Name: hierarchical and programmable one-pot oligosaccharide synthesis
Uploaded: 2019-09-06T13:00:00
Description: Watch this Scientific Journal Video about Hierarchical and Programmable One-Pot Oligosaccharide Synthesis at JoVE.com

This work was supported by Academia Sinica including the Summit Program, Ministry of Science and Technology [MOST 104-0210-01-09-02, MOST 105-0210-01-13-01, MOST 106-0210-01-15-02], and NSF (1664283).

1. Auto-CHO software manipulation
<ol>
	<li>Java Runtime Environment installation: make sure the Java Runtime Environment (JRE) has been installed in the device. If JRE has been installed, go to the next step, &#8220;software initialization&#8221;; otherwise, download and install JRE according to the user&#8217;s operating system found at: &#60;https://www.oracle.com/technetwork/java/javase/downloads/index.html&#62;.</li>
	<li>Software initialization: go to the Auto-CHO website at &#60;https://sites.google.com/view/aut...

<ol>
	<li>Apweiler, R., Hermjakob, H., Sharon, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+frequency+of+protein+glycosylation,+as+deduced+from+analysis+of+the+SWISS-PROT+database.">On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.</a> Biochimica Et Biophysica Acta. 1473 (1), 4-8 (1999).</li><li>Sears, P., Wong, C. -. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+Automated+Synthesis+of+Oligosaccharides+and+Glycoproteins.">Toward Automated Synthesis of Oligosaccharides and Glycoproteins.</a> Science. 291 (5512), 2344-2350 (2001).</li><li>Kulkarni, S. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#8220;One-Pot&#8221;+Protection,+Glycosylation,+and+Protection-Glycosylation+Strategies+of+Carbohydrates.">&#8220;One-Pot&#8221; Protection, Glycosylation, and Protection-Glycosylation Strategies of Carbohydrates.</a> Chemical Reviews. 118 (17), 8025-8104 (2018).</li><li>Zhang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programmable+One-Pot+Oligosaccharide+Synthesis.">Programmable One-Pot Oligosaccharide Synthesis.</a> Journal of the American Chemical Society. 121 (4), 734-753 (1999).</li><li>Cheng, C. -. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hierarchical+and+programmable+one-pot+synthesis+of+oligosaccharides.">Hierarchical and programmable one-pot synthesis of oligosaccharides.</a> Nature Communications. 9 (1), 5202 (2018).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> ChemDraw. , (2019).</li><li>Cheeseman, J. R., Frisch, &. #. 1. 9. 8. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Predicting magnetic properties with chemdraw and gaussian. , (2000).</li><li>Yap, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PaDEL-descriptor:+An+open+source+software+to+calculate+molecular+descriptors+and+fingerprints.">PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints.</a> Journal of Computational Chemistry. 32 (7), 1466-1474 (2011).</li><li>Ceroni, A., Dell, A., Haslam, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+GlycanBuilder:+a+fast,+intuitive+and+flexible+software+tool+for+building+and+displaying+glycan+structures.">The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.</a> Source Code for Biology and Medicine. 2, 3 (2007).</li><li>Damerell, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+GlycanBuilder+and+GlycoWorkbench+glycoinformatics+tools:+updates+and+new+developments.">The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments.</a> Biological Chemistry. 393 (11), 1357-1362 (2012).</li></ol>

The Auto-CHO software was developed for assisting chemists to proceed hierarchical and programmable one-pot synthesis of oligosaccharides5. Auto-CHO was built by Java programming language. It is a GUI software and cross-platform, which currently supports Windows, macOS, and Ubuntu. The software can be downloaded free of charge for the Auto-CHO website at &#60;https://sites.google.com/view/auto-cho/home&#62;, and its source code with MIT license can be accessed from the GitHub at &#60;https://githu...

Carbohydrates are ubiquitous in nature1,2, but their presence and mode of action remain an uncharted territory, mainly due to difficult access to this class of molecules3. Unlike automated synthesis of oligopeptides and oligonucleotides, the development of automated synthesis of oligosaccharides remains a formidable task, and progress has been relatively slow.
To tackle this problem, Wong et al. developed the first automated method for the synthesis of oligosaccharides using a programmable software program called Optimer4, which guides the selection of BBLs from a library of ~50 BBLs for sequential one-pot reactions. Each BBL was designed and synthesized with well-defined reactivity tuned by various protecting groups. Using this approach, the complexities of protecting manipulation and intermediate purification can be minimized during synthesis, which have been considered the most difficult issues to overcome in the development of automated synthesis. Despite this advance, the method is still quite restricted, as the number of BBLs is too small and the Optimer program can only handle certain small oligosaccharides. For more complex oligosaccharides that require more BBLs and multiple passes of one-pot reactions and fragment condensation, an upgraded version of the software program, Auto-CHO5, has been developed.
In Auto-CHO, more than 50,000 BBLs with defined reactivity to the BBL library have been added, including 154 synthetic and 50,000 virtual ones. These BBLs were designed by machine learning based on basic properties, calculated NMR chemical shifts6, 7, and molecular descriptors8, which affect the structure and reactivity of the BBLs. With this upgraded program and new set of BBLs available, the synthesis capacity is expanded, and as demonstrated, several oligosaccharides of interest can rapidly be prepared. It is believed that this new development will facilitate the synthesis of oligosaccharides for the study of their roles in various biological processes and their impacts on the structures and functions of glycoproteins and glycolipids. It is also thought that this work will benefit the glycoscience community significantly, given that this method is available to the research community free of charge. Synthesis of the essential human embryonic stem cell marker, SSEA-45, is demonstrated in this work.

<table>
	<tbody>
		<tr>
			<td>Acetonitrile</td>
			<td>Sigma-Aldrich</td>
			<td>75-05-8</td>
			<td></td>
		</tr>
		<tr>
			<td>Anhydrous magnesium sulfate</td>
			<td>Sigma-Aldrich</td>
			<td>7487-88-9</td>
			<td></td>
		</tr>
		<tr>
			<td>Cerium ammonium molybdate</td>
			<td>TCI</td>
			<td>C1794</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane</td>
			<td>Sigma-Aldrich</td>
			<td>75-09-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Drierite</td>
			<td>Sigma-Aldrich</td>
			<td>7778-18-9</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl acetate</td>
			<td>Sigma-Aldrich</td>
			<td>141-78-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>67-56-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Molecular sieves 4 &#197;</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>n-Hexane</td>
			<td>Sigma-Aldrich</td>
			<td>110-54-3</td>
			<td></td>
		</tr>
		<tr>
			<td>N-Iodosuccinimide</td>
			<td>Sigma-Aldrich</td>
			<td>516-12-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium bicarbonate</td>
			<td>Sigma-Aldrich</td>
			<td>144-55-8</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium thiosulfate</td>
			<td>Sigma-Aldrich</td>
			<td>10102-17-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Toluene</td>
			<td>Sigma-Aldrich</td>
			<td>108-88-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Trifluoromethanesulfonic acid</td>
			<td>Sigma-Aldrich</td>
			<td>1493-13-6</td>
			<td></td>
		</tr>
	</tbody>
</table>

hierarchical and programmable one-pot oligosaccharide synthesis

This article presents a general experimental protocol for programmable one-pot oligosaccharide synthesis and demonstrates how to use Auto-CHO software for generating potential synthetic solutions. The programmable one-pot oligosaccharide synthesis approach is designed to empower fast oligosaccharide synthesis of large amounts using thioglycoside building blocks (BBLs) with the appropriate sequential order of relative reactivity values (RRVs). Auto-CHO is a cross-platform software with a graphical user interface that provides possible synthetic solutions for programmable one-pot oligosaccharide synthesis by searching a BBL library (containing about 150 validated and &#62;50,000 virtual BBLs) with accurately predicted RRVs by support vector regression. The algorithm for hierarchical one-pot synthesis has been implemented in Auto-CHO and uses fragments generated by one-pot reactions as new BBLs. In addition, Auto-CHO allows users to give feedback for virtual BBLs to keep valuable ones for further use. One-pot synthesis of stage-specific embryonic antigen 4 (SSEA-4), which is a pluripotent human embryonic stem cell marker, is demonstrated in this work.

The Auto-CHO search result based on default parameter settings indicates SSEA-4 can be synthesized by a [2 + 1 + 3] one-pot reaction. Figure 3 shows the software screenshot of the SSEA-4 search result. When a trisaccharide reducing end acceptor is selected (Figure 3, label 1), the program shows four potential solutions for the query. The first solution has one fragment (Figure 3, label 2), and its ca...

Watch this Scientific Journal Video about Hierarchical and Programmable One-Pot Oligosaccharide Synthesis at JoVE.com

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

This protocol demonstrates how to use the Auto-CHO software for hierarchical and programmable one-pot synthesis of oligosaccharides. It also describes the general procedure for RRV determination&#160;experiments and one-pot glycosylation of SSEA-4.

This article presents a general experimental protocol for programmable one-pot oligosaccharide synthesis and demonstrates how to use Auto-CHO software for ...

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