Do Young Kim
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Research Subjects
Do Young Kim has a total of 17 co-authors. Here are the top co-authors by number of shared publications:
- Hak Joong Kim
Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
4 shared publications Jimin Park
Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
2 shared publicationsSeungwoo Kim
Department of Chemistry and Center for Proteogenome Research Korea University Seoul, 02841, Republic of Korea
2 shared publications- Suyeon Yeom
Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
2 shared publications Arjun Gontala
Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
1 shared publication- Chul Hee Choi
Chungnam National University
1 shared publication
Latest Publications
- Open Access
- 16 January 2025
- Published by Royal Society of Chemistry (RSC) in RSC Chemical Biology
- Vol. 6 (3) , 387-393
Siderophore-based targeted antibody recruitment for promoting immune responses towards Gram-negative pathogens
Antibody-recruiting molecules (ARMs) have emerged as a promising strategy for enhancing immune responses against pathogens and cancer cells. In this study, we developed a novel class of antibacterial ARMs utilizing siderophores, small iron-chelating compounds, as targeting motifs. Siderophores naturally exhibit high specificity for bacterial pathogens due to their role in iron acquisition, making them ideal candidates for selective targeting. We identified a potent ARM, GNP3, comprising MECAM, a siderophore mimetic, and 2,4-dinitrophenyl (DNP), a motif recognized by endogenous antibodies, connected via a flexible linker. GNP3 binds simultaneously to both anti-DNP antibody and the siderophore receptor, FepA, facilitating the targeted deposition of antibodies on the surface of FepA-expressing bacterial cells, such as Escherichia coli and Pseudomonas aeruginosa. This GNP3-induced opsonization promoted robust immune responses, including complement-dependent cytotoxicity (CDC) in the presence of serum and macrophage-mediated phagocytosis. Moreover, GNP3 effectively triggered CDC activity against serum-resistant uropathogenic E. coli. The results suggest that siderophore-based ARMs, by harnessing the immune defense system, represent a promising complementary approach to traditional antibiotics for overcoming recalcitrant bacterial infections.
- 16 January 2025
- Published by Royal Society of Chemistry (RSC) in RSC Chemical Biology
- Vol. 6 (3) , 387-393
Open AccessSiderophore-based targeted antibody recruitment for promoting immune responses towards Gram-negative pathogens
Antibody-recruiting molecules (ARMs) have emerged as a promising strategy for enhancing immune responses against pathogens and cancer cells. In this study, we developed a novel class of antibacterial ARMs utilizing siderophores, small iron-chelating compounds, as targeting motifs. Siderophores naturally exhibit high specificity for bacterial pathogens due to their role in iron acquisition, making them ideal candidates for selective targeting. We identified a potent ARM, GNP3, comprising MECAM, a siderophore mimetic, and 2,4-dinitrophenyl (DNP), a motif recognized by endogenous antibodies, connected via a flexible linker. GNP3 binds simultaneously to both anti-DNP antibody and the siderophore receptor, FepA, facilitating the targeted deposition of antibodies on the surface of FepA-expressing bacterial cells, such as Escherichia coli and Pseudomonas aeruginosa. This GNP3-induced opsonization promoted robust immune responses, including complement-dependent cytotoxicity (CDC) in the presence of serum and macrophage-mediated phagocytosis. Moreover, GNP3 effectively triggered CDC activity against serum-resistant uropathogenic E. coli. The results suggest that siderophore-based ARMs, by harnessing the immune defense system, represent a promising complementary approach to traditional antibiotics for overcoming recalcitrant bacterial infections.
- Open Access
- 19 February 2024
- Published by Royal Society of Chemistry (RSC) in Chemical Society Reviews
- Vol. 53 (7) , 3253-3272
Targeted protein degradation directly engaging lysosomes or proteasomes
This review delineates emerging technologies for targeted protein degradation that directly involve lysosomes or proteasomes. It explores their unique features, advantages, and limitations, offering perspectives on future therapeutic applications.
- 19 February 2024
- Published by Royal Society of Chemistry (RSC) in Chemical Society Reviews
- Vol. 53 (7) , 3253-3272
Open AccessTargeted protein degradation directly engaging lysosomes or proteasomes
This review delineates emerging technologies for targeted protein degradation that directly involve lysosomes or proteasomes. It explores their unique features, advantages, and limitations, offering perspectives on future therapeutic applications.
- 12 December 2023
- Published by American Chemical Society (ACS) in Organic Letters
- Vol. 25 (50) , 9008-9013
Carboxylate-Directed Pd-Catalyzed β-C(sp3)–H Arylation of N-Methyl Alanine Derivatives for Diversification of Bioactive Peptides
This study presents a Pd(II)-catalyzed method for the β-C(sp3)-H arylation of N-Cbz- or N-Fmoc-protected N-methyl alanines, providing ready access to building blocks for N-methylated peptide synthesis. For this transformation, the native carboxylate was exploited as the directing group, attributing its success to the use of a monoprotected amino-pyridine ligand. Its synthetic utility was demonstrated by facile generation of nine analogues of the naturally occurring N-methylated cyclic peptide cycloaspeptide A.
- 12 December 2023
- Published by American Chemical Society (ACS) in Organic Letters
- Vol. 25 (50) , 9008-9013
Carboxylate-Directed Pd-Catalyzed β-C(sp3)–H Arylation of N-Methyl Alanine Derivatives for Diversification of Bioactive Peptides
This study presents a Pd(II)-catalyzed method for the β-C(sp3)-H arylation of N-Cbz- or N-Fmoc-protected N-methyl alanines, providing ready access to building blocks for N-methylated peptide synthesis. For this transformation, the native carboxylate was exploited as the directing group, attributing its success to the use of a monoprotected amino-pyridine ligand. Its synthetic utility was demonstrated by facile generation of nine analogues of the naturally occurring N-methylated cyclic peptide cycloaspeptide A.
- 8 February 2023
- Published by American Chemical Society (ACS) in ACS Infectious Diseases
- Vol. 9 (3) , 554-566
Cytoplasmic Delivery of an Antibiotic, Trimethoprim, with a Simple Bidentate Catechol Analog as a Siderophore Mimetic
Concerns about antibiotic-resistant Gram-negative pathogens are escalating, and accordingly siderophore-based intracellular antibiotic delivery is attracting more attention as an effective means to overcome these infections. Despite the successful clinical translation of this strategy, the delivery potential of siderophores has been limited to periplasm targeting, and this has appreciably restricted the repertoire of applicable antibiotics. To overcome this shortcoming of the current technology, this study focused on investigating the capability of simple bidentate catechol analogs to function as vehicles for cytoplasmic antibiotic delivery. Specifically, by employing trimethoprim, an inhibitor of dihydrofolate reductase located in the cytoplasm, as a model antibiotic, a chemical library of chelator-antibiotic conjugates featuring four different catechol analogs was prepared. Then, their various pharmacological properties and antimicrobial activities were evaluated. Analysis of these characterization data led to the identification of the active conjugates exhibiting notable iron- and trimethoprim-dependent potency against Escherichia coli. Further characterization of these hit molecules using E. coli mutant strains revealed that 2,3-dihydroxybenzoate could effectively deliver several corresponding conjugates to the cytoplasm by exploiting the siderophore uptake machineries present across the outer and inner membranes, originally designated for the native siderophore of E. coli, enterobactin. Considering the synthetic simplicity, such a catechol analog could have appreciable usage in potentiating cytoplasm-active antibiotics against recalcitrant Gram-negative pathogens.
- 8 February 2023
- Published by American Chemical Society (ACS) in ACS Infectious Diseases
- Vol. 9 (3) , 554-566
Cytoplasmic Delivery of an Antibiotic, Trimethoprim, with a Simple Bidentate Catechol Analog as a Siderophore Mimetic
Concerns about antibiotic-resistant Gram-negative pathogens are escalating, and accordingly siderophore-based intracellular antibiotic delivery is attracting more attention as an effective means to overcome these infections. Despite the successful clinical translation of this strategy, the delivery potential of siderophores has been limited to periplasm targeting, and this has appreciably restricted the repertoire of applicable antibiotics. To overcome this shortcoming of the current technology, this study focused on investigating the capability of simple bidentate catechol analogs to function as vehicles for cytoplasmic antibiotic delivery. Specifically, by employing trimethoprim, an inhibitor of dihydrofolate reductase located in the cytoplasm, as a model antibiotic, a chemical library of chelator-antibiotic conjugates featuring four different catechol analogs was prepared. Then, their various pharmacological properties and antimicrobial activities were evaluated. Analysis of these characterization data led to the identification of the active conjugates exhibiting notable iron- and trimethoprim-dependent potency against Escherichia coli. Further characterization of these hit molecules using E. coli mutant strains revealed that 2,3-dihydroxybenzoate could effectively deliver several corresponding conjugates to the cytoplasm by exploiting the siderophore uptake machineries present across the outer and inner membranes, originally designated for the native siderophore of E. coli, enterobactin. Considering the synthetic simplicity, such a catechol analog could have appreciable usage in potentiating cytoplasm-active antibiotics against recalcitrant Gram-negative pathogens.