Introduction
The goal of pharmaceuticals is to prevent or cure disease through drug therapy by specifically targeting cells, proteins, enzymes, genes, etc. It is often crucial to understand the structure, function, and relevant mechanisms involved with the target when designing an effective drug candidate. Furthermore, being able to know the effects on structure after drug-binding can provide insight into the functionality of a specific target. Because of this fact, it is common practice for research labs to develop protein crystals and use methods like x-ray diffraction, electron density mapping, and nuclear magnetic resonance spectroscopy to model the full structure. In this case, P2Y12, a member of P2Y receptor, was modeled when binded to ADZ1283, an engineered receptor inhibitor.The molecular scene shows the chemical of P2Y12 with the anionic side chains in red and charged nucleic acids and ligands in grey for contrast.
Image analysis of P2Y12 crystals is used to model protein structure in complex with AstraZeneca’s novel ADZ1283: Ethyl 6-(4(-((benzylsulphonyl)carbamoyl)piperidin-1yl)-5-cyano-2-methylnicotinate. ADZ1283 functions to block the P2Y12 receptor as a means to treat thrombosis. ADZ1283-binding leads to unique protein structure, unfound in other P2Y receptors. Helix V of seven transmembrane helices is found to be . This change along with the discovery of a potential second active within P2Y12 has implications on how P2Y12 uses it’s seven transmembrane helical bundle interact with ADP in the bloodstream.
As a member of a large class of G-protein-coupled receptors, P2Y12 is often an initial role player in signal transduction and cellular response due to external environmental factors. In the case of P2Y12, the receptor responds to ADP concentrations in the extracellular matrix and on a larger scale the blood stream. There is importance is understanding how P2Y12's structure receives ADP as an activator. In turn, knowledge of how P2Y12 is affected when properly inhibited can lead to improved drug design in terms of bioavailability, binding affinity, and effectiveness of inhibition. Ultimately, pharmaceuticals will be better able to prevent and treat cardiovascular diseases and medical conditions (thrombosis, hypercoagulable states) and more immediate dangers (stroke, embolism, and heart attacks).
Overall Structure
The is made up of eight alpha helices. There are seven transmembrane alpha helices and a carboxy-terminal helix VII, which is parallel to the membrane bilayer.
There is only one disulphide bond the amino terminus with helix VII
Helix V: straight conformation because there are no proline or glycine residues to destabilize its structure
- Polar vs nonpolar:
Polar regions are pink. Nonpolar, or hydrophobic, regions are grey.
-N to C termini:
The protein shown in displays the the N and C termini
Binding Interactions
The of P2Y12 is colored in purple, and the ligand (AZD1283) is colored in yellow. The binding site for AZD1283, pocket 1, is composed of helices III–VII, while pocket II contains helices I-III and VII is not represented here. The two pockets are separated by two residues, Y1053 and K2807, which makes the pocket II not a binding site for AZD1283. With the observation of the AZD1283-bound P2Y12R with residue C97 belong to pocket 2, the active metabolites drugs might occupy this pocket.
Additional Features
Acute coronary syndrome, a condition in which there is sudden blockage of blood flow to the heart, is majorly caused by a disease known as atherothrombosis. This disease is characterized by blocked arteries due to thrombosis: formation of a clot within a blood vessel. The P2Y12 protein is an important platelet receptor inhibitor that can be combined with aspirin in the management of ACS. It regulates certain functions through purinergic signaling, which is a form of extracellular signaling mediated by purine nucleotides and nucleosides like ADP and ATP.[5]
The P2Y12 receptor is mainly found on the surface of blood platelets, and functions as a regulator in platelet activation and blood clotting. The P2Y12 receptor is a G-protein coupled receptor, linked to the cAMP-signaling pathway. It mediates platelet activation by decreasing intracellular cAMP levels through inhibition of an AC-mediated signaling pathway. Acting as a chemoreceptor, P2Y12 utilizes ADP as an agonist, which initiates ADP-induced platelet aggregation. Clopidogrel in covalent binding complex with P2Y12 acts as an antiplatelet agent, specifically as an ADP receptor inhibitor to decrease platelet aggregation and inhibit thrombus formation.
Clopidogrel is a pro-drug and thienopyridine-type inhibitor of the P2Y12 receptor, which requires Cytochrome P450 to hepatic ally transform it to exert its anti platelet effect. is a membrane protein, characteristic of alternating hydrophobic and polar groups. The central heme group is stabilized by several side chains. The Fe2+ atom that makes up the heart of the heme group is surrounded by a highly hydrophobic porphyrin ring . The role of the heme group in biological systems is to facilitate oxygen transport as well as aid in electron transfer as part of the electron transport chain. The heme group of the hemeprotein Cytochrome P450 acts as a catalyst for the metabolism of clopidogrel. Shown below is the activation of Clopidogrel in vivo. CYP2C19 is an enzymatic member of the cytochrome P450 mixed-function oxidase system. The final step is a hydrolysis to yield the active metabolite.
Quiz Question 1
Below is the structure for AZD1283. shows a representation of the pocket where AZD1283 binds to P2Y12R. The dark salmon molecule is AZD1283 which is surrounded by magenta colored amino acids which are polar and gray colored ones which are hydrophobic.List 3 amino acid residues from the scene that should participate in hydrogen bonding with AZD1283 and 3 that should not. Why might the amino acids that don't hydrogen bond with AZD1283 still be present in the pocket?
See Also
Credits
Introduction - Adam Murphy
Overall Structure - Cora Ricker
Drug Binding Site - Duy Nguyen
Additional Features - Lauren Timmins
Quiz Question 1 - Aidan Finnerty
References
- ↑ Zhang K, Zhang J, Gao ZG, Zhang D, Zhu L, Han GW, Moss SM, Paoletta S, Kiselev E, Lu W, Fenalti G, Zhang W, Muller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q. Structure of the human P2Y12 receptor in complex with an antithrombotic drug. Nature. 2014 May 1;509(7498):115-8. doi: 10.1038/nature13083. Epub 2014 Mar 23. PMID:24670650 doi:http://dx.doi.org/10.1038/nature13083
1. Savi, P., et al. "P2Y 12, a new platelet ADP receptor, target of clopidogrel." Biochemical and biophysical research communications 283.2 (2001): 379-383.
2. https://en.wikipedia.org/wiki/Cytochrome_P450
3. https://en.wikipedia.org/wiki/Clopidogrel
4. https://en.wikipedia.org/wiki/P2Y12
5. https://en.wikipedia.org/wiki/Purinergic_signalling
