Yibo Wang, Ph.D.Assistant Professor
Drug Discovery & Chemical Biology Group, Chemical Biology Laboratory
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
5625 Renmin Street, Changchun, China, 130022
Phone: +86-431-85262240                          
E-mail: yibo.wang@ciac.ac.cn		    

——————————————————————————————————————————————————————————————————————————-

Funding Support

1. Role: PI
    Time Period: Jan 1, 2019 – Dec 31, 2021
    Amount: RMB￥275, 000.00
    Granting Agency: National Natural Science Foundation of China
    Title: Role of glycosylation in dsRNA recognition of TLR3 via molecular dynamics simulation

2. Role: PI
    Time Period: Jan 1, 2019 – Dec 31, 2021
    Amount: RMB￥300, 000.00
    Granting Agency: Changchun Institute of Applied Sciences, Chinese Academy of Sciences
    Title: Fund for member of Youth Innovation Promotion Association of CIAC

3. Role: PI
    Time Period: Dec 1, 2018 – Dec 31, 2019
    Amount: RMB￥50, 000.00
    Granting Agency: Open Funds of State Key Laboratory of Oncology in South China
    Title: The discovery of peptide inhibitors for the transmembrane domain oligomerization of Epstein–Barr virus latent membrane protein 1(LMP-1)

Work Experience

  • Committee Member of the Jilin Pharmaceutical Association (Specialty: Pharmacology)                                                                 2018-
  • Assistant Professor, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences (Collaborator: Dr. Xiaohui Wang), Changchun, Jilin, China                                                                                                                                                                                                                                                                         2017-
  • Post-Doc, Icahn School of Medicine at Mount Sinai (Advisor: Dr. Marta Filizola), New York, NY, US                                             2016−2017

Academic Background

  • Ph.D., Biochemistry, University of Calgary (Advisor: Dr. Sergei Noskov), Calgary, Alberta, Canada                                              2011−2016

       Dissertation: Molecular Mechanisms of Ion and Solute Interactions with Voltage-Gated Ion Channels (04/2016)

  • Graduate Student, Physical Chemistry, Jilin University (Advisor: Dr. Xu-ri Huang), Changchun, Jilin, China                                   2008–2011
  • B.S., Material Chemistry, Jilin University, Changchun, Jilin, China                                                                                                         2004−2008

Expertise

  • Extensive experience in using and modifying MD simulation software products to study properties of molecules of biological and pharmaceutical relevance;
  • Kinetic analysis via Markov State Model;
  • Force-field development and applications (additive and polarizable force-fields);
  • Free energy simulations of protein-ligand recognition;
  • Homology modeling;
  • Molecular drug design and binding site prediction;
  • Efficiently setting up and running massively parallel simulations on various platforms (CPU/GPU);
  • Data handing and analysis by programming;
  • Excellent teamwork skills with experimental and theoretical researchers.

Research Projects

  • Post-Doc Study – Icahn School of Medicine at Mount Sinai, New York, USA(advisor: Dr. Marta Filizola)                                         2016-2017

       The role of sodium ion regulating the G protein-coupled receptors (GPCRs) was studied using enhanced sampling methods and Markov State Model analysis.

  • Ph.D. Study – University of Calgary, Canada(advisor: Dr. Sergei Noskov)                                                                                            2011-2016

Selectivity Study of Ion Channels with Additive and Polarizable Force Fields:

Ion channels are membrane proteins to control ion transport across the cell membrane. I performed free energy perturbation and potential of mean force calculations with massively parallel simulations (~2000 simulations per system) on BlueGene and other high performance computing platforms, by rebuilding the single- or multi-dimensional free energy profiles, to unveil mechanisms of ion channels distinguishing ionic species.

Antiarrhythmic or Antifungal Molecule Design and Interaction Study with Human Ion Channels:

Many antiarrhythmic agents used for maintenance of sinus rhythm or antifungal drugs can block human potassium channels and cause serious side effects like fainting or sudden death. To optimize current drugs, a database for drug-like molecules was designed based on current drugs with Schrödinger. The binding locations for drugs or drug derivatives were investigated by rigid, flexible and induced fit docking with Schrödinger, Gold and AutoDock. The binding affinities and binding paths to ion channels for a small number of drug candidacies or present drugs were studied based on the potential of mean force calculations. Kinetic information was also estimated from free energy profiles.

  • M.Sc. Study – Jilin University, China  (advisor: Dr. Xuri Huang)                                                                                                            2008−2011

Pathway Study on Small Molecule Release or Transport:

Small molecules were released from ligand delivery protein or transported by channels following their unique path. The residue-ligand interactions were investigated during the ligand transportation. And a new protocol was designed to reveal the optimum path for drug molecules releasing from a drug-deliver protein.

Awards:

  • Faculty of Graduate Studies Travel Award                                                           03/2016
  • Graduate Research Scholarship                                                                          01/2016
  • Eyes High International Doctoral Scholarship                                                      09/2015
  • Eyes High International Doctoral Scholarship                                                      09/2014
  • Bettina Bahlsen Memorial Graduate Scholarship                                                 09/2014
  • Graeme Bell and Norma Kay Sullivan-Bell Graduate Scholarship                       09/2012
  • National Graduates Scholarship                                                                           09/2010
  • Scholarship for Excellent First-year Graduates                                                    09/2010
  • Excellent Graduate Student Financial Assistance Scholarship                            10/2010
  • National Graduates Scholarship                                                                           09/2009
  • First Prize of Graduate Scholarship                                                                      09/2009

Qualifications and Skills

  • Programming and Scripting Languages: FORTRAN 77, Python, C-shell scripting
  • Software: CHARMM, NAMD, Gromacs, Gaussian, Schrödinger, Gold, AutoDock, PyEMMA.
  • Computational Methodologies
    • Markov State Model build and analysis;
    • Free energies calculation and decomposition of protein-ligand association;
    • Steered molecular dynamics simulation for ligand releasing from protein;
    • Potential of mean force computation by umbrella sampling;
    • Free energy perturbation simulation for protein-ligand binding affinities.

Publications: ($Denotes principal contribution)

  1. Wang, Y.;Finol-Urdaneta, R. K.; French, R. J.; Noskov, S. Y., Bases of sodium channel selectivity among organic cations.Biophysical Journal, 2019, (Revisions requested)
  2. Hu, X.; Wang, Y.; Hunkele, A.; Provasi, D.;Pasternak, G.; Filizola, M.*, Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis PLoS Computational Biology 2019, 15(1): e1006689
  3. Zhang X.; Cui, F.*; Chen, H.; Zhang, T.; Yang, K.; Wang Y.; Jiang Z.; Rice, K.C.; Watkins, L.R.; Hutchinson, M.R.; Li, Y.; Peng, Y. and Wang, X.*, Dissecting the Innate Immune Recognition of Opioid Inactive Isomer (+)-Naltrexone Derived Toll-like Receptor 4 (TLR4) Antagonists. Journal of Chemical Information and Modeling,  2018, 58(4),816-825
  4. Yang, P.; Perissinotti, L.; López-Redondo, F.; Wang, Y.; DeMarco, K.; Jeng, M.; Vorobyov, I; Harvey, R.*; Kurokawa, J.; Noskov, S.*; Clancy, C.*, A multiscale computational modeling approach predicts mechanisms of female sex risk in the setting of arousal-induced arrhythmias. Journal of Physiology (London), 2017, 595(14),4695-4723
  5. Wang, Y.$; Guo, J.$; Perissinotti, L.$; Lees-Miller, J.$; Teng, G.; Durdagi, S.; Duff, H.*; Noskov, S.*, Role of the pH in state-dependent blockade of hERG currents. Scientific Reports, 2016, 6:32536
  6. Ngo, V.; Wang, Y.; Haas, S.; Noskov, S. Y.; Farley, R. A.*, K+ block is the mechanism of functional asymmetry in bacterial Nav channels. PLOS Computational Biology 2016, 12(1): e1004482.
  7. Lees-Miller, J. P$.; Guo, J.$; Wang, Y.; Perissinotti, L. L.; Noskov, S. Y.*; Duff, H. J.*, Ivabradine prolongs phase 3 of cardiac repolarization and blocks the hERG1 (KCNH2) current over a concentration-range overlapping with that required to block HCN4. Journal of Molecular and Cellular Cardiology 2015, 85, 71-78.
  8. Chamberlin, A.$; Qiu, F.$; Wang, Y.$; Noskov, S. Y.*; Larsson, H. P.*, Mapping the gating and permeation pathways in the voltage-gated proton channel Hv1. Journal of Molecular Biology 2015, 427 (1), 131-45.
  9. Wang, Y.$; Chamberlin, A. C.$; Noskov, S. Y.*, Molecular strategies to achieve selective conductance in NaK channel variants. Journal of Physical Chemistry B 2014, 118 (8), 2041-9.
  10. Chamberlin, A.$; Qiu, F.$; Rebolledo, S.; Wang, Y.; Noskov, S. Y.*; Larsson, H. P.*, Hydrophobic plug functions as a gate in voltage-gated proton channels. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 2014, 111 (2), E273-E282.
  11. Finol-Urdaneta, R. K.$; Wang, Y.$; Al-Sabi, A.; Zhao, C. F.; Noskov, S. Y.*; French, R. J.*, Sodium channel selectivity and conduction: Prokaryotes have devised their own molecular strategy. Journal of General Physiology 2014, 143 (2), 157-171.
  12. Feng, X. L.; Zhao, X.; Yu, H.; Wang, Y.; Sun, T. D.; Huang, X. R.*, Molecular Dynamics of an Extremely Thermophilic Ribose Binding Protein. Acta Chim Sinica 2012, 70 (5), 606-610.
  13. Wang, Y.; Zhao, X.; Sun, B. L.; Yu, H.; Huang, X. R.*, Molecular dynamics simulation study of the vanillate transport channel of Opdk. Archives of Biochemistry and Biophysics 2012, 524 (2), 132-139.
  14. Wang, Y.; Zhao, X.*; Yu, H.; Huang, X. R.*, Releasing of the chromophore from the drug delivery protein C-1027: A molecular dynamics simulations study. Journal of Structural Biology 2010, 172 (3), 284-293.

Selected Presentations:

  • Talk:Yibo Wang, Na+ channel Study with Polarizable Force Field. The 7th Kananaskis Symposium on Molecular Simulation, Kananaskis, Canada  02/2016
  • Poster: Yibo Wang, Laura Perissinotti, Jiqing Guo, Henry Duff, Sergei Noskov, Molecular Origins of State-dependent hERG1 Blockade by Dofetilide. The 59th BPS Annual Meeting, Baltimore, USA   02/2015
  • Poster: Yibo Wang, Adam Chamberlin, Chunfeng Zhao, Sergei Noskov, Strategies to Achieve Selective Conductance in K- and Na- Selective Ion Channels. The 58th BPS Annual Meeting, San Francisco, USA  02/2014
  • Talk:Yibo Wang, Molecular Dynamics Study of hERG Blockers. The 5th Kananaskis Symposium on Molecular Simulation, Kananaskis, Canada  02/2014
  • Invited Talk: Yibo Wang, Study of Three Typical Ion Channels via Molecular Dynamics. Telluride Workshop: Biophysics of ion Channels, Telluride, USA  07/2013
  • Talk:Yibo Wang, Molecular Mechanism Study of Mutant NaK Channels. The 4th Kananaskis Symposium on Molecular Simulation, Kananaskis, Canada  01/2013
  • Poster:Yibo Wang, Chunfeng Zhao, Rocio Finol-Urdaneta, Sergei Noskov, Robert French, Functional Study of the Sodium Ion Channel Permeation with Molecular Simulations. CSHAsia 2012 Conference, Suzhou, China  09/2012
  • Invited Talk: Drug discovery Targeting Transmembrane Protein-protein Interactions. Moscow，Russia  08/2019

Journal Reviewer:

Current Medicinal Chemistry, Biophysical Journal, BMC Pharmacology and Toxicology, PLOS Computational Biology, Current Topics in Membranes, Journal of Molecular Modeling, Journal of Biomolecular Structure & Dynamics, Journal of Theoretical and Computational Chemistry

Teaching Experience:

  • BCEM 553: Molecular Biophysics (Dr. Sergei Noskov)                                        2015
  • BCEM 577: Biomolecular Simulation (Dr. Peter Tieleman)                                  2014