Yousong Ding

Yousong Ding, Ph.D.

Associate Professor

Department: Medicinal Chemistry
Business Phone: (352) 273-7742
Business Email: dingyous@ufl.edu

About Yousong Ding

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 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.

Related Links:

Teaching Profile

Courses Taught
2014-2024
PHA7980 Research for Doctoral Dissertation
2016-2017,2019-2024
PHA6435 Biosynthetic Logic of Medicinal Natural Products
2014-2021,2023-2024
PHA7979 Advanced Research
2015,2020
PHA6971 Research for Master’s Thesis
2014-2018,2020-2023
PHA6905C Research Procedures in Medicinal Chemistry
2015,2018-2023,2023-2024
PHA6935 Selected Topics in Pharmacy
2015-2016,2018-2021,2020-2024
GMS6009 Principles of Drug Action and Therapeutics
2014-2018,2020-2024,2023-2024
PHA6910 Supervised Research
2015-2018,2020-2023
PHA5439 Prin Med Chem-Pcol I
2014-2015,2018
PHA6447 Drug Design
2018
CHM7979 Advanced Research
2018
CHM7980 Research for Doctoral Dissertation
2016-2017
PHA5878C Pt Care 3: Cv and Pulm
2016-2017
PHA5782C Patient Care 2
2016-2017
PHA6934 Seminar in Medicinal Chemistry
2016,2021-2023,2023-2024
PHA4913 Undergraduate Research in Medicinal Chemistry
2016
PHA5906 Research in Med Chem
2015-2016
PHA5438 Medicinal Chemistry 2
2014
PHA5433 Funda Medicinal Chem
2021
PHA6894 Introduction to Graduate Studies
2021
PHA5930 Sem Pharm Research
2022-2024
PHA6467C Drug Design II
2022-2023
PHA6740 Fundamentals of Grant Writing in the Pharmaceutical Sciences

Research Profile

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.

Open Researcher and Contributor ID (ORCID)

0000-0001-8610-0659

Publications

2024
Biosynthesis of Dolastatin 10 in Marine Cyanobacteria, a Prototype for Multiple Approved Cancer Drugs
Organic Letters. 26(7):1321-1325 [DOI] 10.1021/acs.orglett.3c04083. [PMID] 38330916.
2023
Biosynthesis of Lyngbyastatins 1 and 3, Cytotoxic Depsipeptides from an Okeania sp. Marine Cyanobacterium
Journal of Natural Products. 86(1):85-93 [DOI] 10.1021/acs.jnatprod.2c00782. [PMID] 36546857.
2023
Carbohydrate-Small Molecule Hybrids as Lead Compounds Targeting IL-6 Signaling.
Molecules (Basel, Switzerland). 28(2) [DOI] 10.3390/molecules28020677. [PMID] 36677735.
2023
Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease
Communications Biology. 6(1) [DOI] 10.1038/s42003-023-04590-y. [PMID] 37024599.
2023
Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics.
Marine drugs. 21(2) [DOI] 10.3390/md21020076. [PMID] 36827117.
2023
Design, synthesis and evaluation of halogenated phenazine antibacterial prodrugs targeting nitroreductase enzymes for activation
RSC Medicinal Chemistry. 14(8):1472-1481 [DOI] 10.1039/d3md00204g. [PMID] 37593580.
2023
Design, Synthesis, and Evaluation of Carbonate-Linked Halogenated Phenazine-Quinone Prodrugs with Improved Water-Solubility and Potent Antibacterial Profiles
ACS Infectious Diseases. 9(4):899-915 [DOI] 10.1021/acsinfecdis.2c00558. [PMID] 36867688.
2023
Heterologous Production of the C33–C45 Polyketide Fragment of Anticancer Apratoxins in a Cyanobacterial Host
Organic Letters. 25(13):2238-2242 [DOI] 10.1021/acs.orglett.3c00462. [PMID] 36961224.
2023
Recent progress in unraveling the biosynthesis of natural sunscreens mycosporine-like amino acids
Journal of Industrial Microbiology and Biotechnology. 50(1) [DOI] 10.1093/jimb/kuad038. [PMID] 37950572.
2022
A roadmap for the functional annotation of protein families: a community perspective
Database. 2022 [DOI] 10.1093/database/baac062. [PMID] 35961013.
2022
Biochemical and structural characterization ofHaemophilus influenzaenitroreductase in metabolizing nitroimidazoles
RSC Chemical Biology. 3(4):436-446 [DOI] 10.1039/d1cb00238d. [PMID] 35441146.
2022
Methods of DNA introduction for the engineering of commensal microbes
Engineering Microbiology. 2(4) [DOI] 10.1016/j.engmic.2022.100048.
2022
Structural and biochemical studies of an iterative ribosomal peptide macrocyclase
Proteins: Structure, Function, and Bioinformatics. 90(3):670-679 [DOI] 10.1002/prot.26264. [PMID] 34664307.
2021
A Modular Synthetic Route Involving N-Aryl-2-nitrosoaniline Intermediates Leads to a New Series of 3-Substituted Halogenated Phenazine Antibacterial Agents
Journal of Medicinal Chemistry. 64(11):7275-7295 [DOI] 10.1021/acs.jmedchem.1c00168. [PMID] 33881312.
2021
Aldoximes are precursors of auxins in Arabidopsis and maize.
The New phytologist. 231(4):1449-1461 [DOI] 10.1111/nph.17447. [PMID] 33959967.
2021
Bacterial translation machinery for deliberate mistranslation of the genetic code
Proceedings of the National Academy of Sciences. 118(35) [DOI] 10.1073/pnas.2110797118. [PMID] 34413202.
2021
Biocatalytic synthesis of peptidic natural products and related analogues
iScience. 24(5) [DOI] 10.1016/j.isci.2021.102512. [PMID] 34041453.
2021
Biosynthesis and Heterologous Production of Mycosporine-Like Amino Acid Palythines
The Journal of Organic Chemistry. 86(16):11160-11168 [DOI] 10.1021/acs.joc.1c00368. [PMID] 34006097.
2021
Fungal Epithiodiketopiperazines Carrying α,β‐Polysulfide Bridges from Penicillium steckii YE, and Their Chemical Interconversion
ChemBioChem. 22(2):416-422 [DOI] 10.1002/cbic.202000403. [PMID] 32816319.
2021
Heterologous production of cyanobacterial compounds
Journal of Industrial Microbiology and Biotechnology. 48(3-4) [DOI] 10.1093/jimb/kuab003. [PMID] 33928376.
2021
Metabolite profiling reveals organ‐specific flavone accumulation in Scutellaria and identifies a scutellarin isomer isoscutellarein 8‐O‐β‐glucuronopyranoside
Plant Direct. 5(12) [DOI] 10.1002/pld3.372. [PMID] 34977451.
2021
The Ferric-Superoxo Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide
Biochemistry. 60(31):2436-2446 [DOI] 10.1021/acs.biochem.1c00416. [PMID] 34319079.
2020
Cyanobacterial Dihydroxyacid Dehydratases Are a Promising Growth Inhibition Target
ACS Chemical Biology. 15(8):2281-2288 [DOI] 10.1021/acschembio.0c00507. [PMID] 32786290.
2020
Waikikiamides A–C: Complex Diketopiperazine Dimer and Diketopiperazine–Polyketide Hybrids from a Hawaiian Marine Fungal Strain Aspergillus sp. FM242
Organic Letters. 22(11):4408-4412 [DOI] 10.1021/acs.orglett.0c01411. [PMID] 32433885.
2019
A Promiscuous Cytochrome P450 Hydroxylates Aliphatic and Aromatic C−H Bonds of Aromatic 2,5‐Diketopiperazines
ChemBioChem. 20(8):1068-1077 [DOI] 10.1002/cbic.201800736. [PMID] 30604585.
2019
Chemical and Metagenomic Studies of the Lethal Black Band Disease of Corals Reveal Two Broadly Distributed, Redox-Sensitive Mixed Polyketide/Peptide Macrocycles
Journal of Natural Products. 82(1):111-121 [DOI] 10.1021/acs.jnatprod.8b00804. [PMID] 30636420.
2019
Direct Aromatic Nitration System for Synthesis of Nitrotryptophans in Escherichia coli
ACS Synthetic Biology. 8(4):857-865 [DOI] 10.1021/acssynbio.8b00534.
2019
Front Cover: A Promiscuous Cytochrome P450 Hydroxylates Aliphatic and Aromatic C−H Bonds of Aromatic 2,5‐Diketopiperazines (ChemBioChem 8/2019)
ChemBioChem. 20(8):974-974 [DOI] 10.1002/cbic.201900174.
2019
Rapid kill assessment of an N-arylated NH125 analogue against drug-resistant microorganisms.
MedChemComm. 10(5):712-716 [DOI] 10.1039/c8md00613j. [PMID] 31191861.
2018
A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate
Nature Communications. 9(1) [DOI] 10.1038/s41467-018-04154-3. [PMID] 29725007.
2018
Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces.
Molecular plant pathology. 19(7):1733-1741 [DOI] 10.1111/mpp.12656. [PMID] 29316196.
2018
High-Yield Production of Herbicidal Thaxtomins and Thaxtomin Analogs in a Nonpathogenic Streptomyces Strain.
Applied and environmental microbiology. 84(11) [DOI] 10.1128/AEM.00164-18. [PMID] 29602787.
2018
One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins
ACS Catalysis. 8(11):10761-10768 [DOI] 10.1021/acscatal.8b03317.
2018
Photosynthetic Production of Sunscreen Shinorine Using an Engineered Cyanobacterium
ACS Synthetic Biology. 7(2):664-671 [DOI] 10.1021/acssynbio.7b00397.
2018
Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters.
Microbial cell factories. 17(1) [DOI] 10.1186/s12934-018-0874-2. [PMID] 29454348.
2017
Antimicrobial peptide-inspired NH125 analogues: bacterial and fungal biofilm-eradicating agents and rapid killers of MRSA persisters
Organic & Biomolecular Chemistry. 15(26):5503-5512 [DOI] 10.1039/c7ob01028a.
2017
Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity
Proceedings of the National Academy of Sciences. 114(34):8980-8985 [DOI] 10.1073/pnas.1706894114. [PMID] 28784797.
2017
Engineered P450 biocatalysts show improved activity and regio-promiscuity in aromatic nitration.
Scientific reports. 7(1) [DOI] 10.1038/s41598-017-00897-z. [PMID] 28405004.
2016
An artificial self-sufficient cytochrome P450 directly nitrates fluorinated tryptophan analogs with a different regio-selectivity.
Biotechnology journal. 11(5):624-32 [DOI] 10.1002/biot.201500416. [PMID] 26743860.
2016
Irisin exerts dual effects on browning and adipogenesis of human white adipocytes.
American journal of physiology. Endocrinology and metabolism. 311(2):E530-41 [DOI] 10.1152/ajpendo.00094.2016. [PMID] 27436609.
2016
Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp.
Molecular plant-microbe interactions : MPMI. 29(8):640-50 [DOI] 10.1094/MPMI-04-16-0068-R. [PMID] 27502745.

Grants

Jul 2023 ACTIVE
Accessing and expanding microbial bioactive chemical diversity by synthetic biology and new enzymology
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Nov 2022 ACTIVE
Efficient and Resilient Biomanufacturing in Variable Gravity
Role: Co-Project Director/Principal Investigator
Funding: US DEPT OF DEFENSE DARPA
Sep 2022 – Feb 2024
Visiting Scholar Agreement: Biocatalytic routes to antiviral agents
Role: Principal Investigator
Funding: AGROPARIS TECH
Aug 2022 ACTIVE
Integrative Multidisciplinary Discovery Platform to Unlock Marine Natural Products Therapeutic Opportunities
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Feb 2022 – Jan 2023
Efficacy and toxicology studies of thaxtomin A and analogs of thaxtomin A
Role: Principal Investigator
Funding: BIOTELLIGA
Sep 2021 ACTIVE
Engineering Native E. coli to Detect, Report, and Treat Colorectal Cancer
Role: Principal Investigator
Funding: UNIV OF CALIFORNIA SAN DIEGO via NATL INST OF HLTH NCI
Jul 2021 ACTIVE
Novel Imine Formation by ATP Grasp Enzymes
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Jun 2020 – Jun 2022
NMR console upgrade for structural biology and metabolomics
Role: Faculty
Funding: NATL INST OF HLTH OD
Oct 2018 – Jul 2019
Testing of Early Feasibility of Streptomyces albus J1074-thx2 as a Production Strain of the Herbicide Thaxtomin
Role: Principal Investigator
Funding: KOCH BIOLOGICAL SOLUTIONS LLC
Jul 2018 – Jun 2023
Accessing and expanding microbial chemical diversity by synthetic biology and new enzymology
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Jun 2016 – May 2018
Developing synthetic biology approaches for the production of nitroaromatics
Role: Principal Investigator
Funding: UF DSR OPPORTUNITY FUND
May 2016 – May 2019
Engineering Biosystems for aromatic nitration
Role: Principal Investigator
Funding: US AIR FORCE RESEARCH LABORATORY
Jul 2015 ACTIVE
UF component for SRI program
Role: Project Manager
Funding: UNIV OF CENTRAL FLORIDA SPACE INST via FL LEGISLATURE
Jul 2015 – Dec 2017
Engineering Irisin for Understanding its Benefits to Obestiy
Role: Principal Investigator
Funding: US ARMY MED RES ACQUISITION
Jun 2015 – May 2016
Developing Biotechnological approaches for producing
Role: Principal Investigator
Funding: OAK RIDGE ASSO UNIVERSITIES
Jan 2012 – Dec 2016
Institutional Research Grant
Role: Project Manager
Funding: AMERICAN CANCER SOCIETY

Education

Principal Scientist
2012-2013 · Bioprocess Development Group, Pfizer
Postdoctoral Fellow
2010-2012 · California Institute of Technology
Ph.D.
2010 · University of Michigan, Ann Arbor
M.S.
2004 · University of Nebraska
B.S.
2000 · Peking University

Contact Details

Phones:
Business:
(352) 273-7742
Emails:
Business:
dingyous@ufl.edu
Addresses:
Business Mailing:
PO Box 100485
GAINESVILLE FL 32610
Business Street:
MSB P6-27
1345 Center Drive
GAINESVILLE FL 326103003