• GPCR activation mechanism
  • GPCR signalling
  • Protein-ligand interactions
  • computer-aided drug design
  • Enzyme catalysis

About

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Academic Experiences

Prof. 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, Prof. 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. Prof. Yuan worked at Idorsia (previously known as Actelion) Pharmaceutical Ltd in Basel as a specialist in computer-aided drug design (CADD) for 5 years. 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. In 2019, Prof. Yuan was offered a full professor position by the Shenzhen Institute of Advanced Technology, Chinese Academy of Science. He is also the director of the "Research Center for Computer-aided Drug Discovery".

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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.

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Our team


Secretary

MingYing Chen

I obtained my Postgraduate Diploma Diploma from Swiss Hotel Management School in Switzerland. Then I worked as an assistant accountant in West Palm Beach, USA for 2 years. After that, I went back to China and worked as the general manager assistant for one year. I enjoy hiking, music, movie and gym.




Postdocs

RongFeng Zou

I obtained my Ph.D degree at KTH Royal Institute of Technology, Sweden. My research interests are focused on the computational studies of biomolecular systems using enhanced sampling methods. I am also interested in developing novel methods for modern drug discovery. I like cooking and traveling in leisure time.




Shu Li

I completed my Ph.D. in Computational Biology and Biophysics at Peking University. During my graduate study, I employed molecular dynamics simulations to investigate the functional dynamics of membrane proteins and developed the coarse-grained force field. My research interests is to study the protein-protein interactions as well as the structures and dynamics of proteins.


XueYing Wang

I obtained my Ph.D degree in chemical genomics from Peking University in 2019. My research interests are focused on medicinal chemistry and computer-aided drug discovery. I also like art and music in my free time.





MuPeng Luo

I received my Ph.D. degree in Organic Chemistry at Shanghai Advanced Research Institute , Chinese Academy of Sciences. My research interests are mainly focused on the rational design of enzymes and their application in drug discovery and fine chemicals industry. In my leisure time, I like listening to music, reading, fishing and running.




LiuQing Chen

I obtained my Ph.D. degree from the Shanghai JiaoTong University. My research is mainly focused on the crystal structure analysis of enzyme used in synthetic biology. My research interest is to combine structural and computational information for the rational engineering of proteins. I like fitness and running.




Yang Yang

I received my PhD in computer-aided drug design from Shanghai Institute of Materia Medica, Chinese Academy of Sciences. Then I worked as a postdoc at Scripps Research Institute in California. I am enthusiastic about data science and drug discovery research. I am also into traveling and reading for leisure.




Haojie Guo

I obtained my Ph.D degree at Shanghai Institute of Applied Physics, Chinese Academy of Sciences. During my PhD, my research direction was macromolecular crystallography. My research interests are focused on structure and function of membrane proteins, and computer-aided drug discovery. I like playing basketball in my leisure time.




PhD Students

WenQiang Cui

I am a PhD student at SIAT, majoring in chemical biology. My research interests are network pharmacology, molecular dynamics simulation and drug design. In my spare time, I like doing sports and watching movies.





Graduate Students

Bing Bai

I am studying for a master's degree in computer science at SIAT. My research interests are the application of artificial intelligence in drug discovery, including machine learning, deep learning and so on. My hobby is playing basketball.





YuanYuan Hou

I am studying at SIAT as a postgraduate, majoring in computer technology.I have a strong interest in deep learning and data mining, and I hope to continue my research in the field of computational biology. In my free time, I like assembling toys, computers and home appliances. I like jogging as well.





ShiYu Wang

I am a postgraduate student in CADD center, majoring in chemistry. My research interests are deep learning for drug discovery, such as QSAR and molecular generation. I like watching movies and riding bikes in my spare time.





He Yang

I'm pursuing for my master's degree in SIAT since I graduated from Sun Yat-Sen University in summer of 2020. My research insterests is computer aided drug design (CADD), and my hobbies are basketball and jogging.





Undergraduate Students

YinZhen Chen

I come from JiNan University in Guangzhou. I am an exchange student in SIAT. My major is Biology and I am interested in Bioinformatics and Computational Biology. I like running and playing mobile games.




Publications

* corresponding authors #joint first authors

2020
(47) Chan S.#, Wu Y.#, Tan L.#, Vogel H. Cheng J.*, Wu D.*, Yuan S.*, Enhancing the Signaling of GPCRs via Orthosteric Ions. ACS Central Science (2020). (doi:10.1021/acscentsci.9b01247)

(46) Liu K., Wu L., Yuan S., et. al, Structural basis of CXC chemokine receptor 2 activation and signalling. Nature (2020). (doi:10.1038/s41586-020-2492-5)

(45) Hua T., Li X., et. al, Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-Gi Complex Structures. Cell (2020). (doi:10.1016/j.cell.2020.01.008)

(44) Cui W., Aouidate A., Wang S., Yu Q., Li Y., Yuan S.*, Discovering anti-cancer drugs via computational methods. Frontiers in Pharmacology (2020). (doi:10.3389/fphar.2020.00733)

(43) Dong Q.#, Yuan S.#, Wu L.#, et.al , Structure‑guided engineering of a Thermobifida fusca cutinase for enhanced hydrolysis on natural polyester substrate. Bioresources and Bioprocessing (2020). (doi:10.1186/s40643-020-00324-8)


2019
(42) Chan S., Shan H., Dahoun T., Vogel H., Yuan S.*, Advancing Drug Discovery via Artificial Intelligence. Trends in Pharmacological Sciences (2019). (doi:10.1016/j.tips.2019.06.004)

(41) 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)

(40) Liu L, Chan S, Mo T, Ding W, Yu S., Zhang Q.*, Yuan S.*, Movements of the Substrate-Binding Clamp of Cypemycin Decarboxylase CypD. Journal of Chemical Information and Modeling (2019). (doi:10.1021/acs.jcim.9b00156)

(39) Yuan S.*, Dahoun T., Brugarolas M., Pick H., Filipek S., Vogel H.*, Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds, Communications Biology (2019). (doi:10.1038/s42003-019-0384-8)

(38) Chen X., Xu Y., Qu L., et al, Molecular Mechanism for Ligand Recognition and Subtype Selectivity of α2C Adrenergic Receptor. Cell Reports (2019). (doi:10.1016/j.celrep.2019.10.112)

(37) Zheng L., Falschlunger C., Huang K, Mairhofer E, Yuan S, et. al. Hatchet ribozyme structure and implications for cleavage mechanism. Proc Natl Acad Sci USA (2019). (10.1073/pnas.1902413116)


2018
(36) WIPO 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)

(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)

(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)

(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)

(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)

(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)

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)

(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)

(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)

(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)

(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)

(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)

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)

(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)

(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)

(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)

(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)

(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)

(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 )


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)

(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)

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)

(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)

(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)

(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)

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)

(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)

(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 )

(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 )

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)

(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)

(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)

(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)

(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) 

News

sofos

Uncover the molecular mechanism of CXCR2

Scientific Work    Shuguang Yuan    2 July 2020   

Chemokines and their receptors mediate cell migration, which influences multiple fundamental biological processes and disease conditions, such as inflammation and cancer. Our team has successfully illuminated the molecular mechanism of CXCR2 binding to its endogenous ligand IL8 peptide. CXCR2 has been considered to play an essential role in different oncology pathway and our findings provided new insights into cancer drug discovery. This work has been published in Nature recently.

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sofos

Computational pharmacy identified anti-2019-nCoV virus drug candiates

Anti-2019-nCoV drug discovery    Dr. Shuguang Yuan    26 January 2020   

Our team has identified several potential anti-2019-nCoV drug candiates via computational pharmacy. We have computatinally screened 2400+ FDA and othere resource approved drugs as well as 6700+ nature products from Chinese medicines. Finally, several drug molecules were identified. We are actively working on both biochemical experiments as well as clinical studies.

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ACS Central Science

Explore a completely new drug binding mode for GPCR

Scientific progress    Dr. Shuguang Yuan    23 January 2020   

Our team has found a completely new binding mode for GPCR drugs recently. In this work, it is the first time that Orthosteric metal ions were identified to coordinate with both drug molecules and GPCRs. Our computational predictions were vailidated by crystal structures, biochemical mutations as well as organic synthesis. This work has been published in ACS Central Science which is entitled "Enhancing the Signaling of GPCRs via Orthosteric Ions".

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Merry Christmas and Happy New Year

Merry Christmas and Happy New Year

New Year Wishes    Dr. Shuguang Yuan    24 December 2019   

Joyeux Noel et Bonne Année.

Merry Christmas and Happy New Year.

Fröhliche Weihnachten und ein Glückliches Neues Jahr.

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China HighTech Fair 2019

collaboration with HuaWei    Dr. Shuguang Yuan    13-17 November 2019   

Our team presented our recent achievements in the China HighTech Fair 2019. We also established a joined project with HuaWei Cloud Computing which was also demonstrated in this event. Our project, which was entitled "A complete workflow for computational drug discovery", obtained the "Excellent Product" award.
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From computational molecular basis of GPCR to modern drug discovery

Invited talk    Dr. Shuguang Yuan    10-12 November 2019   

Prof. Shuguang Yuan was invited to give a talk in recent conference "From free energy pertubation to biomedicine: bridging experiment and computation". The tile of his talk was "From computational molecular basis of GPCR to modern drug discovery".
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Welcome Prof. Horst Vogel to join our team

New member    Dr. Shuguang Yuan    10 November 2019   

Prof. Horst Vogel joined our team as a full-time "Chief Scientst". Prof. Vogel will focus on membrane protein related biotechnology innovation as well as modern drug discovery.
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Advancing Drug Discovery via Artificial Intelligence

Scientific work    Dr. Shuguang Yuan    15 July 2019   

Our work, which is entitled "Advancing Drug Discovery via Artificial Intelligence", has been published in Trends in Pharmacological Sciences. In this work, we depicted how to use AI to advance modern drug discovery during the preclinical stage.
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Contact

  1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, China
   yuanshg"AT"gpcrm.org
   Website: www.gpcrm.org

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