High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1
Abstract
:1. Introduction
2. Results and Discussion
2.1. Virtual Screening and Molecular Docking of ZINC Lead-Like Compounds
2.2. Physiochemical and ADME/T Properties
2.3. Analyses of the NDM-1 and Screened Inhibitors Interaction
2.3.1. NDM-1 and Meropenem Interaction
2.3.2. NDM-1 and ZINC10936382 Interaction
2.3.3. NDM-1 and ZINC30479078 Interaction
2.3.4. NDM-1 and ZINC41493045 Interaction
2.3.5. NDM-1 and ZINC7424911 Interaction
2.3.6. NDM-1 and ZINC84525623 Interaction
2.4. Molecular Mechanics—General Born Surface Area (MM-GBSA) Estimation
Molecular Dynamics (MD) Simulation
2.5. IC50 Value Determination
2.6. Steady State Enzyme Kinetics
3. Materials and Methods
3.1. Materials
3.2. Experimental Procedures
3.3. Retrieval and Preparation of Ligands
3.4. Preparation of Protein, Active Site Prediction, and Grid Generation
3.5. Virtual Screening and Molecular Docking
3.6. Validation of Docking Protocol
3.7. Determination of Physiochemical and ADME/T Properties
3.8. Molecular Mechanics—Generalized Born Surface Area (MM-GBSA) Calculations
3.9. Molecular Dynamics (MD) Simulation
3.10. Cloning, Expression and Purification of NDM-1
3.11. Determination of IC50
3.12. Enzyme Kinetics
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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S. No. | ZINC ID | Docking Score * | Glide g-Score * | Glide e-Model * | XP g-Score * |
---|---|---|---|---|---|
1. | ZINC10936382 | −8.322 | −8.322 | −68.183 | −8.322 |
2. | ZINC30479078 | −9.046 | −9.046 | −66.578 | −9.046 |
3. | ZINC41493045 | −7.714 | −7.714 | −64.597 | −7.714 |
4. | ZINC7424911 | −8.254 | −8.265 | −63.254 | −8.254 |
5. | ZINC84525623 | −8.790 | −8.790 | −64.740 | −8.790 |
6. | Control (Meropenem) | −6.413 | −6.413 | −56.140 | −6.413 |
Structure/Name of Compounds | Mol. Weight (g/mol) | HBD b | HBA c | Tpsa d (Å2) | Net Charge | RB e |
---|---|---|---|---|---|---|
ZINC10936382 | 393.418 | 1 | 5 | 65.4 | 0 | 3 |
ZINC30479078 | 416.452 | 1 | 4 | 66.5 | 0 | 5 |
ZINC41493045 | 372.428 | 0 | 6 | 89.2 | 0 | 3 |
ZINC7424911 | 339.358 | 1 | 5 | 80.5 | 0 | 3 |
ZINC84525623 | 378.428 | 2 | 4 | 84.5 | 0 | 3 |
ZINC Id | QPpolrz (13 to 70) | QPlogS (−6 to 0.5) | QPlogPC16 (4 to 18) | QPlogPoct (8 to 43) | QPlogPw (5 to 48) | QPlogPo/w (−2 to 6) | QPlogKp (−8 to −1) | QPlog Khsa (−1.5 to 1.2) |
---|---|---|---|---|---|---|---|---|
ZINC10936382 | 43.299 | −6.736 | 11.702 | 18.741 | 9.631 | 4.843 | −1.346 | 0.813 |
ZINC30479078 | 48.327 | −5.251 | 12.043 | 20.834 | 10.492 | 2.723 | −2.811 | 0.636 |
ZINC41493045 | 40.603 | −4.524 | 11.974 | 18.573 | 11.572 | 2.070 | −2.946 | −0.429 |
ZINC7424911 | 41.415 | −5.717 | 12.778 | 19.790 | 12.387 | 3.337 | −2.263 | 0.450 |
ZINC84525623 | 42.420 | −3.863 | 12.527 | 21.290 | 15.816 | 2.284 | −3.107 | −0.003 |
Compounds/ZINC IDs | Molecular Interactions | Nature of Interactions | Distance (Å) | Docking Binding Energy (∆G), kcal/mol | Docking Binding Affinity (Kd), M−1 | MM-GBSA Binding Energy, kcal/mol |
---|---|---|---|---|---|---|
Control (Hydrolyzed Meropenem) | Lys211:HZ1–Lig:O Asn220:HN–Lig:O Asn220:HD21–Lig:O Lig:H–His250:NE2 Lig:H–His120:NE2 Lig:H–His189:NE2 ZN2–Lig:O Trp93–Lig:C | Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Other (Metal–Acceptor) Hydrophobic (Pi–Alkyl) | 2.72 1.99 1.85 2.59 2.76 2.32 2.92 5.25 | −6.413 | 5.05 × 104 | −52.971 |
ZINC10936382 | Gln123:HN–Lig:O Asn220:HD22–Lig:O ZN2–Lig:O ZN1–Lig His122–Lig His250–Lig Val73–Lig His122–Lig Lig–Val73 | Hydrogen Bond Hydrogen Bond Other (Metal–Acceptor) Electrostatic Hydrophobic (Pi–Pi Stacked) Hydrophobic (Pi–Pi Stacked) Hydrophobic (Alkyl) Hydrophobic (Pi–Alkyl) Hydrophobic (Pi–Alkyl) | 2.08 2.93 2.86 4.97 4.94 4.80 3.98 4.26 5.18 | −8.322 | 1.27 × 106 | −61.432 |
ZINC30479078 | Gln123:HN–Lig:O Asp124:HN–Lig:O Asp124:OD2–Lig Val73:CG1–Lig His122–Lig Lig–Val73 | Hydrogen Bond Hydrogen Bond Electrostatic Hydrophobic (Pi–Sigma) Hydrophobic (Pi–Alkyl) Hydrophobic (Pi–Alkyl) | 2.67 2.18 3.70 3.61 4.04 5.00 | −9.046 | 4.31 × 106 | −70.643 |
ZINC41493045 | His122:HD1–Lig:O Asn220:HD21–Lig:O ZN1–Lig:O ZN2–Lig His250–Lig Lys211–Lig His250–Lig | Hydrogen Bond Hydrogen Bond Other (Metal–Acceptor) Electrostatic Hydrophobic (Pi–Pi Stacked) Hydrophobic (Alkyl) Hydrophobic (Pi–Alkyl) | 2.66 1.82 3.08 3.76 4.42 5.26 5.15 | −7.714 | 4.54 × 105 | −62.523 |
ZINC07424911 | Lig:HN–Asp212:OD2 Lig:HN–His250:O Asn220:HN–Lig Asp124:OD2–Lig His250–Lig Trp93–Lig Trp93–Lig Ala215–Lig | Hydrogen Bond Hydrogen Bond Hydrogen Bond Electrostatic Hydrophobic (Pi–Pi Stacked) Hydrophobic (Pi–Pi T–shaped) Hydrophobic (Pi–Pi T–shaped) Hydrophobic (Alkyl) | 2.76 2.72 2.93 4.24 3.97 5.47 4.84 4.34 | −8.254 | 1.13 ×106 | −60.619 |
ZINC84525623 | Gln123:HN–Lig:O Gln123:HN–Lig:O Asp124:HN–Lig:O Lys211:HZ1–Lig:O Asn220:HN–Lig:O His189:CE1–Lig:O ZN2–Lig Asp124:OD2–Lig Val73:CG1–Lig His250–Lig His250–Lig Lig–Val73 His250–Lig | Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Hydrogen Bond Carbon–Hydrogen Bond Electrostatic Electrostatic Hydrophobic (Pi–Sigma) Hydrophobic (Pi–Pi Stacked) Hydrophobic (Pi–Pi T-shaped) Hydrophobic (Alkyl) Hydrophobic (Pi–Alkyl) | 2.66 2.16 2.08 2.71 2.10 3.57 3.66 4.33 3.58 5.47 5.26 5.46 4.72 | −8.790 | 2.80 × 106 | −96.388 |
Substrates | NDM-1 | NDM-1 + ZINC84525623 * | ||||
---|---|---|---|---|---|---|
Km (µM) | kcat (s−1) | kcat/Km (µM−1 s−1) | Km (µM) | kcat (s−1) | kcat/Km (µM−1 s−1) | |
Ampicillin Cefotaxime Imipenem Meropenem Nitrocefin | 88.9 ± 3.1 57.7 ± 3.3 68.4 ± 4.6 58.4 ± 4.1 29.0 ± 2.0 | 438.2 ± 10.5 330.8 ± 16.4 665.8 ± 14.4 285.8 ± 17.3 279.7 ± 18.2 | 4.93 ± 0.21 5.73 ± 0.43 9.73 ± 0.69 4.89 ± 0.45 9.64 ± 0.91 | 111.3 ± 6.2 87.9 ± 5.7 93.6 ± 5.1 80.3 ± 6.4 54.9 ± 4.7 | 97.8 ± 6.1 104.5 ± 6.3 123.1 ± 7.8 125.7 ± 6.0 123.5 ± 6.4 | 0.88 ± 0.07 1.19 ± 0.10 1.32 ± 0.11 1.56 ± 0.14 2.25 ± 0.22 |
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Rehman, M.T.; AlAjmi, M.F.; Hussain, A.; Rather, G.M.; Khan, M.A. High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1. Int. J. Mol. Sci. 2019, 20, 819. https://doi.org/10.3390/ijms20040819
Rehman MT, AlAjmi MF, Hussain A, Rather GM, Khan MA. High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1. International Journal of Molecular Sciences. 2019; 20(4):819. https://doi.org/10.3390/ijms20040819
Chicago/Turabian StyleRehman, Md Tabish, Mohamed F AlAjmi, Afzal Hussain, Gulam Mohmad Rather, and Meraj A Khan. 2019. "High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1" International Journal of Molecular Sciences 20, no. 4: 819. https://doi.org/10.3390/ijms20040819