Hak Joong Kim

We highlight recent advances in cell-surface glycan engineering and its applications for studying glycan-mediated biological events and developing therapeutics.

Mycobacterium avium is a major causative agent of nontuberculous mycobacterial pulmonary disease, which poses therapeutic challenges owing to its intrinsic drug resistance and the need for prolonged multidrug regimens. In this study, we identified two novel nucleoside analogs, MCCB-04-35 and MCCB-04-37, as potential therapeutic candidates against M. avium infection. Both compounds exhibited significant bacteriostatic activity in vitro and in infected macrophages, with minimal cytotoxicity. Time–kill kinetics and MIC assays confirmed their potent inhibitory effects, particularly against slow-growing mycobacteria. Checkerboard synergy testing revealed additive to synergistic interactions with clinically used antibiotics such as clarithromycin and ciprofloxacin. In a mouse model of chronic lung infection, both compounds significantly reduced pulmonary bacterial burden, inflammatory cytokine levels, and histopathological damage. Transcriptomic analysis of treated M. avium revealed the downregulation of key metabolic pathways, including oxidative phosphorylation and nitrogen metabolism, indicating disruption of intracellular energy homeostasis. These findings suggest that MCCB-04-35 and MCCB-04-37 exert antimicrobial effects through metabolic interference and may serve as effective therapeutic agents either alone or in combination for treating M. avium infections. IMPORTANCE: Pulmonary disease caused by Mycobacterium avium complex (MAC) is notoriously difficult to treat due to intrinsic antibiotic resistance and the need for prolonged multidrug therapy, often poorly tolerated with suboptimal outcomes. The identification of new therapeutic candidates with novel mechanisms of action is urgently needed. Here, we report two novel nucleoside analogs, MCCB-04-35 and MCCB-04-37, exhibiting strong anti-mycobacterial activity against M. avium both in vitro and in vivo , with minimal cytotoxicity. These compounds showed additive to synergistic effects when combined with existing antibiotics such as clarithromycin. In a mouse model of chronic lung infection, they significantly reduced bacterial burden, inflammation, and tissue damage. Transcriptomic profiling revealed downregulation of metabolic pathways essential for bacterial energy production, suggesting a unique mechanism of antimicrobial action. Our findings provide promising leads for the development of more effective treatments for MAC pulmonary disease, either as monotherapy or in combination with current drugs.

DNA-encoded library (DEL) technology enables high-throughput small-molecule discovery but is typically performed using purified proteins under in vitro conditions that do not reflect native intracellular environments. Here, we present a microfluidic agarose μ-droplet platform for cellular-context DEL screening. The porous hydrogel droplets provide mechanically stable yet permeable microenvironments that protect weak protein–ligand interactions while enabling efficient buffer exchange and ligand diffusion. Importantly, mild cell permeabilization within droplets selectively retained chromatin-associated proteins, allowing screening directly in a cellular context. Using BRD4 as a model target, we validated intracellular ligand engagement by fluorescence imaging and super-resolution microscopy. Small-scale DEL screening selectively enriched JQ1 in both bead-based and cell-based formats, and large-scale DEL screening across millions of encoded compounds successfully identified hit molecules by sequencing. This agarose μ-droplet–based strategy expands DEL technology toward biologically relevant and chromatin-associated targets under near-native conditions.

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.

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.

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.

Tauopathy is characterized by the abnormal aggregation of tau proteins. In order to develop drugs for tauopathies, a variety of different therapeutic strategies have been investigated. Synapse loss is a hallmark of tauopathies and is reportedly related to cognitive impairment in Alzheimer's disease as well. Emerging evidence suggests that pathogenic tau species are linked to synaptic dysfunction and synapse loss in tauopathies. As such, a potential therapeutic approach to ameliorate synaptic dysfunction and counteract synaptic loss due to pathogenic tau holds promise. This review highlights the pathological links between tau pathology and synaptic integrity and current efforts to develop therapeutics rescuing synaptic dysfunction for tauopathies, which will help to understand the association between tau and synapses and develop disease‐modifying drugs for tauopathies.

Proteomics has played a central role in the identification of reliable disease biomarkers, which are the basis of precision medicine, a promising approach for tackling recalcitrant diseases such as cancer, that elude conventional treatments. Among proteomic methodologies, targeted proteomics employing stable isotope-labeled (SIL) internal standards is particularly suited for the clinical translation of biomarker information owing to its high throughput and accuracy in the quantitative analysis of patient-derived proteomes. Using SIL internal standards ensures the utmost level of confidence in detection and precision in targeted MS experiments. For successfully establishing assays based on targeted proteomics, it is crucial to secure broad coverage when selecting the SIL standard peptide panel. However, cysteinyl peptides have often been excluded because of cysteine's high chemical reactivity. To address this limitation, a new cysteine building block was developed by incorporating a sulfhydryl group configured with an S-carbamidomethyl group, which is commonly used in proteome sampling. This compound was found to be chemically stable and applicable to a variety of solid-phase peptide synthesis (SPPS) campaigns. Furthermore, a direct comparison of the synthesized SIL peptides and tryptic endogenous peptides demonstrated the potential utility of an SPPS flow based on the new cysteine building block for improving the success of targeted proteomic applications.

Because of the wide use of Fingolimod for the treatment of multiple sclerosis (MS) and its cardiovascular side effects such as bradycardia, second-generation sphingosine 1-phosphate receptor 1 (S1P1) agonist drugs for MS have been developed and approved by FDA. The issue of bradycardia is still present with the new drugs, however, which necessitates further exploration of S1P1 agonists with improved safety profiles for next-generation MS drugs. Herein, we report a tetrahydroisoquinoline or a benzo[c]azepine core-based S1P1 agonists such as 32 and 60 after systematic examination of hydrophilic groups and cores. We investigated the binding modes of our representative compounds and their molecular interactions with S1P1 employing recent S1P1 cryo-EM structures. Also, favorable ADME properties of our compounds were shown. Furthermore, in vivo efficacy of our compounds was clearly demonstrated with PLC and EAE studies. Also, the preliminary in vitro cardiovascular safety of our compound was verified with human iPSC-derived cardiomyocytes.

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.