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Yun Lyna Luo, PhD

Yun Lyna Luo, PhD

Associate Professor, Biotechnology and Pharmaceutical Sciences

College of Pharmacy

luoy@westernu.edu

Phone: (909) 469-8377 | Fax: (909) 469-5600

Website: https://sites.google.com/site/lynayunluo/

Join year: 2013 Aug

  • Education
    • Postdoc, Argonne National Laboratory, US 2011-2013
    • Postdoc, University of Chicago, US 2008-2011
    • Ph.D. Ecole Normale Supérieure, University of Paris VI, France 2004-2007
    • BS. MS. Zhejiang University, China 1997-2004
  • Courses

    · Molecular Simulation and Drug Design, 3 Credit Hours

    · Pharmacological Basis of Therapeutics I-IV (Medicinal Chemistry topics), 48 Lecture hours/year

    · Advanced Pharmaceutical Sciences II (Drug Metabolism, Acid-base Chemistry, Drug Design topics), 12 Lecture hours/year

    · Graduate Seminar, 2 Credit Hours, Facilitator

    · Interprofessional Practice & Education, Facilitator

  • Research Interest

    As a computational chemistry/biophysics research group, we investigate the structural dynamics of complex biomolecules and conduct mechanism-based drug design.

    The ongoing projects are:

    Mechanical and chemical gating of mechanosensitive Piezo channels;

    Gating and molecular permeation of connexin hemichannels;

    Gating mechanism of HCN channels;

    Computational method for reversible covalent drug design;

    Computational method for protein allosteric network analysis;

  • Research Grant

    Research Grants (active)

    NIH R01GM130834 (PI, WesternU) 09/2019-05/2028

    Mechanisms of mechanical and chemical gating in mechanosensitive piezo1 channels

    NIH R01GM139164 (co-I, U Miami) 05/2021-05/2024

    Activation mechanism in HCN channels

    NIH R01 (co-I, UC Davis) 04/2022-03/2027

    Gating and regulation of connexin hemichannels

    NIH R01 (co-I, City of Hope) 09/2023-08/2028

    Targeting protein arginine methyltransferase to eradicate acute myeloid leukemia

    NIH R61-R33 (co-I, Yale University) 11/2023-10/2027

    Targeting the sperm-specific calcium channel CatSper for contraception

    Tower Cancer Research Foundation(co-I, City of Hope) 01/2023-12/2027

    A Novel Approach to Elicit Anti-tumor Immunity Against Acute Myeloid Leukemia

  • Awards

    Invited Talks (since 2013)

    1. Mar 2024 Ligand Recognition and Molecular Gating, Gordon Research Conference, Ventura, CA

    2. Mar 2024 Symposium of Modeling Molecular Recognition, ACS National Meeting, New Orleans, LA

    3. Nov 2023 Department of Anesthesiology, Washington University, St. Louis, MO

    4. Oct 2023 Department of Physiology and Membrane Biology, UC Davis, Davis, CA

    5. May 2023 Computer-Aided Drug Design Symposium, University of Maryland, Baltimore, MD

    6. Apr 2023 Distinguished Lecture Series in Physiology, UC Davis, Davis, CA

    7. Mar 2023 Molecular Mechanics session, ACS National Meeting, Indianapolis, IN

    8. Mar 2023 Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI

    9. Feb 2023 Biophysical Society Annual Meeting, San Diego, SD

    10. Jan 2023 Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Huston, TX

    11. Aug 2022 ACS Award Symposium for Computers in Chemical & Pharmaceutical Research, Chicago, IL

    12. Jul 2022 ISQBP President’s meeting, Innsbruck, Austria (virtual)

    13. May 2022 Ion channels and transporters: From molecule to human, EMBO|FEBS Lecture course, Erice, Italy

    14. Apr 2022 Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MS

    15. Aug 2021 Molecular Mechanics session, ACS National Meeting (virtual)

    16. Jun 2021 Workshop on Free Energy Methods in Drug Design (virtual)

    17. Apr 2021 ACS Spring National Meeting (virtual)

    18. Jan 2020 Department of Biochemistry and Biophysics, U Pennsylvania, Philadelphia, PA

    19. Jan 2020 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA

    20. Jan 2020 Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX

    21. Aug 2019 Recent Advances in Kinase Drug Discovery Symposium, ACS National Meeting, San Diego, CA.

    22. Mar 2019 Biophysical Society Annual Meeting, Membrane Transport Subgroup, Boston, MS.

    23. Aug 2018 ACS National Meeting, Boston, MS.

    24. Jun 2018 Worldwide Chinese Computational Biology and Molecular Simulation Conference, Guangzhou, China

    25. Jun 2018 Westlake Institute for Advanced Study, Hangzhou, China

    26. Oct 2017 Department of Pharmacology, Physiology and Neuroscience,Rutgers, Newark, NJ

    27. Jun 2017 CECAM workshop, Lausanne, Switzerland

    28. May 2017 Southern California Theoretical Chemistry Symposium, Irvine, CA

    29. Dec 2016 School of Pharmacy, Xiamen University, China

    30. June 2016 Canadian Chemistry Conference, Halifax, Canada

    31. July 2015 School of Pharmacy, Zhejiang University, China

    32. Mar. 2015 ACS National Meeting, Denver, CO

    33. Feb 2015 Rutgers, New Jersey Medical School, Newark, NJ

    34. Aug 2014 Telluride Science Research Center Molecular Recognition Workshop, Telluride, CO

    35. Apr 2014 Big Bang Science Club, Western University of Health Sciences, Pomona, CA

    36. Mar 2013 Department of Chemistry, University of Texas-Pan American, Edinburg, TX

    37. Mar 2013 ACS National Meeting, New Orleans, LA

    38. Feb 2013 Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ

    39. Jan 2013 Department of Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA

    40. Jan 2013 Department of Chemistry, Illinois Institute of Technology, Chicago, IL

  • Organizations

    Editorial Board Member: Communications Biology -Nature(since 2022)

    Guest Editor:Nature Commun & Commun BiologyJoint Collection

    "Methods and Applications in Multiscale Structure Biology" (2023-2024)

    Guest Editor: J Computational Chemistry, "Membrane Protein Simulations and Free Energy Approaches" (2020)

    Member of

    Biophysical Society (BPS)

    BPS Membrane Transport Subgroup (Chair-elect 2023)

    American Chemical Society (ACS)

    ACS Division of Computers in Chemistry (Programing committee 2022)

    International Society of Quantum Biology and Pharmacology (ISQBP) (Councilor-elect 2023)

    Biophysics Colab (Outreach taskforce 2022)

    Society of General Physiologists (SGP)

    American Association for the Advancement of Science (AAAS)

    American Association of Colleges of Pharmacy (AACP)

    Chinese American Faculty Association (CAFA) Southern California (President-elect 2020)

    Meeting Organizer of

    American Chemical Society Spring Annual Meeting, Molecular Mechanics Sessions, Indianapolis, Mar, 2023

    67th Biophysical Society Annual Meeting, Membrane Transport Subgroup Symposium, San Diego, Feb, 2023

    67th Biophysical Society Annual Meeting, Mechanosensitive Membrane Protein Platform, San Diego, Feb, 2023

    66th Biophysical Society Annual Meeting, Membrane Transport Subgroup Symposium, San Francisco, Feb, 2022

    Membrane Protein Simulations and Free Energy Approaches, ACS, Boston, Aug, 2018

    Computational Methods to Address Challenges in Drug Discovery, CECAM Workshop, Lausanne, June, 2017

    Journal Reviewer of

    Nature Communications; Science Advances, eLife; Communication Biology; PNAS, Biophysical Journal; Journal of the American Chemical Society (JACS); Journal of Chemical Theory and Computation (JCTC); Journal of General Physiology (JGP); Journal of Chemical Information and Modeling (JCIM); The Journal of Physical Chemistry B (JPCB).; Journal of Medicinal Chemistry (JMC); The Journal of Chemical Physics (JCP), Journal of Computational Chemistry (JCC); Trends in Biochemical Sciences; PROTEINS: Structure, Function, and Bioinformatics; BBA – Biomembrane;, Scientific Reports; Current Opinion in Structural Biology; European Journal of Medicinal Chemistry; Bioorganic & Medicinal Chemistry Letters; ACS Omega; International Journal of Molecular Science;, Journal of Molecular Graphics and Modeling; Computational Biology and Chemistry; PLOS One; PeerJ; Frontiers Oncology, Computational Biology and Chemistry; Journal of Biomolecular Structure & Dynamics

    Grant Proposal Reviewer of

    NIH Macromolecular Structure and Function B Study Section - MSFB

    ACS Petroleum Research Fund

    AACP New Investigator Award Grants

    Centre Européen de Calcul Atomique et Moléculaire (CECAM) Workshop Proposals

    Natural Sciences and Engineering Research Council (NSERC) of Canada Discovery Grants

  • Committees

    College Reward and Recognition Committee (chair 2016-2017)

    College Student Performance Committee (chair 2019-2020)

    College Tenure and Promotion Committee (chair 2023-2024)

    Vice chair of Department of Pharmaceutical Sciences (2018-2019)

    University Awards Committee

    College Curriculum Committee

    College Faculty Secretary

    College Peer Evaluation Committee

    Master of Science in Pharmaceutical Sciences (MSPS) Admission Committee

    MSPS Graduate Program Committee

    MSPS Self-Study Committee

  • Publications

    Editorials

    1. Reliability and Reproducibility Checklist for Molecular Dynamics Simulations, Commun Biol2023, 6,268.

    2. Im, W., Banavali, N., Luo, Y., Celebrating Benoit Roux's 60th Birthday: Quantifying Biology at the Membrane. J Comput Chem 2020, 41, 385-386

    Invited viewpoint

    3. Luo, Y., Mechanism-Based and Computational-Driven Covalent Drug Design. J Chem Inf Model 2021, 61, 5307-5311

    Book Chapters

    4. Delemotte, L & Luo, Y.,Molecular Dynamics. Handbook ofIon channels, 2nd Edition.

    5. Luo, Y., Lacroix, J., Ion Channels in Biophysics and Physiology:Methods & Challenges to Study Mechanosensitive Ion Channels. Adv Exp Med Biol 2021, 1349, 33-49.

    6. Botello-Smith, W., Luo, Y., Concepts, Practices, and InteractiveTutorial forAllosteric Network Analysis of Molecular Dynamics Simulations. Methods Mol Biol 2021, 2302, 311-334.

    7. Luo, Y., Lacroix, J., Prabhu, S., Antibody-Drug Conjugates: The 21st Century Magic Bullets for Cancer, Section V Case Studies, Chapter 12: Ado-Trastuzumab Emtansine, Springer, 2015.

    Patent

    8. Inhibitors of protein arginine methyltransferase 9 and uses thereof, U.S. Patent Application No. 63/378,798

    9. Isoform-specific calpain inhibitors, methods of identification, and use thereof, U.S. Patent 20190030114

    10. Calpain-2 selective inhibitor compounds for treatment of glaucoma, U.S. Patent 20210179543

    Preprints and Peer-reviewed articles (corresponding *)

    11. Wen, C., Luo, Y.*, Madsen, J.*, Optimizing coarse-grained models for large-scale membrane protein simulations, doi.org/10.1101/2024.05.13.594009

    12. Lin, Y., Wijerathne, T., Bhatt, A., Jiang, W., Sterling J., Lacroix, J.*, Luo, Y.*, Minimal mechanism for current rectification through ion channels, bioRxiv.

    13. Li, S.*, Wu, B., Luo, Y., Han, W.*, Simulation of functional motion of super large biomolecules with a mixed-resolution model, J. Chem. Theory Comput., 2024

    14. Dong, H., et. al., Luo, Y., Ling, L.*, Targeting PRMT9 mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anti-cancer immunity, Nature Cancer, 2024

    15. Baudry, M., Wang, Y., Bi, X., Luo, Y.,et al., Identification and neuroprotective properties of NA-184, a calpain-2 inhibitor, Pharmacology Research & Perspectives, 2024

    16. Jiang, W., Wijerathne, T., Zhang, H., Lin, Y., Jo, S., Im, W., Lacroix, J., Luo, Y.*, Structural and thermodynamic framework for PIEZO1 modulation by small molecules, PNAS, 120, e2310933120, 2023

    17. Baudry, M., Luo, Y., Bi, X., Calpain-2 inhibitors as therapy for traumatic brain injury, Neurotherapeutics, 20, 1592-1602, 2023

    18. Jiang, W.*, Lacroix, J, Luo, Y.*, Importance of molecular dynamics equilibrium protocol on protein-lipid interaction near channel pore, Biophysical Reports, 2, 100080, 2022

    19. Lin, Y., Luo, Y.*, Unifying Single-channel permeability from rare-event sampling and steady-state flux, Frontiers in Molecular Biosciences: Biological Modeling and Simulation, 2022

    20. Jiang, W., Del Rosario, J.S., Botello-Smith, W., Zhao, S., Lin, Y., Zhang, Han., Lacroix, J.*, Rohacs, T.*, Luo, Y.*, Crowding-induced opening of the mechanosensitive Piezo1 channel in silico. Commun. Biol. 4, 84, 2021

    21. Jiang, W., Ling, Y., Luo, Y.*, Mechanical properties of anionic asymmetric bilayers from atomistic simulations, J. Chem. Phys., 2021

    22. Jiang, W., Lin, Y., Botello-Smith, W., Contreras, J.*, Harris, A.*, Maragliano, L.*, Luo, Y.*, Free energy and kinetics of cAMP permeation through connexin26 hemichannel via applied voltage and milestoning, Biophys. J., 2021

    23. Sterling, J.*, Jiang, W., Botello-Smith, W., Luo, Y.*, Ion pairing and dielectric decrement in glycosaminoglycan brushes, J. Phys. Chem. B., 2021

    24. Botello-Smith, W, Luo, Y.*, Investigating protein-protein allosteric network using current-flow scheme, J. Comput. Chem, 2020, 41, 552-560

    25. Gaete PS, Lillo MA, López W, Liu Y, Jiang W, Luo Y, Harris AL, Contreras JE., A novel voltage-clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels, J Gen Physiol. 2020, 2;152(11):e202012607.

    26. Anderson, S., Tabassum, A., Yeon, J., Sharma, G., Santos, P., Soong, T., Thu, Y., Nies, I., Kurita, T., Chandler, A., Alsamarah, A., Kanassatega, R., Luo, Y.*, Botello-Smith, W.*, Andresen, B.*, In silico prediction of ARB resistance: A first step in creating personalized ARB therapy. PLOS Comput. Biol., 2020.

    27. Xie, C.; Jiang, W.; Lacroix, J.J.;Luo, Y.*; Hao, J*. Insight into Molecular Mechanism for Activin A-Induced Bone Morphogenetic Protein Signaling.Int. J. Mol. Sci.2020,21, 6498.

    28. Sun J, Liu Y, Zhu G, ... Luo Y, Baudry M, Bi X., PKA and Ube3a regulate SK2 channel trafficking to promote synaptic plasticity in hippocampus: Implications for Angelman Syndrome,Sci. Rep.2020, 10, 9824.

    29. Botello-Smith W, Zhang H, Ozkan AD, Jiang W, Pham CN, Lacroix J* and Luo Y*, A molecular Mechanism for the Chemical Activation of the Mechanosensitive Piezo1 Channel, Nat. Commun., DOI: 10.1038/s41467-019-12501-1.

    30. Zhu Y, He X, Lin YC, ... Marcucci G, Luo Y, Li L., Targeting PRMT1-mediated FLT3 methylation disrupts maintenance of MLL-rearranged acute lymphoblastic leukemia, Blood, DOI: 10.1182/blood.2019002457.

    31. Botello-Smith, W., Luo, Y.*, Robust determination of protein allosteric signaling pathways, J. Chem. Theory Comput., 2019, 15, 2116-2126.

    32. Capuccino, J., Chatterjee, P., Garcia, I., Botello-Smith, W., Zhang, H., Harris, A., Luo, Y.*, Contreras, J.*, The connexin26 human mutation N14K disrupts cytosolic intersubunit interactions and promotes channel opening, J. Gen. Physiol., 2019, 151, 382-341.

    33. Zhang, H., Jiang, W., Chatterjee P., Luo, Y.*, Ranking reversible covalent drugs: from free energy perturbation to fragment docking, J. Chem. Inf. Model, 2019, 59, 2093-2102.

    34. He X, Zhu Y, Lin YC, ... Marcucci G, Luo Y, Li L., PRMT1-mediated FLT3 arginine methylation promotes maintenance of FLT3-ITD+ acute myeloid leukemia, Blood, 2019, 134, 548-560.

    35. Lacroix, J.*, Botello-Smith, W., Luo, Y., Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1, Nat. Commun., 2018, 9, 2029.

    36. Q. Fei, D. Kent, W. Botello-Smith, F. Nur, S. Nur, A. Alsamarah, P. Chatterjee, M. Lambros*, Y. Luo*, Molecular mechanism of resveratrol’s lipid membrane protection, Sci. Rep., 2018, 8, 1587.

    37. Abrams C, Peinado A, Mahmoud R, ... Botello-Smith W, Freidin M, Luo Y., Alterations at Arg76 of human connexin 46, a residue associated with cataract formation, cause loss of gap junction formation but preserve hemichannel function. Am. J. Physiol. Cell Physiol.2018, 315, 623-635.

    38. Chatterjee, P., Yadav, M., Chauhan, N., Huang, Y., Luo, Y., Cancer cell metabolism featuring Nrf2. Curr. Drug Discov. Technol. 2018, doi: 10.2174/1570163815666180911092443.

    39. M. Liu, K. Huang, L. Qian, ... Z. Wang, Y. Luo, Y. Huang, Effects of bioactive constituents in the Traditional Chinese Medicinal formula Si-Wu-Tang on Nrf2 signaling and neoplastic cellular transformation, Phytomedicine, 2018, 40, 1-9.

    40. P. Chatterjee,W. Botello-Smith,H. Zhang,L Qian,A. Alsamarah,D. Kent,J. Lacroix,M. Baudry,Y. Luo*,Can relative binding free energy predict selectivity of reversible covalent inhibitors?J. Am. Chem. Soc.2017, 139, 17945-17952.

    41. W. Botello-Smith, A. Alsamarah, P. Chatterjee, C. Xie, J.J. Lacroix, J.Hao*, Y. Luo*, Polymodal allosteric regulation of type 1 serine/threonine kinase receptors via a conserved electrostatic lock, PLOS Comput. Biol.,2017, 13, e1005711.

    42. Y. Luo*, A. R. Rossi, A. L. Harris, Computational Studies of Molecular Permeation through Connexin26 Channels, Biophys. J., 2016, 110, 584-599.

    43. W. Lopez, J. Ramachandran, A. Alsamarah, Y. Luo, A. L. Harris, and J. E. Contreras, Mechanism of gating by calcium in connexin hemichannels, Proc. Natl. Acad. Sci. U S A,2016, 113, E7986-E7995.

    44. Y. Luo*, A. Alsamarah, K. Zhang, J. Hao*. Development of New Therapeutic Agents for Fibrodysplasia Ossificans Progressiva. Curr Mol Med., 2016, 16, 4-11.

    45. A. Alsamarah, AE, LaCuran, P. Oelschlaeger, J. Hao, Y. Luo*, Uncovering molecular bases underlying bone morphogenetic protein receptor inhibitor selectivity. PLOS ONE, 2015, 10, e0132221.

    46. J. Sun, G. Zhu, Y. Liu, S. Standley, A. Ji, R. Tunuguntla, Y. Wang, C. Claus, Y. Luo, M. Baudry, X. Bi, UBE3A regulates synaptic plasticity and learning and memory by controlling SK2 channel endocytosis. Cell Rep., 2015, 12, 359-360.

    Work Before WesternU

    47. W. Jiang, J. C. Phillips, L. Huang, M. Fajer, Y. Meng, J. C. Gumbart, Y. Luo, K. Schulten, B. Roux, Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun., 2014, 185 (3), 908-916.

    48. R. M. Venable, Y. Luo, K. Gawrisch, B. Roux, R. W. Pastor, Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data. J. Phys. Chem. B. 2013 117 (35), 10183-10192.

    49. P. E. M. Lopes, J. Huang, J. Shim, Y. Luo, H. Li, B. Roux and A. D. MacKerell, Jr., Polarizable Force field for peptides and protein based the Classical Drude Oscillator. J. Chem. Theory Comput., 2013 9 (12), 5430-5449.

    50. Y. Luo, W. Jiang, H. Yu, A. D. MacKerell, Jr., and B. Roux, Calibrating the potential function for accurate ion pairing in molecular dynamics simulations of concentration electrolytes solutions. Faraday Discussions, 2013, 160, 135-149.

    51. W. Jiang, Y. Luo (co-1st), L. Maragliano, B. Roux, Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J. Chem. Theory Comput., 2012, 8 (11), 4672-4680.

    52. Y. Luo, E. Harder, R. S. Faibish and B. Roux, Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane. J. Mem. Sci. 2011, 384 (1-2), 1-9.

    53. J. Herrou, G. Rotskoff, Y. Luo, B. Roux and S. Crosson, The structural basis of a protein partner switch that regulates stress-dependent transcription. Proc. Natl. Acad. Sci. U S A, 2012, 109 (21): E1415-23.

    54. Y. Luo and B. Roux, Simulation of osmotic pressure in concentrated aqueous salt solutions. J. Phys. Chem. Lett. 2010, 1 (1), 183–189

    55. Y. Luo, B. Egwolf, D. E. Walters, and B. Roux, Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter: I. Single ion potential of mean force calculations and diffusion coefficient. J. Phys. Chem. B, 2010, 114 (2), 952–958

    56. B. Egwolf, Y. Luo, D. E. Walters, and B, Roux, Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter:II. Multi ion effects studies with grand canonical monte carlo/brownian dynamics simulations. J. Phys. Chem. B, 2010, 114 (8), 2901–2909

    57. Y. Luo, F. Barbault, C. Gourmala, Y. M. Zhang, F. Maurel, Y. Z. Hu and B. T. Fan, Cellular interaction through LewisX cluster: theoretical studies.J. Mol. Model, 2008, 14, 901-910.

    58. C. Gourmala, Y. Luo, F. Barbault, Y. M. Zhang, S. Ghalem, F. Maurel and B. T. Fan, Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations. J. Mol. Struct.: THEOCHEM, 2007, 821, 22-29.

    59. Y. Luo, C. Gourmala, D. Dong, F. Barbault, B. T. Fan, Y. Z. Hu, Y. M. Zhang*, First synthesis of two deoxy Lewisx pentaosyl glycosphingolipids. Glycoconjugate J., 2008, 25, 335-344.

    60. F. Barbault, J. Rebehmed, C. Teixeira, Y. Luo, O. Smila-Castro, F. Maurel, B. T. Fan, Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site. Eur. J. Med. Chem. 2008, 43, 1648-56.