Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71
Abstract
:1. Introduction
2. Results and Discussion
2.1. Rational Design and Screening
2.2. Stability of the Simulated Complexes
2.3. Number of Contact Atoms and H-Bonds
2.4. Key Binding Residues
2.5. Predicted Binding Affinity of the Potent Rupintrivir Analog
3. Materials and Methods
3.1. System Preparation and Compound Screening
3.2. Molecular Dynamics Simulations
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 | Compound | ||||
---|---|---|---|---|---|
MM/PBSA | MM/GBSA | MM/PBSA | MM/GBSA | ||
P1′-1 | −9.14 | −6.5 | P2-m9 | 0.4 | 0.94 |
P1′-2 | 0.17 | 4.98 | P2-m10 | 3.25 | 8.96 |
P1-1 | 7.82 | 5.02 | P3-1 | 0.43 | 3.24 |
P1-2 | 20.41 | 17.58 | P3-2 | 5.67 | 7.82 |
P1-3 | 1.37 | 1.91 | P3-3 | 2.54 | 4.15 |
P1-4 | 8.28 | 4.21 | P3-4 | −4.9 | −2.54 |
P1-5 | 17.76 | 14.31 | P4-1 | 1.98 | 6.27 |
P2-p1 | 6.38 | 5.49 | P4-2 | 1.73 | 4.25 |
P2-p2 | 14.17 | 14.15 | P4-3 | 2.28 | 7.36 |
P2-p3 | 1.48 | 2.14 | P4-4 | 12.74 | 12.79 |
P2-p4 | 7.55 | 9.22 | P4-5 | −5.34 | −5.68 |
P2-p5 | 7.85 | 11.03 | P4-6 | 4.46 | 2.51 |
P2-p6 | 0.73 | 3.55 | P4-7 | 4.65 | 4.29 |
P2-p7 | 1.37 | 5.18 | P4-8 | 3.32 | 2.94 |
P2-p8 | 6.65 | 7.74 | P4-9 | 6.58 | 4.92 |
P2-p9 | 0.65 | 1.38 | P4-10 | 0.75 | 1.27 |
P2-p10 | 1.56 | 3.93 | P4-11 | 4.89 | 3.34 |
P2-m1 | 20.47 | 18.36 | P4-12 | 13.28 | 11.89 |
P2-m2 | 18.59 | 17.29 | P4-13 | 1.57 | 0.47 |
P2-m3 | −12.12 | −4.2 | P4-14 | 1.64 | 0.96 |
P2-m4 | 2.41 | 6.29 | P4-15 | 12.68 | 11.51 |
P2-m5 | 8.74 | 12.38 | P4-16 | 1.55 | 1.12 |
P2-m6 | 1.75 | 1.35 | P4-17 | 3.03 | 2.52 |
P2-m7 | 0.49 | 2.03 | P4-18 | 4.12 | 4.44 |
P2-m8 | 1.98 | 4.71 | P4-19 | −5.55 | −6.68 |
CV-A16 | EV-A71 | |
---|---|---|
P4-5 | 22.5 ± 5.0 | 16.1 ± 4.7 |
P4-19 | 22.1 ± 5.3 | 17.4 ± 4.8 |
P1′-1 | 19.3 ± 4.3 | 17.8 ± 4.5 |
P2-m3 | 24.3 ± 4.3 | 22.1 ± 4.5 |
P3-4 | 17.9 ± 4.8 | 21.6 ± 4.8 |
Rupintrivir | 23.7 ± 4.7 | 20.0 ± 5.0 |
CV-A16 | EV-A71 | |
---|---|---|
P4-5 | 4.8 ± 1.1 | 3.6 ± 1.3 |
P4-19 | 4.0 ± 1.2 | 4.4 ± 1.2 |
P1′-1 | 4.0 ± 1.0 | 5.1 ± 1.1 |
P2-m3 | 6.5 ± 1.2 | 5.6 ± 1.5 |
P3-4 | 3.3 ± 1.3 | 4.8 ± 1.1 |
Rupintrivir | 4.5 ± 0.9 | 4.7 ± 1.1 |
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Sripattaraphan, A.; Sanachai, K.; Chavasiri, W.; Boonyasuppayakorn, S.; Maitarad, P.; Rungrotmongkol, T. Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71. Molecules 2022, 27, 1908. https://doi.org/10.3390/molecules27061908
Sripattaraphan A, Sanachai K, Chavasiri W, Boonyasuppayakorn S, Maitarad P, Rungrotmongkol T. Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71. Molecules. 2022; 27(6):1908. https://doi.org/10.3390/molecules27061908
Chicago/Turabian StyleSripattaraphan, Amita, Kamonpan Sanachai, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Phornphimon Maitarad, and Thanyada Rungrotmongkol. 2022. "Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71" Molecules 27, no. 6: 1908. https://doi.org/10.3390/molecules27061908