Amino-3,5-Dicyanopyridines Targeting the Adenosine Receptors. Ranging from Pan Ligands to Combined A1/A2B Partial Agonists
Abstract
:1. Introduction
2. Results
2.1. Chemistry
2.2. Pharmacological Assays
2.3. Molecular Docking Studies
3. Discussion
3.1. Structure–Activity Relationships
3.2. Molecular Docking Investigation and In Silico ADMET Prediction.
4. Conclusions
5. Materials and Methods
5.1. Chemistry
5.1.1. General Methods
5.1.2. Synthesis of the target compounds 1–4, 6–13, and 20
5.1.3. Synthesis of the Target Compounds 14–17
5.1.4. Synthesis of 2-amino-4-phenylpyridine-3,5-dicarbonitrile (18)
5.1.5. 2-Amino-6-[(2-hydroxyethyl)amino]-4-(4-methoxyphenyl)pyridine-3,5-dicarbonitrile (19)
5.1.6. Synthesis of 4-substituted-2-amino-6-(phenylsulfanyl)pyridine-3,5-dicarbonitriles 21–27 [18,24–26]
5.1.7. Synthesis of 2-amino-4-substituted-6-sulfanylpyridine-3,5-dicarbonitriles 33–40 [14,18,20,21]
5.1.8. Synthesis of 2-amino-4-methyl-6-sulfanylpyridine-3,5-dicarbonitrile (39) [22,23]
5.1.9. Synthesis of 2-amino-6-chloro-4-phenylpyridine-3,5-dicarbonitrile (42) [27]
5.2. Pharmacological Assays
5.2.1. Cell Culture and Membrane Preparation.
5.2.2. Competition Binding Experiments
5.2.3. Cyclic AMP Assays.
5.2.4. Data Analysis
5.3. Molecular Modelling
- Conformational Analysis of ligands. The algorithm generated conformations from a single 3D conformation by conducting a systematic search. In this way, all combinations of angles were created for each ligand.
- Placement. A collection of poses was generated from the pool of ligand conformations using Alpha Triangle placement method. Poses were generated by superposition of ligand atom triplets and triplet points in the receptor binding site. The receptor site points are alpha sphere centres which represent locations of tight packing. At each iteration, a random conformation was selected, a random triplet of ligand atoms and a random triplet of alpha sphere centres were used to determine the pose.
- Scoring. Poses generated by the placement methodology were scored using the Alpha HB scoring function, which combines a term measuring the geometric fit of the ligand to the binding site and a term measuring hydrogen bonding effects.
- Induced Fit. The generated docking conformations were subjected to energy minimization within the binding site and the protein sidechains are included in the refinement stage. In detail, the protein backbone is set as rigid while the side chains are not set to “free to move” but are set to “tethered”, where an atom tether is a distance restraint that restrains the distance not between two atoms but between an atom and a fixed point in space.
- Rescoring. Complexes generated by the Induced Fit methodology stage were scored using the Alpha HB scoring function. Gold tool was used with default efficiency settings through MOE interface, by selecting GoldScore as scoring function [31].
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
ABMECA | N6-(4-Aminobenzyl)-N-methylcarboxamidoadenosine |
AC | Adenylate Cyclase |
ADMET | Absorption, Distribution, Metabolism, Excretion, Toxicity |
Ado | Adenosine |
AR | Adenosine Receptor |
BSA | Bovine Serum Albumin |
CCPA | 2-Chloro-N6-cyclopentyladenosine |
CHO | Chinese Hamster Ovary |
CPA | N6-Cyclopentyladenosine |
DPCPX | 8-Cyclopentyl-1,3-dipropylxanthine |
EL | Extracellular loop |
EtOAc | Ethyl Acetate |
DMF | Dimethylformamide |
DMSO | Dimethylsulfoxide |
EDTA | Ethylendiaminotetracetic Acid |
HEPES | 4-(2-Hydroxyethyl)-1-piperazine-1-ethane sulfonic Acid |
MOE | Molecular operating environment; |
NECA | 5′-(N-Ethylcarboxamido)adenosine |
rt | room temperature |
SARs | Structure-Activity Relationships |
THF | Tetrahydrofuran |
TM | Transmembrane |
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cAMP Assays | Binding Experiments a | |||||
---|---|---|---|---|---|---|
EC50 (nM) b Efficacy, c % | Ki (nM) or I% | |||||
hA2B | hA1 d | hA2A e | hA3 f | |||
R1 | R2 | |||||
1 | ˃1000 (12%) | 25% | 4% | 574 ± 46 | ||
2 | 227 ± 21 (36%) | 26% | 1% | 1% | ||
3 | 27 ± 3 (56%) | 16 ± 2 | 17% | 8% | ||
4 | ˃1000 (14%) | 77 ± 6 | 1% | 8% | ||
5g | 11.7 ± 1.2 (62%) | 8.21 ± 0.73 | 221 ± 19 | 85 ± 6 | ||
6 | 12 ± 1 (100%) | 83 ± 7 | 38 ± 3 | 48 ± 4 | ||
7 | 109 ± 12 (32%) | 30 ± 4 | 865 ± 68 | 850 ± 62 | ||
8 | 18 ± 2 (76%) | 0.78 ± 0.08 | 139 ± 12 | 410 ± 38 | ||
9 | ˃1000 (4%) | 419 ± 32 | 32% | 21% | ||
10 | 78 ± 6 (78%) | 5.32 ± 0.42 | 47 ± 4 | 212 ± 19 | ||
11 | 36 ± 3 (30%) | 8.32 ± 0.78 | 227 ± 21 | 388 ± 29 | ||
12 | 260 ± 24 (44%) | 31% | 8% | 1% | ||
13 | CH3 | ˃1000 (1%) | 74 ± 8 | 331 ± 32 | 510 ± 53 | |
14 | ˃1000 (1%) | 140 ± 12 | 115 ± 10 | 19% | ||
15 | NHCH2CH2OH | ˃1000 (1%) | 943 ± 87 | 1% | 1% | |
16 | ˃1000 (1%) | 1% | 1% | 1% | ||
17 | ˃1000 (1%) | 27% | 1% | 25% | ||
18 | H | ˃1000 (1%) | 15% | 16% | 5% | |
19 | NHCH2CH2OH | ˃1000 (1%) | 14% | 2% | 15% | |
20 | SCH2COOCH3 | ˃1000 (1%) | 987 ± 81 | 1% | 5% | |
P453 g | 9.52 ± 0.91 (70%) | 235 ± 24 | 764 ± 72 | 474 ± 45 | ||
LUF5833 h | 19 ± 7 (81%) | 2.4 ± 1 | 28 ± 1 | 171 ± 109 |
compd | Efficacy, b % | EC50 (nM) c |
---|---|---|
3 | 39 ± 4 | 19.6 ± 1.7 |
8 | 34 ± 3 | 1.34 ± 0.11 |
11 | 52 ± 4 | 8.87 ± 0.64 |
DPCPX | 100 ± 9 | 1.52 ± 0.12 |
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Catarzi, D.; Varano, F.; Varani, K.; Vincenzi, F.; Pasquini, S.; Dal Ben, D.; Volpini, R.; Colotta, V. Amino-3,5-Dicyanopyridines Targeting the Adenosine Receptors. Ranging from Pan Ligands to Combined A1/A2B Partial Agonists. Pharmaceuticals 2019, 12, 159. https://doi.org/10.3390/ph12040159
Catarzi D, Varano F, Varani K, Vincenzi F, Pasquini S, Dal Ben D, Volpini R, Colotta V. Amino-3,5-Dicyanopyridines Targeting the Adenosine Receptors. Ranging from Pan Ligands to Combined A1/A2B Partial Agonists. Pharmaceuticals. 2019; 12(4):159. https://doi.org/10.3390/ph12040159
Chicago/Turabian StyleCatarzi, Daniela, Flavia Varano, Katia Varani, Fabrizio Vincenzi, Silvia Pasquini, Diego Dal Ben, Rosaria Volpini, and Vittoria Colotta. 2019. "Amino-3,5-Dicyanopyridines Targeting the Adenosine Receptors. Ranging from Pan Ligands to Combined A1/A2B Partial Agonists" Pharmaceuticals 12, no. 4: 159. https://doi.org/10.3390/ph12040159
APA StyleCatarzi, D., Varano, F., Varani, K., Vincenzi, F., Pasquini, S., Dal Ben, D., Volpini, R., & Colotta, V. (2019). Amino-3,5-Dicyanopyridines Targeting the Adenosine Receptors. Ranging from Pan Ligands to Combined A1/A2B Partial Agonists. Pharmaceuticals, 12(4), 159. https://doi.org/10.3390/ph12040159