Potency of LSD
Client: Dr. Derek Ng.
Media: UCSF Chimera, Adobe Photoshop, Adobe Illustrator.
Audience: Educated lay audience.
Format: Two-page spread in a popular science magazine.
Objective: Render an illustration showing relationship between the molecular structure and function of lysergic acid diethylamide (LSD). I aimed to make the content engaging and readable for a lay audience.
UCSF Chimera was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311.
Last updated in June, 2019.
Earlier version (Jan 2019)
Work up from PDB (Chimera to Photoshop)
Early draft layouts
Ishchenko, A., Wacker, D., Kapoor, M., Zhang, A., Han, G. W., Basu, S., … Cherezov, V. (2017). Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody. Proceedings of the National Academy of Sciences, 114(31), 8223–8228. https://doi.org/10.1073/pnas.1700891114
Duration of action of ecstasy.
Dasgupta, A. (2017). Challenges in Laboratory Detection of Unusual Substance Abuse: Issues with Magic Mushroom, Peyote Cactus, Khat, and Solvent Abuse. Advances in Clinical Chemistry (1st ed., Vol. 78). Elsevier Inc. https://doi.org/10.1016/bs.acc.2016.07.004
Duration of psilocybin activity.
Kang, Y., Zhou, X. E., Gao, X., He, Y., Liu, W., Ishchenko, A., … Xu, H. E. (2015). Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature, 523(7562), 561–567. https://doi.org/10.1038/nature14656
Used to inform the structure of arrestin that I should depict.
Passie, T., Halpern, J. H., Stichtenoth, D. O., Emrich, H. M., Hintzen, A. (2008). The pharmacology of lysergic acid diethylamide: A review. CNS Neuroscience & Therapeutics, 14(4). https://doi.org/10.1111/j.1755-5949.2008.00059.x
Average duration of LSD activity.
PDB ID: 1CF1 – Bovine inactive arrestin
Not human but so far the most appropriate structure I could find, used in Kang et al., 2015 and Scheerer & Sommer, 2017
PDB ID: 5MAM – Human insulin in complex with serotonin
Used to obtain 3D structure of serotonin.
PDB ID: 5TVN – Human LSD-bound 5-HT2BR (Wacker et al., 2017)
Used directly in illustration as secondary structure and surface structure model, close-up of binding pocket with LSD interacting with specific residues, 3D structure of LSD.
Removed cytochrome b562 (UniProt P0ABE7) and rebuilt missing loop with (UniProt P41595).
Orientation in the membrane from Orientations of Proteins in Membranes Database.
Quibell, R., Prommer, E. E., Mihalyo, M., Twycross, R., & Wilcock, A. (2011). Ketamine*. Journal of Pain and Symptom Management, 41(3), 640–649. https://doi.org/10.1016/j.jpainsymman.2011.01.001
Duration of ketamine activity.
Scheerer, P., & Sommer, M. E. (2017). Structural mechanism of arrestin activation. Current Opinion in Structural Biology, 45, 160–169. https://doi.org/10.1016/j.sbi.2017.05.001
Used to inform structure of arrestin to use/approximately how the protein should probably approach my receptor (see Kang et al., 2015).
UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem.2004 Oct;25(13):1605-12.
Program used for molecular structure visualizations: stick models and surface models for activated 5-HT2BR, and reference for 3D structure of receptors rendered in Adobe Photoshop.
Wacker, D., Wang, C., Katritch, V., Han, G. W., Huang, X.-P., Vardy, E., McCorvy, J. D., Jiang, Y., Chu, M., Siu, F. Y., Liu, W., Xu, H. E., Cherezov, V.. Roth, B. L., Stevens, R. C. (2013). Structural Features for Functional Selectivity at Serotonin Receptors. Science, 340(6132), 615–619. https://doi.org/10.1126/science.1232808
Detailed explanation of conformational characteristics in LSD/5-HT2BR likely related to biased arrestin signalling (these are better summarized visually in Wacker et al., 2017).
Wacker, D., Wang, S., McCorvy, J. D., Betz, R. M., Venkatakrishnan, A. J., Levit, A., Lansu, K., Schools, Z. L., Che, T., Nichols, D. E., Shoichet, B. K., Dror, R. O. Roth, B. L. (2017). Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell, 168(3), 377–389.e12. https://doi.org/10.1016/j.cell.2016.12.033
Main source for this illustration on the LSD/5-HT2BR structure-function relationship, specific LSD conformation most likely responsible for long residence time.
Adopted similar visualization strategies for the receptor-ligand complex (secondary structure overview); close-up of orthosteric binding site; surface model of receptor with EL2 “lid”; close-up of motifs/conformational changes associated with biased signalling.
Describes rotation of LSD at diethylamide when binding.
Confirms that 5-HT2BR is a good model for 5-HT2AR (no crystal model for the latter yet).