XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

Linda C Johansson; Benjamin Stauch; John D McCorvy; Gye Won Han; Nilkanth Patel; Xi-Ping Huang; Alexander Batyuk; Cornelius Gati; Samuel T Slocum; Chufeng Li; Jessica M Grandner; Shuming Hao; Reid H J Olsen; Alexandra R Tribo; Sahba Zaare; Lan Zhu; Nadia A Zatsepin; Uwe Weierstall; Saïd Yous; Raymond C Stevens; Wei Liu; Bryan L Roth; Vsevolod Katritch; Vadim Cherezov

doi:10.1038/s41586-019-1144-0

XFEL structures of the human MT₂ melatonin receptor reveal the basis of subtype selectivity

Nature. 2019 May;569(7755):289-292. doi: 10.1038/s41586-019-1144-0. Epub 2019 Apr 24.

Authors

Linda C Johansson^#^{1

2}, Benjamin Stauch^#^{1

2}, John D McCorvy^{3

4}, Gye Won Han^{1

2}, Nilkanth Patel^{1

5}, Xi-Ping Huang^{3

6}, Alexander Batyuk⁷, Cornelius Gati^{8

9}, Samuel T Slocum^{3

6}, Chufeng Li^{10

11}, Jessica M Grandner^{1

5}, Shuming Hao^{1

2}, Reid H J Olsen³, Alexandra R Tribo³, Sahba Zaare¹⁰, Lan Zhu¹¹, Nadia A Zatsepin^{10

11}, Uwe Weierstall^{10

11}, Saïd Yous¹², Raymond C Stevens^{1

2

5}, Wei Liu¹¹, Bryan L Roth^{13

14

15}, Vsevolod Katritch^{16

17

18}, Vadim Cherezov^{19

20

21}

Affiliations

¹ Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
² Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
³ Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁴ Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
⁵ Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
⁶ National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁷ Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
⁸ Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
⁹ Department of Structural Biology, Stanford University, Stanford, CA, USA.
¹⁰ Department of Physics, Arizona State University, Tempe, AZ, USA.
¹¹ School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
¹² Université de Lille, CHU Lille, Inserm, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France.
¹³ Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.
¹⁴ National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.
¹⁵ Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.
¹⁶ Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.
¹⁷ Department of Chemistry, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.
¹⁸ Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. katritch@usc.edu.
¹⁹ Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.
²⁰ Department of Chemistry, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.
²¹ Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. cherezov@usc.edu.

^# Contributed equally.

Abstract

The human MT₁ and MT₂ melatonin receptors^1,2 are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns³. Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer³, and MT₂ has also been implicated in type 2 diabetes^4,5. Here we report X-ray free electron laser (XFEL) structures of the human MT₂ receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon⁶ at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants: H208^5.46A (superscripts represent the Ballesteros-Weinstein residue numbering nomenclature⁷) and N86^2.50D, obtained in complex with 2-PMT. Comparison of the structures of MT₂ with a published structure⁸ of MT₁ reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [³H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT₁ and MT₂, but in addition the MT₂ structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT₂. Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Crystallization
Diabetes Mellitus, Type 2 / genetics
Electrons*
Humans
Indenes / chemistry
Indenes / metabolism
Lasers*
Ligands
Melatonin / analogs & derivatives
Melatonin / chemistry
Melatonin / metabolism
Models, Molecular*
Molecular Docking Simulation
Molecular Dynamics Simulation
Mutation
Receptor, Melatonin, MT1 / chemistry
Receptor, Melatonin, MT1 / metabolism
Receptor, Melatonin, MT2 / chemistry*
Receptor, Melatonin, MT2 / genetics
Receptor, Melatonin, MT2 / metabolism*
Structure-Activity Relationship
Substrate Specificity

Substances

2-phenylmelatonin
Indenes
Ligands
Receptor, Melatonin, MT1
Receptor, Melatonin, MT2
ramelteon
Melatonin

Abstract

Publication types

MeSH terms

Substances

Grants and funding