Article
Chemistry, Physical
Zherui Chen, Weiguo Liu, Jingyue Sun, Cong Chen, Yongchen Song
Summary: Adding amphiphilic peptides as green KHIs substitutes can effectively inhibit hydrate growth by utilizing the vdW interaction between hydrophobic groups and water molecules. Peptides consisting of alanine and lysine (5AK) and alanine and threonine (5AT) have been studied, and it is found that 5AK with more hydrophobic binding sites exhibits a higher inhibitory effect. Additionally, the addition of threonine further improves the inhibitory effect of the peptide. These findings provide theoretical guidance for the development of new KHIs.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Thermodynamics
Mina Maddah, Mitra Maddah, Kiana Peyvandi
Summary: Antifreeze proteins (AFPs) have been shown to inhibit hydrate growth by binding to specific amino acids and providing a hydrate binding site on the surface. Thr2 and Thr35 are the main adsorption sites, providing a good shape complementary to replace on the half-cages of hydrate surface.
JOURNAL OF CHEMICAL THERMODYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Jeong-Hwan Kim, Kyoung-Ik Min
Summary: Using a tyrosine-rich short peptide, gold-peptide superstructures with diverse shapes can be synthesized through UV irradiation-induced mineralization of gold ions, allowing for controlled fabrication in different solvent environments. This study sheds light on the design and development of diverse gold-peptide superstructures for various applications, including catalysis, sensing, imaging, and photothermal therapy.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Reyhane Chamani, Mohammad Hossein Taleqani, Aylar Imanpour, Mehri Khatami
Summary: Cleavage of collagen NC1 alpha 1 to alpha 3 (IV) domains produces antiangiogenic proteins called Arresten, Canstatin, and Tumstatin. This study found that Tumstatin-derived peptides were more effective, with amino acids L78, V82, and D84 being essential for their activity. In vitro and in vivo experiments compared the efficacy of a nine amino acid peptide derived from Tumstatin (Tum) to the corresponding sequences in Arresten (Ars) and Canstatin (Can). CD spectroscopy, MD, and docking simulations were performed to evaluate the structure and interaction of the peptides with integrin alpha v beta 3. Results showed that the peptides inhibited cell viability, migration, tube formation, and tumor growth, with Canstatin-derived peptide being the most potent. CD measurement and DSSP calculation revealed that Canstatin had a more coil conformation. MD simulations showed that Canstatin had more fluctuation, fewer intramolecular interactions, and less structural compactness compared to Tumstatin and Arresten. The Canstatin-derived peptide interacted closely with integrin alpha v beta 3 near the RGD binding site, with the most negative binding energy and more interactions. In conclusion, this study identified an active peptide derived from Canstatin for the first time and showed that the peptide sequence affected its structure and interaction with its receptor.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2022)
Article
Pharmacology & Pharmacy
Si-Yuan Yao, Jia-Fan Wang, Zheng Xu, Yue Meng, Yue Xue, Fan Yang, Wen-Bing Yao, Xiang-Dong Gao, Song Chen
Summary: SNP-9 is a neuroprotective peptide that can decrease oligomeric amyloid beta (Aβ) levels by co-assembling with toxic Aβ oligomers. The peptide also regulates abnormal hyperphosphorylation of tau by binding to calcyclin-binding protein. These findings suggest that SNP-9 may be a potential therapeutic intervention for Alzheimer's disease (AD).
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Food Science & Technology
Jiamin Dang, Shuangkui Du, Liying Wang
Summary: This study demonstrated the inhibitory properties of corn gluten peptides on soluble epoxide hydrolase (sEH). Through virtual screening and experimental testing, peptides with high inhibitory activity were identified, which may serve as candidates for novel natural inhibitors.
Article
Food Science & Technology
Jaff Ribeiro da Silva, Mariana Barros de Cerqueira e Silva, Biane Oliveira Philadelpho, Victoria Cruz de Souza, Johnnie Elton Machado dos Santos, Marcelo Santos Castilho, Ederlan de Souza Ferreira, Eduardo Maffud Cilli
Summary: The newly designed peptides Pyr-GF and GSTLN enhance the inhibitory effect of pravastatin on HMGCoAR, with the combination showing more significant inhibition compared to pravastatin alone. The peptides demonstrate a cholesterol-lowering effect and act as adjuvants when combined with pravastatin, with Pyr-GF mainly targeting the catalytic site and GSTLN targeting the NADPH site of HMGCoAR.
Article
Biochemistry & Molecular Biology
Sivashanmugam Muthukumaran, K. N. Sulochana, Vetrivel Umashankar
Summary: The study focused on designing inhibitory peptides targeting ODC by investigating the interacting interfaces of native ODC forms. Peptide3 and Peptide4 were identified as potentially targeting ODC, showing significant decreases in intracellular polyamine levels, cell adhesion, and cell cycle perturbation in Y79 cells, making them promising therapeutic agents for retinoblastoma.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Food Science & Technology
Haopeng Dai, Min He, Guilin Hu, Zhongrong Li, Abdulbaset Al-Romaima, Zhouwei Wu, Xiaocui Liu, Minghua Qiu
Summary: The study aimed to investigate the ACE inhibitory effect of bioactive peptides from green coffee beans. Through in vitro and in silico methods, it was found that two peptides have the potential to be used as antihypertensive agents.
Article
Chemistry, Medicinal
Begum Nurpelin Saglik, Derya Osmaniye, Serkan Levent, Ulviye Acar Cevik, Betul Kaya Cavusoglu, Yusuf Ozkay, Zafer Asim Kaplancikli
Summary: This study focused on the design, synthesis, and evaluation of novel compounds as selective COX-2 inhibitors, which showed significant inhibition potencies against COX-2 enzyme. Molecular modelling studies helped to understand the binding properties and selectivity of these derivatives on COX-2 enzyme.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Ruoxuan Xu, Dinghang Hu, Jinlian Lin, Jie Tang, Ruoting Zhan, Guiyou Liu, Lei Sun
Summary: In this study, the cytotoxicity and DNA binding affinity of Anthraycline dutomycin and its derivative SW91 were investigated. The results showed that dutomycin has more significant inhibition of cell growth and higher DNA binding affinity.
Article
Microbiology
Bruna Agrillo, Alessandra Porritiello, Lorena Gratino, Marco Balestrieri, Yolande Therese Proroga, Andrea Mancusi, Loredana Cozzi, Teresa Vicenza, Principia Dardano, Bruno Miranda, Pablo V. Escriba, Marta Gogliettino, Gianna Palmieri
Summary: This study investigated the structural and functional characteristics of lysine-to-arginine substitution in antimicrobial peptides (AMPs), and reported the properties of a new RiLK1 derivative named RiLK3. The results showed that lysine-to-arginine replacement not only did not improve the antimicrobial activity of RiLK1, but completely abolished its activity against the hepatitis A virus. Therefore, the substitution of lysine with arginine has complex effects on antimicrobial efficacy and selectivity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Polymer Science
Alexis Dupre-Demorsy, Olivier Coutelier, Mathias Destarac, Clemence Nadal, Valerie Bourdon, Tsuyoshi Ando, Hiroharu Ajiro
Summary: In this study, bulk reversible addition-fragmentation chain-transfer (RAFT) polymerization of N-methyl-N-vinylacetamide (NMVA) was explored using four different RAFT agents. Poly(N-methyl-N-vinyl acetamide) (PNMVA) with predetermined M_n and relatively low dispersities (D < 1.5) was successfully synthesized at an unusually high [V-70](0)/[RAFT agent](0) ratio. In addition, two double hydrophilic diblock copolymers, poly(ethylene oxide)-b-poly(N-methyl-N-vinylacetamide) (PEO-b-PNMVA) and poly(N-isopropylacrylamide)-b-poly(N-methyl-N-vinylacetamide) (PNIPAAm-b-PNMVA), were synthesized, with the latter exhibiting reversible formation of colloidal aggregates in water.
Article
Biochemistry & Molecular Biology
Hona Hosseinpoor, Sara Moghadam Farid, Aida Iraji, Sadegh Askari, Najmeh Edraki, Samanesadat Hosseini, Akram Jamshidzadeh, Bagher Larijani, Mahshid Attarroshan, Somayeh Pirhadi, Mohammad Mahdavi, Mehdi Khoshneviszadeh
Summary: A series of novel compounds were designed, synthesized, and evaluated for their tyrosinase inhibitory activities, antioxidant activities, and melanin content reduction. Compound 9j showed significant anti-tyrosinase activity and reduction in melanin content.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Edward Ntim Gasu, John Kenneth Mensah, Lawrence Sheringham Borquaye
Summary: New antimicrobial peptides were designed using the chemophysical properties of a peptide extracted from Olivancillaria hiatula and computational tools. These peptides have antibacterial and antivirulence activities and may combat infections by interfering with quorum sensing.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Meng Liu, James D. Farrell, Xianren Zhang, Jure Dobnikar, Stefano Angioletti-Uberti
Summary: We propose a classical density functional theory model to study the self-assembly of polymeric surfactants on curved surfaces. Phase separation driven by size alone is thermodynamically unfavorable on cylindrical and spherical surfaces. By coupling surface topography and polymeric surfactants, non-uniform patterns can be designed on surfaces.
Article
Chemistry, Multidisciplinary
Lingzhi Li, Shixin Li, Yan Xu, Luyao Ren, Lin Yang, Xia Liu, Yanhui Dai, Jian Zhao, Tongtao Yue
Summary: Nanoscale plastics can cross biological barriers through interactions with the cell membrane, and the competition between polymer-polymer interactions and polymer-lipid interactions regulates the interface processes of nanoplastic translocation, transformation, and membrane perturbation. Different materials and aging properties of nanoplastics play key roles in their fate and toxicity to mammalian cells.
ENVIRONMENTAL SCIENCE-NANO
(2023)
Review
Chemistry, Multidisciplinary
Mengying Qi, Xudong Wang, Jiahao Chen, Yin Liu, Yun Liu, Jianbo Jia, Lingxiangyu Li, Tongtao Yue, Lirong Gao, Bing Yan, Bin Zhao, Ming Xu
Summary: This article mainly discusses the transformations of silver nanoparticles in the gastrointestinal tract, their absorption by epithelial cells, and the mechanisms underlying their oral toxicity. It also highlights the knowledge gaps and future research directions in this field.
Review
Chemistry, Multidisciplinary
Xiliang Yan, Tongtao Yue, David A. A. Winkler, Yongguang Yin, Hao Zhu, Guibin Jiang, Bing Yan
Summary: Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. This review discusses the role of artificial intelligence (AI) and molecular simulation in transforming nanotoxicity data into critical information, by constructing quantitative nanostructure-toxicity relationships and elucidating toxicity-related molecular mechanisms. Several obstacles must be overcome for AI and molecular simulation to have their full impact, including the lack of high-quality nanomaterials, standardized nanotoxicity data, model-friendly databases, specific and universal nanodescriptors, and realistic simulation of nanomaterials. The review also provides a comprehensive summary of current capability gaps and tools required to fill these gaps, as well as a perspective on future trends and challenges.
Article
Chemistry, Physical
Xiaohua Yang, Xiangyang Liu, Jinhui Han, Zhiping Liu, Xianren Zhang
Summary: In this study, quantum chemical calculations were used to evaluate carbonates with different fluorinated patterns to meet the requirements of antioxidation, stabilize SEI films, and modify solvation structures. The results showed that both the quantity and position of fluorine substitutions have a significant impact on the oxidation and reduction potentials. It was also found that fluorination weakens the coordination ability of carbonates, which is beneficial for the construction of a good SEI.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Shixin Li, Fang Huang, Tie Xia, Yan Shi, Tongtao Yue
Summary: Phosphatidylinositol 4,5-bisphosphate (PIP2) is a critical molecule located at the inner leaflet of cell membrane, having anchoring and signaling functions. The interaction between PIP2 and the outer lipid domain is influenced by the length of sphingomyelin (SM) acyl chains, leading to either accumulation or expulsion of PIP2. These findings provide molecular insights into the regulatory mechanism of cell signal transduction.
Article
Biology
Ying Xu, Dingka Song, Wei Wang, Shixin Li, Tongtao Yue, Tie Xia, Yan Shi
Summary: This study reveals the role of Clec12a in modulating lipid sorting and phagocyte activation induced by monosodium uric acid (MSU) crystals. While the ITIM motif of Clec12a is dispensable, the transmembrane domain of Clec12a disrupts MSU-induced lipid raft recruitment and attenuates downstream signals. This provides new insights into the molecular mechanisms of solid particle-induced immune activation and potential strategies for inflammation control.
LIFE SCIENCE ALLIANCE
(2023)
Article
Engineering, Environmental
Yingjie Liu, Tongtao Yue, Lu Liu, Bowen Zhang, Hao Feng, Shixin Li, Xia Liu, Yanhui Dai, Jian Zhao
Summary: Extracellular polymeric substances (EPS) play a significant role in modifying the fate and toxicity of nanoplastics at the microbial-aquatic interface. Through molecular dynamics simulations and experiments, this study provides insights into the assembly of EPS and its regulatory effects on the aggregation of differently charged nanoplastics and their interactions with bacterial membranes. The findings show that EPS forms micelle-like structures driven by hydrophobic and electrostatic interactions, and different components of EPS can promote or suppress its assembly depending on their hydrophobicity and charge. EPS can reduce the adsorption of hydrophobic nanoplastics and alleviate their aggregation through electrostatic repulsion. Additionally, EPS can modulate the binding interactions between nanoplastics and bacterial membranes by reducing the surface charge.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Engineering, Environmental
Zhen Luo, Dongfang Xu, Yan Xu, Jian Zhao, Guoqing Hu, Tongtao Yue
Summary: In this study, the interaction between carbon nanotubes (CNTs), pulmonary surfactant (PS), and coexisting contaminants was investigated. It was found that PS can solubilize some of the contaminants adsorbed on CNTs, while also increasing the bioaccessibility of certain compounds. These findings suggest that the toxicity profile of PS-modified CNTs should consider the presence of coexisting contaminants and the aggregation state of CNTs.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Changsheng Chen, Hongguang Zhang, Xianren Zhang
Summary: In this study, we used molecular dynamics to investigate how a two-component surfactant mixture can cooperatively reduce the interfacial tension of a flat vapor-liquid interface. Our simulation results showed that the addition of a secondary surfactant to a given insoluble surfactant can either further reduce or increase the interfacial tension, indicating positive or negative synergistic effects, respectively. The synergistic mechanisms were found to depend on the structure complementary effect between different surfactant components. Furthermore, we confirmed that the symmetry of head-tail distributions in the surfactant mixture plays a key role in determining the positive or negative synergistic effect.
Article
Nanoscience & Nanotechnology
Changsheng Chen, Xianren Zhang, Masao Doi
Summary: One permanent characteristic of small systems' thermodynamics is their dependence on the environment or ensemble. In this study, the gas-liquid transition in soft nano-confinement is discussed, with a focus on the change in phase behavior under different confinement conditions.
Article
Chemistry, Physical
Xiaohua Yang, Xiangyang Liu, Jinhui Han, Zhiping Liu, Xianren Zhang
Summary: Designing solvents or additives with high oxidation stability and good solid-electrolyte interphase (SEI) is crucial for lithium secondary batteries.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Yang Bai, Yaqin Wang, Zelong Qiao, Yongping Yang, Luanjie Deng, Chuanjie Li, Xiudong Chen, Shitao Wang, Yan Huang, Xianren Zhang, Dapeng Cao
Summary: In this study, an efficient trifunctional electrocatalyst was developed, with Fe2P and Co nanoparticles embedded in porous carbon. The catalyst exhibited excellent catalytic performance for oxygen reduction reaction, oxygen evolution reaction, and hydrogen evolution reaction, making it suitable for fuel cells, metal-air batteries, and water electrolyzers.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
Article
Chemistry, Physical
Jiawei Wang, Yan Huang, Xianren Zhang, Dapeng Cao, Shitao Wang
Summary: A one-step electroless deposition method was developed to prepare a carbon-based catalyst, RuPd/NPSC, which showed excellent catalytic activity for the HER under acidic and alkaline conditions.
SUSTAINABLE ENERGY & FUELS
(2022)
Article
Chemistry, Physical
Hongguang Zhang, Shan Chen, Zhenjiang Guo, Xianren Zhang
Summary: In this study, molecular dynamics simulations were used to investigate the effect of surfactant-like molecules on the dissolution of bulk nanobubbles. The results show that the concentration of dissolved gas and the molecular structure of surfactants determine the stability of bulk nanobubbles. When the interfaces of nanobubbles are saturated with surfactants, the fate of the bubbles can either remain stable or be completely dissolved. As gas dissolves, the bubbles shrink and insoluble surfactants form a monolayer with increasing density until the surface tension reaches a very low level. The chemical structure of surfactants crucially affects the bubble stability by changing the elastic energy of the monolayer. Two basic conditions for stable nanobubbles at low gas saturation are identified: vanishing surface tension due to bubble dissolution and positive spontaneous curvature of the surfactant monolayer.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)