Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation
The P2Y<sub>12</sub> receptor is an important member of the purinergic receptor family, known for its critical role in platelet activation and thrombosis. In our previously published study, the acridinone analogue NSC618159 was identified as a potent antagonist of P2Y<sub>12</su...
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| Format: | Article |
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MDPI AG
2023-05-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/28/9/3878 |
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| author | Belal O. Al-Najjar Fadi G. Saqallah |
| author_facet | Belal O. Al-Najjar Fadi G. Saqallah |
| author_sort | Belal O. Al-Najjar |
| collection | DOAJ |
| description | The P2Y<sub>12</sub> receptor is an important member of the purinergic receptor family, known for its critical role in platelet activation and thrombosis. In our previously published study, the acridinone analogue NSC618159 was identified as a potent antagonist of P2Y<sub>12</sub>. In this work, we investigate the conformational changes in P2Y<sub>12</sub> when bound to NSC618159 using molecular dynamics simulations on the receptor’s active and inactive forms (4PXZ and 4NTJ, respectively). It was observed that it took the systems about 7 ns and 12 ns to stabilise when NSC618159 was in complex with the active and inactive forms of P2Y<sub>12</sub>, respectively. Additionally, the binding pocket of the crystal structure 4PXZ expanded from 172.34 Å<sup>3</sup> to an average of 661.55 Å<sup>3</sup> when bound to NSC618159, with a maximum pocket volume of 820.49 Å<sup>3</sup>. This expansion was attributed to the pulled away transmembrane (TM) helices and the adoption of a more open conformation by extracellular loop 2 (EL2). In contrast, 4NTJ’s pocket volume was mostly consistent and had an average of 1203.82 Å<sup>3</sup>. Moreover, the RMSF profile of the NSC618159-4PXZ complex showed that residues of TM-I and TM-VII had similar fluctuations to the 4NTJ crystal structure, representing the inactive form of P2Y<sub>12</sub>. Finally, the energy components and binding affinities of NSC618159 towards the active and inactive forms of P2Y<sub>12</sub> were predicted using the MM-PBSA approach. According to the results, the binding affinity of NSC618159 towards both active (4PXZ) and inactive (4NTJ) forms of P2Y<sub>12</sub> was found to be almost identical, with values of −43.52 and −41.68 kcal/mol, respectively. In conclusion, our findings provide new insights into the conformational changes of P2Y<sub>12</sub> upon binding to NSC618159 and may have implications for the development of new P2Y<sub>12</sub> antagonists with enhanced potency and specificity. |
| first_indexed | 2024-03-11T04:11:55Z |
| format | Article |
| id | doaj.art-290ca8059d5e429ea72213a3818c13c6 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T04:11:55Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-290ca8059d5e429ea72213a3818c13c62023-11-17T23:24:41ZengMDPI AGMolecules1420-30492023-05-01289387810.3390/molecules28093878Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and ConformationBelal O. Al-Najjar0Fadi G. Saqallah1Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 19328, JordanDepartment of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 19328, JordanThe P2Y<sub>12</sub> receptor is an important member of the purinergic receptor family, known for its critical role in platelet activation and thrombosis. In our previously published study, the acridinone analogue NSC618159 was identified as a potent antagonist of P2Y<sub>12</sub>. In this work, we investigate the conformational changes in P2Y<sub>12</sub> when bound to NSC618159 using molecular dynamics simulations on the receptor’s active and inactive forms (4PXZ and 4NTJ, respectively). It was observed that it took the systems about 7 ns and 12 ns to stabilise when NSC618159 was in complex with the active and inactive forms of P2Y<sub>12</sub>, respectively. Additionally, the binding pocket of the crystal structure 4PXZ expanded from 172.34 Å<sup>3</sup> to an average of 661.55 Å<sup>3</sup> when bound to NSC618159, with a maximum pocket volume of 820.49 Å<sup>3</sup>. This expansion was attributed to the pulled away transmembrane (TM) helices and the adoption of a more open conformation by extracellular loop 2 (EL2). In contrast, 4NTJ’s pocket volume was mostly consistent and had an average of 1203.82 Å<sup>3</sup>. Moreover, the RMSF profile of the NSC618159-4PXZ complex showed that residues of TM-I and TM-VII had similar fluctuations to the 4NTJ crystal structure, representing the inactive form of P2Y<sub>12</sub>. Finally, the energy components and binding affinities of NSC618159 towards the active and inactive forms of P2Y<sub>12</sub> were predicted using the MM-PBSA approach. According to the results, the binding affinity of NSC618159 towards both active (4PXZ) and inactive (4NTJ) forms of P2Y<sub>12</sub> was found to be almost identical, with values of −43.52 and −41.68 kcal/mol, respectively. In conclusion, our findings provide new insights into the conformational changes of P2Y<sub>12</sub> upon binding to NSC618159 and may have implications for the development of new P2Y<sub>12</sub> antagonists with enhanced potency and specificity.https://www.mdpi.com/1420-3049/28/9/3878P2Y<sub>12</sub>molecular dynamicsMM-PBSAP2Y<sub>12</sub> antagonists |
| spellingShingle | Belal O. Al-Najjar Fadi G. Saqallah Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation Molecules P2Y<sub>12</sub> molecular dynamics MM-PBSA P2Y<sub>12</sub> antagonists |
| title | Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation |
| title_full | Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation |
| title_fullStr | Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation |
| title_full_unstemmed | Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation |
| title_short | Unlocking the Conformational Changes of P2Y<sub>12</sub>: Exploring an Acridinone Compound’s Effect on Receptor Activity and Conformation |
| title_sort | unlocking the conformational changes of p2y sub 12 sub exploring an acridinone compound s effect on receptor activity and conformation |
| topic | P2Y<sub>12</sub> molecular dynamics MM-PBSA P2Y<sub>12</sub> antagonists |
| url | https://www.mdpi.com/1420-3049/28/9/3878 |
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