering, Istanbul Medeniyet University, Istanbul, Turkey
2Ali Riza Veziroglu Vocational School, Kocaeli University, Kocaeli, Turkey

Citation: Ipek C, et al.: Molecular Docking Study of the Benzylidene-bis-(4-Hydroxycoumarin) Derivatives as Antiviral to Coronavirus COVID-19

Received: 12-Jan-2024 Accepted: 29-Jan-2024 Published: 05-Feb-2024, DOI: 10.31858/0975-8453.15.2.81-87

Copyright: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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