Virtual Screening, Synthesis, and Biological Evaluation of Some Carbohydrazide Derivatives as Potential DPP-IV Inhibitors
Abstract
:1. Introduction
2. Results and Discussion
2.1. Virtual Screening of the Designed Derivatives
2.1.1. In Silico ADMET Analysis
2.1.2. Molecular Docking
2.2. In vitro DPP-IV Enzyme Assay
2.3. In Vivo Antidiabetic Activity
3. Materials and Methods
3.1. Virtual Screening of the Designed Derivatives
3.1.1. In Silico ADMET Analysis
3.1.2. Molecular Docking
3.2. Chemistry
3.2.1. Synthesis of ethyl 6-Methyl-2-oxo-4- -1,2,3,4-tetrahydropyrimidine-5-carboxylate
3.2.2. Synthesis of 6-Methyl-2-oxo-4-substituted-1,2,3,4 Tetrahydropyrimidine-5-carbohydrazide
3.2.3. Synthesis of 6-Methyl-2-oxo-4-substituted-N’-((E) Substituted-methylidene)-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide Derivatives
- Characterization data(E)-N-Benzylidene-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (1a).
- (E)-N-(2-Hydroxybenzylidene)-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (1b).
- (E)-N-(2-Methoxybenzylidene)-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (1c).
- (E)-N-(4-Methoxybenzylidene)-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (1d).
- (E)-N-Benzylidene-4-(2-chlorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-5-carbohydrazide (2a).
- (E)-4-(2-Chlorophenyl)-N-(2-hydroxybenzylidene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (2b).
- (E)-4-(2-Chlorophenyl)-N-(2-methoxybenzylidene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (2c).
- (E)-4-(2-Chlorophenyl)-N-(4-methoxybenzylidene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (2d).
- (E)-N-Benzylidene-4-(2,4-dichlorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (3a).
- (E)--4-(2,4-Dichlorophenyl)-N-(2-hydroxybenzyldene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (3b).
- (E)-N-(2,4-Diclorobenzylidene)-4-(2-methoxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (3c).
- (E)-N-(2,4-Diclorobenzylidene)-4-(4-methoxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (3d).
- (E)-N-Benzylidene-4-(2-fluorophenyl)-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (4a).
- (E)--4-(2-Fluorophenyl)-N-(2-hydroxybenzyldene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (4b).
- (E)--4-(2-Fluorophenyl)-N-(2-methoxybenzyldene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (4c).
- (E)--4-(2-Fluorophenyl)-N-(4-methoxybenzyldene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (4d).
- (E)-N-Benzylidene-4-(2,4-difluorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (5a).
- (E)--4-(2,4-Difluorophenyl)-N-(2-hydroxybenzyldene)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (5b).
- (E)-N-(2,4-Difluorobenzylidene)-4-(2-methoxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (5c).
- (E)-N-(2,4-Difluorobenzylidene)-4-(4-methoxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carbohydrazide (5d).
3.3. In Vitro DPP-IV Enzymatic Assay
3.4. In Vivo Antidiabetic Activity
3.4.1. Animals and Ethical Approvals
3.4.2. Acute Toxicity Studies
3.4.3. STZ-Induced T2DM Model
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Codes | Ar | Ar’ | Codes | Ar | Ar’ |
---|---|---|---|---|---|
1a | Phenyl | Phenyl | 3c | 2,4-dichlorophenyl | 2-methoxyphenyl |
1b | Phenyl | 2-hydroxyphenyl | 3d | 2,4-dichlorophenyl | 4-methoxyphenyl |
1c | Phenyl | 2-methoxyphenyl | 4a | 2-fluorophenyl | Phenyl |
1d | Phenyl | 4-methoxyphenyl | 4b | 2-fluorophenyl | 2-hydroxyphenyl |
2a | 2-chlorophenyl | Phenyl | 4c | 2-fluorophenyl | 2-methoxyphenyl |
2b | 2-chlorophenyl | 2-hydroxyphenyl | 4d | 2-fluorophenyl | 4-methoxyphenyl |
2c | 2-chlorophenyl | 2-methoxyphenyl | 5a | 2,4-difluorophenyl | Phenyl |
2d | 2-chlorophenyl | 4-methoxyphenyl | 5b | 2,4-difluorophenyl | 2-hydroxyphenyl |
3a | 2,4-dichlorophenyl | Phenyl | 5c | 2,4-difluorophenyl | 2-methoxyphenyl |
3b | 2,4-dichlorophenyl | 2-hydroxyphenyl | 5d | 2,4-difluorophenyl | 4-methoxyphenyl |
Compound Codes | Lipinski Rule of Five | Veber’s Rule | |||||
---|---|---|---|---|---|---|---|
Log P (<5) | Mol. Wt. (<500 Da) | HBA (<10) | HBD (<5)s | Violations | Total Polar Surface Area (Å2) (<140 Å2) | No. of Rotatable Bonds (<10) | |
NL | 3.29 | 419.37 | 10 | 01 | 0 | 59.97 | 03 |
1a | 1.97 | 334.37 | 3 | 3 | 0 | 82.59 | 5 |
1b | 1.61 | 350.37 | 4 | 4 | 0 | 102.82 | 5 |
1c | 2.1 | 364.4 | 4 | 3 | 0 | 91.82 | 6 |
1d | 2.07 | 364.4 | 4 | 3 | 0 | 91.82 | 6 |
2a | 2.44 | 368.82 | 3 | 3 | 0 | 82.59 | 5 |
2b | 2.06 | 384.82 | 4 | 4 | 0 | 102.82 | 5 |
2c | 2.61 | 398.84 | 4 | 3 | 0 | 91.82 | 6 |
2d | 2.59 | 398.84 | 4 | 3 | 0 | 91.82 | 6 |
3a | 2.98 | 403.26 | 3 | 3 | 0 | 82.59 | 5 |
3b | 2.58 | 419.26 | 4 | 4 | 0 | 102.82 | 5 |
3c | 3.16 | 433.29 | 4 | 3 | 0 | 91.82 | 6 |
3d | 3.12 | 433.29 | 4 | 3 | 0 | 91.82 | 6 |
4a | 2.24 | 352.36 | 4 | 3 | 0 | 82.59 | 5 |
4b | 1.86 | 368.36 | 5 | 4 | 0 | 102.82 | 5 |
4c | 2.41 | 382.39 | 5 | 3 | 0 | 91.82 | 6 |
4d | 2.38 | 382.39 | 5 | 3 | 0 | 91.82 | 6 |
5a | 2.56 | 370.35 | 5 | 3 | 0 | 82.59 | 5 |
5b | 2.19 | 386.35 | 6 | 4 | 0 | 102.82 | 5 |
5c | 2.73 | 400.38 | 6 | 3 | 0 | 91.82 | 6 |
5d | 2.7 | 400.38 | 6 | 3 | 0 | 91.82 | 6 |
Compound Codes | Pharmacokinetics | Drug-Likeness | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GI abs. | BBB pen. | P-gp sub. | CYP1A2 | CYP2C19 | CYP2C9 | CYP2D6 | CYP3A4 | Log Kp (Skin Permeation, cm/s) | Ghose | Egan | Muegge | Bioavailability Score | |
Inhibitors | |||||||||||||
NL | H | Y | Y | N | N | N | Y | N | –7.43 | Y | Y | Y | 0.55 |
1a | H | N | Y | N | N | N | N | N | –6.87 | 0 | 0 | 0 | 0.55 |
1b | H | N | Y | N | N | N | N | N | –7.22 | 0 | 0 | 0 | 0.55 |
1c | H | N | Y | N | N | Y | N | N | –7.07 | 0 | 0 | 0 | 0.55 |
1d | H | N | Y | N | N | Y | N | N | –7.07 | 0 | 0 | 0 | 0.55 |
2a | H | N | Y | N | N | Y | N | N | –6.63 | 0 | 0 | 0 | 0.55 |
2b | H | N | Y | N | N | N | N | N | –6.99 | 0 | 0 | 0 | 0.55 |
2c | H | N | Y | N | N | Y | N | Y | –6.84 | 0 | 0 | 0 | 0.55 |
2d | H | N | Y | N | N | Y | N | Y | –6.84 | 0 | 0 | 0 | 0.55 |
3a | H | N | Y | Y | Y | Y | N | Y | –6.4 | 0 | 0 | 0 | 0.55 |
3b | H | N | Y | Y | N | N | N | Y | –6.75 | 0 | 0 | 0 | 0.55 |
3c | H | N | Y | Y | Y | Y | N | Y | –6.6 | 0 | 0 | 0 | 0.55 |
3d | H | N | Y | Y | Y | Y | N | Y | –6.6 | 0 | 0 | 0 | 0.55 |
4a | H | N | Y | N | N | N | N | N | –6.91 | 0 | 0 | 0 | 0.55 |
4b | H | N | Y | N | N | N | N | N | –7.26 | 0 | 0 | 0 | 0.55 |
4c | H | N | Y | N | N | Y | N | Y | –7.11 | 0 | 0 | 0 | 0.55 |
4d | H | N | Y | N | N | Y | N | Y | –7.11 | 0 | 0 | 0 | 0.55 |
5a | H | N | Y | N | N | N | N | N | -6.95 | 0 | 0 | 0 | 0.55 |
5b | H | N | Y | N | N | N | N | N | –7.29 | 0 | 0 | 0 | 0.55 |
5c | H | N | Y | N | N | Y | N | Y | –7.15 | 0 | 0 | 0 | 0.55 |
5d | H | N | Y | N | N | Y | N | Y | –7.15 | 0 | 0 | 0 | 0.55 |
Compound Codes | Parameters | |||||||
---|---|---|---|---|---|---|---|---|
LD50 (mg/kg) | Toxicity Class | Prediction Accuracy (%) | Hepatotoxicity (Probability) | Carcinogenicity (Probability) | Immunotoxicity (Probability) | Mutagenicity (Probability) | Cytotoxicity (Probability) | |
NL | 800 | 4 | 23 | I (0.60) | A (0.50) | A (0.80) | I (0.65) | I (0.71) |
1a | 711 | 4 | 54.26 | A (0.64) | A (0.71) | I (0.98) | I (0.60) | I (0.72) |
1b | 1644 | 4 | 54.26 | A (0.64) | A (0.66) | I (0.65) | I (0.62) | I (0.78) |
1c | 1880 | 4 | 54.26 | A (0.61) | A (0.60) | A (0.55) | I (0.59) | I (0.80) |
1d | 1880 | 4 | 54.26 | A (0.62) | A (0.60) | I (0.89) | I (0.59) | I (0.77) |
2a | 1000 | 4 | 54.26 | A (0.59) | A (0.52) | I (0.96) | I (0.69) | I (0.76) |
2b | 1000 | 4 | 23 | A (0.62) | A (0.52) | A (0.69) | I (0.70) | I (0.79) |
2c | 1000 | 4 | 23 | A (0.61) | I (0.53) | A (0.84) | I (0.68) | I (0.77) |
2d | 1190 | 4 | 100 | A (0.69) | I (0.62) | A (0.96) | I (0.97) | I (0.93) |
3a | 1000 | 4 | 54.26 | A (0.59) | A (0.52) | I (0.93) | I (0.69) | I (0.76) |
3b | 1190 | 4 | 100 | A (0.69) | I (0.62) | A (0.96) | I (0.97) | I (0.93) |
3c | 1000 | 4 | 23 | A (0.61) | I (0.53) | A (0.91) | I (0.68) | I (0.77) |
3d | 1000 | 4 | 23 | A (0.61) | I (0.53) | A (0.50) | I (0.68) | I (0.77) |
4a | 1000 | 4 | 23 | A (0.60) | A (0.57) | I (0.97) | I (0.68) | I (0.77) |
4b | 1644 | 4 | 23 | A (0.64) | A (0.55) | A (0.59) | I (0.67) | I (0.79) |
4c | 711 | 4 | 23 | A (0.63) | I (0.51) | A (0.78) | I (0.66) | I (0.78) |
4d | 1880 | 4 | 23 | A (0.63) | I (0.51) | I (0.76) | I (0.66) | I (0.78) |
5a | 1000 | 4 | 23 | A (0.60) | A (0.57) | I (0.60) | I (0.68) | I (0.77) |
5b | 1644 | 4 | 23 | A (0.64) | A (0.55) | A (0.97) | I (0.67) | I (0.79) |
5c | 711 | 4 | 23 | A (0.63) | I (0.51) | A (0.98) | I (0.66) | I (0.78) |
5d | 1880 | 4 | 23 | A (0.63) | I (0.51) | A (0.91) | I (0.66) | I (0.78) |
Active Amino Acid Residues | Atom from Ligand | Bond Length (Å) | Bond Type | Bond Category | Ligand Energy | Docking Scores |
---|---|---|---|---|---|---|
(kcal/mol) | ||||||
Native Ligand | ||||||
TYR662 | N-H | 1.66907 | Hydrogen Bond | Conventional Hydrogen Bond | 447.3 | −9.1 |
ARG125 | Pi-Orbitals | 4.39768 | Electrostatic | Pi-Cation | ||
ARG358 | 3.52293 | |||||
ARG358 | 5.41244 | Hydrophobic | Pi-Alkyl | |||
PHE357 | Aromatic Carbon | 3.79334 | ||||
1b | ||||||
GLU378 | N | 4.2858 | Electrostatic | Attractive Charge | 299.89 | −9.4 |
GLU378 | N | 4.09602 | ||||
SER349 | H | 2.37918 | Hydrogen Bond | Conventional Hydrogen Bond | ||
SER376 | H | 2.55398 | ||||
SER376 | NH | 2.862 | ||||
THR351 | O | 1.98084 | ||||
THR351 | O | 1.67832 | ||||
GLU378 | C | 3.06114 | Carbon Hydrogen Bond | |||
THR350 | Pi-Orbitals | 3.1604 | Pi-Donor Hydrogen Bond | |||
SER376 | 3.06845 | |||||
PHE396 | 4.9139 | Hydrophobic | Pi-Pi T-shaped | |||
CYS394 | Alkyl | 5.29122 | Pi-Alkyl | |||
VAL354 | 5.28734 | |||||
2b | ||||||
ARG560 | NH | 2.90874 | Hydrogen Bond | Conventional Hydrogen Bond | 343.49 | −9.3 |
ASN562 | H | 2.81998 | ||||
LYS512 | Pi-Orbitals | 3.51422 | Hydrophobic | Pi-Sigma | ||
ILE529 | 3.43887 | |||||
ARG560 | 3.75323 | |||||
PHE559 | 5.21502 | Pi-Pi T-shaped | ||||
PRO475 | Cl | 5.41082 | Alkyl | |||
LYS512 | Cl | 4.09612 | ||||
ALA564 | Pi-Orbitals | 5.11889 | Pi-Alkyl | |||
PRO475 | 4.72305 | |||||
PHE559 | 5.12368 | |||||
3b | ||||||
GLU205 | N | 5.12407 | Electrostatic | Attractive Charge | 340.69 | −9.3 |
GLU205 | N | 5.23339 | ||||
HIS740 | H | 2.57758 | Hydrogen Bond | Conventional Hydrogen Bond | ||
PHE357 | Pi-Orbitals | 3.79816 | Hydrophobic | Pi-Pi Stacked | ||
TYR662 | 4.0191 | |||||
TYR547 | 4.68336 | |||||
TYR666 | 4.89163 | Pi-Pi T-shaped | ||||
SER630; TYR631 | 4.99633 | Amide-Pi Stacked | ||||
LYS554 | Cl | 4.43461 | Alkyl | |||
VAL656 | Pi-Orbitals | 5.41552 | Pi-Alkyl | |||
TYR547 | Cl | 4.69875 | ||||
TYR547 | Cl | 4.67797 | ||||
4a | ||||||
PHE559 | F | 3.12032 | Hydrogen Bond;Halogen | Carbon Hydrogen Bond;Halogen (Fluorine) | 316.76 | −9.5 |
VAL558 | F | 3.51875 | Halogen | Halogen (Fluorine) | ||
LEU514 | Pi-Orbitals | 4.68451 | Hydrophobic | Pi-Alkyl | ||
PRO510 | 5.49372 | |||||
LYS512 | 4.13088 | |||||
ILE529 | 4.76619 | |||||
5b | ||||||
ILE102 | H | 2.81295 | Hydrogen Bond | Conventional Hydrogen Bond | 316.62 | −9.6 |
HIS100 | H | 1.85943 | ||||
ILE102 | O | 2.2207 | ||||
ASN74 | F | 3.14132 | Halogen | Halogen (Fluorine) | ||
LYS71 | Pi-Orbitals | 4.97015 | Electrostatic | Pi-Cation | ||
TYR105 | 5.06176 | Hydrophobic | Pi-Pi T-shaped | |||
ILE76 | 5.43513 | Pi-Alkyl | ||||
ILE102 | 5.10056 |
3D-Docking Poses | 2D-Docking Poses |
---|---|
Native Ligand | |
Compound 1b | |
Compound 2b | |
Compound 3b | |
Compound 4a | |
Compound 5b | |
Compound Code | % Inhibition at 50 µM | IC50 (µM) | Compound Code | % Inhibition at 50 µM | IC50 (µM) |
---|---|---|---|---|---|
1a | 40.74 ± 0.38 | 58.95 ± 0.0012 | 3c | 61.00 ± 0.08 | 33.73 ± 0.0024 |
1b | 42.69 ± 0.28 | 54.73 ± 0.0025 | 3d | 63.25 ± 0.05 | 32.38 ± 0.0021 |
1c | 56.47 ± 0.37 | 39.72 ± 0.0027 | 4a | 64.78 ± 0.33 | 30.47 ± 0.0025 |
1d | 57.74 ± 0.38 | 38.26 ± 0.0050 | 4b | 63.80 ± 0.16 | 31.75 ± 0.0027 |
2a | 61.25 ± 0.16 | 32.41 ± 0.0033 | 4c | 60.40 ± 0.08 | 34.94 ± 0.0016 |
2b | 65.50 ± 0.08 | 31.93 ± 0.0029 | 4d | 57.74 ± 0.38 | 38.62 ± 0.0025 |
2c | 63.25 ± 0.05 | 33.97 ± 0.0025 | 5a | 44.20 ± 0.28 | 65.31 ± 0.0021 |
2d | 64.78 ±0.33 | 31.72 ± 0.0021 | 5b | 70.70 ± 0.37 | 28.13 ± 0.0029 |
3a | 61.25 ± 0.16 | 33.91 ± 0.0029 | 5c | 58.54 ± 0.27 | 37.63 ± 0.0026 |
3b | 61.00 ± 0.08 | 33.79 ± 0.0021 | 5d | 62.28 ± 0.29 | 34.13 ± 0.0027 |
Sitagliptin | 101.7 ± 0.09 | 0.018 ± 0.0012 | --- |
Treatment Group | Fasting Blood Glucose (mg/dL) ± SEM | |||
---|---|---|---|---|
On Day 1 | On Day 7 | On Day 14 | On Day 21 | |
Diabetic control | 265.33 ± 6.27 | 269.66 ± 7.96 | 275.33 ± 1 0.04 | 280.00 ± 13.29 |
Sitagliptin (10 mg/kg) | 240.16 ± 9.88 | 178.66 ± 6.92 *** | 175.16 ± 8.61 *** | 133.50 ± 11.80 *** |
Compound 1b (50 mg/kg) | 261.00 ± 8.44 | 215.03 ± 3.29 * | 187.05 ± 6.48 * | 160.12 ± 6.18 * |
Compound 5b (50 mg/kg) | 253.83 ± 4.49 | 182.00 ± 8.11 * | 167.16 ± 6.23 ** | 157.33 ± 5.75 ** |
Compound 4c (50 mg/kg) | 264.66 ± 5.70 | 237.16 ± 9.01 | 194.83 ± 4.81 * | 169.66 ± 8.53 * |
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Jadhav, P.B.; Jadhav, S.B.; Zehravi, M.; Mubarak, M.S.; Islam, F.; Jeandet, P.; Khan, S.L.; Hossain, N.; Rashid, S.; Ming, L.C.; et al. Virtual Screening, Synthesis, and Biological Evaluation of Some Carbohydrazide Derivatives as Potential DPP-IV Inhibitors. Molecules 2023, 28, 149. https://doi.org/10.3390/molecules28010149
Jadhav PB, Jadhav SB, Zehravi M, Mubarak MS, Islam F, Jeandet P, Khan SL, Hossain N, Rashid S, Ming LC, et al. Virtual Screening, Synthesis, and Biological Evaluation of Some Carbohydrazide Derivatives as Potential DPP-IV Inhibitors. Molecules. 2023; 28(1):149. https://doi.org/10.3390/molecules28010149
Chicago/Turabian StyleJadhav, Prerana B., Shailaja B. Jadhav, Mehrukh Zehravi, Mohammad S. Mubarak, Fahadul Islam, Philippe Jeandet, Sharuk L. Khan, Nazmul Hossain, Salma Rashid, Long Chiau Ming, and et al. 2023. "Virtual Screening, Synthesis, and Biological Evaluation of Some Carbohydrazide Derivatives as Potential DPP-IV Inhibitors" Molecules 28, no. 1: 149. https://doi.org/10.3390/molecules28010149
APA StyleJadhav, P. B., Jadhav, S. B., Zehravi, M., Mubarak, M. S., Islam, F., Jeandet, P., Khan, S. L., Hossain, N., Rashid, S., Ming, L. C., Sarker, M. M. R., & Azlina, M. F. N. (2023). Virtual Screening, Synthesis, and Biological Evaluation of Some Carbohydrazide Derivatives as Potential DPP-IV Inhibitors. Molecules, 28(1), 149. https://doi.org/10.3390/molecules28010149