General

Shuguang Yuan, Full professor, Shenzhen Institutes of Advanced Technology, Chinse Academy of Science

Email: shuguang.yuan@siat.ac.cn

Research Keywords

• Computational biology

• Cell signalling 

• Artificial intelligence 

• Modern drug discovery

• Molecular simulations 

• Rational protein design  


Education

EPFL, Switzerland

09.2012 – 06.2013 PhD, computational biology


Polish Academy of Science, Poland

05.2011– 08.2012 PhD, computational biology


KULeuven University, Belgium

10.2009– 05.2011 PhD, computational biology


Shanghai Institute of Organic Chemistry, CAS, China

09.2005 – 03.2009 Master, structural and computational biology


Taiyuan University of Science and Technology, China 

09.2000 – 07.2004 Bachelor, Material science


Experience

   
Work Experience

Shenzhen Institutes of Advanced Technology, Chinse Academy of Science

02.2019-present director of computer-aided drug discovery, full professor

 

University of Warsaw, Poland

04.2018 – present Affiliated professor, computational biology

 

Actelion/Idorsia Pharmaceutical Ltd, Switzerland

03.2014 – present Expert in computational biology

 

EPFL, Switzerland

07.2013 – 03.2014 Postdoc, computational biology


Teaching Experience

05.2017 – present University of Warsaw, “Applying computational methods to modern drug discovery”

 

06.2014 – present Actelion/Idorsia Pharmaceutical Ltd, “computational supports of drug lead optimization”

 

08.2016 Fachhochschule Nordwestschweiz (FHNW), “The first step of Chinese”

 

01.2016 – 08.2016 Actelion/Idorsia Pharmaceutical Ltd, “Rational drug discovery through Web browsers”

 

03.2012 – 08.2012 University of Warsaw, “The principle of computational biology”

 

10.2010 – 03.2011 KULeuven University, “Molecular simulations of protein systems”


Publications

   
Papers

2020
(44) 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)

(43) 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)


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) 

Patents

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)


Monograph

Latek D., et al, Yuan S., Filipek, S., Modeling of Membrane Proteins, Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes doi: 10.1007/978-3-642-28554-7_12 (2014). 357-431


Latek D., et al, Yuan S., Filipek, S., Modeling of Membrane Proteins: From Bioinformatics to Molecular Quantum Mechanics, Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes doi: 10.1007/978-3-319-95843-9_12 (2019)    


Research Interests

Computer-Aided Drug Discovery

Artificial Intelligence 

Computational Biology

Conferences

05.2019 Cold Spring Harbor Aisa, Suzhou, China

Membrane Proteins: Structure & Function


10.2018 Tsinghua University, Shenzhen, China

Computational methods in modern drug discovery

 

06.2018 University Heidelberg, Heidelberg, Germany

The activation mechanism and drug discovery of G protein-coupled receptors

 

04.2018 CompAllo: Towards a Unified Approach to the Analysis and Design of Allostery, CECAM workshop, Lausanne, Switzerland

The activation mechanism and drug discovery of G protein-coupled receptors

 

03.2018 Multiscale modelling in electrophysiology: from atoms to organs, CECAM workshop, Lugano, Switzerland

The activation mechanism of G protein-coupled receptors signalling

 

12.2017 The Shanghai Institute of Materia Medica (SIMM), CAS, Shanghai, China; The Shanghai Institute of Plant Physiology & Ecology (SIPP), CAS, Shanghai, China; The ShanghaiTech University, CAS, Shanghai, China; Zhejiang University, Hangzhou, China; The Tianjin Institute of Industrial Biotechnology (TIB), CAS, Tianjin, China

Applying computational biology to basic research and modern drug discovery

 

11.2017 The 5th iHuman Forum, Shanghai, China

The ligand stereo selectivity of G protein-coupled receptors – a point from view from computational biology

 

09.2017 European Synthetic Cellular Signaling Circuits, Bristol, UK

Applying computational methods to modern drug discovery

 

05.2017 Membrane Protein and Function, the Cold Spring Harbor Asian Conference, Suzhou, China

Computational biology in GPCR mechanistic study and drug discovery

 

05.2017 The Peking University; Nankai University, China

From lead to clinic drug: the power of computational biology


Students

现指导学生

白冰  硕士研究生  085211-计算机技术  

崔文强  博士研究生  0703Z1-化学生物学  

王世玉  硕士研究生  070300-化学  

杨合  硕士研究生  085600-材料与化工  

陈亭利  硕士研究生  086000-生物与医药  

侯园园  硕士研究生  085211-计算机技术  

Honors & Distinctions


Grants

10.2018   Main applicant, Anton2 the specialized Supercomputer, USA National Research Council (peer reviewed)

 

10.2017     Main applicant, Polish National Supercomputer Center (peer reviewed)

 

10.2016     Main applicant, Polish National Supercomputer Center, Polish National Supercomputer Center (peer reviewed)

 

11.2015    Main applicant, Anton the specialized Supercomputer, USA National Research Council (peer reviewed)

 

10.2013     Main applicant, European Union Council and ETH        Marie Curie ETH postdoc fellowship (peer reviewed)     

 

01.2013     Co-applicant, European Union Council FP7 Frame Synthetic Cellular Signaling Circuits research project grant (peer reviewed)

 

11.2012     Main applicant, Anton the specialized Supercomputer, USA National Research Council (peer reviewed)


Membership

04.2016 – present editorial board, “Journal of Bioinformatics, Computational and Systems Biology”

 

01.2015 – present reviewer board, “Angewandte Chemie”, “Nature Communications”, “Communications Biology”, “ChemMedChem”, “Scientific Reports”, “Current Protein and Peptide Science”, “Computational Biology and Chemistry”, “Journal of Bioinformatics, Computational and Systems Biology”, “Chemometrics and Intelligent Laboratory Systems”, “Computational and Structural Biotechnology Journal”

 

09.2015 – present membership, American Chemical Society

 

06.2013 – present membership, Swiss Chemical Society

 

05.2011 – present life time membership, Marie Curie Association