Screening and Analysis of Potential Inhibitors of SHMT2
Abstract
:1. Introduction
2. Results and Discussion
2.1. Virtual Screening Results
2.2. Result from Molecular Dynamics Simulation
2.3. Binding Free Energies
2.4. Identification of Hot Spots
2.5. Analysis of Binding Mechanism
3. Method
3.1. Molecular Docking
3.2. Consensus Scoring
3.3. Molecular Clustering
3.4. Molecular Dynamics Simulation
3.5. Binding Free Energy Calculation
4. Conclusions and Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Residue | IE | ||||||
---|---|---|---|---|---|---|---|
TYR105_B | −5.05 | 0.05 | 0.71 | −0.28 | −4.57 | 0.39 | −4.18 |
LEU166_A | −4.50 | −0.07 | 0.55 | −0.35 | −4.36 | 0.44 | −3.92 |
ARG425_A | −3.18 | −0.08 | 0.02 | −0.22 | −3.46 | 0.24 | −3.22 |
TYR106_B | −2.40 | 0.13 | −0.17 | −0.17 | −2.61 | 0.15 | −2.46 |
LYS409_A | −1.82 | −0.01 | 0.06 | −0.17 | −1.94 | 0.14 | −1.80 |
GLU98_B | −1.75 | −0.22 | 0.23 | −0.14 | −1.88 | 0.17 | −1.71 |
TYR176_A | −1.93 | 0.00 | 0.34 | −0.19 | −1.78 | 0.16 | −1.62 |
PHE320_B | −2.11 | −0.55 | 1.14 | −0.12 | −1.64 | 0.21 | −1.43 |
ASN408_A | −1.37 | −0.31 | 0.15 | −0.11 | −1.63 | 0.23 | −1.40 |
LEU172_A | −1.74 | −0.30 | 0.59 | −0.13 | −1.59 | 0.21 | −1.38 |
HIP171_A | −1.21 | −0.17 | −0.01 | −0.09 | −1.48 | 0.23 | −1.25 |
ASN410_A | −1.38 | −0.38 | 0.52 | −0.10 | −1.33 | 0.25 | −1.08 |
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Chen, B.; Zhang, J.Z.H. Screening and Analysis of Potential Inhibitors of SHMT2. Biophysica 2023, 3, 651-667. https://doi.org/10.3390/biophysica3040044
Chen B, Zhang JZH. Screening and Analysis of Potential Inhibitors of SHMT2. Biophysica. 2023; 3(4):651-667. https://doi.org/10.3390/biophysica3040044
Chicago/Turabian StyleChen, Bojin, and John Z. H. Zhang. 2023. "Screening and Analysis of Potential Inhibitors of SHMT2" Biophysica 3, no. 4: 651-667. https://doi.org/10.3390/biophysica3040044