Chlorogenic Acid and Cinnamaldehyde in Breast Cancer Cells: Predictive Examination of Pharmacokinetics and Binding Thermodynamics with the Key Mediators of PI3K/Akt Signaling
Abstract
1. Introduction
2. Materials and Methods
2.1. Retrieval and Preparation of Target Proteins and Ligands
2.2. Molecular Docking Approach
2.3. Approach to Pharmacokinetic Analysis of Chlorogenic Acid and Cinnamaldehyde
2.4. Drug-Likeness Analysis
3. Results
3.1. Predicted Molecular Docking Results
3.2. Predicted Pharmacokinetic Results for Chlorogenic Acid and Cinnamaldehyde
4. Discussion
4.1. Molecular Docking
4.2. Pharmacokinetics of Chlorogenic Acid and Cinnamaldehyde
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ligand | Akt Binding | Parameters | |
---|---|---|---|
1 | Chlorogenic acid | XYZ coordinates Binding energy Interacting amino acids | 25.140333; 6.181083; 8.167583 −8.2 kcal/mol Asp 274; Lys 276; Asn 279; Leu 295; Phe 309; Cys 310; Gly 311 |
2 | Cinnamaldehyde | XYZ coordinates Binding energy Interacting amino acids | 27.003800; 6.254100; 9.233900 −5.4 kcal/mol Leu 156; Gly 157; Val 164; Ala 177; Ala 230; Met 281 |
3 | Spirocyclic sulfonamides inhibitor (co-crystallized ligand) | XYZ coordinates | 28.185902; 2.786537; 11.33597 |
4 | Capivasertib (the first FDA-approved Akt inhibitor for treatment of breast cancer) The binding energies of FDA-approved drugs ranged from −5.6 to −6.9 kcal/mol [22] | XYZ coordinates Binding energy | 30.194838; 2.264703; 12.38245 −8.5 kcal/mol |
Ligand | PI3K Binding | Parameters | |
---|---|---|---|
1 | Chlorogenic acid | XYZ coordinates Binding energy Interacting amino acids | 58.764226; −8.98519; 81.31416 −8.5 kcal/mol Ser7; Ile121; Lys672; Ser673; Met 675; His676; Ile713; Asn803; Val845 |
2 | Cinnamaldehyde | XYZ coordinates Binding energy Interacting amino acids | 57.478300; −7.86420; 83.815100 −6.2 kcal/mol Trp669; Lys672; Glu674; His676; Val706; Met709; Ile 713; Ile841; Gly842; Asp 843 |
3 | Pyridopyrimidinones inhibitors (co-crystallized ligand) | XYZ coordinates | 54.042978; 4.928485; 87.43672 |
Ligand | PDK1 Binding | Parameters | |
---|---|---|---|
1 | Chlorogenic acid | XYZ coordinates Binding energy Interacting amino acids | 37.643194; −27.85712; −11.5306 −8.2 kcal/mol Leu88; Val96; Ala109; Lys111; Ser160; Ala 162; Glu209; Leu212; Thr222; Asp223 |
2 | Cinnamaldehyde | XYZ coordinates Binding energy Interacting amino acids | 34.57870; −28.64820; −12.19540 −5.8 kcal/mol Leu88; Val96; Ala109; Lys111; Leu159; Ser160; Ala162; Leu212; Thr222 |
3 | 7-azaindoles inhibitor (co-crystallized ligand) | XYZ coordinates | 34.78813; −27.57596; −12.39844 |
S/N | Parameters | Predicted | Value | Recommendation | Implication |
---|---|---|---|---|---|
CGA | CA | ||||
1 | Number of rotatable bonds | 5 | 2 | ≤10, per Veber’s rule | Contributes to molecule conformational flexibility to permeate cell membrane and interact with receptors |
2 | Molecular weight (g/mol) | 354.31 | 132.16 | ≤500 g/mol | Small molecules cross cell membrane and have better oral bioavailability |
3 | Caco-2 permeability (LogPapp) | −6.49 | −4.767 | ≥0.9 | Low intestinal wall permeability |
4 | P-glycoprotein pump substrate | No | No | Not removed by the efflux pump in the GIT | |
5 | BBB permeability | No | Yes | ||
6 | Octanol/water partition coefficient (Lipophilicity, Log Po/w) | −0.39 | 1.97 | 0–5 | Lower value is suggestive of hydrophilicity or lipophobicity of the compound, which therefore becomes membrane impermeable |
S/N | Parameters | Prediction | Reference | Implication | |
---|---|---|---|---|---|
CGA | CA | ||||
1 | PPB (%) | 64.8 | 94.9 | <90 | High plasma protein binding suggests drugs remain unavailable to tissue to elicit therapeutic effects |
2 | Volume distribution(l/kg) | 0.976 | 0.384 | 0.4–20 | Low volume reaching extravascular tissue based on blood tissue perfusion |
S/N | Parameters | Prediction | Reference | Implication | |
---|---|---|---|---|---|
CGA | CA | ||||
1 | CLplasma (mL/min/kg) | 11.086 | 3.34 | 5–15 mL/min/kg Moderate clearance plasma rate | Varied bioavailability in the systemic circulation and plasma removal rate; this may impact volume distribution and half-life |
2 | T1/2 (hr) | 1.395 | 2.758 | 1–4 h short half-life | Its effect wears off quickly, and 50% is removed quickly from the body. |
S/N | Parameters | Prediction | |
---|---|---|---|
CGA | CA | ||
1 | Lethal Dose 50 (LD50) | 5000 mg/kg | 1850 mg/kg |
2 | Hepatotoxicity | Inactive | Inactive |
3 | Neurotoxicity | Inactive | Active |
4 | Cardiotoxicity | Inactive | Active |
5 | Cytotoxicity | Inactive | Inactive |
6 | Mutagenicity | Inactive | Active |
7 | Nephrotoxicity | Fairly active | Inactive |
8 | Pulmonary | Fairly active | Inactive |
9 | Immunotoxicity | Active | Active |
S/N | Parameters | Prediction | Optimal Value | Implication | |
---|---|---|---|---|---|
CGA | CA | ||||
1 | Number of H-bond acceptors | 9 | 1 | ≤10 | High number increases polarity and H-bonding with targets but impacts membrane penetration due to hydrophilicity conferment for CGA, but insufficient H-bond forming group in CA, making CA more lipophilic and membrane-penetrating. Undesired H-bonding in CGA, with groups such as P-gp, caused by H-bond donors. |
2 | Number of H-bond donors | 6 | 0 | ≤5 | |
3 | Topological polar surface area (TPSA)(Å2) | 164.75 | 17.07 | 0–140 Å2 | The more surface area covered by polar atoms in a drug, the poorer the drug cell permeability and effectiveness to reach target tissues. 60–80 Å2 required to penetrate mammary tissues. |
4 | Number of rotatable sigma bonds | 5 | 2 | ≤10 | Moderate amount confers appropriate degree of flexibility to the drug, which is important for drug conformational change to cross cell membrane and interact with target at its active site. |
5 | Number of heavy atoms | 25 | 10 | <36 | Appropriate number indicative of good binding affinity (target selectivity) and ligand efficiency (ligand binding energy) |
6 | Number of aromatic heavy atoms | 6 | 6 | 2–4 | Higher increases drug hydrophobicity, which may enhance the ligand binding affinity but may reduce target selectivity via pi orbital stacking with aromatic amino acid side chains of undesired proteins |
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Olayiwola, Y.; Gollahon, L. Chlorogenic Acid and Cinnamaldehyde in Breast Cancer Cells: Predictive Examination of Pharmacokinetics and Binding Thermodynamics with the Key Mediators of PI3K/Akt Signaling. Biomedicines 2025, 13, 1810. https://doi.org/10.3390/biomedicines13081810
Olayiwola Y, Gollahon L. Chlorogenic Acid and Cinnamaldehyde in Breast Cancer Cells: Predictive Examination of Pharmacokinetics and Binding Thermodynamics with the Key Mediators of PI3K/Akt Signaling. Biomedicines. 2025; 13(8):1810. https://doi.org/10.3390/biomedicines13081810
Chicago/Turabian StyleOlayiwola, Yusuff, and Lauren Gollahon. 2025. "Chlorogenic Acid and Cinnamaldehyde in Breast Cancer Cells: Predictive Examination of Pharmacokinetics and Binding Thermodynamics with the Key Mediators of PI3K/Akt Signaling" Biomedicines 13, no. 8: 1810. https://doi.org/10.3390/biomedicines13081810
APA StyleOlayiwola, Y., & Gollahon, L. (2025). Chlorogenic Acid and Cinnamaldehyde in Breast Cancer Cells: Predictive Examination of Pharmacokinetics and Binding Thermodynamics with the Key Mediators of PI3K/Akt Signaling. Biomedicines, 13(8), 1810. https://doi.org/10.3390/biomedicines13081810