Ding Laboratory

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 associate 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 interest 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 and was promoted to Associate Professor in 2020.

Research Interests

One primary goal of the Ding laboratory is to discover and develop small molecules and biologics as new therapeutic leads for the treatment and management of obesity, cancer, and infectious diseases.  Nature has offered a vast array of strategies and solutions to address these unmet medical needs. The Ding laboratory aims to understand and apply these strategies available in nature.

Research Area #1: Deciphering and employing the biosynthetic logic of bioactive natural products for drug discovery.  Natural organisms produce a number of bioactive small molecules that have inspired the development of about 50 % of marketed drugs and continuously serve as a prolific source of new drug leads.  We will identify the biosynthetic gene clusters of potential natural products directly from microbial genomes and then produce these compounds by expressing their clusters in heterologous hosts.  Through designing novel production routes, developing capable hosts, and creating new/improved biocatalysts, the Ding laboratory will optimize chemical productivity and diversify the structures of select candidates.

Research Area #2: Engineering microbiome strains to sense, monitor and respond to human diseases.  The microbiome is tightly associated with human health and diseases.  The Ding lab is interested in developing microbiome strains as tools and therapeutic agents for treating and managing human diseases, particularly cancer, obesity, and infections.  Currently, through a multi-institutional collaboration, the Ding lab is engineering human native bacteria for colon cancer diagnosis and treatment using synthetic biology approaches.

Research Area #3: Discovering and engineering proteins for biotechnological and biomedical applications. An essential component of the central dogma of biology, proteins are fundamental building blocks of life processes and have demonstrated a wide range of applications.  The Ding laboratory is interested in discovering proteins of new functions and engineering them for applications.  For example, the Ding laboratory has developed biocatalysts from different types of enzymes in natural product biosynthetic pathways and employed them to produce value-added chemicals.  In addition, the Ding laboratory is interested in engineering biomedically important proteins as tools and therapeutic agents (e.g., protease inhibitors and cancer glycan-specific binding proteins).

We are recruiting talented postdoc scholars and graduate students in all three areas. 

Please feel free to contact Dr. Ding (yding@cop.ufl.edu) for more details.

Alumni:

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
• The National High Magnetic Field Laboratory (NHMFL)

Ding Lab Publications

2021

1. Askey BC, Liu D, Rubin GM, Kunik A R, Song YH, Ding Y,* Kim J.* Metabolite profiling reveals organ-specific flavone accumulation in Scutellaria and identifies a scutellarin isomer isoscutellarein 8-O-β-glucuronopyranoside. Plant Direct. 2021, just accepted. doi: https://doi.org/10.1101/2021.09.25.461812 (*: co-corresponding author)
2. Li H, Donelan W, Wang F, Zhang P, Yang Y, Ding Y,* Tang D,* Li S.* GLP-1 induces the expression of FNDC5 derivatives that execute lipolytic actions. Front Cell Dev. Biol. 2021, 9: 777026. (*: co-corresponding author)
3. Dhakal D, Chen M, Luesch H,* Ding Y.* Heterologous production of cyanobacterial compounds. J. Ind. Microbiol. Biotechnol. 2021, 48(3-4):kuab003. (*: co-corresponding author)
4. Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience. 2021, 24: 102512. (Cover art)
5. Jiang G, Zhang P, Ratnayake R, Yang G, Zhang Y, Zuo R, Powell M, Huguet-Tapia JC, Abboud KA, Dang LH, Teplitski M, Paul V, Xiao R, Ahammad KH, Zaman U, Hu Z, Cao S, Luesch H, Ding Y. Fungal epithiodiketopiperazines carrying α,β-polysulfide bridges from Penicillium steckii YE, and their chemical interconversion. Chembiochem. 2021, 22: 416-422.
6. Chen M, Rubin GM, Jiang G, Raad Z, Ding Y. Biosynthesis and heterologous production of mycosporine-like amino acid palythines. J. Org. Chem. 2021, 86: 11160-11168.
7. Perez VC, Dai R, Bai B, Tomiczek B, Askey BC, Zhang Y, Rubin GM, Ding Y, Grenning A, Block AK, Kim J. Aldoximes are precursors of auxins in Arabidopsis and maize. New Phytol. 2021, 231: 1449-1461.
8. Vargas-Rodriguez O, Badran AH, Hoffman KS, Chen M, Crnković A, Ding Y, Krieger JR, Westhof E, Söll D, Melnikov S. Bacterial translation machinery for deliberate mistranslation of the genetic code. Proc. Natl. Acad. Sci. USA. 2021, 118: e2110797118.
9. Li G, Patel K, Zhang Y, Pugmire JK, Ding Y, Bruner SD. Structural and biochemical studies of an iterative ribosomal peptide macrocyclase. Proteins. 2021, doi: 10.1002/prot.26264.
10. Martin CP, Chen M, Martinez MF, Ding Y,* Caranto JD.* The ferric-superoxo intermediate of the TxtE nitration pathway resists reduction, facilitating its reaction with nitric oxide. Biochemistry. 2021, 60: 2436-2446. (*: co-corresponding author)
11. Yang H, Kundra S, Chojnacki M, Liu K, Fuse MA, Abouelhassan Y, Kallifidas D, Zhang P, Huang G, Jin S, Ding Y, Luesch H, Rohde KH, Dunman PM, Lemos JA, Huigens RW 3rd. A modular synthetic route involving N-aryl-2-nitrosoaniline intermediates leads to a new series of 3-substituted halogenated phenazine antibacterial agents. J. Med. Chem. 2021, 64: 7275-7295.

2020

1. Rubin GM, Ding Y. Recent advances in the biosynthesis of RiPPs from multicore-containing precursor peptides. J. Ind. Microbiol. Biotechnol. 2020, 47: 659-674.
2. Zhang P, MacTavish BS, Yang G, Chen M, Roh J, Newsome KR, Bruner SD,* Ding Y.* Cyanobacterial dihydroxyacid dehydratases are a promising growth inhibition target. ACS Chem. Biol. 2020, 15: 2281-2288. (*: co-corresponding author) (Cover Art)
3. Wang F, Sarotti AM, Jiang G, Huguet-Tapia JC, Zheng SL, Wu X, Li C, Ding Y,* Cao S.* Waikikiamides A-C: Complex diketopiperazine dimer and diketopiperazine-polyketide hybrids from a Hawaiian marine fungal strain Aspergillus FM242. Org. Lett. 2020, 22: 4408-4412. (*: co-corresponding author)

2019

1. Li H, Zhang Y, Wang F, Donelan W, Zona MC, Li S, Reeves W, Ding Y, Tang D, Yang L. Effects of irisin on the differentiation and browning of human visceral white adipocytes. Am. J. Transl. Res. 2019, 11: 7410-7421.
2. Zuo R, Ding Y. Direct aromatic nitration system for synthesis of nitrotryptophans in Escherichia coli. ACS Syn. Biol. 2019, 19, 8: 857-865.
3. Abouelhassan Y, Zhang P, Ding Y, Huigens RW. Rapid kill assessment of an N-arylated NH125 analogue against drug-resistant microorganisms. MedChemComm 2019, 10: 712-716.
4. Gunasekera SP, Meyer JL, Ding Y, Abboud KA, Luo D, Campbell JE, Angerhofer A, Goodsell JL, Raymundo LJ, Liu J, Ye T, Luesch H, Teplitski M, Paul VJ. Chemical and metagenomic studies of the lethal black band disease of corals reveal two broadly distributed, redox-sensitive mixed polyketide/peptide macrocycles. J. Nat. Prod. 2019, 82: 111-121.
5. Jiang G, Zhang Y, Powell MM, Hylton SM, Hiller NW, Loria R, Ding Y. A promiscuous cytochrome P450 hydroxylates aliphatic and aromatic C-H bonds of aromatic 2,5-diketopiperazines. Chembiochem. 2019, 20: 1068-1077.

2018

1. Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-pot biocombinatorial synthesis of herbicidal thaxtomins. ACS Catal. 2018, 8: 10761-10768.
2. Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous production of microbial ribosomally synthesized and post-translationally modified peptides. Front Microbiol. 2018, 9:1801. doi: 10.3389/fmicb.2018.01801.
3. Hanson A, Amthor J, Sun J, Niehaus T, Gregory J, Bruner SD, Ding Y. Redesigning thiamin synthesis: Prospects and potential payoffs, Plant Sci. 2018, 273:92-99.
4. Jiang G, Zhang Y, Powell MM, Zhang P, Zuo R, Zhang Y, Kallifidas D, Tieu AM, Luesch H, Loria R*, Ding Y*. High-yield production of herbicidal thaxtomins and analogs in a nonpathogenic Streptomyces Appl. Environ. Microbiol. 2018, 84. pii: AEM.00164-18. doi: 10.1128/AEM.00164-18. (*: co-corresponding author)
5. Kallifidas D, Jiang G, Ding Y, Luesch H. Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters, Microb. Cell Fact. 2018, 17:25, doi: 10.1186/s12934-018-0874-2.
6. 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, Nat. Commun. 2018, 9: 1780, doi:10.1038/s41467-018-04154-3
7. Yang G, Cozad M, Holland D, Zhang Y, Luesch H, Ding Y. Photosynthetic production of sunscreen shinorine using an engineered cyanobacterium, ACS Syn. Biol. 2018, 7: 664-671.
8. Zhang Y, Jiang G, Ding Y*, Loria R*. Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces, Mol. Plant Pathol. 2018, 19: 1733-1741. (*: co-corresponding author)