In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases
Abstract
:1. Introduction
2. Materials and Methods
2.1. In Silico Docking Study
2.2. Chemistry
2.3. Cells and Materials
2.4. Cell Fusion Assay Using Dual Split Proteins (DSP)
2.5. Enzyme Assays
2.6. Pseudovirus Assay
2.7. Cell Toxicity Assay
3. Results
3.1. Design Rational
3.2. In Silico Evaluation
3.3. Chemistry
3.4. In Vitro Evaluations
3.4.1. TMPRSS2 Inhibition Assay
3.4.2. Cell Fusion Assays
3.4.3. Pseudovirus Entry and Cell Viability Assays
3.4.4. Thrombin and Factor Xa Enzyme Inhibition Assays
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Compound | Binding Score 1 | Established Interactions |
---|---|---|
7 | −5.7172 | Three hydrogen bonds between (Gly464, Cys465, and Ser436) and the protons of one amidine group. |
Hydrogen bond between His279 with a proton of the other amidine group. | ||
Attractive charge between Asp435 and one amidine group. | ||
π-sulfur interaction between Cys465 and the phenyl (linker) group. | ||
8 | −6.5412 | Hydrogen bond between His279 with protons of one amidine group. |
π-σ interaction between Val280 and the phenyl (linker) group. | ||
π-alkyl interaction between Val280 and the furan central ring. | ||
Alkyl interaction between Cys465 and isopropyl substitution on one amidine group. | ||
9 | −6.0349 | C-H bond between Ser436 and protons of the tetrahydropyrimidine ring. |
C-H bond between Gly464 and protons of the tetrahydropyrimidine ring. | ||
π-alkyl interaction between Val280 and the phenyl (linker) group. | ||
Alkyl interaction between Cys465 and the tetrahydropyrimidine ring. | ||
10 | −6.2871 | Salt bridge between Asp435 and one amidine group. |
Three hydrogen bonds between (Asp435, Gly464, and Trp461) and the protons of one amidine group. | ||
Two hydrogen bonds between His279 and the other amidine group. | ||
Two amide-π stacked interactions between Cys437 and the benzimidazole ring. | ||
Amide-π stacked interactions between Trp461 and the benzimidazole ring. | ||
11 | −7.4058 | Hydrogen bond between Cys465 with protons of one amidine group. |
Hydrogen bond between Gly391 with protons of the other amidine group. | ||
Alkyl interaction between Cys465 and isopropyl substitution on one amidine group. | ||
π-π T-shaped interaction between His296 and the benzimidazole ring. | ||
π -alkyl interaction between Val280 and the benzimidazole ring. | ||
12 | −6.4987 | Salt bridge between Asp435 and one amidine group. |
Two hydrogen bonds between Ser436 and (the same) amidine group. | ||
Hydrogen bond between Ser441 with a proton of the benzimidazole ring. | ||
π-alkyl interaction between Val280 and the benzimidazole ring. | ||
13 | −7.6965 | Salt bridge between Asp435 and one amidine group. |
Hydrogen bond between Ser436 and (the same) amidine group. | ||
Hydrogen bond between Ser441 with a proton of the benzimidazole ring. | ||
Hydrogen bond between His279 with a proton of the other benzimidazole ring. | ||
π-donor hydrogen bond between Thr393 with a proton of the benzimidazole ring. | ||
π-alkyl interaction between Val278 with the (same) benzimidazole ring. | ||
π-σ interaction between Val278 with the (same) benzimidazole ring. | ||
π-alkyl interaction between Val280 and the phenyl (linker) group. | ||
π-alkyl interaction between Val280 and the pyridine central ring. | ||
Amide-π stacked interaction between Cys437 and the benzimidazole ring. | ||
14 | −8.4438 | Two hydrogen bonds between Ser441 and Ser436 with a proton of one amidine group. |
Hydrogen bond between His279 with a proton of the benzimidazole ring. | ||
Two π-alkyl interaction between Val278 with the (same) benzimidazole ring. | ||
π-π interaction between His296 with the (other) benzimidazole ring. | ||
π-alkyl interaction between Val278 with the phenyl (linker) group. | ||
π-alkyl interaction between Val280 with the phenyl (linker) group. | ||
π-alkyl interaction between Val280 with the pyridine central ring. | ||
π-donor hydrogen bond between Thr393 with a proton of the benzimidazole ring. | ||
π-sulfur interaction between Cys281 with the phenyl (linker) group. |
Compound | TMPRSS2 IC50 (µM) | S2TA Assay | CoTF Assay IC50 (µM) | |
---|---|---|---|---|
% Inhibition 1 | IC50 (µM) | |||
7 | 82.7 | 39.91 | >100 | >100 |
10 | 5.57 | 89.53 | 16.93 | 37.84 |
11 | >10 2 | 44.17 | >100 | >100 |
12 | 4.89 | 55.42 | >100 | >100 |
13 | 72.4 | 93.98 | 13.70 | 37.00 |
14 | >100 | 97.33 | 10.87 | 30.97 |
Pentamidine | 3.98 | 71.30 | 32.27 | >100 |
Nafamostat | <0.001 | 89.32 | 0.007115 | >100 |
Compound | SARS-CoV-2 Pseudovirus | Cell Viability Inhibition IC50 (µM) | |
---|---|---|---|
% Inhibition 1 | IC50 (µM) | ||
7 | 2.66 | >100 | >100 |
10 | 19.57 | >100 | >100 |
11 | 27.02 | >100 | >100 |
12 | 17.07 | >100 | >100 |
13 | 20.53 | >100 | >100 |
14 | 77.44 | 83.66 | >100 |
Pentamidine | 69.48 | 45 | >100 |
Nafamostat | 87.34 | 0.06 | >100 |
Compound | IC50 (µM) | |
---|---|---|
Thrombin | Factor Xa | |
7 | 79.1 | 30.9 |
10 | 0.921 | 5.93 |
11 | >1 1 | >1 1 |
12 | 0.862 | 34.1 |
13 | 0.929 | 4.89 |
14 | 2.25 | >10 1 |
Pentamidine | 1.51 | 6.22 |
Nafamostat | 0.0341 | 1.74 |
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Hassan, A.H.E.; El-Sayed, S.M.; Yamamoto, M.; Gohda, J.; Matsumoto, T.; Shirouzu, M.; Inoue, J.-i.; Kawaguchi, Y.; Mansour, R.M.A.; Anvari, A.; et al. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses 2023, 15, 1171. https://doi.org/10.3390/v15051171
Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue J-i, Kawaguchi Y, Mansour RMA, Anvari A, et al. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses. 2023; 15(5):1171. https://doi.org/10.3390/v15051171
Chicago/Turabian StyleHassan, Ahmed H. E., Selwan M. El-Sayed, Mizuki Yamamoto, Jin Gohda, Takehisa Matsumoto, Mikako Shirouzu, Jun-ichiro Inoue, Yasushi Kawaguchi, Reem M. A. Mansour, Abtin Anvari, and et al. 2023. "In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases" Viruses 15, no. 5: 1171. https://doi.org/10.3390/v15051171
APA StyleHassan, A. H. E., El-Sayed, S. M., Yamamoto, M., Gohda, J., Matsumoto, T., Shirouzu, M., Inoue, J. -i., Kawaguchi, Y., Mansour, R. M. A., Anvari, A., & Farahat, A. A. (2023). In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses, 15(5), 1171. https://doi.org/10.3390/v15051171