Yousong Ding, Ph.D.

Yousong Ding

Assistant Professor

Medicinal Chemistry

OFFICE: Medical Science Building, P6-27

EMAIL: yding@cop.ufl.edu

PHONE: 352-273-7742

CV: Link to CV

 

Education

  • 2012-2013       Principal Scientist, Bioprocess Development Group, Pfizer, Kalamazoo, MI
  • 2010-2012       Postdoctoral Fellow, California Institute of Technology, Pasadena, CA
  • 2004-2010       Ph.D. in Medicinal Chemistry, University of Michigan, Ann Arbor, MI
  • 2001-2004       M.S. Chemistry, University of Nebraska, Lincoln, NE
  • 1996-2000       B.S. Applied Chemistry, Peking University, China

Biographical Sketch

Yousong Ding, Ph.D., an assistant professor of medicinal chemistry, received his B.S. in applied chemistry from Peking University. He pursued his M.S. studies about fungal secondary metabolite biosynthesis at the University of Nebraska under the direction of Dr. Liangcheng Du. He further expanded his expertise in the natural product field during his Ph.D. training with Dr. David Sherman at the University of Michigan. Dr. Ding then worked as a postdoctoral scholar in Dr. Frances H. Arnold’s laboratory at the California Institute of Technology. In the Arnold laboratory, he applied principles of protein engineering and synthetic biology to develop biocatalysts for the production of valuable chemicals and to understand herbicide metabolism. His long-term interests in developing drug molecules led him to take a position in Pfizer. This position allowed him to gain experience in pharmaceutical bioprocess development, and correspondingly he generated various types of biocatalysts used in bio-routes for lowering manufacturing costs of several drugs. In 2013, Dr. Ding started his position as an assistant professor in the Department of Medicinal Chemistry at the University of Florida. His research interests include natural product biosynthesis, drug discovery and development, synthetic biology, protein engineering, and chemical biology.

Research Interests

One primary goal of the Ding laboratory is to discover and develop small molecules and biologics as new therapeutic leads that address significant unmet medical needs such as drugs for obesity, cardiovascular, cancer, and infectious diseases. Nature offers a vast array of small molecules that have inspired the development of a number of marketed drugs, and continuously serve as a prolific source of new drug leads. The Ding laboratory is particularly interested in deciphering and employing the biosynthetic logics of these small molecules for drug discovery. One strategy employed in the laboratory involves identification and analysis of natural product biosynthetic systems from microbial genome data, heterologous production of encoded chemicals, structure determination, and bioactivity evaluation. Through designing novel production routes, developing capable hosts, and creating new/improved biocatalysts, the Ding laboratory will optimize chemical productivity and diversify structures of select candidates. In another research area, the Ding laboratory is interested in developing biocatalysts from different types of enzymes in natural products biosynthetic pathways and employing them to produce value-added chemicals. Researchers in the Ding laboratory gain broad training spanning organic chemistry, medicinal chemistry, biochemistry, microbiology, molecular biology, cell biology, protein engineering, synthetic biology, and bioprocess development.

Group Members


Current:

  • Ran Zuo (5th yr, M.S. in Biochemistry and Cell Biology, Chinese Academy of Sciences)
  • Guangde Jiang (4rd yr, M.S. in Medicinal Chemistry, China Pharmaceutical University)
  • Peilan Zhang (4rd yr, B.S. in Pharmacy, Sichuan University)
  • Yi Zhang (4rd yr, M.S. in Medicinal Chemistry, China Pharmaceutical University)
  • Manyun Chen (1st yr, M.S. in Pharmaceutical Science, University of Southern California)
  • Dake Liu (1st yr, B.S. in Medicinal Chemistry, China Pharmaceutical University)
  • Magan Powell (undergraduate)
  • Monica Cozad (MS student in Microbiology)
  • Steven Crichton (undergraduate)
  • Destin Holland (undergraduate)
  • Jaehyeok Roh (PharmD)
  • Ashley Womer (undergraduate)

Former:

High School Students:

  • Julius Chai
  • Padmavathi Reddy
  • Kathryn Wulber

Undergraduate Students:

  • Kimberly Loudermilk
  • Sunny Aroda
  • Nina Jovic
  • Nicholas Lee
  • Evelina Dedic
  • Erica Christenson
  • Harrison J Bonilla
  • Mishal P Mehta
  • Wesley Dickerson
  • Nilay S Dharma
  • Kyle Volland
  • Albert Tieu
  • Sara Kearny (Wheaton College)
  • Jada Brooks (Bethune-Cookman University)
  • Ariana E. Santiago (REU, University of Puerto Rico)

Pharm.D. Students:

  • XiaoBin Chen
  • Julian Rashid
  • Joshua L McBride

Visiting Scholars:

  • Hongfen Yang
  • Yu Shan
  • Chao Jiang
  • Tariq Ismail

Postdoc Scholar:

  • Guang Yang

 

University of Florida Affiliations

  • Center for Natural Products, Drug Discovery and Development (CNPD3)
  • Emerging Pathogens Institute (EPI)
  • UF Health Cancer Center
  • UF Informatics Institute
  • UF Biodiversity Institute

Ding Lab Publications

  1. Zhang Y, Jiang G, Ding Y, Loria R. Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces, under review.
  2. Jiang G, Zhang P, Ratnayake R, Yang G, Zhang Y, Zuo R, Powell M, Abboud KA, Dang LH, Teplitski M, Paul V, Xiao R, Luesch H, Ding Y. Interconversion of fungal epithiodiketopiperazines bearing α,β-polysulfide bridges and possessing antiaging and cytotoxic activity, under review.
  3. Zhang Y, Li K, Yang G, McBride JL, Bruner SD, Ding Y. A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate, under review.
  4. Yang G, Zhang Y, Lee NK, Cozad MA, Kearney SE, Luesch H, Ding Y. Cyanobacterial Sfp-type phosphopantetheinyl transferases functionalize carrier proteins of diverse biosynthetic pathways, Sci. Rep. 2017, 7: 11888. doi: 10.1038/s41598-017-12244-3.
  5. Zhang P, Li K, Yang G, Xia C, Polston JE, Li G, Li S, Lin Z, Yang LJ, Bruner SD, Ding Y. Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity, Proc. Natl. Acad. Sci. U. S. A. 2017, 114: 8980-8985.
  6. Basak A, Abouelhassan Y, Zuo R, Yousaf H, Ding Y, Huigens RW. Antimicrobial peptide-inspired NH125 analogues: bacterial and fungal biofilm-eradicating agents and rapid killers of MRSA persisters, Org. Biomol. Chem. 2017, 15: 5503-5512.
  7. Zuo R, Zhang Y, Jiang C, Hackett JC, Loria R, Bruner SD, Ding Y. Engineered P450 biocatalysts show improved activity and regio-promiscuity in aromatic nitration, Sci. Rep. 2017, 7: 842. doi: 10.1038/s41598-017-00897-z.
  8. Li K, Condurso H, Li G, Ding Y, Bruner, SD. Precursor protein-directed peptide macrocyclization in ribosomal peptide biosynthetic pathways, Nat. Chem. Biol. 2016, 12: 973-979.
  9. Zhang Y, Bignell DR, Zuo R, Fan Q, Huguet-Tapia JC, Ding Y, Loria R. Promiscuous pathogenicity islands and phylogeny of pathogenic Streptomyces Mol. Plant. Microbe Interact. 2016, 29: 640-650.
  10. Zhang Y, Xie C, Wang H, Foss RM, Clare M, George EV, Li S, Katz A, Cheng H, Ding Y, Tang D, Reeves WH, Yang LJ. Irisin exerts dual effects on browning and adipogenesis of human white adipocytes. Am. J. Physiol. Endocrinol. Metab. 2016, 311: E530-541.
  11. Tu D, Cheng X, Gao Y, Yang P, Ding Y, Jiang C. Palladium-catalysed direct C-2 methylation of indoles. Org. Biomol. Chem. 2016, 14: 7443-7446.
  12. Zuo R, Garrison AT, Basak A, Zhang P, Huigens RW*, Ding Y*. In vitro antifungal and antibiofilm activities of halogenated quinoline analogues against Candida albicans and Cryptococcus neoformans. Int. J. Antimicrob. Agents. 2016, 48: 208-211. (*: co-corresponding author)
  13. Le J, Gao Y, Ding Y*, Jiang C*. Cu-mediated C2-dehydrogenative homocoupling of indoles via C-H activation assisted by a removable N-pyrimidyl group. Tetrahedron Lett. 2016, 57, 1728-1731 (*: co-corresponding author)
  14. Zuo R, Zhang Y, Huguet-Tapia JC, Mehta M, Dedic E, Bruner SD, Loria R, Ding Y. An artificial self-sufficient cytochrome P450 directly nitrates fluorinated tryptophan analogs with different regio-selectivity. Biotechnol. J. 2016 Jan 7. doi: 10.1002/biot.201500416.
  15. Zhang Y, Loria R, Ding Y. Applications of natural products from soil microbes. Soil Ecosystem Services doi:10.2136/2015.soilecosystemsservices.2015.0023
  16. Xie C, Zhang Y, Tran TD, Wang H, Li S, George EV, Zhuang H, Zhang P, Kandel A, Lai Y, Tang D, Reeves WH, Cheng H, Ding Y*, Yang LJ*. Irisin controls growth, intracellular Ca2+ signals, and mitochondrial thermogenesis in cardiomyoblasts. Plos One 2015, 10: e0136816. (*: co-corresponding author)
  17. Yang G, Ding Y. Recent advances in biocatalyst discovery, development and their applications. Bioorg. Med. Chem. 2014, 22: 5604-5612.

Selected Publications Prior to Independent Career

  1. Ding Y, Rath CM, Bolduc KL, Håkansson K, Sherman DH. Chemoenzymatic synthesis of cryptophycin anticancer agents by an ester bond-forming non-ribosomal peptide synthetase module. J. Am. Chem. Soc. 2011, 133:14492-14495.
  2. Ding Y, Wet JR, Cavalcoli J, Li S, Greshock TJ, Miller KA, Finefield JM, Sunderhaus JD, McAfoos TJ, Tsukamoto S, Williams RM, Sherman DH Genome-based characterization of two prenylation steps in the assembly of the stephacidin and notoamide anticancer agents in a marine Aspergillus J. Am. Chem. Soc. 2010, 132: 12733-12740.
  3. Ding Y, Gruschow S, Greshock TJ, Finefield J, Sherman DH, Williams RW. Detection of VM55599 and Pre-paraherquamide from Aspergillus japonicus and Penicillium fellutanum: Biosynthetic Implications. J. Nat. Prod. 2008, 71: 1574-1578
  4. Ding Y, Williams RM, Sherman DH. Isolation and characterization of a 4-dimethylallyltryptophan synthase from Malbranchea aurantiaca. J. Biol. Chem. 2008, 283: 16068-16076
  5. Ding Y, Seufert WH, Beck ZQ, Sherman DH. Analysis of the cryptophycin P450 epoxidase reveals substrate tolerance and cooperativity. J. Am. Chem. Soc. 2008, 130: 5492-5498