Article
Biochemistry & Molecular Biology
Qingxin Li, Qiwei Huang, Congbao Kang
Summary: In this study, the TM domain of SARS-CoV-2 spike protein was analyzed using solution NMR spectroscopy. The results revealed a helical structure, an unstructured linker, and important amino acid residues. These findings provide valuable insights into the function of the spike protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Alexander S. Paramonov, Ekaterina N. Lyukmanova, Alexander G. Tonevitsky, Alexander S. Arseniev, Zakhar O. Shenkarev
Summary: Thionins are small cationic cysteine-rich peptides involved in plant immune response, with Viscotoxin A3 (VtA3) from mistletoe demonstrating antimicrobial and cytotoxic activity. The structure of VtA3 in membrane-mimicking media was studied, showing stability and potential ion channel formation. VtA3 interacts with membranes and can form oligomers in certain conditions, with potential implications for membrane disruption mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Steven R. LaPlante, Valerie Roux, Fatma Shahout, Gabriela LaPlante, Simon Woo, Maria M. Denk, Sacha T. Larda, Yann Ayotte
Summary: This research protocol focuses on monitoring the solution behavior of drugs using NMR to reveal nano-entities formed due to self-associations. By employing various NMR techniques and other characterization methods, the properties of drugs in solution can be evaluated within days for compounds in a library.
Article
Biochemistry & Molecular Biology
Oleg Batishchev, Natalia Kuzmina, Andrey A. Mozhaev, Alexander S. Goryashchenko, Ekaterina D. Mileshina, Alexander N. Orsa, Eduard Bocharov, Igor E. Deyev, Alexander G. Petrenko
Summary: This study provides insights into the structural and activation mechanisms of IRR, identifying two conformations of inactive IRR in neutral media and two presumably active IRR conformations at pH 9.0, all showing formation of intracellular catalytic domains responsible for autophosphorylation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Fei Zhao, Zhihao Zhu, Linshan Xie, Feng Luo, Huixia Wang, Yanli Qiu, Weiling Luo, Fang Zhou, Dongxiang Xue, Zhihui Zhang, Tian Hua, Dong Wu, Zhi-Jie Liu, Zhiping Le, Houchao Tao
Summary: Detergents are commonly used in membrane protein studies, but the limited diversity of traditional detergents restricts their applications to structurally distinct proteins. In this study, the authors report the cross-conjugation of two series of monomeric detergents to construct a library of dimeric detergents for a wider range of applications. Optimum detergents were identified through systematic evaluation and hybrid detergents enabled high-quality studies of different proteins. The findings suggest that the use of cross-coupling chemistries can greatly expand the diversity of detergents for future studies on membrane proteins.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Xi Hu, Yu Sun, Xiaoqi Zhou, Bo Zhang, Hanxi Guan, Fan Xia, Shuangying Gui, Xueqian Kong, Fangyuan Li, Daishun Ling
Summary: Drug loading affects the rigidity of polymeric micelles, and micelles with moderate drug loading exhibit higher cellular uptake and cytotoxicity. NMR measurements reveal the impact of drug loading on micellar rigidity.
Article
Immunology
Safaa A. Faheem, Reem M. Hazem, Norhan M. Elsayed, Yasser M. Ahmed, Noha M. Saeed
Summary: The study aimed to assess the involvement of Wnt/beta-catenin signaling in CsA-induced hepatotoxicity and whether knockdown of this pathway by NCL can attenuate CsA-induced hepatotoxicity. The results showed that NCL can significantly decrease liver enzymes activities, improve histopathological alterations induced by CsA, alleviate oxidative stress and inflammation. Moreover, NCL inhibited Wnt/beta-catenin signaling and increased the expression of PPAR-gamma.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Chemistry, Physical
Caihua Zhou, Guang Fan, Lingjuan Deng
Summary: This study investigates the helical conformers and absorption spectra of three types of 8-aminoquinoline oligoamides. The results reveal that the oligoamides connected with beta-pinene have stable conformers and the absorption band strength is influenced by the degree of polymerization.
CHEMICAL PHYSICS LETTERS
(2022)
Review
Chemistry, Medicinal
Hyeonyeong Im, Ji-Hyun Park, Seowoo Im, Juhyeong Han, Kyungmin Kim, Yun-Hee Lee
Summary: The high incidence of obesity has led to an increased need to discover new therapeutic targets. Recent research has shown that G-protein coupled receptors (GPCRs) could be potential therapeutic targets to regulate adipose tissue metabolism.
ARCHIVES OF PHARMACAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Shaoqin Zheng, Jiahui Lin, Zhongqiu Pang, Hui Zhang, Yinuo Wang, Lanjing Ma, Haijiao Zhang, Xi Zhang, Maorong Chen, Xinjun Zhang, Chao Zhao, Jun Qi, Liu Cao, Min Wang, Xi He, Ren Sheng
Summary: In this study, researchers discovered that cholesterol binds specifically to the Fzd5 receptor, enabling its maturation and trafficking to the plasma membrane. Cholesterol stimulates tumor growth in Wnt-addicted pancreatic ductal adenocarcinoma through Fzd5-mediated signaling, while a natural compound can inhibit this process. These findings reveal a novel mechanism by which Fzd5 acts as a cholesterol sensor and suggest potential therapeutic opportunities for Wnt-dependent cancers.
Article
Chemistry, Multidisciplinary
Meifang Yang, Weiling Luo, Wei Zhang, Huixia Wang, Dongxiang Xue, Yiran Wu, Suwen Zhao, Fei Zhao, Xing Zheng, Houchao Tao
Summary: We report a new strategy based on Ugi reaction for the rapid expansion of detergent diversity. The new detergents were comprehensively evaluated in terms of physical properties and thermal stabilization, and were applied in the study of membrane proteins. The results not only have potential applications in membrane protein research, but also provide insights into the structural-physical relationship of detergents.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Chemistry, Physical
Yuan -Yuan Hu, Xiao-Lin Liu, Hai -Dan Yao, Yang -lin Jiang, Kang Li, Ming-Qing Chen, Peng Wang, Jian-Ping Zhang
Summary: The effects of Polyethylene glycol (PEG) on B800 and B850 excitonic properties of the Light-Harvesting complex 2 (LH2) from Rhodobacter sphaeroides 2.4.1 were investigated. PEG addition in micellar solutions caused LH2 aggregation and enhanced B850 excitonic coupling between inter-complexes, as well as conformational changes of the bound carotenoid (Car). In liposomes, PEG addition resulted in approximately 37% fluorescence quenching of B850 excitons in the embedded LH2s by altering the surrounding hydration state.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Food Science & Technology
Yuyuan Hu, Chuanguo Ma, Ruinan Yang, Shujing Guo, Tong Wang, Jun Liu
Summary: The aim of this study is to investigate the molecular interaction between phytosterol glycosyl derivatives and bile salts, and their impact on cholesterol solubilization. It was found that the introduction of phytosterol glycosyl derivatives into cholesterol-loaded bile salt micelles resulted in a sharp decrease in cholesterol solubility, along with changes in micelle properties. Nuclear magnetic resonance revealed that the structural change was caused by the insertion of beta-sitosterol glycosyl derivatives via hydrogen bonds with sodium taurocholate. The glycosyl moiety of beta-sitosterol glycosyl derivatives significantly influenced the hydrogen-bond interactions.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Roya Ahmadi, Bakhtyar Sepehri, Mehdi Irani, Raouf Ghavami
Summary: In this study, structure-based drug design methods were used to optimize carbamazepine (CBZ) for enhanced binding capacity to the N6W binding site of FZD8. Two compounds, 79 and 82, showed the smallest binding energies to the N6W binding site. Compounds C79 and C82 were synthesized by replacing a hydrogen atom of the seven-membered ring in CBZ with benzoate and nicotinate groups, respectively. Docking results also indicated that a trifluoromethyl on one of the phenyl rings was favorable for improving the FZD8 inhibition activity of the molecule. Molecular dynamics simulation showed that the FZD8-C82 complex was stable and had stronger binding to the N6W binding site compared to C79 and CBZ.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2023)
Article
Endocrinology & Metabolism
Sung-Jin Bae, Yunju Jo, Min Kyoung Cho, Jung-Sook Jin, Jin-Young Kim, Jaewon Shim, Yun Hak Kim, Jang-Kyung Park, Dongryeol Ryu, Hyun Joo Lee, Jongkil Joo, Ki-Tae Ha
Summary: Endometriosis is a common gynecological disease, and its underlying mechanisms are not fully understood. This study identified differentially expressed genes associated with endometriosis and revealed multiple signaling pathways involved in its pathogenesis. Validation of gene expression was also done through immunohistochemistry and western blot analysis.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dipayan Mondal, Sk Abdul Amin, Md Moinul, Kalpataru Das, Tarun Jha, Shovanlal Gayen
Summary: Kinases are important signalling enzymes that make up 20% of the druggable genome. Protein kinases are responsible for regulating various cellular activities, and their deregulation can lead to diseases like cancer. Researchers are actively developing inhibitors based on different chemical scaffolds. Indole scaffold has shown to be versatile and used in the design of inhibitors against various tyrosine kinases.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Hyun-Chul Kim, Jongho Yoon, Sukbin Yoon, Youngmee Kim, Suk Joong Lee, Seong Huh
Summary: N-doped porous metal-organic framework derived carbons were synthesized and activated with KOH, resulting in improved gas sorption and electrochemical capacitive properties. The N-doped MDC-700-2KOH showed high specific capacitance and specific energy, as well as excellent cycling performance.
Article
Chemistry, Physical
Md. Moinul, Sk. Abdul Amin, Samima Khatun, Sanjib Das, Tarun Jha, Shovanlal Gayen
Summary: This study discusses the HDAC8 inhibition and selectivity of indole-based HDAC inhibitors through literature review and molecular modeling. The discovery of a potent and selective indole-based iHDAC8 has attracted significant attention in the development of indole-based HDAC inhibitors. QAAR models have been developed to predict/selective inhibitors against HDAC8.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Review
Chemistry, Organic
Pankaj Lal Kalar, Swatantra Agrawal, Sandhya Kushwaha, Shovanlal Gayen, Kalpataru Das
Summary: The synthesis of organofluorine compounds is important in pharmaceuticals, agrochemicals, and materials due to their enhanced properties. Green synthetic methodologies have gained research interest due to their advantages over conventional methods. This review highlights recent developments in green methods for the synthesis of organofluorine compounds and their applications in various biological activities. It also discusses the synthesis of biologically active fluorinated compounds using green approaches.
CURRENT ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Manisha Malani, Manthan S. Hiremath, Surbhi Sharma, Manisha Jhunjhunwala, Shovanlal Gayen, Chittaranjan Hota, Jayabalan Nirmal
Summary: Patients with chronic diseases undergo long-term systemic drug treatment, but ocular barriers can falsely recognize these drugs and allow them to enter the eye from the bloodstream, leading to toxicity. Understanding the role of organic cation transporter (OCT1) in ocular barriers is important for the entry of systemic drugs into the eye. Machine learning and computer simulation models were used to predict potential OCT1 substrates from various systemic drugs causing ocular toxicity. The accuracy of the machine learning model was around 80%, and it identified previously unknown potential OCT1 substrates.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
In-Hwan Choi, Ja-Min Gu, Hyun-Chul Kim, Youngmee Kim, Seong Huh
Summary: A new three-dimensional Zn-MOF material with excellent gas sorption abilities has been synthesized.
BULLETIN OF THE KOREAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Qiwei Huang, Hui Qi Ng, Yong Yao Loh, Zhiyuan Ke, Wan Hsin Lim, CongBao Kang
Summary: Ubiquitin-conjugating enzyme E2 T (UBE2T) is an important enzyme involved in protein ubiquitination and has been associated with various diseases. Despite the lack of a druggable pocket, efforts have been made to develop inhibitors for UBE2T. In this study, the backbone resonance assignments of human UBE2T without the C-terminal region were reported, providing valuable information for drug discovery and understanding the mechanism of action of UBE2T inhibitors.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biophysics
Qingxin Li, Hui Qi Ng, Ying Ru Loh, CongBao Kang
Summary: Dengue virus is a significant human pathogen in tropical and subtropical regions, and its genome encodes important non-structural proteins for assembly and replication. Dengue NS2B, a membrane protein involved in protein-protein interactions, has critical transmembrane helices and a cytoplasmic region that acts as a cofactor for viral NS3 protease. We have reported the backbone resonance assignments for a dengue NS2B construct called mini-NS2B, containing only transmembrane regions, which will aid in determining NS2B structure and identifying small molecules that bind to the transmembrane regions.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biochemistry & Molecular Biology
Qingxin Li, Congbao Kang
Summary: RNA-binding proteins (RBPs) are crucial for regulating the functions of RNA molecules. Small molecules that can interact with RBPs have been developed as potential drug candidates. This article discusses the perspectives on developing small molecule regulators of RBPs, including small molecules that affect RBP-RNA interactions, bifunctional molecules that target both RNA and RBP, and other molecules that influence the stability of RNA or RBPs. The importance of bifunctional molecules in overcoming challenges in drug discovery is emphasized.
Article
Biochemistry & Molecular Biology
Sourav Sardar, Jyotisha, Sk. Abdul Amin, Samima Khatun, Insaf Ahmed Qureshi, Umesh Kumar Patil, Tarun Jha, Shovanlal Gayen
Summary: HDAC1 is an important target for cancer epigenetics and different molecular modeling techniques have been used to study its interactions with natural inhibitors. By analyzing the molecular structures of these inhibitors, certain amino acid residues have been identified as potential binding sites. The stability of the HDAC1-natural inhibitors complexes has also been evaluated.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biotechnology & Applied Microbiology
Dai Di Chen, Qingxin Li, Jin Chuan Wu
Summary: Pomelo-peel-derived carbons (PPCs) are a promising adsorbent for removing purine compounds from beverages to produce low-purine, healthier products for treating hyperuricemia. They also have the potential to be used as food additives for removing purines in stomach.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Arijit Bhattacharya, Sk Abdul Amin, Prabhat Kumar, Tarun Jha, Shovanlal Gayen
Summary: HDAC10, a class-IIb HDAC, is involved in cancer progression, and the search for selective inhibitors is hindered by the lack of crystal/NMR structure. Ligand-based modeling techniques and machine learning were used in this study to screen potential HDAC10 inhibitors, and structural fingerprints were identified using Bayesian classification and Recursive partitioning models.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Chemistry, Organic
Seungjin Lee, In Guk Park, Jin Won Choi, Jin Young Son, Jin Woo Lee, Jae-Seoun Hur, Youngmee Kim, Sang-Jip Nam, Hahk-Soo Kang, Stephen T. Deyrup, Minsoo Noh, Sang Hee Shim
Summary: Three unprecedented caged xanthone [6,6,6,6,6] polyketides, Daldipyrenones A-C (1-3), were discovered from an endolichenic fungus, Daldinia pyrenaica 047188. The structures of 1-3 were determined using spectroscopic analysis and chemical derivatization. Daldipyrenones are likely formed by the combination of a chromane biosynthesis intermediate and a spiro-azaphilone through radical coupling or Michael addition, resulting in the formation of a bicyclo[2.2.2]octane ring. Genome sequencing revealed two biosynthetic gene clusters responsible for the formation of two biosynthetic intermediates, suggesting a proposed biosynthetic pathway. Daldipyrenone A (1) exhibited significant antimelanogenic activity and moderate adiponectin-secretion promoting activity with lower EC50 values than positive controls.
Article
Nanoscience & Nanotechnology
Do Nam Lee, Yeong Rim Kim, Youngmee Kim, Bong Joo Park, Su Jung Lee, Sung-Jin Kim, Jae Ho Shin
Summary: Metal-organic frameworks (MOFs) can serve as potential scaffolds for therapeutic nitric oxide (NO) delivery. The researchers achieved controlled release of therapeutic NO by loading it onto Cu-MOF, which exhibited good stability and anticancer activity.
ACS APPLIED BIO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Sukbin Yoon, In-Hwan Choi, Youngmee Kim, Seong Huh
Summary: The diethylammonium counter-cations of InBTB MOF can be effectively exchanged with cationic trans-[Co(en)(2)Cl-2](+) complex ions through a simple cation-exchange process. The heterogenized trans-[Co(en)(2)Cl-2]@InBTB catalytic system showed high recyclability for hydrogen peroxide decomposition and exhibited trans-cis isomerization. The catalytic ability of trans-[Co(en)(2)Cl-2]@InBTB could be maintained up to seven times of recycling.
