About

Academic Experiences

Dr Shuguang Yuan obtained his master degree in biochemistry and structural biology from the Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences in 2009. Following that, his doctoral dissertation was funded by the Maria Curia Fellowship. It was conducted in three different institutes in Europe: EPFL(Switzerland), Polish Academy of Science(Poland) and KULeuven University(Belgium). In his research, he investigated the principles of various biological systems including enzymes, kinases, ion channels, transporters and, in particular, G protein-coupled receptors (GPCRs). In June 2013, he was awarded with a PhD title with the honor of distinguished thesis. Following that, he was offered the Marie Curie ETH Postdoc Fellowship. In 2014, Dr. Yuan proposed a theory about the activation mechanism and the continuous water channel of GPCRs (Nature Communications, 2014), which are widely recognized in this area. Dr. Yuan is currently working at a leading pharmaceutical company in Basel as a specialist in computer-aided drug design (CADD). In the past few years, he has advanced two of his designed molecules into clinical trials. In 2016, he was invited to join the editorial board of the Journal of Bioinformatics, Computational and Systems Biology. In 2018, he was honored with a title of "affiliate professor" by the University of Warsaw.

Research Scopes

Currently, Dr. Shuguang Yuan is focused on the signalling mechanism and computer aided drug discovery (CADD) of G protein-coupled receptors (GPCRs). GPCRs regulate central human physiological responses to neurotransmitters, hormones, and environmental stimuli, and are among the most important therapeutic targets for many diseases including diabetes, pain, cancer, Alzheimer's disease and so on. About 40% of all marketed medicines are targeting GPCRs. Besides that, he is also interested in investigating enzyme catalytic mechanisms and enzyme engineerings. Furthermore, ligand-gated ion channels, transporters, kinase and disordered proteins are also within his research scopes. Dr. Yuan wishes that his work can benefit the entire human health exensively.

Research network

Dr. Shuguang Yuan has established an extensively international collaboration network in the area of structural biology, biochemistry and medicinal chemistry. These include the University of Southern California, iHuman Institute of the ShanghaiTech Unviersity, Case Western Reserve University, Swiss Federal Institute of Technology Lausanne (EPFL), University of California Los Angeles(UCLA), Max-Planck Institute, University of Copenhagen, Shanghai Institute of Organic Chenistry (SIOC, CAS), Fudan University, to name a few. Dr. Shuguang Yuan is involved in the GPCR Glisten network. He has also established extensive industrial network for drug discovery.

Publications

* corresponding authors #joint first authors
JCR-1=top 5%, JCR-2=6-20%, JCR-3=21-50%, JCR-4=50-100%

2019
(37) Chan S., Li Y., Dahoun T., Vogel H., Yuan S.*, New binding sites, new opportunities for GPCR drug discovery. Trends in Biochemical Sciences (2019). (doi:10.1016/j.tibs.2018.11.011,JCR-1)

2018
(36) Patent: Aissaoui H., Guerry P., Lehembre F., Pothier J., Pouzol L., Richard S., Yuan S., Piperidine CXCR7 receptor modulators. (2018). (patent no. WO 2018/019929 A1)

(35) Chan S., Wang J., Palczewski K., Filipek S., Vogel H.*, Liu Z.*, Yuan S.*, Exploring a new ligand binding site of G protein-coupled receptors. Chemical Science (2018). (cover story, doi:10.1039/C8SC01680A, JCR-1)

(34) Chan S., Pan L., Li Y., Yuan S.*, Rationalization of stereoselectivity in enzyme reactions. Computational Molecular Science (2018). (cover story, doi:10.1002/wcms.1403, JCR-1)

(33) Yan Y., Liu Q., Zang X., Yuan S., Bat-Erdene U., Nguyen C., Gan J., Zhou J.*, Jacobsen S.*, Tang Y.*, Resistance-Gene Directed Discovery of a Natural Product Herbicide with a New Mode of Action. Nature (2018). (doi:10.1038/s41586-018-0319-4, JCR-1)

(32) Peng Y., McCorvy J., Harpsøe K., Lansu K, Yuan S., et. al. Roth B.*, Stevens R.*, Liu Z.*, 5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology. Cell (2018). (doi:10.1016/j.cell.2018.01.001, JCR-1)

(31) Ernst I., Haase M., Ernst S., Yuan S., Kuhn A., Leptihn S., Large conformational changes of a highly dynamic Pre-Protein Binding Domain in SecA. Communications Biology (2018). (doi:10.1038/s42003-018-0133-4)

(30) Li W, Zhou Y, You W, Yang M, Ma Y, Wang M, Wang Y, Yuan S., Xiao Y*, Development of Photoaffinity Probe for the Discovery of Steviol Glycosides Biosynthesis Pathway in Stevia rebuadiana and Rapid Substrate Screening, ACS Chemical Biology (2018). (doi:10.1021/acschembio.8b00285, JCR-2)

(29) Zhou Y, Li W, You W, Di Z, Wang M, Zhou H, Yuan S., Wong NK, Xiao Y*, Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes. Chemical Communications (2018). (doi:10.1039/C7CC09951G, JCR-2)

2017
(28) Sun Z., Wu L., Bocola M., Chan S., Lonsdale R., Kong X., Yuan S.*, Zhou J.*, Reetz M.*, Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. Journal of the American Chemical Society (2017). (doi:10.1021/jacs.7b10278, JCR-1)

(27) Yuan H., Zhang J., Cai Y., Wu S., Yang K., Chan S., Huang W., Jin W., Li Y., Yin Y., Igarashi Y., Yuan S.*, Zhou J.*, Tang G.*, GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection. Nature communications (2017). (doi:10.1038/s41467-017-01508-1, JCR-1)

(26) Chan S., McCarthy D., Li J., Palczewski K., Yuan S.*, Designing Safer Analgesics via µ-Opioid Receptor Pathways. Trends in Pharmacological Sciences (2017). (doi:10.1016/j.tips.2017.08.004, JCR-1)

(25) Wang J., Llie A., Yuan S.*, Reetz M.*, Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe. Journal of the American Chemical Society (2017). (doi:10.1021/jacs.7b06019, JCR-1)

(24) Yuan S.*, Chan S., Hu Z.Q., Implementing WebGL and HTML5 in macromolecular visualization and modern computer-aided drug design. Trends in Biotechnology (2017). (doi:10.1016/j.tibtech.2017.03.009, JCR-1)

(23) Yuan S.*, Chan S., Hu Z.Q.,Using PyMOL as a platform for computational drug design. Computational Molecular Science (2017) (cover story, doi:10.1002/wcms.1303, JCR-1)

2016
(22) Yuan S.*, Peng Q., Palczewski K., Vogel H., Filipek S*. Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1A Receptor. Angewandte Chemie Int Ed Engl (2016). (doi:10.1002/anie.201603766, JCR-1)

(21) Yuan S.*, Chan H. C., Vogel H., Filipek S., Stevens R.C.*, Palczewski, K*. The Molecular Mechanism of P2Y1 Receptor Activation. Angewandte Chemie Int Ed Engl (2016) (doi:10.1002/anie.201605147, JCR-1)

(20) Zhang Z, Ma K., Yuan S., Luo Y., Jiang S., Hawara E., Pan S., Ma W.* Song, J*. Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family. Nature structural & molecular biology (2016), (doi:10.1038/nsmb.3279, JCR-1)

(19) Yuan S.*, Chan S., Filipek S., Vogel H., PyMOL and Inkscape bridge the data and the data visualization. Structure (2016) (doi:10.1016/j.str.2016.11.012, JCR-2)

(18) Chan H. C., Filipek S.*, Yuan S.*, The Principles of Ligand Specificity on beta-2-adrenergic receptor. Scientific Reports (2016), (doi:10.1038/srep34736, JCR-3)

(17) Yuan S.*, Filipek S., Vogel*, H. A Gating Mechanism of the Serotonin 5-HT3 Receptor. Structure (2016) (doi:10.1016/j.str.2016.03.019, JCR-2)

(16) Ji X., Liu W., Yuan S., Ding W.*, Zhang Q*. Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chemical Communications (2016), (doi: 10.1039/C6CC05661J JCR-2)

2015
(15) Yuan S.*, Palczewski K., Peng Q., Kolinski M., Vogel H., Filipek S*. The Mechanism of Ligand-Induced Activation or Inhibition of mu- and kappa-Opioid Receptors. Angewandte Chemie Int Ed Engl (2015) (VIP paper, doi:10.1002/anie.201501742, JCR-1)

(14) Baud O., Yuan S., Veya L., Filipek S., Vogel H*., Pick H*. Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles. Scientific Reports (2015), (doi:10.1038/srep14948, JCR-3)

2014
(13) Yuan S.*, Hu Z., Filipek S., Vogel H*. W246 Opens a Gate for a Continuous Intrinsic Water Pathway during Activation of the Adenosine A Receptor. Angewandte Chemie Int Ed Engl (2014), (doi:10.1002/anie.201409679, JCR-1)

(12) Yuan S.*, Filipek S., Palczewski K., Vogel H*. Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway. Nature communications (2014), (doi:10.1038/ncomms5733, JCR-1)

(11) Kong X, Yuan S., Li L., Chen S., Xu J. H., Zhou J* . Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates. Proc Natl Acad Sci U S A (2014), (doi:10.1073/pnas.1404915111, JCR-1)

(10) Kufareva I., Katritch V., Participants of GPCR contests, Stevens R. C., Abagyan R* . Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure (2014), (doi:10.1016/j.str.2014.06.012, JCR-2)

2013
(9) Yuan S.*, Vogel H., Filipek S*. The Role of Water and Sodium Ions in the Activation of the mu-Opioid Receptor. Angewandte Chemie Int Ed Engl (2013), (doi:10.1002/anie.201302244, JCR-1)

(8) Yuan S.*, Wu R., Latek D., Trzaskowski B., Filipek S*. Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations. PLoS Computational Biolology (2013), (doi:10.1371/journal.pcbi.1003261, JCR-2)

(7) Wu Y., Yuan S., Chen S., Wu D., Chen J., Wu J*. Enhancing the production of galacto-oligosaccharides by mutagenesis of Sulfolobus solfataricus beta-galactosidase. Food chemistry (2013), (doi:10.1016/j.foodchem.2012.11.052 JCR-2)

(6) Le Roy K., Vergauwen R., Struyf T., Yuan S., Lammens W., Matrai J., De Maeyer M., Van den Ende W*. Understanding the role of defective invertases in plants: tobacco Nin88 fails to degrade sucrose. Plant physiology (2013), (doi:10.1104/pp.112.209460 JCR-1)

before 2013
(5) Yuan S., Le Roy K., Venken T., Lammens W., Van den Ende W., De Maeyer M*. pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity? PloS one (2012), (doi:10.1371/journal.pone.0037453, JCR-3)

(4) Yuan S., Ghoshdastider U., Trzaskowski B., Latek D., Debinski A., Pulawski W., Wu R., Gerke V., Filipek*, S. The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations. PloS one (2012), (doi:10.1371/journal.pone.0047114, JCR-3)

(3) Trzaskowski B., Latek D., Yuan S., Ghoshdastider U., Debinski A., Filipek S*. Action of molecular switches in GPCRs - theoretical and experimental studies. Curr Med Chem (2012), (PMID:22300046, JCR-2)

(2) Lammens W., Le Roy K., Yuan S., Vergauwen R., Rabijns A., Van Laere A., Strelkov S. V., Van den Ende W*. Crystal structure of 6-SST/6-SFT from Pachysandra terminalis, a plant fructan biosynthesizing enzyme in complex with its acceptor substrate 6-kestose. The Plant journal : for cell and molecular biology (2012), (doi:10.1111/j.1365-313X.2011.04858.x, JCR-2)

(1) Zheng C., Liu H. H., Yuan S., Zhou J., Zhang B*. Molecular basis of LMAN1 in coordinating LMAN1-MCFD2 cargo receptor formation and ER-to-Golgi transport of FV/FVIII. Blood (2010), (doi:10.1182/blood-2010-04-278325, JCR-1)

News

A work on GPCR ligand binding sites

Scientific work Dr. Shuguang Yuan 03 January 2019

Our work entitled "New Binding Sites, New Opportunities for GPCR Drug Discovery" has been published in "Trends in Biochemical Sciences" recently. We elaborated the latest progress of GPCR ligand binding sites as well as their implications. Our work provides new insights towards GPCR drug discovery.

Merry Christmas and Happy New Year

New Year Wishes Dr. Shuguang Yuan 15 December 2018

Joyeux Noel et Bonne Année.

Merry Christmas and Happy New Year.

Fröhliche Weihnachten und ein Glückliches Neues Jahr.

A cover story in Computational Molecular Science

Scientific work Dr. Shuguang Yuan 5 December 2018

Our recent work entitled "Rationalization of stereoselectivity in enzyme reactions" has been published in "Computational Molecular Science". Our work has been selected as a cover story. Congratuationas to all contributors.
read more

A top downloaded article

Frequently downloaded paper Dr. Shuguang Yuan 26 October 2018

Our article "Using PyMOL as a platform for computational drug design", published in Computational Molecular Science, was one of the journal's top 20 most downloaded recent papers! Amongst articles published between July 2016 and June 2018, this article received some of the highest downloads in the 12-months post online publication. Congratuations to all contributors.
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A new webpage of Prof. Vogel

new webpage Dr. Shuguang Yuan 16 October 2018

A new webpage http://hv.gpcrm.org of Prof. Horst Vogel is lauched recently.
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An invited talk on the progress of painkiller

Invited guest Dr. Shuguang Yuan 1 October 2018

Dr. Yuan invited Dr. Hui Wang from ETH Zurich, to give a scientific talk entitled "Programming human cell functions for personalized medicine" at Idorsia. Dr. Wang is going to talk about her recent contributions to a new technology to treat chronic pain, allowing non-invasive and side effect-free control of pain suppression. This interesting work of Dr. Wang has been published in Nature Biomedical Engineering (doi:10.1038/s41551-018-0192-3) recently.
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A cover story in Chemical Science

Scientific work Dr. Shuguang Yuan 20 July 2018

Our team has found a new ligand binding pocket next to the highly conserved D2.50 residue of GPCRs, using all-atom long time scale molecular dynamics simulations. This has been confirmed by the follow-up mutagenesis studies which were finished at the iHuman Institute in ShanghaiTech University. Systimatical analysis on over 200 GPCRs crystal structures indicated that this potential new binding site widely exists in most family A GPCRs. This story is going to be published as a back side cover story in Chemical Science (doi:10.1039/C8SC01680A). Congratuations to all contributors.
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Scientific Exchanging and Collobrations

Scientific network Dr. Shuguang Yuan 11, July 2018, Basel, Switzerland

Prof. Zhijie Liu, the executive director of the iHuman Institute at the ShanghaiTech Unviersity, has been invited by Dr. Yuan to Idorsia at Basel for a sceintific talk on the latest progesses of GPCR research.
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Scientific Communications

Scientific Communications Dr. Shuguang Yuan 30, June 2018, Lausanne, Switzerland

Dr. Yuan had an extenstive discussion with both Prof. Jacques Dubochet (the Nobel Prize laureate in Chemistry 2017) and Prof. Horst Vogel on the latest progess of structrual biology as well as how to advance society and economy using sciences.
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Scientific Exchanging

invited talk Dr. Shuguang Yuan 15, June 2018, Heidelberg, Germany

Dr. Yuan has been invited to the Heidelberg University in Germany for a talk. He is going to give a presention on the activation mechanism and drug discovery of GPCRs.
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New publications

Scientific Work Dr. Shuguang Yuan 14, December 2017

Dr. Yuan has found a new catalytic binding site for enzyme CCH which is different from the one observed in the crystal structure. This result was confirmed by subsequent mutagenesis study. Dr. Yuan also captured the substrate entrance pathway and product leaving pathway, using metaMD simulations. A catalytic mechanism was proposed for CCH by Dr. Yuan. This work was published in Nature Communications (doi:10.1038/s41467-017-01508-1) recenntly. Besides that, Dr. Yuan introudced quantum mechanics (QM), as well as molecular dynamics (MD) simulations, to reveal the stereoselectivity of enzyme LEH. A catalytic mechanism was also proposed by Dr. Yuan. This work was published in JACS (doi:10.1021/jacs.7b10278) recently.
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Cold Spring Harbor Conference on membrane protein

invited talk Dr. Shuguang Yuan May 15-19 2017, Suzhou, China

Dr. Yuan has been invited to the Cold Spring Harbor Conference on membrane protein. He will give a talk on a successful story of odorant receptor drug discovery.
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Highlighted work

Scientific news Dr. Shuguang Yuan April 20 2017

Our work on PyMOL and Computer-Aided Drug Discovery (CADD) appeals to a broad scientific audience. It has been highlighted in the Wiley Advanced Science News.
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A cover story is selected by the WIREs Computational Molecular Science

Publication Dr. Shuguang Yuan Feb 2017,Wiley Online Library

The publication (doi:10.1002/wcms.1298) entitled "Using PyMOL as a platform for computational drug design" has been selected as a cover story (doi:10.1002/wcms.1303)for WIREs Computational Molecular Science. It would be published online in February, 2017
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The 4th annual Shanghai iHuman Forum

invited talk Dr. Shuguang Yuan 5-6 November 2016, Shanghai, China

Dr. Shuguang Yuan is invited by Prof. Raymond C Stevens to the 4th anuual Shanghai iHuman Forum. He will deliver a talk on the "Principle of GPCRs ligand specificities"
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A gating mechanism of the 5HT3 ligand-gated ion channel

Publication Dr. Shuguang Yuan 3 May 2016

Our recent work on illuminating the activation mechanism of the 5HT3 serotonin ligand-gated ion channel has been published in Structure (doi:10.1016/j.str.2016.03.019). Congratuations to all contributors.
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GPCRs Activation

GPCR signalling

Protein-ligand interaction

Rational drug design

Enzyme catalysis