A Caltech Library Service

High-throughput identification of crystalline natural products from crude extracts enabled by microarray technology and microED

Delgadillo, David A. and Burch, Jessica E. and Kim, Lee Joon and de Moraes, Lygia and Niwa, Kanji and Williams, Jason and Tang, Melody J. and Lavallo, Vincent G. and Chhetri, Bhuwan K. and Jones, Christopher G. and Hernandez Rodriguez, Isabel and Signore, Joshua A. and Marquez, Lewis and Bhanushali, Riya and Greene, Madison and Woo, Sunmin and Kubanek, Julia and Quave, Cassandra and Tang, Yi and Nelson, Hosea M. (2023) High-throughput identification of crystalline natural products from crude extracts enabled by microarray technology and microED. . (Unpublished)

[img] PDF - Submitted Version
Creative Commons Attribution Non-commercial No Derivatives.

[img] PDF - Supplemental Material
Creative Commons Attribution Non-commercial No Derivatives.


Use this Persistent URL to link to this item:


The structural determination of natural products (NPs) can be arduous due to sample heterogeneity. This often demands itera-tive purification processes and characterization of complex molecules that may only be available in miniscule quantities. Microcrystal electron diffraction (microED) has recently shown promise as a method to solve crystal structures of NPs from nanogram quantities of analyte. However, its implementation in NP discovery remains hampered by sample throughput and purity requirements akin to traditional NP-discovery workflows. In the methods described herein, we leverage the resolving power of transmission electron microscopy (TEM) and the miniaturization capabilities of DNA microarray technology to address these challenges through the establishment of an NP screening platform, array electron diffraction (ArrayED). In this workflow, an array of HPLC fractions taken from crude extracts are deposited onto TEM grids in picoliter-sized droplets. This multiplexing of analytes on TEM grids enables 1200 or more unique samples to be simultaneously inserted into a TEM equipped with an autoloader. Selected area electron diffraction analysis of these microarrayed grids allows for rapid identification of crystalline metabolites. In this study, ArrayED enabled structural characterization of 14 natural products, including four novel crystal structures and two novel polymorphs, from 20 crude extracts. Moreover, we identify several chemical species that would not be detected by standard mass spectrometry (MS) or UV/Vis and crystal forms that would not be characterized using traditional methods.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Delgadillo, David A.0000-0002-0897-4470
Burch, Jessica E.0000-0002-3578-1770
Kim, Lee Joon0000-0002-0786-7614
de Moraes, Lygia0000-0001-9176-8725
Niwa, Kanji0000-0003-0772-0935
Lavallo, Vincent G.0000-0001-8945-3038
Jones, Christopher G.0000-0003-4308-1368
Marquez, Lewis0000-0002-3782-5204
Woo, Sunmin0000-0001-7561-2333
Kubanek, Julia0000-0003-4482-1831
Quave, Cassandra0000-0001-9615-7886
Tang, Yi0000-0003-1597-0141
Nelson, Hosea M.0000-0002-4666-2793
Additional Information:The content is available under CC BY NC ND 4.0 License. We thank the Proteomics Exploration Lab at Caltech for mass spectrometry support, Dr. S. Chen and the Caltech Cryo-EM facility for materials and advice, Dr. S. Virgil for helpful discussions, for figures of instruments, and D. Cascio for assistance in crystallography with recrystallization screens. We also thank the government of Fiji for allowing us to perform research in their territorial waters and M.E. Hay and D. Rasher for performing field collections of Halymenia sp. This research was funded by NIH NCCIH 1R01AT011990 (H.M.N., C.L.Q., Y.T., and J.K.), NIH ICBG U19-TW007401 (J.K.), Packard Foundation (H.M.N.), Pew Charitable Trust (H.M.N.). Author Contributions. D.A.D, L.J.K and H.M.N designed the workflow. J.E.B. processed and refined structures. L.S.M., M.J.T., I.H.R., V.G.L. and J.A.S. screened microarrays. L.J.K. and C.G.J. aided in recrystallization and data collection. K.N., J.W., B.K.C., L.M., M.G., and R.B. provided the crude extracts utilized. The manuscript was written through contributions of all authors. / All authors have given approval to the final version of the manuscript.
Funding AgencyGrant Number
David and Lucile Packard FoundationUNSPECIFIED
Pew Charitable TrustUNSPECIFIED
Record Number:CaltechAUTHORS:20230328-625661000.2
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120489
Deposited By: George Porter
Deposited On:30 Mar 2023 15:56
Last Modified:30 Mar 2023 15:56

Repository Staff Only: item control page