PMC:7784829 / 12424-26386 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7784829","sourcedb":"PMC","sourceid":"7784829","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7784829","text":"Molecular docking studies\nThe three-dimensional structure of the SARS-CoV spike protein and SARS-CoV-2 Spike protein RBD has been solved. The PDB files of the SARS-CoV spike protein (6CRV) and the Spike protein RBD of the SARS-CoV-2 (6M0J) was downloaded from the PDB databank. These structures were used to predict the ability of the binding of curcumin and its derivatives to the spike proteins of the two corona viruses. Curcumin and 24 of its derivatives (Figure 1 and Supplementary Figure 2) were docked on to 6CRV and 6M0J. Tables 2 and 3 gives the binding energies of curcumin and its derivatives with 6CRV (binding energies ranged from −10.98 to −5.12 kcal/mol) and with 6M0J (binding energies ranged −10.01 to −5.33 kcal/mol) respectively. Visual examination of the computationally docked optimal binding poses of curcumin and its derivatives on 6CRV and 6MOJ revealed the important role of various types of interactions viz. hydrogen bonding and hydrophobic interactions, including π–π stacking, π–cation, and π–σ interactions in the stability of the binding of the curcumin/derivatives to the spike protein (6CRV and 6M0J). All compounds showed one or more hydrogen bonds with 6CRV and 6M0J except a few.\nFigure 2. Molecular docking of Bis-demethoxy curcumin on SARS-CoV spike protein (6CRV). (A) 3 D structure of SARS-CoV Spike Glycoprotein Macromolecule (6CRV). (B) Binding Interaction of Bis-demethoxy curcumin with amino acid residues of SARS-CoV Spike glycoprotein (PDB ID-6CRV). (C) Superimposed binding mode of Bis-demethoxy curcumin with SARS-CoV Spike protein. (D) 2 D representation of the binding interaction of Bis-demethoxy curcumin with SARS-CoV Spike protein.\nTable 2. Molecular docking results of curcumin and its derivatives with SARS-CoV Spike protein (6CRV). The top hits with the binding energy lesser than -8.4 are in bold.\nCompound Binding Energy (ΔG) Ligand Efficiency Intermolecular energy XPH-Bond\nCurcumin –10.1 –0.14 –8.24 –10.9724\nBHBC –8.28 –0.13 –7.87 –3.42239\nMNC –8.01 –0.43 –6.98 –8.01452\nBDMC –10.98 –0.18 –8.94 –14.0467\n1 –5.12 –0.25 –4.17 0\n2 –8.55 –0.41 –6.56 –18.4317\n3 –6.56 –0.21 –4.92 –11.1148\n4 –8.69 –0.13 –6.94 –19.1539\n5 –7.03 –0.19 –5.93 –8.47153\n6 –6.59 –0.36 –5.12 –7.41531\n7 –7.96 –0.21 –6.14 –7.98548\n8 –7.55 –0.19 –5.14 –6.14537\n9 –6.91 –0.21 –5.18 0\n10 –7.75 –0.21 –6.14 –6.73473\n11 –8.02 –0.19 –6.19 –17.2465\n12 –7.85 –0.38 –6.25 –14.6321\n13 –5.94 –0.29 –4.12 –11.3576\n14 –8.75 –0.25 –7.19 –21.1412\n15 –7.87 –0.38 –7.26 –0.473228\n16 –8.47 –0.25 –6.88 –8.458912\nDMC –7.89 –0.21 –6.41 –10.47057\nFAC –7.17 –0.36 –5.15 –9.14873\nIBC –7.91 –0.23 –7.17 –6.90341\nIVC –7.43 –0.44 –6.67 –19.9864\nSYC –6.82 –0.26 –5.45 –9.44678\nAbbreviations: BHBC: 3-5-di-tert-butyl-4-hydroxybenzaldehyde curcumin, MNC: 4-methoxy-1-naphthaldehyde curcumin, BDMC: Bis-demethoxy curcumin, DMC: Demethoxy curcumin, FAC: Ferulic-acid curcumin, IBC: Ibuprofen curcumin, IVC: Isovanillin curcumin, SYC: Syringaldehyde curcumin.\nTable 3. Molecular docking analysis of curcumin and its derivatives with SARS-CoV-2 Spike protein Receptor binding domain (6M0J). The top hits with the binding energy lesser than -8.4 are in bold.\nCompound Binding Energy (ΔG) Ligand Efficiency Intermolecular energy XPH-Bond\nCurcumin –9.81 –0.15 –8.35 –15.1512\nBHBC −5.33 –0.13 –7.96 0\nMNC –7.96 –0.27 –7.38 –4.24687\nBDMC –10.01 –0.12 –9.18 –13.9824\n1 –7.58 –0.36 –6.19 –18.3489\n2 –8.81 –0.31 –8.38 1.2654\n3 –6.14 –0.34 –5.45 –6.95102\n4 –8.88 –0.18 –7.98 –14.0321\n5 –6.23 –0.26 –5.88 –3.5891\n6 –7.16 –0.37 –6.15 –10.1688\n7 –6.89 –0.25 –5.98 –9.12515\n8 –5.49 –0.12 –3.90 –5.92265\n9 –6.92 –0.18 –6.22 –6.96719\n10 –7.03 –0.24 –6.33 –7.0\n11 –6.88 –0.27 –6.23 –6.44363\n12 –7.95 –0.41 –5.70 –2.5581\n13 –6.11 –0.39 –5.42 –7.34943\n14 –7.45 –0.19 –6.40 –10.5367\n15 –5.74 –0.39 –5.51 –2.36748\n16 –7.83 –0.27 –7.48 –6.64321\nDMC –5.98 –0.19 –5.38 –5.99913\nFAC –5.85 –0.38 –5.25 –6.46613\nIBC –6.65 –0.15 –6.20 –1.52841\nIVC –8.96 –0.43 –7.73 –12.2707\nSYC –5.87 –0.29 –5.43 –4.4411\nAbbreviations: BHBC: 3-5-di-tert-butyl-4-hydroxybenzaldehyde curcumin, MNC: 4-methoxy-1-naphthaldehyde curcumin, BDMC: Bis-demethoxy curcumin, DMC: Demethoxy curcumin, FAC: Ferulic-acid curcumin, IBC: Ibuprofen curcumin, IVC: Isovanillin curcumin, SYC: Syringaldehyde curcumin. In 6CRV, it was found that ARG99, GLY100, TRP 101, ILE116, ILE117, ASN118, VAL123, MET144, SER165, ASP166, PHE168, ARG183, PHE185, LYS198, ILE219, PHE220 were the major amino acids involved in hydrogen bonding, hydrophobic and van der Waals interaction with most of the curcumin compounds. However, majority of the curcumin compounds exhibited hydrogen bonding with ARG99, MET144, LYS198 except compound 1 and 9. In addition, all the compounds exhibited hydrophobic (π–π stacking, π–cation, and π–σ) interactions with ASP166, VAL123, PHE185 and van der Waals interaction with GLY100, TRP 101, ILE117, ASN118, ARG183, ILE116, PHE168, SER165, PHE220, ILE219.\nAll compounds showed one or more hydrogen bonding interactions with spike RBD of the SARS-CoV-2 (6M0J) except 3-5-di-tert-butyl-4-hydroxybenzaldehyde curcumin. It was found that ARG355, TYR396, PRO426, ASP428, THR430, GLY431, PHE429, PHE 464, GLU516, SER514, LEU517 and PHE515 were the major amino acids involved in hydrogen bonding hydrophobic and van der Waals interaction with the all of curcumin compounds. However, majority of the curcumin compounds exhibit hydrogen bonding with ARG355, LEU517 and THR430. In addition, the compounds exhibited hydrophobic (π–π stacking, π–cation, and π–σ) and van der Waals interactions with PHE464, GLY431, GLU516, SER514, PHE515, TYR396, PRO426, ASP428 and PHE429.\nThe curcumin derivative with the best binding affinity was Bis-demethoxycurcumin for both 6CRV (ΔG = −10.98 kcal/mol) and 6M0J (ΔG = −10.01 kcal/mol). The native compound, curcumin, demonstrated a binding energy of −9.81 kcal/mol for 6M0J and −10.1 kcal/mol for 6CRV. Binding mode of Bis-demethoxycurcumin with SARS-CoV Spike protein and SARS-CoV-2 Spike protein RBD is shown in Figure 2 and 3, respectively.\nFigure 3. Molecular docking of Bis-demethoxy curcumin on SARS-CoV-2 spike protein receptor binding domain (6M0J). (A) 3D structure of SARS-CoV-2 spike protein RBD bound with ACE2 protein Macromolecule. (B) Binding Interaction of Bis-demethoxy curcumin with amino acid residue of spike protein RBD of SARS-CoV-2 (PDB ID-6M0J). (C) Superimposed binding mode of Bis-demethoxy curcumin, docked with SARS-CoV-2 spike protein RBD. (D) 2D representation of the binding interaction of Bis-demethoxy curcumin with SARS-CoV-2 spike RBD.\n\nIn-silico drug-likeness and pharmacokinetic property prediction\nAll the structures used for docking were analysed for in silico drug-likeness based on the Lipinski’s rules using pkCSM server (Table 4). The lipophilicity (expressed as LogP) predicted for all the compounds were found to be well above the traditionally cut-off value of 5 used for drug design. Curcumin and its derivatives, used in this study, show suitable MW values (MW \u003c 500) essential for a successful penetration through biological membranes. The surface area (SA) for all the compounds was observed to be in the range 115.89 − 240.65 Å2 which is well within the limit. All compounds, except 5-di-tert-butyl-4-hydroxybenzaldehyde curcumin (BHBC), 4-methoxy-1-naphthaldehyde curcumin (MNC), Syringaldehyde curcumin (SYC) and compound-16, fall into the appropriate range indicating good bioavailability of the candidate molecule. The number of hydrogen bond acceptors (HBA, ≤10) and donors (HBD, ≤5) for all the compounds were in accordance with the Lipinski’s rule of five.\nTable 4. In-silico prediction of drug-likeness for curcumin derivatives[a].\nCompound MW LogP SA HBA HBD nviolations Rotatable bonds\nBHBC 534.78 8.93 236.0 4 3 1 6\nMNC 538.59 6.14 232.11 7 2 1 11\nBDMC 308.33 3.83 133.51 4 3   5\n1 270.353 4.21 115.89 3 1   4\n2 332.739 3.79 136.57 5 4   4\n3 314.337 3.77 133.64 5 4   4\n4 322.36 4.36 139.56 3 3   4\n5 364.441 4.93 159.62 4 0   5\n6 320.388 4.95 141.45 4 3   1\n7 325.32 3.60 138.02 5 1   6\n8 329.193 4.45 125.75 2 1   4\n9 462.181 5.24 164.71 7 2   0\n10 351.358 4.13 149.74 4 5   1\n11 360.375 5.07 149.89 2 1   3\n12 419.565 6.24 185.40 9 4   1\n13 389.495 5.22 171.67 4 4   1\n14 342.778 3.81 143.82 4 2   2\n15 469.629 4.38 208.20 6 5   1\n16 486.564 6.19 211.58 11 6 1 0\nDMC 342.391 3.20 146.43 5 2   9\nFAC 550.604 4.7 232.81 9 2   15\nIBC 556.655 5.24 240.62 7 1   15\nIVC 504.535 4.69 214.22 8 3   11\nSYC 430.453 3.77 180.12 10 8 1 3\n[a]  MW = Molecular weight, LogP = octanol-water partition coefficient, SA = Surface Area, HBA = Number of hydrogen bond acceptor, HBD = Number of hydrogen bond donor, nviolations = violations from Lipinski’s rule. BHBC: 3-5-di-tert-butyl-4-hydroxybenzaldehyde curcumin, MNC: 4-methoxy-1-naphthaldehyde curcumin, BDMC: Bis-demethoxy curcumin, DMC: Demethoxy curcumin, FAC: Ferulic-acid curcumin, IBC: Ibuprofen curcumin, IVC: Isovanillin curcumin, SYC: Syringaldehyde curcumin. Additionally, a variety of key ADMET (Absorption, Distribution, Metabolism and Excretion) properties have also been calculated with the aid of pkCSMserver. The results are listed in Table 5. All curcumin derivatives showed moderate to high water solubility ranging from −2.91 log mol/L (BHBC) to −6.99 log mol/L (compound-12), in addition to high Caco-2 permeability (permeation \u003e 0.90) except compound BHBC and MNC (permeation = 0.67 and 0.43 respectively) which showed moderate permeability. Intestinal absorption (IA) has been found to be greater than 85% indicating good permeation across the intestinal membrane. Further, all curcumin compounds showed good permeation through skin (permeation \u003e −2.5). Additionally, all curcumin compounds showed no inhibition towards P-glycoprotein I and P-glycoprotein II, except compounds BHBC, MNC, compound-13 and Ferrulic acid curcumin (FAC) which demonstrated inhibition towards P-glycoprotein I. Furthermore, all curcumin compounds showed poor BBB permeability and moderate CNS permeability except Isovanillin curcumin (IVC) and SYC. All showed inhibition towards the metabolizing enzyme CYP3A4 except BHBC, compounds-8, -11, -14, -15 and -16, while except compound-15, all showed inhibition towards CYP2C9. All curcumin derivatives were found to show the total clearance in the range 0.10 log mL/min/kg (compound-1 and -4) to 1.01 log mL/min/kg (compound-15). Further, all curcumin derivatives except compound 15 were found to act as OCT2 substrate, thus indicating that these compounds will not have any adverse interactions and no negative effect on renal clearance.\nTable 5. In-silico ADME prediction for curcumin derivatives[a].\nComp Absorption Distribution Metabolism Excretion\n  WS CP IA SP PI-1 PI-2 VD FU BBB CNS CI-1 CI-2 TC RS\nBHBC –2.91 0.67 88.62 –2.73 Yes Yes –0.39 0.31 –0.67 –0.85 No Yes 0.15 No\nMNC –3.64 0.43 100 –2.73 Yes Yes –1.45 0.33 –0.39 –2.73 Yes Yes 0.26 No\nBDMC –4.43 1.01 95.92 –2.99 No No –0.22 0.08 –0.72 –2.11 Yes Yes 0.12 No\n1 –4.66 1.25 91.80 –2.51 No No 0.18 0.06 0.01 –1.45 Yes Yes 0.10 No\n2 –3.23 0.93 89.16 –2.76 No No –0.07 0.12 –1.07 –2.29 Yes Yes 0.05 No\n3 –3.19 0.94 89.70 –2.76 No No –0.02 0.13 –1.06 –2.27 Yes Yes 0.06 No\n4 –4.11 0.92 87.64 –3.07 No No 0.09 0 –0.74 –1.85 Yes Yes 0.10 No\n5 –6.39 1.06 94.85 –2.49 No No 0.25 0 –0.03 –1.30 Yes Yes 0.22 No\n6 –5.42 1.43 90.49 –2.73 No No 0.05 0 –0.33 –1.29 Yes Yes 0.23 No\n7 –4.54 1.04 91.97 –2.73 No No –0.37 0 0.28 –2.20 Yes Yes 0.13 No\n8 –5.09 1.66 90.44 –2.29 No No 0.27 0 0.16 –1.47 No Yes 0.14 No\n9 –7.03 1.13 93.34 –2.51 No No 0.37 0 0.46 –1.26 Yes Yes 0.26 No\n10 –4.89 0.94 91.50 –2.74 No No –0.04 0 –0.24 –1.93 Yes Yes 0.11 No\n11 –5.93 1.28 89.16 –2.59 No No 0.36 0 0.66 –1.40 No Yes 0.13 No\n12 –6.99 1.02 91.30 –2.75 No No 0.66 0 –0.32 –1.85 Yes Yes 1.04 No\n13 –5.42 1.27 92.76 –2.80 Yes Yes 0.54 0 –0.02 –1.58 Yes Yes 0.26 No\n14 –4.20 1.12 90.31 –2.92 No No –0.04 0.01 –0.31 –1.33 No Yes 0.08 No\n15 –3.76 0.97 88.86 –2.79 No No 1.90 0.16 –0.20 –1.26 No No 1.01 Yes\n16 –6.92 0.90 94.67 –2.73 No No –0.59 0.07 –0.72 –2.62 No Yes 0.41 No\nDMC –3.95 0.99 92.03 –2.74 No No –0.06 0.12 –0.23 –2.66 Yes Yes 0.32 No\nFAC –4.02 1.41 83.68 –2.76 Yes Yes –0.58 0.24 –0.91 –3.26 Yes Yes 0.55 No\nIBC –4.36 0.91 91.72 –2.73 No No –0.88 0.18 –0.53 –2.77 Yes Yes 0.62 No\nIVC –3.95 0.96 89.31 –2.73 No No –0.60 0.24 –1.37 –3.02 Yes Yes 0.16 No\nSYC –3.89 1.01 89.15 –2.73 No No 0.28 0.17 –1.47 –3.14 Yes Yes 0.23 No\n[a]  Abbreviations: WS—Water solubility (log mol/L), CP—Caco2 permeability (log Papp in 10-6 cm/s), IA—Human intestinal absorption (% Absorbed), SP—Skin permeability (log Kp),PI-1—P-glycoprotein I inhibitor, PI-2—P-glycoprotein II inhibitor, VD—Human volume ofdistribution (log L/kg), FU—Fraction unbound (human) (Fu), BBB—BBB permeability (logBB), CNS—CNS permeability (log PS), CI-1—CYP3A4 inhibitor, CI-2—CYP2C9 inhibitor,TC—Total clearance (log mL/min/kg), RS—Renal OCT2 (organic cation transporter 2) substrate. 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