Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species
Abstract
1. Introduction
2. Results and Discussion
2.1. Kauranes 302 and Its Derivative 302a Have Dual In Vitro Enzymatic Activity against L. major PTR1/DHFR-TS
2.2. Hybrid Model of L. major DHFR-TS and Molecular Docking Calculations
2.3. Kaurane 302 and Its Derivative 302a May Have the Potential to Inhibit DHFR-TS in Different Species of Leishmania from the New World
2.4. Molecular Dynamics Simulations for L. major and L. braziliensis DHFR-TS Interacting with 302 and MTX
2.5. Free Energy Calculations by the Molecular Mechanics Poisson–Boltzmann Surface Area Approach (MM/PBSA) Method
3. Materials and Methods
3.1. LmDHFR-TS Enzyme Inhibition Assay
3.2. Isolation of Compound 148
3.3. Synthesis of 16ß,17-Isopropylidenedioxy-ent-kauran-3-one (4)
3.4. Hybrid Models of Leishmania DHFR-TS
3.5. Molecular Docking Calculations
3.6. Molecular Dynamics Simulations
3.7. Binding Free Energies Using the Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) Method
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Compound | 4 | 135 | 302 | 301 | 302a | 301a | MTX |
---|---|---|---|---|---|---|---|
IC50 (µM) | 7.6 | 11.2 | 6.3 | 8.8 | 4.5 | 7.9 | 1.4 |
Confidence Interval (95%) | 6.9–8.1 | 10.2–12.1 | 5.8–6.9 | 8.0–9.9 | 3.9–5.2 | 7.1–8.4 | 1.1–1.8 |
Kiapp | 0.81 | 1.20 | 0.68 | 0.94 | 0.48 | 0.85 | 0.15 |
Structure | MolDock Score (kJ/mol) | RMSD (A) | SD |
---|---|---|---|
4 | −70.25 | 0.68 | 5.7 |
135 | −62.85 | 1.23 | 8.6 |
301 | −73.34 | 1.09 | 10.3 |
302 | −76.53 | 1.13 | 4.9 |
301a | −72.26 | 0.89 | 9.8 |
302a | −81.43 | 1.29 | 6.4 |
2,4-diamine | −72.34 | 1.55 | 8.9 |
MTX | −107.60 | 0.24 | 5.9 |
L. braziliensis | L. panamensis | L. amazonensis | |||||||
---|---|---|---|---|---|---|---|---|---|
Structure | VINA Score (kcal/mol) | SD | RMSD | VINA Score (kcal/mol) | SD | RMSD | VINA Score (kcal/mol) | SD | RMSD |
4 | −10.70 | 0.05 | 0.13 | −10.96 | 0.07 | 0.46 | −10.68 | 0.04 | 0.11 |
135 | −10.50 | 0 | 0.21 | −10.19 | 0.03 | 0.31 | −10.52 | 0.06 | 0.25 |
302 | −10.90 | 0.05 | 0.55 | −10.44 | 0.05 | 2.73 | −10.55 | 0.15 | 0.86 |
302a | −11.17 | 0.13 | 0.61 | −12.55 | 0.28 | 0.56 | −10.60 | 0.08 | 0.61 |
301 | −10.40 | 0.10 | 0.92 | −10.84 | 0.07 | 1.68 | −10.85 | 0.05 | 0.64 |
301a | −10.66 | 0.20 | 0.45 | −12.54 | 0.08 | 0.86 | −11.14 | 0.15 | 0.79 |
MTX | −9.64 | 0.07 | 1.87 | −9.45 | 0.15 | 1.48 | −9.54 | 0.07 | 1.71 |
Structure | Van der Waals (kJ/mol) | Electrostatic (kJ/mol) | Polar Solvation (kJ/mol) | SASA (kJ/mol) | Binding Energy (kJ/mol) |
---|---|---|---|---|---|
Leishmania major | |||||
302 | −122.6 ± 11.8 | −262.3 ± 1.1 | 263.4 ± 23.5 | −16.7 ± 0.7 | −138.2 ± 12.2 |
302A | −210.2 ± 10.2 | −127.6 ± 3.0 | 219.5 ± 8.6 | −15.9 ± 1.0 | −134.2 ± 16.8 |
MTX | −157.5 ± 12.4 | −399.7 ± 10.9 | 436.4 ± 22.4 | −19.4 ± 1.3 | −140.1 ± 18.6 |
Leishmania braziliensis | |||||
302 | −215.4 ± 5.3 | −23.6 ± 2.2 | 124.2 ± 6.8 | −20.0 ± 0.4 | −134.8 ± 9.5 |
302A | −199.3 ± 6.0 | −31.4 ± 0.6 | 107.4 ± 7.4 | −21.3 ± 0.6 | −144.5 ± 5.0 |
MTX | −216.4 ± 5.5 | −51.5 ± 3.5 | 194.6 ± 8.0 | −22.6 ± 0.8 | −95.9 ± 9.2 |
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Herrera-Acevedo, C.; de Menezes, R.P.B.; de Sousa, N.F.; Scotti, L.; Scotti, M.T.; Coy-Barrera, E. Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species. Antibiotics 2023, 12, 663. https://doi.org/10.3390/antibiotics12040663
Herrera-Acevedo C, de Menezes RPB, de Sousa NF, Scotti L, Scotti MT, Coy-Barrera E. Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species. Antibiotics. 2023; 12(4):663. https://doi.org/10.3390/antibiotics12040663
Chicago/Turabian StyleHerrera-Acevedo, Chonny, Renata Priscila Barros de Menezes, Natália Ferreira de Sousa, Luciana Scotti, Marcus Tullius Scotti, and Ericsson Coy-Barrera. 2023. "Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species" Antibiotics 12, no. 4: 663. https://doi.org/10.3390/antibiotics12040663
APA StyleHerrera-Acevedo, C., de Menezes, R. P. B., de Sousa, N. F., Scotti, L., Scotti, M. T., & Coy-Barrera, E. (2023). Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species. Antibiotics, 12(4), 663. https://doi.org/10.3390/antibiotics12040663