Molecular Docking and Drug-Likeness of Salicornia-Derived Phytochemicals Against HER Receptors
Abstract
1. Introduction
2. Materials and Methods
2.1. Retrieval and Preparation of Proteins
2.2. Ligand Selection and Preparation
2.3. Molecular Docking Analysis and Visualization
2.4. In Silico ADME Analysis
2.5. Toxicity Analysis of Selected Compounds
3. Results and Discussion
3.1. Molecular Docking Analysis
3.1.1. Molecular Docking Analysis of Bioactive Compounds from S. herbacea and S. brachiata with HER1 Receptor
3.1.2. Molecular Docking Analysis of Bioactive Compounds from S. herbacea and S. brachiata with the HER2 Receptor
3.1.3. Molecular Docking Analysis of Bioactive Compounds from S. herbacea and S. brachiata with the HER4 Receptor
3.2. Drug-Likeness Properties of the Selected Phytochemicals According to Lipinski’s Rule of Five
3.3. Pharmacokinetic Properties of Selected Phytochemicals According to SwissADME Analysis
3.4. Toxicity Analysis
3.5. Prediction of Organ-Specific Toxicity of the Selected Compounds in S. herbacea
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Phytochemical | Binding Energy (ΔG) (kcal/mol) | Number of H Bonds | Amino Acids Involved in Hydrogen Bonding |
---|---|---|---|
3,5-di-O-caffeoylquinic acid | −8.7 | 7 | ASP770, ARG767, LEU703, SER768, ARG831, ALA767, ALA766, ARG705 |
3-O-caffeoylquinic acid | −7.7 | 4 | ARG831, ARG776, ILE1018, LEU778 |
Myricetin | −7.6 | 3 | ARG831, ARG776, LEU703 |
Quercetin | −7.5 | 3 | GLY873, ALA859, GLU758 |
Stigmasterol | −7.5 | 0 | - |
Gefitinib | −7.4 | 2 | LEU703, ARG831 |
Dovitinib | −8.1 | 3 | ARG776, VAL769, ALA767 |
Phytochemical | Binding Energy (ΔG) (kcal/mol) | Number of H Bonds | Amino Acids Involved in Hydrogen Bonding |
---|---|---|---|
3,5-di-O-caffeoylquinic acid | −8.5 | 7 | ARG98, ASP769, ARG978, TYR835, ALA706, VAL839, TYR772 |
Stigmasterol | −8.1 | 0 | - |
3-O-caffeoylquinic acid | −8.0 | 3 | GLU770, ARG868, GLU766 |
Kaempferol | −7.8 | 3 | GLU770, GLY865, ASN758 |
Gefitinib | −7.8 | 3 | LYS 957, VAL839, ASN708 |
Dovitinib | −9.0 | 2 | GLU766, ARG868 |
Phytochemical | Binding Energy (ΔG) (kcal/mol) | Number of H Bonds | Amino Acids Involved in Hydrogen Bonding |
---|---|---|---|
3,5-di-O-caffeoylquinic acid | −8.3 | 5 | GLN988, ARG837, VAL986, GLN707, PRO705, GLN 982 |
Stigmasterol | −7.9 | 1 | GLN988 |
Hesperitin | −7.7 | 5 | ASN706, ILE987, TYR833, MET775, SER774 |
Myricetin | −7.6 | 3 | ILE987, ASN706, TYR833 |
3-O-caffeoylquinic acid | −7.5 | 6 | ASP990, ASP991, GLN707, ARG782, ASN706, SER774 |
Quercetin | −7.5 | 2 | ILE987, SER774 |
Isorhamnetin | −7.4 | 6 | ASP991, ARG837, TYR833, SER774, ARG782, ASP776 |
Acacetin | −7.3 | 2 | ARG837, ASN706 |
Rhamnetin | −7.3 | 3 | ARG782, ASP991, GLN707 |
Gefitinib | −7.2 | 2 | ASN706, ARG837 |
Dovitinib | −8.5 | 2 | ASP813, GLN988 |
Phytochemical | Mass (g/mol) | Hydrogen Bond Donor | Hydrogen Bond Acceptor | Log P | Molar Refractivity |
---|---|---|---|---|---|
3,5-di-O-caffeoylqunic acid | 516.45 | 7 | 12 | 0.81 | 126.90 |
Myricetin | 318.24 | 6 | 8 | 1.69 | 80.06 |
Quercetin | 302.24 | 5 | 7 | 1.99 | 78.03 |
Hesperitin | 302.28 | 3 | 6 | 2.19 | 78.06 |
Isorhamnetin | 478.40 | 7 | 12 | −0.24 | 114.63 |
Stigmasterol | 412.69 | 1 | 1 | 7.80 | 132.75 |
Rhamnetin | 82.50 | 4 | 7 | 2.29 | 82.50 |
Kaempferol | 286.24 | 4 | 6 | 1.90 | 76.01 |
Acacetin | 284.26 | 2 | 5 | 3.35 | 78.46 |
Gefitinib | 446.90 | 1 | 7 | 4.32 | 121.66 |
Dovitinib | 392.43 | 3 | 4 | 2.21 | 120.28 |
3-O-caffeoylquinic acid | 354.31 | 6 | 9 | −0.75 | 83.50 |
Phytochemical | ESOL (Log S) | GIA | BBB Permeant | P-gp Substrate | CYP3A4 Inhibitor | CYPIA2 Inhibitors | Bioavailability Score |
---|---|---|---|---|---|---|---|
3,5-di-O-caffeoylquinic acid | −3.65 | Low | No | Yes | No | No | 0.11 |
3-O-caffeoylquinic acid | −1.62 | Low | No | No | No | No | 0.11 |
Myricetin | −3.01 | Low | No | No | Yes | Yes | 0.55 |
Quercetin | −3.16 | High | No | No | Yes | Yes | 0.55 |
Hesperitin | −3.62 | High | No | Yes | Yes | Yes | 0.55 |
Isorhamnetin | −3.26 | Low | No | Yes | No | No | 0.17 |
Stigmasterol | −7.46 | Low | No | No | No | No | 0.55 |
Rhamnetin | −3.36 | High | No | No | Yes | Yes | 0.55 |
Gefitinib | −5.05 | High | Yes | No | Yes | No | 0.56 |
Dovitinib | −3.66 | High | No | Yes | No | Yes | 0.55 |
Compounds Name | Oral LD50 Value (mg/Kg) | Predicted Toxicity Class | Prediction Accuracy (%) | Average Similarity (%) |
---|---|---|---|---|
3,5-di-O-caffeoylquinic acid | 5000 | 5 | 71.63 | 69.26 |
3-O-caffeoylquinic acid | 5000 | 5 | 71.21 | 69.26 |
Myricetin | 159 | 3 | 100 | 100 |
Quercetin | 159 | 3 | 100 | 100 |
Stigmasterol | 890 | 4 | 89.38 | 70.97 |
Kaempferol | 3919 | 5 | 82.46 | 70.97 |
Isorhamnetin | 5000 | 5 | 87.48 | 70.97 |
Rhamnetin | 5000 | 5 | 86.79 | 70.97 |
Hesperitin | 2000 | 4 | 77.77 | 69.26 |
Acacetin | 4000 | 5 | 83.54 | 70.97 |
Gefitinib | 2935 | 5 | 51.88 | 67.38 |
Dovitinib | 1072 | 4 | 53.59 | 67.38 |
Compounds Name | Hepatotoxicity | Neurotoxicity | Nephrotoxicity | Respirotoxicity | Cardiotoxicity |
---|---|---|---|---|---|
3,5-di-O-caffeoylquinic acid | 0.70 I | 0.87 I | 0.52 A | 0.52 A | 0.88 I |
3-O-caffeoylquinic acid | 0.72 I | 0.89 I | 0.56 A | 0.57 A | 0.99 I |
Myricetin | 0.69 I | 0.89 I | 0.62 A | 0.83 A | 0.99 I |
Quercetin | 0.69 I | 0.89 I | 0.62 A | 0.83 A | 0.99 I |
Stigmasterol | 0.87 I | 0.54 A | 0.89 I | 0.82 A | 0.85 I |
Kaempferol | 0.68 I | 0.89 I | 0.62 A | 0.83 A | 0.91 I |
Isorhamnetin | 0.72 I | 0.88 I | 0.64 A | 0.85 A | 0.82 A |
Rhamnetin | 0.73 I | 0.86 I | 0.59 A | 0.82 A | 0.71 I |
Hesperitin | 0.70 I | 0.87 I | 0.67 A | 0.86 A | 0.99 A |
Acacetin | 0.72 I | 0.84 I | 0.63 A | 0.78 A | 0.64 A |
Gefitinib | 0.73 A | 0.83 A | 0.51 I | 0.98 A | 0.81 I |
Dovitinib | 0.54 A | 0.96 A | 0.75 I | 0.98 A | 0.87 I |
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Withana, T.N.; Perera, D.; Fernando, T.D. Molecular Docking and Drug-Likeness of Salicornia-Derived Phytochemicals Against HER Receptors. Curr. Issues Mol. Biol. 2025, 47, 495. https://doi.org/10.3390/cimb47070495
Withana TN, Perera D, Fernando TD. Molecular Docking and Drug-Likeness of Salicornia-Derived Phytochemicals Against HER Receptors. Current Issues in Molecular Biology. 2025; 47(7):495. https://doi.org/10.3390/cimb47070495
Chicago/Turabian StyleWithana, Thiwanga N., Dinum Perera, and Tharani D. Fernando. 2025. "Molecular Docking and Drug-Likeness of Salicornia-Derived Phytochemicals Against HER Receptors" Current Issues in Molecular Biology 47, no. 7: 495. https://doi.org/10.3390/cimb47070495
APA StyleWithana, T. N., Perera, D., & Fernando, T. D. (2025). Molecular Docking and Drug-Likeness of Salicornia-Derived Phytochemicals Against HER Receptors. Current Issues in Molecular Biology, 47(7), 495. https://doi.org/10.3390/cimb47070495