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Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

Abstract

The neuromodulator melatonin synchronizes circadian rhythms and related physiological functions through the actions of two G-protein-coupled receptors: MT1 and MT2. Circadian release of melatonin at night from the pineal gland activates melatonin receptors in the suprachiasmatic nucleus of the hypothalamus, synchronizing the physiology and behaviour of animals to the light–dark cycle1,2,3,4. The two receptors are established drug targets for aligning circadian phase to this cycle in disorders of sleep5,6 and depression1,2,3,4,7,8,9. Despite their importance, few in vivo active MT1-selective ligands have been reported2,8,10,11,12, hampering both the understanding of circadian biology and the development of targeted therapeutics. Here we docked more than 150 million virtual molecules to an MT1 crystal structure, prioritizing structural fit and chemical novelty. Of these compounds, 38 high-ranking molecules were synthesized and tested, revealing ligands with potencies ranging from 470 picomolar to 6 micromolar. Structure-based optimization led to two selective MT1 inverse agonists—which were topologically unrelated to previously explored chemotypes—that acted as inverse agonists in a mouse model of circadian re-entrainment. Notably, we found that these MT1-selective inverse agonists advanced the phase of the mouse circadian clock by 1.3–1.5 h when given at subjective dusk, an agonist-like effect that was eliminated in MT1- but not in MT2-knockout mice. This study illustrates the opportunities for modulating melatonin receptor biology through MT1-selective ligands and for the discovery of previously undescribed, in vivo active chemotypes from structure-based screens of diverse, ultralarge libraries.

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Fig. 1: Large library docking finds novel, potent melatonin receptor ligands.
Fig. 2: Affinity, efficacy and potency of MT1-selective inverse agonists on human and mouse MT1 and MT2 receptors.
Fig. 3: In vivo, MT1-selective inverse agonists decelerate re-entrainment rate and induced a phase advance in circadian activity when administered at subjective dusk.

Data availability

Probe pairs (two similar ligands with and without activity) of inverse agonists selective for MT1 and agonists selective for hMT2 are available by arrangement with Sigma (Extended Data Fig. 3). The identities of the compounds docked in this study are freely available from the ZINC database (http://zinc15.docking.org) and active compounds may be purchased from Enamine. Raw data are available for Fig. 1, Extended Data Tables 1, 2 and Extended Data Figs. 1, 2 in Supplementary Tables 1 (MT1 and MT2 affinities, MT1 DOCK energies and ranks) and 2 (compound purity information). Bias information for Extended Data Fig. 3 is included in Supplementary Table 3. For Fig. 2, data from the GPCRome screens, concentration–response curves, and competition binding and LC–MS experiments are included in Supplementary Data 15 and synthesis routes and spectra of compounds in Supplementary Data 6, 7. Further data for Fig. 3 are included in Extended Data Figs. 4, 5, 7 and Supplementary Table 4. Raw data values and transformed data for in vitro cell-based assays as well as in vivo data for phase shift and re-entrainment are available for Figs. 2, 3 and Extended Data Figs. 4 (re-entrainment), 5 (phase shift), 6, 7a–c.

Code availability

DOCK3.7 is freely available for non-commercial research (http://dock.compbio.ucsf.edu/DOCK3.7/). A web-based version is freely available to all at http://blaster.docking.org/. The ultra-large library used here is freely available at http://zinc15.docking.org/.

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Acknowledgements

This study was supported by US NIH awards U24DK1169195 (to B.L.R. and B.K.S.), R35GM122481 (to B.K.S.), the NIMH Psychoactive Drug Screening Contract (to B.L.R.), GM133836 (to J.J.I.), ES023684 (to M.L.D.), UL1TR001412 and KL2TR001413 (to the University at Buffalo), a PhRMA Foundation Fellowship (73309 to A.J.J.), Jacobs School of Medicine and Biomedical Sciences unrestricted funds (to M.L.D.), R35GM127086 (to V.C.), EMBO ALTF 677-2014 (to B.S.), HFSP long-term fellowship LT000046/2014-L (to L.C.J.), a postdoctoral fellowship from the Swedish Research Council (to L.C.J.) and the National Science Foundation (NSF) BioXFEL Science and Technology Center 1231306 (to B.S. and V.C.). We thank G. Wilding from the Biostatistics, Epidemiology and Research Design (BERD) Core of the Clinical and Translational Science Institute at the University at Buffalo for statistical advice regarding analyses of in vivo data.

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Authors

Contributions

B.K.S., B.L.R. and M.L.D. conceived the study. R.M.S. performed the docking and structure-based optimization. J.D.M. and H.J.K. performed the initial binding and functional assays and analyses, assisted by T.C. A.J.J. performed the 2-[I125]iodomelatonin and GTP-perturbation assays. S.S. performed the profiling studies. G.C.G. performed the in vivo mouse pharmacology experiments and all animal husbandry. Y.S.M. and O.S. directed the compound synthesis, purification and characterization experiments. B.S., L.C.J., V.C., B.L.R., X.-P.H. and J.D.M. determined and validated the structures of the MT1 and MT2 receptor types, and made them available before publication. T.K. performed signalling bias calculations. J.J.I. created the ultra-large libraries. B.L.R. supervised the pharmacology studies; B.K.S. supervised the docking and compound optimization; M.L.D. supervised the binding studies and the in vivo circadian rhythm experiments in mice. M.L.D. G.C.G. designed all in vivo experiments. R.M.S., B.K.S., M.L.D., G.C.G., J.D.M., H.J.K. and B.L.R. wrote the paper with contributions from other authors.

Corresponding authors

Correspondence to Brian K. Shoichet or Bryan L. Roth or Margarita L. Dubocovich.

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Competing interests

B.K.S. and J.J.I. are founders of a company, BlueDolphin LLC, that works in the area of molecular docking. All other authors declare no competing interests.

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Peer review information Nature thanks Derk-Jan Dijk, Irina Kufareva and Ieva Sutkeviciute for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Concentration–response curves of the initial 15 compounds in cAMP assays.

af, Inhibition of isoproterenol-stimulated cAMP mediated by hMT1 (a, c, e) or hMT2 (b, d, f) in HEK293T cells by melatonin and the 15 initial compounds. Data are normalized to the melatonin response. The 15 initial compounds were split into three graphs for clarity, melatonin response curves are the same across graphs in a, c, e and b, d, f. Data are mean ± s.e.m. of four biologically independent experiments (n = 4) run in triplicate, unless otherwise indicated, in which case the number of biologically independent experiments is indicated in parentheses next to the compound name. Source Data

Extended Data Fig. 2 Concentration–response curves of notable analogues based on initial hits in cAMP assays.

af, Inhibition of isoproterenol-stimulated cAMP mediated by hMT1 (a, c, e) or hMT2 (b, d, f) in HEK293T cells by melatonin and select analogues. Data are normalized to the melatonin response. The compounds were split into three graphs for clarity, melatonin response curves are the same across graphs in a, c, e and b, d, f. Data are mean ± s.e.m. of four biologically independent experiments (n = 4) run in triplicate, unless otherwise indicated, in which case the number of biologically independent experiments is indicated in parentheses next to the compound name. Source Data

Extended Data Fig. 3 Small changes in the ligand structure have large effects on the activity and selectivity of the melatonin receptor.

a, Docked pose of ZINC151209032, an MT1-selective direct-docking hit. b, Docked pose of ZINC497291360, a close analogue of ZINC151209032 that has twofold selectivity for MT2 over MT1. c, Docked pose of ZINC151192780, an analogue for which the MT2 selectivity increases to 89-fold over MT1. d, Docked pose of ZINC485552623, which adds a bulkier 2-chloro-3-methylthiophene into a proposed MT2-selective hydrophobic cleft, resulting in a fully MT2-selective agonist without detectable MT1 activity. All docked poses are overlaid onto the crystallographic pose of 2-phenylmelatonin in transparent blue. e, Concentration–response curves of the four analogues binding to MT1 and MT2. Data are normalized to the melatonin response and are mean ± s.e.m. of four biologically independent experiments (n = 4) run in triplicate. f, Bias plots of ZINC482850041 and ZINC608506688 relative to melatonin signalling. Mean values (Supplementary Table 3) are presented as solid lines and the shading indicates the 95% confidence interval. Data in f are normalized to the melatonin response and represent mean ± s.e.m. of three biologically independent experiments (n = 3) run in triplicate, except for ZINC608506688 for Gi activation (n = 4). Source Data

Extended Data Fig. 4 MT1-selective inverse agonists decelerate the re-entrainment rate in vivo via MT1 receptors.

Data are an extension of Fig. 3a–c. ae, Representative actograms of running wheel activity in wild-type (WT) C3H/HeN mice treated with vehicle (VEH) (a), 30 μg melatonin (MLT) per mouse (b), UCSF7447 (‘7447) (c), UCSF3384 (‘3384) (d) or 300 μg luzindole (LUZ) per mouse (e) immediately before the new dark onset (black dots) after an abrupt advance in the dark onset of 6 h in a 12:12 light:dark cycle (grey, dark phase; white, light phase). Compounds were administered once a day for 3 days (see Methods for additional details). fk, Representative actograms of running wheel activity for C3H/HeN mice treated with vehicle (wild-type (f), MT1KO (h), MT2KO (j)) or inverse agonist UCSF7447 (wild-type (g), MT1KO (i), MT2KO (k)) after a 6-h advance in dark onset. Mice were kept on a 12:12 light:dark cycle. UCSF7447 (30 μg per mouse) was administered for three consecutive days immediately before the new dark onset (black dots). l, The inverse agonist UCSF3384 decelerates the rate of re-entrainment of the rhythm of running wheel activity onset in C3H/HeN wild-type mice. Data are expressed in hours advanced each day for wild-type mice treated with vehicle or UCSF3384 (two-way repeated-measures ANOVA; treatment × time interaction: F16,647 = 1.99, P = 0.0122). m, The inverse agonist UCSF7447 does not modulate the rate of re-entrainment of the onset of a running wheel activity rhythm in C3H/HeN MT1KO mice. Data are expressed in hours advanced each day for MT1KO mice treated with vehicle or UCSF7447 (mixed-effect two-way repeated-measures ANOVA; treatment × time interaction: F16,474 = 1.44, P = 0.117). n, The inverse agonist UCSF7447 decelerates the rate of re-entrainment of the onset of a running wheel activity rhythm in C3H/HeN MT2KO mice. Data are expressed in hours advanced each day for MT2KO mice treated with vehicle or UCSF7447 (mixed-effect two-way repeated-measures ANOVA; treatment × time interaction: F16,683 = 2.57, P = 0.000686). Data are mean + s.e.m. *P < 0.05, **P < 0.01; multiple comparisons were corrected using Tukey’s post-test (P < 0.05). The dotted line in l–n indicates the new dark onset. Additional details of all statistical analyses as well as n numbers for each condition can be found in the Methods, ‘Statistics and reproducibility’. All treatments were given as a subcutaneous injection. Source Data

Extended Data Fig. 5 MT1-selective inverse agonists induce a phase advance in circadian activity at CT 10 that is mediated by MT1 in vivo.

Data are an extension of Fig. 3d–f. ae, Representative actograms of running wheel activity from individual C3H/HeN wild-type mice kept in constant dark (grey bars) treated with vehicle (a), melatonin (b), UCSF7447 (c), UCSF3384 (d) or luzindole (e). All treatments were 30 μg per mouse except for luzindole, which was 300 μg per mouse as described in the Methods. Mice were treated at dusk (CT 10; 2 h before the onset of running wheel activity) for three consecutive days (black dots). Red lines indicate the best-fit line of pre-treatment onsets and blue lines indicate the best-fit line of post-treatment onsets, which were both used for phase shift determinations (see Methods for more details). The corresponding quantification can be found in Fig. 3d. fh, Representative actograms of running wheel activity from individual C3H/HeN wild-type mice kept in the constant dark treated with vehicle (f), melatonin (g) or UCSF7447 (h; all treatments were 0.9 μg per mouse) at CT 10. The corresponding quantification can be found in Fig. 3d. ik, Representative actograms of running wheel activity from individual C3H/HeN wild-type mice kept in the constant dark treated with melatonin (i) at CT 2 (10 h before the onset of running wheel activity) or vehicle (j) compared with UCSF7447 (k; all treatments were 30 μg per mouse) at CT 6 (6 h before the onset of running wheel activity). The corresponding quantification can be found in Extended Data Fig. 7. lq, Representative actograms of running wheel activity from individual C3H/HeN wild-type (l, m), MT1KO (n, o) and MT2KO (p, q) mice kept in constant dark treated with vehicle (white; l, n, p) or UCSF7447(blue; m, o, q; 30 μg per mouse) at CT 10. The corresponding quantification can be found in Fig. 3e. rw, Representative actograms of running wheel activity from individual C3H/HeN wild-type (r, s), MT1KO (t, u) and MT2KO (v, w) mice kept in constant dark treated with vehicle (white; r, t, v) or UCSF7447(blue; s, u, w; 30 μg per mouse) at CT 2. The corresponding quantification can be found in Fig. 3f. All treatments were given by subcutaneous injection.

Extended Data Fig. 6 Concentration–response curves and Schild plots of the inverse agonists UCSF7447 and UCSF3384 in cAMP assays.

a, b, d, e, Modulation of hMT1-mediated (a, d) or hMT2-mediated (b, e) inhibition of isoproterenol-stimulated cAMP in HEK293T cells by melatonin in the presence of UCSF7447 (a, b) or UCSF3384 (d, e) for a range of concentrations. Data are normalized to the effect of isoproterenol alone and are mean ± s.e.m. of three biologically independent experiments (n = 3) run in triplicate. c, f, Schild plots depicting the competitive antagonism of melatonin by UCSF7447 (c) and UCSF3384 (f). Schild analysis of hMT1 (purple) and hMT2 (teal) show the competitive antagonism of UCSF7447 (hMT1, pKB = 7.4 ± 0.1, slope = 0.98 ± 0.03; hMT2, pKB = 6.2 ± 0.1, slope = 1.3 ± 0.4) (c) and UCSF3384 (hMT1, pA2 = 7.9 ± 0.1, slope = 0.80 ± 0.04; hMT2 pKB = 6.7 ± 0.1, slope = 1.0 ± 0.1) (f). Data are mean ± s.e.m. of three biologically independent experiments (n = 3) run in triplicate. Source Data

Extended Data Fig. 7 Differential phase shift profile for the inverse agonist UCSF7447 compared to the agonist melatonin and a prototype antagonist (luzindole) across the circadian cycle.

ac, C3H/HeN mice were kept in constant dark and treated with vehicle, melatonin, luzindole or UCSF7447 (all treatments were 30 μg per mouse except for luzindole, which was 300 μg per mouse, subcutaneously). Mice were treated at CT 2, 6 or 10 (10, 6 or 2 h before the onset of running wheel activity) for three consecutive days (Methods). a, CT 2 phase shift data were compared using one-way ANOVA (F3,11 = 28.16, P = 1.85 × 10−5). b, CT 6 phase shift data were compared using one-way ANOVA (F3,26 = 0.61, P = 0.61). c, CT 10 phase shift data were compared using one-way ANOVA (F3,17 = 35.13, P = 1.66 × 10−7). All multiple comparisons were made compared with vehicle using a Dunnet’s post hoc test (P < 0.05). Values for melatonin and UCSF7447 at CT 10 were pooled from previous data for comparison to luzindole. Data are mean ± s.e.m. ****P < 0.0001 for comparisons with vehicle. All treatments were given by subcutaneous injection. Source Data

Extended Data Table 1 Active molecules from the initial docking screen
Extended Data Table 2 Some of the potent analogues from initial hits
Extended Data Table 3 Pharmacokinetics of three melatonin receptor type-selective ligands
Extended Data Table 4 Probe pairs of in vivo tested molecules

Supplementary information

Supplementary Information

This file contains Supplementary Tables 2-5 and Supplementary Data 2-7.

Reporting Summary

Supplementary Table 1

All Molecules tested against MT1/MT2 | Excel file containing all molecules that were tested against the melatonin receptors organized by cluster with DOCK scores, closest known melatonin receptor ligands by ECFP4 Tanimoto coefficient, affinities at both receptors, and any close patented molecules.

Source Data

This file contains source Data for Supplementary Data 3.

Source Data

This file contains source Data for Supplementary Data 4.

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Stein, R.M., Kang, H.J., McCorvy, J.D. et al. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature 579, 609–614 (2020). https://doi.org/10.1038/s41586-020-2027-0

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