About

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".

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.

Our team

Research associate professors

Nicole Holzmann

I received my PhD in Theoretical Chemistry from the Philipps-Universität Marburg, Germany. Then I worked as a Postdoc for the CNRS at the Université de Lorraine (France) and as a Computational Scientist at the STFC (UK). My research comprises various areas of computational life sciences including classical and ab initio MD simulations, DFT/TD-DFT calculations as well as bonding analyses.

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.

Ashish Kumar Agrahari

I completed my PhD in computational biology from VIT University Vellore, India. During my PhD I performed In-Silico SNP prediction, molecular docking and molecular dynamic simulations of cytoplasmic as well as membrane proteins to unveil the biological information at molecular levels. Yet at the same time I want to explore more in this field. My hobbies include gym, badminton and travelling.

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.

Adnane Aouidate

I received my Ph.D in computer-aided drug design from Moulay Ismail University, Meknes, Morocco in 2019. During my Ph.D I have applied 2D and 3D-QSAR studies, molecular docking and in silico ADMET prediction to design new bioactive molecules. In my free time I enjoy running, playing basketball and listening to music.

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.

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.

WenQiang Cui

I am currently a master student in Northeast Agricultural University. I am a visiting student at Prof. Yuan's group. My research interests are molecular simulation and deep learning. I like playing basketball and watching movies in my free time.

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

2019
(41) 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)

(40) 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)

(39) 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)

(38) 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)

(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

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.
read more

Cold Spring Harbor Conference on membrane protein

invited talk Dr. Shuguang Yuan 6-10 May 2019, Suzhou, China

Dr. Yuan has been invited to the Cold Spring Harbor Conference on membrane protein. He will give a talk about exploring a new ligand binding site of GPCRs.
read more

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 into 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.
read more

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.
read more

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.
read more

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.
read more

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.
read more

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.
read more

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.
read more

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.
read more

Highlighted work

Scientific Work Dr. Shuguang Yuan 20 April 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
read more

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"
read more

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.
read more

GPCRs Activation

GPCR signalling

Protein-ligand interaction

Rational drug design

Enzyme catalysis