In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development
Abstract
:1. Introduction
2. Results and Discussion
2.1. Design of In Silico Screening Protocol/Benchmarking Studies
2.2. Screening of Biogenic Database
2.2.1. Generation I Selection
2.2.2. Generation II Selection
2.3. Kinase Selectivity Screening
2.4. ADME(T) Results & Analysis
3. Conclusions
4. Materials and Methods
4.1. Computational Details
4.1.1. Ligand Preparation
4.1.2. Protein Preparation
4.1.3. Docking
4.1.4. Pharmacophore Modelling
4.1.5. ADME(T) Calculations
4.1.6. DFT Calculations
4.2. Experimental In Vitro Binding Assays
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Enrichment Statistics | Protocol 1 | Protocol 2 | Protocol 3 |
---|---|---|---|
# Actives recovered a | 50 | 42 | 41 |
AU-ROC | 0.8 | 0.76 | 0.77 |
Top-ranked 1% Statistics | |||
# Actives in top 1% | 10 | 15 | 19 |
EF—1% b | 16 | 28 | 34 |
Top-ranked 2% Statistics | |||
# Actives in top 2% | 16 | 16 | 22 |
EF—2% b | 15 | 16 | 22 |
Top-ranked 5% Statistics | |||
# Actives in top 5% | 22 | 22 | 26 |
EF—5% b | 8.8 | 8.8 | 10 |
Compound | Computational a | Experimental | ||
---|---|---|---|---|
Docking Score | Log BB | PSA (Å2) | IC50 (µM) (% Inhibition at 50 µM) | |
1 | −8.21 | −0.55 | 73.6 | 1.63 ± 0.30 |
2 | −8.19 | −0.66 | 74.1 | 20.55 ± 3.80 |
3 | −8.84 | −0.32 | 69.2 | 63.73 ± 3.3 |
4 | −8.37 | −0.41 | 55.1 | 87.51 ± 9.17 |
5 | −8.29 | −0.35 | 66.6 | (20%) |
6 | −8.37 | −0.29 | 89.7 | (11%) |
7 | −8.31 | −0.63 | 95.4 | (10%) |
8 | −8.35 | −0.50 | 66.0 | (10%) |
9 | −8.41 | −0.46 | 71.5 | (9%) |
10 | −8.19 | −0.63 | 138.7 | (6%) |
11 | −8.92 | −0.52 | 117.2 | (2%) |
12 | −8.58 | −0.30 | 54.5 | (NI) b |
Skeletal Structure | ||
Global minimum conformation | ||
t1 | t2 | |
Energy (kcal/mol) a | ||
Relative GPE | 0.0 (0.0) | 7.1 (6.8) |
Relative SPE | 0.0 | 6.3 |
Dihedral Angle (°) b | ||
ω1 [C(2)-C(1)-N-H] | 9.3 | 15.7 |
ω2 [C(2)-C(1)-N-C(1′)] | −138.6 | −128.9 |
ω3 [C(1)-C(2)-O-H] | - | −179.1 |
Compound | Computational a | Experimental | ||
---|---|---|---|---|
Docking Score | Log BB | PSA (Å2) | IC50 (µM) | |
2 | −8.19 | −0.66 | 74.1 | 20.55 ± 3.80 |
13 | −8.32 | −0.70 | 74.1 | 9.4 ± 0.5 |
14 | −8.44 | −0.74 | 74.5 | 9.1 ± 0.2 |
15 | −8.31 | −0.76 | 82.4 | 11.4 ± 0.6 |
16 | −4.79 | −0.41 | 70.0 | 27.1 ± 1.1 |
17 | −7.68 | −0.21 | 69.0 | 14.0 ± 3.1 |
18 | −8.41 | −0.60 | 73.3 | 25.3 ± 3.5 |
19 | −7.54 | −0.76 | 73.0 | 4.9 ± 0.2 |
20 | −7.89 | −0.83 | 81.8 | 9.1 ± 1.7 |
21 | −7.91 | −0.85 | 87.7 | 17.0 ± 2.7 |
22 | −8.40 | −0.85 | 89.4 | 36.7 ± 5.7 |
Kinase | Compound IC50 (µM) | |
---|---|---|
14 | 19 | |
GSK-3α | 2.3 ± 0.4 | 1.7 ± 0.1 |
GSK-3β | 9.1 ± 2.4 | 4.9 ± 0.2 |
PKBβ | 14.9 ± 1.5 | 24.6 ± 0.2 |
ERK2 | 21. 3 ± 2.3 | - |
PKCγ | - | 11.0 ± 1.5 |
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Emmerich, T.D.; Hayes, J.M. In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development. Pharmaceuticals 2023, 16, 661. https://doi.org/10.3390/ph16050661
Emmerich TD, Hayes JM. In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development. Pharmaceuticals. 2023; 16(5):661. https://doi.org/10.3390/ph16050661
Chicago/Turabian StyleEmmerich, Thomas D., and Joseph M. Hayes. 2023. "In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development" Pharmaceuticals 16, no. 5: 661. https://doi.org/10.3390/ph16050661
APA StyleEmmerich, T. D., & Hayes, J. M. (2023). In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development. Pharmaceuticals, 16(5), 661. https://doi.org/10.3390/ph16050661