curriculum vitae · ph.d. research with professor richard w. roberts, california institute of...

CURRICULUM VITAE ———————————————————————

Xin (Cindy) Qi, Ph.D. 1600 SW Archer Rd. Assistant Professor HSC P5-31, PO Box 100485 Department of Medicinal Chemistry Gainesville, FL 32610 College of Pharmacy Tel: (352)-294-5581 (work) University of Florida Email: [email protected]

RESEARCH INTERESTS

General Directions: Drug discovery for anti-cancer, diabetes and HIV/AIDS therapy. Conduct research at the interface between Chemistry and Biology with focus on Medicinal Chemistry. Develop innovative technologies in peptoid synthesis and application, peptide and protein engineering, and microarray high through-put screening. Address biologically significant problems in chemical biology and cancer biology, including signaling pathways, cancer pathogenesis and significant functional roles of regulatory molecules in those biological processes.

Specific Goals: Develop new methods to synthesize cyclic and conformation constrained peptoids. Probe complex signaling pathways such as apoptosis with regulatory molecules obtained

from large peptoid library screening and elucidate their roles in cancer biology. Develop facile peptoid and microarray screening to rapid identify high affinity GPCR

ligands from large combinatorial library for Diabetes therapy using multi-color quantum dots labeled cell-based screening and microarray technology.

Identify biomarkers to target breast cancer through peptoid library and microarray screening technology.

RNA and protein interaction, including HIV RNA, rRNA A site and Box B RNA.

EDUCATION:

The Scripps Research Institute, Scripps Florida Senior Scientist, Chemistry and Cancer Biology June, 2009-June, 2012 UT Southwestern Medical Center, Dallas, TX

Postdoctoral Scholar, Biochemistry/Translational Research/Internal Medicine July, 2005-May, 2009

California Institute of Technology, Pasadena, CA Ph.D., Bioorganic Chemistry May, 2005

Wayne state University, Detroit, MI M.S., Organic Chemistry May, 2000

Peking University, Beijing, P. R. China B.S., Polymer Chemistry July, 1991

FACULTY POSITION: Assistant Professor, UF Department of Medicinal Chemistry 06/05/2012-present

Xin (Cindy) Qi, Department of Medicinal Chemistry, College of Pharmacy, Curriculum Vitae

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INDUSTRIAL EXPERIENCE: Pharmaceutical research and development experience. Aug. 1991-Aug. 1996 Beijing Pharmaceutical Company, Beijing, China, Engineer in pilot synthesis and quality control RESEARCH EXPERIENCES AND ACHIEVEMENTS

Senior Research Associate/Senior Scientist with Professor Thomas Kodadek, The Scripps Research Institute, Florida and UT Southwestern Medical Center Novel Cyclic peptoid targeting oncoprotein prothymosin α in apopotosis

Design and Synthesis of Peptide Tertiary Amides-A fusion of Peptides and Peptoids Rapid identification of Orexin Receptor Binding Ligands using cell-based peptoid screening

accelerated with magnetic beads Facile Peptoid and microarray screening to rapid identify high affinity GPCR ligand from

large combinatorial library Oncoprotein profiling in cancer cells and biosensor development using cyclic peptoid library

Postdoctoral Scholar with Professor Xiaodong Wang, UT Southwestern Medical Center

Role of regulatory molecules and Prothymosin α in apoptosis pathway

Ph.D. Research with Professor Richard W. Roberts, California Institute of Technology Thesis Title: Unnatural Amino Acid Incorporation to Rewrite the Genetic Code and RNA-peptide Interactions Design of Acridine-N peptide conjugates with enhanced binding affinity and specificity to

RNA targets Synthesis of tRNA synthetase inhibitors and incorporation of non-natural amino acid

residues using chemically aminoacylated tRNAs recognizing specific codons The Puromycin route to assess stereo- and regiochemical constraints on peptide bond

formation in eukaryotic ribosomes The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators

M.S. Research with Professor John Montgomery, Wayne State University Developed a nickel-catalyzed three-component synthesis of 1,3 dienes Synthesized indolizidine alkaloids by the nickel-catalyzed cyclization of ynals

B.S. Research with Professor Shuojian Jiang, Peking University Studied the synthesis and curing conditions of epoxy curing agents

TEACHING/MENTORING EXPERIENCE Classroom Teaching at University of Florida:

o 2013-2014, 2014-2015 Fall Semester, PHA 5437, Medicinal Chemistry o 2013-2014, Spring Semester, PHA 6447, Drug Design o 2014-2015, Spring Semester, GMS6009, Principles of Drug Action

Mentored a number of graduate students, undergraduate students and postdocs (UF, Scripps Florida, UT Southwestern Medical Center and Caltech). Under my mentorship,


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eight students were awarded UF HHMI Science for Life awardees, four were awarded UF Scholars.

Served as an instructor for a variety of graduate and undergraduate courses, including Biochemistry, General Chemistry and Organic Synthesis. Presented several invited lectures (UF, Scripps Florida, UT Southwestern Medical Center, Texas A&M and Caltech, USF).

AWARDS AND HONORS Florida Alliance for Health Professionals Diversity (FAHPD) -Florida Health Equity

Research Institute (HERI) Scholars Mentor UF, 2015 UF Health Cancer Center Celebration of Excellence Mentor Outside the Box Award UF, 2014

Clinical and Translational Science Institute Young Investigator Award UF, 2013 Interdisciplinary Center for Biotechnology Research Agilent Award UF, 2012 ResearchFest winner Scripps Florida 2010 Young Investigator Support GRC 2010 Sigma Xi Research winner UT Southwestern Medical Center 2007 Thomas C. Rumble Fellowship Wayne State University 1997 Achievement Award for the Sino-UK Technical Joint Venture Program

Beijing Pharmaceutical Company 1993

PUBLICATIONS Ravil Khaybullin, Xiao Liang, and Xin Qi*, “(S)-N-(N-(((2R,3S,4R,5R)-5-(6-amino-9H-purin-

9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)sulfamoyl)-5-oxopyrrolidine-2-carboxamide”. Molbank, 2015, M864, doi:10.3390/M864.

Jia Lu, Larry Nguyen, Liang Zhao, Tianbing Xia, and Xin Qi*, “Cyclic Mimic of HIV Tat Differentiates Similar TAR RNAs Based on Distinct Dynamic Behaviors”, Biochemistry, 2015, 54 (23), 3687–3693.

Junjie Fu, Ravil Khaybullin, Yanping Zhang, Amy Xia, and Xin Qi*, “Gene Expression Profiling Leads to Discovery of Correlation of Matrix Metalloproteinase 11 and Heparanase 2 in Breast Cancer Progression”, BMC Cancer, 2015, 15:473, doi:10.1186/s12885-015-1410-y

Xiao Liang, Ravil Khaybullin, Junjie Fu, Kevin Goncalves, Amy Xia, and Xin Qi*, "Genetic Code Expansion using Aminoacylated Orthogonal tRNAs in Conjunction with Aminoacyl Sulfamides", Int J of Recent Technology and Engineering, 2015, 3 (6), 78-82.

Junjie Fu, Ravil Khaybullin, Xiao Liang, Madeleine Morin, Amy Xia, Anderson Yeh, and Xin Qi*, “Discovery of Gene Regulation Pattern in Lung Cancer by Gene Expression Profiling Using Human Tissues”, Genomics Data, 2015, 3, 112-115.

Ravil N. Khaybullin, Mei Zhang, Junjie Fu, Xiao Liang, Tammy Li, Alan R. Katritzky, Paul Okunieff and Xin Qi*, “Design and Synthesis of Isosteviol Triazole Conjugates for Cancer Therapy”, Molecules, 2014, 19 (11), 18676-18689.

Junjie Fu, William Allen, Amy Xia, Zhuofan Ma, and Xin Qi*, “Identification of Biomarkers in Breast Cancer by Gene Expression Profiling Using Human Tissues”, Genomics Data, 2014, 2, 299-301.


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Junjie Fu, Timothy Lee and Xin Qi*, “The Identification of High-affinity GPCR Ligands from Large Combinatorial Library Using Multi-color Quantum Dots Labeled Cell-based Screening”, Future Medicinal Chemistry, 2014, 6(7), 809-823.

Jia Lu, Vivian Wong, Yi Zhang, Trung Tran, Liang Zhao, Amy Xia, Tianbing Xia, and Xin Qi*, “Distinct Conformational Transition Patterns of Non-coding 7SK snRNA and HIV TAR RNAs Upon Tat Binding”, Biochemistry, 2014, 53(4), 675-681.

Jia Lu, Liang Zhao, Amy Xia, Tianbing Xia, and Xin Qi*, “Dissect Conformational Distribution and Drug-Induced Population Shift of Prokaryotic rRNA A-Site”, Biochemistry, 2013, 52, 1651-1653.

Xin Qi, Tianbing Xia, “Structure, Dynamics, and Mechanism of Lead Dependent Ribozyme”, BioMolecular Concepts, 2011, 2, 305-314.

Jia Lu, Beena M. Kadakkuzha, Liang Zhao, Martin Fan, Xin Qi, and Tianbing Xia, “Dynamic Ensemble View of the Conformational Landscape of HIV-1 TAR RNA and Allosteric Recognition”, Biochemistry, 2011, 50, 5042-5057.

Xin Qi, John Astle, Thomas Kodadek, “Rapid Identification of Orexin Receptor Binding Ligands using Cell-based Screening Accelerated with Magnetic Beads”, Mol. BioSyst. 2010, 6, 102-107. PMID: 20024071

Xin Qi, Tianbing Xia, Richard Roberts, “Acridine-N Peptide Conjugates Display Enhanced Affinity and Specificity to Box B RNA Targets”, Biochemistry, 2010, 49, 5782-5789.

Xin Qi, Lai Wang, Fenghe Du, “Novel Small Molecules Relieve Prothymosin α- Mediated Inhibition of Apoptosome Formation by Blocking its Interaction with Apaf-1”, Biochemistry, 2010, 49, 1923-1930. NIHMS: 178260

Shelley R. Starck, Yongkai Ow, Vivian Jiang, Maria Tokuyama, Mark Rivera, Xin Qi, Richard W. Roberts, Nilabh Shastri, “A Distinct Translation Initiation Mechanism Generates Cryptic Peptides for Immune Surveillance”, PLoS One 2008, 3(10), e3460. PMCID: PMC 2565129.

Rong-Gui Hu, Jun Sheng, Xin Qi, Zhenming Xu, Terry T. Takahashi, Alexander Varshavsky, “The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators” Nature 2005, 437, 981-986.

Shelley R. Starck, Xin Qi, Brett N. Olsen, Richard W. Roberts, “The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes” J. Am. Chem. Soc. 2003, 125, 8090-8091.

Xin Qi, John Montgomery, “New Three Component Synthesis of 1,3-Dienes Employing Nickel Catalysis” J. Org. Chem. 1999, 64, 9310-9313.

Xin Qi, John Montgomery, "Preparation of 1,3-Dienes by Nickel-Catalyzed Three-Component Couplings" Book of Abstracts, 218th ACS National Meeting, New Orleans, Aug. 22-26, 1999. ORGN-293.

PATENT

1. Xin Qi, Ravil N. Khaybullin, Paul Okunieff and Mei Zhang. “Isosteviol Triazoles and Uses Thereof", US Patent Provisional Application No.: 62/078,853, issued on Nov. 12, 2014.

2. Xin Qi, Ravil N. Khaybullin, and Xiao Liang. “Sulfamide Adenosine Derivatives and Uses Thereof.” U.S. Patent Provisional Application No.: 62/174,362, issued on June 11, 2015.

CONFERENCE PRESENTATIONS AND INVITED TALK


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NIH/NCI for the Minority Cancer Research and Training (MiCaRT) Center RETool invited lecture, "Role of Biomarkers in Fighting Cancer", Gainesville, FL, May 12, 2015.

American Heart Association Eleventh International Kawasaki Disease Symposium, "Identification of biomarkers for Kawasaki Disease Using Metabolomic Approaches", Honolulu, Hawaii, February 2-6, 2015.

University of South Florida, Department of Chemistry, “Design and Synthesis of Novel Molecules with Therapeutic and Diagnostic Applications”, September 3-5, 2014.

University of Michigan OAIC Research Career Development Core annual research retreat, Ann Arbor, MI, May 29-30, 2014.

2014 Claude D. Pepper OAIC annual meeting, Washington DC, April 7-8, 2014. “Drug Discovery to Target Narcolepsy”

Texas A & M University, Department of Biochemistry and Biophysics, “Design and Synthesis of Novel Molecules with Therapeutic and Diagnostic Applications”, September 18, 2013

23rd American Peptide Symposium 2013, Hawaii, June 22-27, 2013. “Identification of Biomarkers to Target Breast Cancer Through Peptoid Library Screening and Microarray Technology”

ASBMB Experimental Biology Meeting 2013, Boston, Apr. 19-24, 2013. “Dissect Conformational Distribution and Drug-Induced Population Shift of Prokaryotic rRNA A-Site”

HHMI Science for Life Research Seminar, “Drug Discovery with Peptoid Library SMART Process”, February. 7, 2013.

ASBMB Experimental Biology Meeting 2012, San Diego, Apr. 21-25, 2012. “Design and Synthesis of Peptide Tertiary Amides-A fusion of Peptides and Peptoids”

UF, Department of Chemistry, “Design and Synthesis of Novel Molecules with Therapeutic and Diagnostic Applications”, November. 2, 2012.

EPS Nanjing International Forum on Pharmaceutical, Nutraceutical and Biotechnology 2011, invited speaker, Nanjing, Sept. 20-22, 2011. “Discovery of Novel Molecules with Therapeutic and Diagnostic Applications”

ASBMB Experimental Biology Meeting 2011, Washington, DC, Apr. 9-13, 2011. “Novel Cyclic Peptoids Targeting Oncoprotein Prothymosin α”

ResearchFest, Scripps Florida, Apr. 20, 2010. “Novel Chemical Screens to Target GPCRs” Gordon Research Conferences, Chemistry and Biology of Peptides, Ventura, CA, Feb. 28-

Mar. 5, 2010. “Facile Peptoid on Bead to Microarray Screening: Rapid Identification of High Affinity GPCR Ligands from Large Combinatorial Libraries”

The Scripps Research Institute Symposium, La Jolla, CA, Oct. 1, 2009. “Rapid Identification of Orexin Receptor Binding Ligands using Cell-based Screening Accelerated with Magnetic Beads”

World’s Best Technologies, WBT showcase 09, Invited presentation, Arlington, TX, March 24-25, 2009. “Rapid Identification of Orexin Receptor Binding Ligands using Cell-based Screening Accelerated with Magnetic Beads”

Metroplex Meeting, Arlington, TX, March 9, 2009. “Rapid Identification of Orexin Receptor Binding Ligands using Cell-based Screening Accelerated with Magnetic Beads”

UT Southwestern Medical Center Symposium, Dec. 5. 2007. “Role of Regulatory molecules and Prothymosin in apoptosis pathway”


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Cell Death Meeting, Cold Spring Harbor laboratory, Cold Spring Harbor, NY, September 26-30, 2007. “Role of Regulatory molecules and Prothymosin in apoptosis pathway”

218th ACS National Meeting, New Orleans, LA, August 22-26, 1999. “Preparation of 1,3-Dienes by Nickel-Catalyzed Three-Component Couplings”

PROFESSIONAL ACTIVITIES

1997- Member, Phi Lambda Upsilon 1998- Member, American Chemical Society 2006- President, Chinese Student and Scholar Association at UTSW Medical Center 2006- Member, Career Committee, Postdoctoral Association at UTSW Medical Center 2006- Board Member, Chinese Association for Science and Technology (CAST), Texas 2007- Member, Sigma Xi 2009- Ad Hoc Reviewer, Journal of the American Chemical Society 2010- Treasurer, Scripps Florida Society of Research Fellows 2011- Distinguished Lecture Series Chair, Scripps Florida Society of Research Fellows 2011- Ad Hoc Reviewer, Nature Chemical Biology 2012- Member, American Society for Biochemistry and Molecular Biology 2012- President, Biotech Club at Scripps Florida 2012- Member, UF Health Cancer Center 2012- Member, American Association of Colleges of Pharmacy 2013- Member, American Heart Association 2013- Member, UF Clinical and Translational Science Institute (CTSI) 2013- Member, UF Emerging Pathogens Institute (EPI) 2013- Member, UF Center for Natural Products, Drug Discovery and Development (CNPD3) 2013- Reviewer, Medicinal Chemistry Letters 2014- Reviewer, Journal of the American Chemical Society 2014- National High Magnetic Field Laboratory (NHMFL) 2014- Reviewer, Molecules 2015- Reviewer, Nature Scientific Reports

RECENT FUNDING

Interdisciplinary Center for Biotechnology Research (ICBR) Agilent Microarray Program Award 11/20/2012

Clinical and Translational Science Institute (CTSI) Pilot Project Program Grant 01/01/2013

American Cancer Society Chris DiMarco Institutional Research Grant 03/01/2013

Oak Ridge Associated Universities (ORAU) Grant Award 05/01/2013

Emerging Pathogens Institute Seed Grant 10/23/2013 UF Health Cancer Center Celebration of Excellence Mentor Outside the Box Award 2014


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University of Michigan OAIC Research Career Development Core (RCDC) Junior Faculty Awardee 01/24/2014

National High Magnetic Field Laboratory Grant 03/12/2014

Mentor Scholarship for 12th Annual Disparities in Health in America 05/2014

Florida Translational Research Program (FTRP): High-Throughput Screening 07/2014

Emerging Pathogens Institute Seed Grant 01/02/2015

Agilent Next Generation Sequence Award 06/04/2015

Citizenship: U. S. Citizen

Xin (Cindy) Qi, Ph.D. UF Health Cancer Center Celebration of Excellence 2014Mentoring Outside the Box Award winner

http://cancer.ufl.edu/administration/events/celebration-of-excellence/celebration-of-excellence-awards-2014/#prettyPhoto


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2015 Research Training Opportunities for Outstanding Leaders (ReTOOL) Program Mentor (student: Tracoyia Roach)

24th American Peptide Symposium with my students Katherine. Larry and Xiao in 2015

curriculum vitae · ph.d. research with professor richard w. roberts, california institute of...

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