Detailed Experimental and In Silico Investigation of Indomethacin Binding with Human Serum Albumin Considering Primary and Secondary Binding Sites
Abstract
:1. Introduction
2. Results and Discussions
2.1. Experimental Investigation of Indomethacin Binding with HSA
2.2. In Silico Investigation of Indomethacin Binding with HSA
3. Materials and Methods
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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Observed | Corrected | |
---|---|---|
KSV1 (mol−1) | 3.4 × 105 (R2 = 0.9952) | 3.0 × 105 (R2 = 0.9971) |
KSV2 (mol−1) | 2.1 × 105 (R2 = 0.9861) | 1.5 × 105 (R2 = 0.9739) |
kb1 (mol−1) | 9.3 × 105 (R2 = 0.9965) | 5.9 × 105 (R2 = 0.9966) |
kb2 (mol−1) | 5.7 × 103 (R2 = 0.9863) | 1.9 × 103 (R2 = 0.9854) |
n1 | 1.08 | 1.05 |
n2 | 0.7 | 0.6 |
35 °C | 45 °C | |
---|---|---|
KSV1 (mol−1) | 2.4 × 105 (R2 = 0.9952) | 2.1 × 105 (R2 = 0.9971) |
KSV2 (mol−1) | 1.3 × 105 (R2 = 0.9861) | 1.0 × 105 (R2 = 0.9739) |
kb1 (mol−1) | 2.9 × 105 (R2 = 0.9965) | 1.8 × 105 (R2 = 0.9966) |
kb2 (mol−1) | 1.7 × 103 (R2 = 0.9863) | 1.4 × 103 (R2 = 0.9854) |
n1 | 1.00 | 0.98 |
n2 | 0.6 | 0.6 |
Warfarin | Ibuprofen | Hemin | Warfarin + Hemin | |
---|---|---|---|---|
KSV1 (mol−1) | 1.2 × 105 | 2.8 × 105 | 2.1 × 105 | 1.1 × 105 |
KSV2 (mol−1) | - | 1.6 × 105 | - | 6.0 × 104 |
kb1 (mol−1) | 2.8 × 104 | 4.7 × 105 | 1.4 × 105 | 3.4 × 103 |
kb2 (mol−1) | - | 1.5 × 103 | - | 9.8 × 102 |
Primary Site | Secondary Site | |||||
---|---|---|---|---|---|---|
Temp (°C) | 25 | 35 | 45 | 25 | 35 | 45 |
∆G (KJ mol−1) | –32.8 | –32.3 | –31.9 | –18.7 | –19.0 | –19.2 |
∆H (KJ mol−1) | –47.4 | –11.6 | ||||
∆S (J mol−1 K−1) | –48.9 | 23.9 |
Name of the Sites | ΔG (kcal/mol) (Program: Auto Dock Vina) | Ki (μM) | Estimated Binding Affinity (kcal/mol) (Program: Prodigy) |
---|---|---|---|
Drug site 1 | −10.1 | 0.04 | −6.5 |
Drug site 2 | −7.96 | 1.46 | −5.4 |
Fatty acid binding site 1 | −8.4 | 0.69 | −5.8 |
Name of the Sites | Hydrogen Bonds | Hydrophobic Interactions |
---|---|---|
Drug site 1 (DS1) | W214 and R218 | K195, K199, S202, L203, A210, F211, A215, L238, D451, and L481 |
Drug site 2 (DS2) | N391 | P384, L387, I388, C392, R410, Y411, V433, C437, R445, A449, and R485 |
Fatty acid binding site 1 (FA1) | None | Leu115, Met123, Phe134, Leu135, Tyr138, Leu139, Ile142, Leu154, Ala158, Tyr161, Phe165, and R186 |
Protein and Protein–Ligand Complexes | RMSD (Å) | RMSF (Å) | Rg (Å) | HBonds (between HSA & Indomethacin | SASA (nm2) | Trace of Covariance Matrix Values (nm2) |
---|---|---|---|---|---|---|
Free HSA | 4.7 | 1.9 | 26.5 | NA | 263.50 | 278.72 |
Drug site 1 | 5.1 | 1.9 | 26.1 | 3 | 265.12 | 297.98 |
Drug site 2 | 6.2 | 1.9 | 26.3 | 2 | 270.65 | 287.46 |
Fatty acid binding site 1 | 5.6 | 1.9 | 26 | 1 | 267.18 | 273.18 |
Protein and Protein–Ligand Complexes | Coil | β-Bridge | Bend | Turn | α-Helix | π-Helix | 310-Helix |
---|---|---|---|---|---|---|---|
Free HSA | 0.13 | 0.00 | 0.00 | 0.07 | 0.71 | 0.01 | 0.01 |
Drug site 1 | 0.14 | 0.00 | 0.00 | 0.08 | 0.70 | 0.00 | 0.01 |
Drug site 2 | 0.14 | 0.00 | 0.00 | 0.07 | 0.70 | 0.00 | 0.01 |
Fatty acid binding site 1 | 0.14 | 0.00 | 0.07 | 0.07 | 0.71 | 0.01 | 0.01 |
Name of the Sites | Number of Water Molecules Added | Number of Counter Ions Added |
---|---|---|
Free HSA | 43,298 | 16 NA |
Drug site 1 | 43,272 | 17 NA |
Drug site 2 | 43,293 | 17 NA |
Fatty acid binding site 1 | 43,299 | 17 NA |
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Ali, M.S.; Muthukumaran, J.; Jain, M.; Tariq, M.; Al-Lohedan, H.A.; Al-Sanea, A.S.S. Detailed Experimental and In Silico Investigation of Indomethacin Binding with Human Serum Albumin Considering Primary and Secondary Binding Sites. Molecules 2023, 28, 2979. https://doi.org/10.3390/molecules28072979
Ali MS, Muthukumaran J, Jain M, Tariq M, Al-Lohedan HA, Al-Sanea ASS. Detailed Experimental and In Silico Investigation of Indomethacin Binding with Human Serum Albumin Considering Primary and Secondary Binding Sites. Molecules. 2023; 28(7):2979. https://doi.org/10.3390/molecules28072979
Chicago/Turabian StyleAli, Mohd Sajid, Jayaraman Muthukumaran, Monika Jain, Mohammad Tariq, Hamad A. Al-Lohedan, and Abdullah Saad S. Al-Sanea. 2023. "Detailed Experimental and In Silico Investigation of Indomethacin Binding with Human Serum Albumin Considering Primary and Secondary Binding Sites" Molecules 28, no. 7: 2979. https://doi.org/10.3390/molecules28072979