Layer-Wise Relevance Analysis for Motif Recognition in the Activation Pathway of the 2- GPCR Receptor.

Mario A Gutiérrez-Mondragón, Caroline König, Alfredo Vellido
Author Information
  1. Mario A Gutiérrez-Mondragón: Computer Science Department, Universitat Politècnica de Catalunya-UPC BarcelonaTech, 08034 Barcelona, Spain.
  2. Caroline König: Computer Science Department, Universitat Politècnica de Catalunya-UPC BarcelonaTech, 08034 Barcelona, Spain. ORCID
  3. Alfredo Vellido: Computer Science Department, Universitat Politècnica de Catalunya-UPC BarcelonaTech, 08034 Barcelona, Spain. ORCID

Abstract

G-protein-coupled receptors (GPCRs) are cell membrane proteins of relevance as therapeutic targets, and are associated to the development of treatments for illnesses such as diabetes, Alzheimer's, or even cancer. Therefore, comprehending the underlying mechanisms of the receptor functional properties is of particular interest in pharmacoproteomics and in disease therapy at large. Their interaction with ligands elicits multiple molecular rearrangements all along their structure, inducing activation pathways that distinctly influence the cell response. In this work, we studied GPCR signaling pathways from molecular dynamics simulations as they provide rich information about the dynamic nature of the receptors. We focused on studying the molecular properties of the receptors using deep-learning-based methods. In particular, we designed and trained a one-dimensional convolution neural network and illustrated its use in a classification of conformational states: active, intermediate, or inactive, of the receptor when bound to the full agonist BI-167107. Through a novel explainability-oriented investigation of the prediction results, we were able to identify and assess the contribution of individual (residues) influencing a particular activation pathway. Consequently, we contribute a methodology that assists in the elucidation of the underlying mechanisms of receptor activation-deactivation.

Keywords

References

  1. Cell. 2013 Jan 31;152(3):532-42 [PMID: 23374348]
  2. Nat Rev Mol Cell Biol. 2002 Sep;3(9):639-50 [PMID: 12209124]
  3. Front Aging Neurosci. 2019 Jul 31;11:194 [PMID: 31417397]
  4. Molecules. 2019 Jun 02;24(11): [PMID: 31159491]
  5. BMC Bioinformatics. 2019 Feb 26;20(1):93 [PMID: 30808287]
  6. Science. 2007 Nov 23;318(5854):1258-65 [PMID: 17962520]
  7. Nat Struct Biol. 2002 Sep;9(9):646-52 [PMID: 12198485]
  8. Int J Mol Sci. 2020 Aug 18;21(16): [PMID: 32824756]
  9. Drug Discov Today. 2017 Feb;22(2):249-269 [PMID: 27890821]
  10. Sci Rep. 2020 Dec 3;10(1):21155 [PMID: 33273642]
  11. Sci Eng Ethics. 2020 Aug;26(4):2051-2068 [PMID: 31650511]
  12. Nat Rev Drug Discov. 2008 Apr;7(4):339-57 [PMID: 18382464]
  13. J Chem Inf Model. 2019 Aug 26;59(8):3353-3358 [PMID: 31265282]
  14. Sensors (Basel). 2021 Jul 01;21(13): [PMID: 34283094]
  15. RSC Adv. 2018 Mar 28;8(22):12127-12137 [PMID: 35539386]
  16. Comput Struct Biotechnol J. 2022 May 18;20:2564-2573 [PMID: 35685352]
  17. Cell. 2020 Apr 2;181(1):81-91 [PMID: 32243800]
  18. Curr Pharm Des. 2019;25(31):3339-3349 [PMID: 31480998]
  19. BMC Bioinformatics. 2019 Dec 24;20(Suppl 25):689 [PMID: 31874614]
  20. Nature. 2015 May 28;521(7553):436-44 [PMID: 26017442]
  21. Chem Rev. 2017 Jan 11;117(1):139-155 [PMID: 27622975]
  22. Nat Commun. 2021 Aug 5;12(1):4721 [PMID: 34354057]
  23. Neuron. 2018 Sep 19;99(6):1129-1143 [PMID: 30236283]
  24. J Mol Graph Model. 2018 Sep;84:96-108 [PMID: 29940506]
  25. Biomedicines. 2020 Aug 31;8(9): [PMID: 32878239]
  26. Sci Robot. 2019 Dec 18;4(37): [PMID: 33137719]
  27. Nat Methods. 2020 Aug;17(8):777-787 [PMID: 32661425]
  28. Nat Chem. 2014 Jan;6(1):15-21 [PMID: 24345941]
  29. Mol Pathol. 2000 Feb;53(1):8-14 [PMID: 10884915]
  30. Proteomics. 2020 Nov;20(21-22):e1900335 [PMID: 32939979]
  31. Interdiscip Sci. 2018 Mar;10(1):43-52 [PMID: 29460086]
  32. IEEE Trans Neural Netw Learn Syst. 2017 Nov.;28(11):2660-2673 [PMID: 27576267]
  33. PLoS One. 2015 Jul 10;10(7):e0130140 [PMID: 26161953]
  34. BMC Biol. 2011 Oct 28;9:71 [PMID: 22035460]
  35. Eur J Radiol. 2019 May;114:14-24 [PMID: 31005165]
  36. Nature. 2009 May 21;459(7245):356-63 [PMID: 19458711]
  37. Pharmaceuticals (Basel). 2020 Sep 18;13(9): [PMID: 32961909]
  38. Cell Rep Methods. 2021 May 17;1(2):100003 [PMID: 35475237]
  39. BMC Bioinformatics. 2021 Feb 5;22(1):47 [PMID: 33546587]
  40. J Chem Inf Model. 2022 Mar 28;62(6):1399-1410 [PMID: 35257580]
  41. Nucleic Acids Res. 2022 May 07;: [PMID: 35524575]

Grants

  1. PID2019-104551RB-I00/AGENCIA ESTATAL DE INVESTIGACIÓN

MeSH Term

Signal Transduction
Receptors, G-Protein-Coupled
Molecular Dynamics Simulation
Molecular Conformation
Adrenergic Agents
Receptors, Adrenergic, beta-2
Ligands
Protein Conformation

Chemicals

Receptors, G-Protein-Coupled
Adrenergic Agents
Receptors, Adrenergic, beta-2
Ligands

Word Cloud

Created with Highcharts 10.0.0receptorsmolecularreceptorparticularpathwaysGPCRscellrelevanceunderlyingmechanismspropertiesactivationGPCRdynamicsconvolutionG-protein-coupledmembraneproteinstherapeutictargetsassociateddevelopmenttreatmentsillnessesdiabetesAlzheimer'sevencancerThereforecomprehendingfunctionalinterestpharmacoproteomicsdiseasetherapylargeinteractionligandselicitsmultiplerearrangementsalongstructureinducingdistinctlyinfluenceresponseworkstudiedsignalingsimulationsproviderichinformationdynamicnaturefocusedstudyingusingdeep-learning-basedmethodsdesignedtrainedone-dimensionalneuralnetworkillustrateduseclassificationconformationalstates:activeintermediateinactiveboundfullagonistBI-167107novelexplainability-orientedinvestigationpredictionresultsableidentifyassesscontributionindividualresiduesinfluencingpathwayConsequentlycontributemethodologyassistselucidationactivation-deactivationLayer-WiseRelevanceAnalysisMotifRecognitionActivationPathway2-Receptornetworksdeeplearninginterpretabilitylayer-wiseproteomicssignalβ2-adrenergic

Similar Articles

Cited By (1)