Discovery of TCP-(MP)-caffeic acid analogs as a new class of agents for treatment of osteoclastic bone loss.

Inhibition of LSD1 was proposed as promising and attractive therapies for treating osteoporosis. Here, we synthesized a series of novel TCP-(MP)-Caffeic acid analogs as potential LSD1 inhibitors to assess their inhibitory effects on osteoclastogenesis by using TRAP-staining assay and try to explore the preliminary SAR. Among them, TCP-MP-CA (11a) demonstrated osteoclastic bone loss both in vitro and in vivo, showing a significant improvement in the in vivo effects compared to the LSD1 inhibitor GSK-LSD1. Additionally, we elucidated a mechanism that 11a and its precursor that 11e directly bind to LSD1/CoREST complex through FAD to inhibit LSD1 demethylation activity and influence its downstream IκB/NF-κB signaling pathway, and thus regulate osteoclastic bone loss. These findings suggested 11a or 11e as potential novel candidates for treating osteoclastic bone loss, and a concept for further development of TCP-(MP)-Caffeic acid analogs for therapeutic use in osteoporosis clinics.

Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii.

Penicillin-binding protein 2 (PBP2), a vital protein involved in bacterial cell-wall synthesis, serves a target for ß-lactam antibiotics. Acinetobacter baumannii is a pathogen notorious for multidrug resistance; therefore, exploration of PBPs is pivotal in the development of new antimicrobial strategies. In this study, the tertiary structure of PBP2 from A. baumannii (abPBP2) was elucidated using X-ray crystallography. The structural analysis demonstrated notable movement in the head domain, potentially critical for its glycosyltransferase function, suggesting that abPBP2 assumes a fully closed conformation. Our findings offer valuable information for developing novel antimicrobial agents targeting abPBP2 that are applicable in combating multidrug-resistant infections.

Interdomain flexibility and putative active site was revealed by crystal structure of MltG from Acinetobacter baumannii.

MltG, positioned within the inner membrane of bacteria, functions as a lytic transglycosylase (LT) essential for integrating into the cell wall by cleaving the newly synthesized glycan strand, emphasizing its critical involvement in bacterial cell wall biosynthesis and remodeling. Current study reported the first structure of MltG family of LT. We have elucidated the structure of MltG from Acinetobacter baumannii (abMltG), a formidable superbug renowned for its remarkable antibiotic resistance. Our structural and biochemical investigations unveiled the presence of a flexible peptidoglycan (PG)-binding domain (PGD) within MltG family, which exists as a monomer in solution. Furthermore, we delineated the putative active site of abMltG via a combination of structural analysis and sequence comparison. This discovery enhances our comprehension of the transglycosylation process mediated by the MltG family, offering insights that could inform the development of novel antibiotics tailored to combat A. baumannii.

Genetically engineered long-acting Esculentin-2CHa(1-30) fusion protein with potential applicability for the treatment of NAFLD.

Esculentin-2CHa(1-30) (?ESC") has been reported as a potent anti-diabetic peptide with little toxicity. However, its very short plasma residence time severely limits the therapeutic efficacy. To address this issue, we genetically engineered a fusion protein of tandem trimeric ESC with an albumin binding domain (ABD) and a fusion partner, SUMO (named ?SUMO-3×ESC-ABD"). The SUMO-3×ESC-ABD, successfully produced from E. coli, showed low cellular and hemolytic toxicity while displaying potent activities for the amelioration of hyperglycemia as well as non-alcoholic fatty liver disease (NAFLD) in vitro. In animal studies, the estimated plasma half-life of SUMO-3×ESC-ABD was markedly longer (427-fold) than that of the ESC peptide. In virtue of the extended plasma residence, the SUMO-3×ESC-ABD could produce significant anti-hyperglycemic effects that lasted for >2 days, while both the ESC or ESC-ABD peptides elicited little effects. Further, twice-weekly treatment for 10 weeks, the SUMO-3×ESC-ABD displayed significant improvement in blood glucose control with a reduction in body weight. Most importantly, a significant improvement in the conditions of NAFLD was observed in the SUMO-3×ESC-ABD-treated mice. Along the systemic effects (by improved glucose tolerance and body weight reduction), direct inhibition of the hepatocyte lipid uptake was suggested as the major mechanism of the anti-NAFLD effects. Overall, this study demonstrated the utility of the long-acting SUMO-3×ESC-ABD as a potent drug candidate for the treatment of NAFLD.

Comparison and analysis of soil microbial communities in organic and conventional paddy fields by farming season.

Interest in soil health and biodiversity conservation has become increasingly important. Consequently, studies comparing the chemical and biological characteristics of organic and traditional paddy soils have been increasing. Soil microorganisms are essential in nutrient cycling; however, their diversity is challenging to ascertain because of their environmental sensitivity and complex interactions. Particularly, in domestic rice cultivation, the soil undergoes multiple irrigation and drainage processes during crop growth, providing a diverse ecological environment for soil microorganisms. The objective of this study is to compare the microbial community and diversity between paddy soils in two agricultural systems. We selected organic and conventional paddy fields in Yangpyeong, Gyeonggi Province, and collected monthly samples from August to November 2022 for analysis. Bacteria and fungi were amplified from the 16S rRNA V3V4 region, ITS 3-4 region respectively, For the comparison of microbial diversity, Alpha diversity indices (Chao1, Shannon, Gini-Simpson indices) were analyzed. The results indicated genus-level differences in microbial communities, with the genera Mucor and Sirastachys exclusively present in organic paddy soils, while the genus Ustilaginoidea was exclusively found in conventional paddy soils. Among them, Ustilaginoidea is reported to be a fungus causing false smut disease, causing damage to crop growth and quality. Additionally, the comparison of microbial diversity between the two farming showed no significant differences (p>0.05). In conclusion, When the microbial communities present in both farming systems were examined, organic farming appeared to be more advantageous than conventional farming regarding crop disease and health. This study provides essential soil chemical and microbiological data for understanding the fundamental characteristics of paddy soils in South Korea.

Water quality seasonal variation assessment of the Gongji and Yaksa streams, Chuncheon, South Korea.

Gongji Stream flows into Lake Uiam, a potable water source for the capital region of Chuncheon, South Korea. Algal blooms often occur downstream of the Gongji stream in combination with drastic flow rate variations. Downstream water quality may also be affected by Yaksa stream. Yaksa stream joins Gongji stream before it reaches Uiam Lake, which is a drinking water source for the city. Limited data exists on the Yaksa stream water quality. Therefore, water quality parameters (pH, electrical conductivity (EC), biological oxygen demand (BOD), total nitrogen (T-N), total phosphorous (T-P), chlorophyll-a (Chl-a), total coliforms, and Escherichia coli (E. coli) concentration) were sampled from Gongji (at sites GJ1 and GJ2) and Yaksa (at sites YS1 and YS2) streams from May to September, 2022. The results revealed the overall water quality of both streams was good (BOD = 0.27-3.66 mg/L; TP = 0.003-0.074 mg/L), except on August 3. On August 3, the concentrations of BOD, TP, total coliforms, and E. coli were elevated, with the highest concentrations in samples from GJ2. The recent heavy rainfall potentially caused sewage inflows near GJ2. The correlation analysis revealed positive linear relationships in the 1-day cumulative precipitation with BOD (r = 0.503), total coliforms (r = 0.547), and TP (r = 0.814). The Yaksa stream may be an Anabaena sp. source, which contaminated samples from YS1, YS2, and GJ2, but not at GJ1 (upstream of the tributary).

Novel Inhibitor of Mixed-Lineage Kinase Domain-Like Protein: The Antifibrotic Effects of a Necroptosis Antagonist.

The pseudokinase mixed-lineage kinase domain-like protein plays a crucial role in programmed cell death via necroptosis. We developed a novel mixed-lineage kinase domain-like inhibitor, P28, which demonstrated potent necroptosis inhibition and antifibrotic effects. P28 treatment directly inhibited mixed-lineage kinase domain-like phosphorylation and oligomerization after necroptosis induction, inhibited immune cell death after necroptosis, and reduced the expression of adhesion molecules. Additionally, P28 treatment reduced the level of activation of hepatic stellate cells and the expression of hepatic fibrosis markers induced by necroptosis stimulation. Unlike the necrosulfonamide treatment, the P28 treatment did not induce cytotoxicity. Finally, the cysteine covalent bonding of P28 was confirmed by liquid chromatography-tandem mass spectrometry.

The structure of AcrIC9 revealing the putative inhibitory mechanism of AcrIC9 against the type IC CRISPR-Cas system.

CRISPR-Cas systems are known to be part of the bacterial adaptive immune system that provides resistance against intruders such as viruses, phages and other mobile genetic elements. To combat this bacterial defense mechanism, phages encode inhibitors called Acrs (anti-CRISPR proteins) that can suppress them. AcrIC9 is the most recently identified member of the AcrIC family that inhibits the type IC CRISPR-Cas system. Here, the crystal structure of AcrIC9 from Rhodobacter capsulatus is reported, which comprises a novel fold made of three central antiparallel ß-strands surrounded by three α-helixes, a structure that has not been detected before. It is also shown that AcrIC9 can form a dimer via disulfide bonds generated by the Cys69 residue. Finally, it is revealed that AcrIC9 directly binds to the type IC cascade. Analysis and comparison of its structure with structural homologs indicate that AcrIC9 belongs to DNA-mimic Acrs that directly bind to the cascade complex and hinder the target DNA from binding to the cascade.

Mychonastes sp. 246 Suppresses Human Pancreatic Cancer Cell Growth via IGFBP3-PI3K-mTOR Signaling.

Previously, we confirmed that Mychonastes sp. 246 methanolic extract (ME) markedly reduced the viability of BxPC-3 human pancreatic cancer cells. However, the underlying mechanism ME remained unclear. Hence, we attempted to elucidate the anticancer effect of ME on BxPC-3 human pancreatic cancer cells. First, we investigated the components of ME and their cytotoxicity in normal cells. Then, we confirmed the G1 phase arrest mediated growth inhibitory effect of ME using a cell counting assay and cell cycle analysis. Moreover, we found that the migration-inhibitory effect of ME using a Transwell migration assay. Through RNA sequencing, Gene Ontology-based network analysis, and western blotting, we explored the intracellular mechanisms of ME in BxPC-3 cells. ME modulated the intracellular energy metabolism-related pathway by altering the mRNA levels of IGFBP3 and PPARGC1A in BxPC-3 cells and reduced PI3K and mTOR phosphorylation by upregulating IGFBP3 and 4E-BP1 expression. Finally, we verified that ME reduced the growth of three-dimensional (3D) pancreatic cancer spheroids. Our study demonstrates that ME suppresses pancreatic cancer proliferation through the IGFBP3-PI3K-mTOR signaling pathway. This is the first study on the anticancer effect of the ME against pancreatic cancer, suggesting therapeutic possibilities and the underlying mechanism of ME action.

Structure of fish TRAF4 and its implication in TRAF4-mediated immune cell and platelet signaling.

Due to an increasing interest in immunity and signal transduction in teleost fish, important key signaling molecules associated with the immune response, including TRAF molecules, have been recently cloned and characterized. To better understand the role of TRAF4 in fish immune signaling and compare it with the human system, our study cloned the TRAF4 gene from the Antarctic yellowbelly rockcod Notothenia coriiceps (ncTRAF4) and purified the protein. Here, we report the first crystal structure of teleost fish TRAF4. Based on biochemical characterization, our findings elucidated the mechanisms through which signaling molecules gain cold adaptivity. Additionally, we identified a platelet receptor GPIbß homolog in N. coriiceps (ncGPIbß) and found that the "RRFERLFKEARRTS" region of this homolog directly binds to ncTRAF4, indicating that ncTRAF4 also recognizes the "RLXA" motif for receptor interactions and further TARF4-mediated cellular signaling. Collectively, our findings provide novel insights into the mechanisms of TRAF4-mediated immune cell and platelet signaling in fish and the structural flexibility-mediated cold adaptiveness of signaling molecules.

Identification of proteomic landscape of drug-binding proteins in live cells by proximity-dependent target ID.

Direct identification of the proteins targeted by small molecules can provide clues for disease diagnosis, prevention, and drug development. Despite concentrated attempts, there are still technical limitations associated with the elucidation of direct interactors. Herein, we report a target-ID system called proximity-based compound-binding protein identification (PROCID), which combines our direct analysis workflow of proximity-labeled proteins (Spot-ID) with the HaloTag system to efficiently identify the dynamic proteomic landscape of drug-binding proteins. We successfully identified well-known dasatinib-binding proteins (ABL1, ABL2) and confirmed the unapproved dasatinib-binding kinases (e.g., BTK and CSK) in a live chronic myeloid leukemia cell line. PROCID also identified the DNA helicase protein SMARCA2 as a dasatinib-binding protein, and the ATPase domain was confirmed to be the binding site of dasatinib using a proximity ligation assay (PLA) and in cellulo biotinylation assay. PROCID thus provides a robust method to identify unknown drug-interacting proteins in live cells that expedites the mode of action of the drug.

Review: An integrated framework for understanding ecological drought and drought resistance.

Droughts are a frequent natural phenomenon that has amplified globally in the 21st century and are projected to become more common and extreme in the future. Consequently, this affects the progress of drought indices and frameworks to categorize drought conditions. Several drought-related indices and variables are required to capture different features of complex drought conditions. Therefore, we explained the signs of progress of ecological drought that were ecologically expressive to promote the integration between the research on and identification of water scarcity situations and analyzed different frameworks to synthesize the drought effects on species and ecosystems. Notably, we present an inclusive review of an integrated framework for an ecological drought. The ecological drought framework affords the advantage of improved methodologies for assessing ecological drought. This is supported by research on water-limited ecosystems that incorporated several drought-related elements and indicators to produce an integrated drought framework. In this framework, we combined multiple studies on drought recovery, early warning signs, and the effects of land management interferences, along with a schematic representation of a new extension of the framework into ecological systems, to contribute to the success and long-term sustainability of ecological drought adaptation, as well as on-the-ground examples of climate-informed ecological drought management in action for an integrated framework for ecological drought. This study provides an integrated approach to the understanding of ecological drought in line with accelerated scientific advancement to promote persistence and plan for a future that irretrievably exceeds the ecosystem thresholds and new multivariate drought indices.

Chelidonium majus Induces Apoptosis of Human Ovarian Cancer Cells via ATF3-Mediated Regulation of Foxo3a by Tip60.

Forkhead transcription factor 3a (Foxo3a) is believed to be a tumor suppressor as its inactivation leads to cell transformation and tumor development. However, further investigation is required regarding the involvement of the activating transcription factor 3 (ATF3)-mediated Tat-interactive protein 60 (Tip60)/Foxo3a pathway in cancer cell apoptosis. This study demonstrated that Chelidonium majus upregulated the expression of ATF3 and Tip60 and promoted Foxo3a nuclear translocation, ultimately increasing the level of Bcl-2-associated X protein (Bax) protein. ATF3 overexpression stimulated Tip60 expression, while ATF3 inhibition by siRNA repressed Tip60 expression. Furthermore, siRNA-mediated Tip60 inhibition significantly promoted Foxo3a phosphorylation, leading to blockade of Foxo3a translocation into the nucleus. Thus, we were able to deduce that ATF3 mediates the regulation of Foxo3a by Tip60. Moreover, siRNA-mediated Foxo3a inhibition suppressed the expression of Bax and subsequent apoptosis. Taken together, our data demonstrate that Chelidonium majus induces SKOV-3 cell death by increasing ATF3 levels and its downstream proteins Tip60 and Foxo3a. This suggests a potential therapeutic role of Chelidonium majus against ovarian cancer.

Gossypol Induces Apoptosis of Human Pancreatic Cancer Cells via CHOP/Endoplasmic Reticulum Stress Signaling Pathway.

Gossypol, a natural phenolic aldehyde present in cotton plants, was originally used as a means of contraception, but is currently being studied for its anti-proliferative and anti-metastatic effects on various cancers. However, the intracellular mechanism of action regarding the effects of gossypol on pancreatic cancer cells remains unclear. Here, we investigated the anti-cancer effects of gossypol on human pancreatic cancer cells (BxPC-3 and MIA PaCa-2). Cell counting kit-8 assays, annexin V/propidium iodide staining assays, and transmission electron microscopy showed that gossypol induced apoptotic cell death and apoptotic body formation in both cell lines. RNA sequencing analysis also showed that gossypol increased the mRNA levels of CCAAT/enhancer-binding protein homologous protein (CHOP) and activating transcription factor 3 (ATF3) in pancreatic cancer cell lines. In addition, gossypol facilitated the cleavage of caspase-3 via protein kinase RNA-like ER kinase (PERK), CHOP, and Bax/Bcl-2 upregulation in both cells, whereas the upregulation of ATF was limited to BxPC-3 cells. Finally, a three-dimensional culture experiment confirmed the successful suppression of cancer cell spheroids via gossypol treatment. Taken together, our data suggest that gossypol may trigger apoptosis in pancreatic cancer cells via the PERK-CHOP signaling pathway. These findings propose a promising therapeutic approach to pancreatic cancer treatment using gossypol.

The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.

Physicochemical properties and freeze-thaw stability of rice flour blends among rice cultivars with different amylose contents.

The effectiveness of the rice flour blends (RFB) for improving the processing suitability of Dodamssal rice flour (DD), a functional rice variety with a relatively high amylose and resistance starch content, was investigated. Physicochemical properties and freeze-thaw stability of RFB composed of DD and four rice flour (RF) samples with different amylose contents were measured at different DD ratios. DD, which has low swelling power and low pasting viscosity properties, has improved some quality in terms of physicochemical properties by blending with other RF. Especially, non-additive behavior was observed in the blend with Geonyang No.2 RF (GY), a medium waxy variety, due to water competition caused by the difference in pasting temperature. The syneresis of DD was reduced by blending with 75% Hanareum No. 4 RF, with a gradual reduction effect observed following a repeated freeze-thaw cycle. GY significantly improved the low freeze-thaw stability of DD with only a 25% blend. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-00989-7.

Chelidonine Induces Apoptosis via GADD45a-p53 Regulation in Human Pancreatic Cancer Cells.

Chelidonium majus has been used as a traditional medicine in China and western countries for various diseases, including inflammation and cancer. However, the anti-cancer effect of chelidonine, a major compound of C. majus extracts, on pancreatic cancer remains poorly understood. In this study, we found that treatment with chelidonine inhibited proliferation of BxPC-3 and MIA PaCa-2 human pancreatic cancer cells. Annexin-V/propidium iodide staining assay showed that this growth inhibitory effect of chelidonine was induced through apoptosis. We found that chelidonine treatment upregulated mRNA levels and transcription factor activity in both cell lines. Increases in protein expression levels of p53, GADD45A, p21 and cleaved caspase-3 were also observed, with more distinct changes in MIA PaCa-2 cells compared to the BxPC-3 cells. These results suggest that chelidonine induces pancreatic cancer apoptosis through the p53 and GADD45A pathways. Our findings provide new insights into the use of chelidonine for the treatment of pancreatic cancer.

Genetic engineering of novel super long-acting Exendin-4 chimeric protein for effective treatment of metabolic and cognitive complications of obesity.

A common bottleneck challenge for many therapeutic proteins lies in their short plasma half-lives, which often makes the treatment far less compliant or even disables achieving sufficient therapeutic efficacy. To address this problem, we introduce a novel drug delivery strategy based on the genetic fusion of an albumin binding domain (ABD) and an anti-neonatal Fc receptor (FcRn) affibody (AFF) to therapeutic proteins. This ABD-AFF fusion strategy can provide a synergistic effect on extending the plasma residence time by, on one hand, preventing the rapid glomerular filtration via ABD-mediated albumin binding and, on the other hand, increasing the efficiency of FcRn-mediated recycling by AFF-mediated high-affinity binding to the FcRn. In this research, we explored the feasibility of applying the ABD-AFF fusion strategy to exendin-4 (EX), a clinically available anti-diabetic peptide possessing a short plasma half-life. The EX-ABD-AFF produced from the E. coli displayed a remarkably (241-fold) longer plasma half-life than the SUMO tagged-EX (SUMO-EX) (0.7 h) in mice. Furthermore, in high-fat diet (HFD)-fed obese mice model, the EX-ABD-AFF could provide significant hypoglycemic effects for over 12 days, accompanied by a reduction of body weight. In the long-term study, the EX-ABD-AFF could significantly reverse the obesity-related metabolic complications (hyperglycemia, hyperlipidemia, and hepatic steatosis) and, moreover, improve cognitive deficits. Overall, this study demonstrated that the ABD-AFF fusion could be an effective strategy to greatly increase the plasma half-lives of therapeutic proteins and thus markedly improve their druggability.

Acid-sensitive oxidative stress inducing and photoabsorbing polysaccharide nanoparticles for combinational anticancer therapy.

Combination therapy, a treatment regimen that combines more than two therapeutic agents to diseased tissues has recently gained increasing attentions in anticancer therapy. As cancer cells are more vulnerable to oxidative stress and heat compared to normal cells, we developed hyperthermia- and oxidative stress-inducing maltodextrin (HTOM) nanoparticles as a platform of combinational photothermal/oxidative anticancer therapy. HTOM was designed to incorporate cinnamaldehyde as an oxidative stress inducer through acid-labile acetal linkage and IR780 as a photoabsorber. HTOM nanoparticles could generate excess reactive oxygen species (ROS) to kill cancer cells effectively. When exposed to near infrared (NIR) laser irradiation (808 nm), HTOM nanoparticles also increased temperature to destroy cancer cells. The combination of NIR laser irradiation with HTOM nanoparticles exhibited significantly higher anticancer activity than HTOM nanoparticles alone and NIR lasers irradiation alone. When combined with NIR laser irradiation on the tumor site, intravenously administrated HTOM nanoparticles effectively eradicated tumors in mouse xenograft models. Our strategy for combination of oxidative stress and photothermal heating may offer a new combinational treatment modality for cancer.

Photo-crosslinking: An Emerging Chemical Tool for Investigating Molecular Networks in Live Cells.

Studying protein-protein interactions (PPIs) is useful for understanding cellular functions and mechanisms. Evaluating these PPIs under conditions as similar as possible to native conditions can be achieved using photo-crosslinking methods because of their on-demand ability to generate reactive species in situ by irradiation with UV light. Various fusion tag, metabolic incorporation, and amber codon suppression approaches using various crosslinkers containing aryl azide, benzophenone, and diazirines have been applied in live cells. Mass spectrometry and immunological techniques are used to identify crosslinked proteins based on their capture transient and context-dependent interactions. Herein we discuss various incorporation methods and crosslinkers that have been used for interactome mapping in live cells.