Article
Biochemistry & Molecular Biology
Iva Lukac, Paul G. Wyatt, Ian H. Gilbert, Fabio Zuccotto
Summary: Water molecules are crucial in protein-ligand binding, and tools exist to predict their position, but predicting their displacement effects remains challenging. A linear-scaling quantum mechanics approach was used to assess water network energetics and stability changes upon ligand modifications, offering valuable insights into SAR data and compound design guidance.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Engineering, Environmental
Mengyao Yao, Jingran Qian, Xiaoni Chen, Jilong Liu, Xiaoqing Yang, Peng Gao, Cheng Zhang
Summary: Agricultural films are widely used in high-intensity agriculture, but the low recovery rate leads to an accumulation of plastic mulch in agricultural soils. This study focuses on the exposure impact of BBP, a chemical introduced into soil ecosystems through the accumulation of plastic mulch, on earthworms. The study explores the effects of BBP on the digestive system, oxidative stress, and neurotoxicity in earthworms, providing insights into the molecular mechanisms underlying these effects.
Article
Chemistry, Multidisciplinary
Nuno M. S. Almeida, Yigitcan Eken, Angela K. Wilson
Summary: This study investigates the impact of PFASs on PPAR gamma and their molecular interactions, identifying two binding sites on PPAR gamma and studying the influence of acidic and basic residues on binding. Furthermore, a comparison of the binding patterns of L-carnitine and PFASs provides insights into mitigation strategies for PFASs.
Article
Environmental Sciences
Minling Gao, Yalei Xu, Xipeng Chang, Zhengguo Song
Summary: The study showed that the application of biochar and iron-manganese oxide modified biochar significantly reduced the accumulation of DBP and DEHP in wheat grains, leading to increased yield, starch and protein content, as well as mineral content. Molecular docking assays indicated that DBP and DEHP could inhibit the activity of starch synthase by binding to it. Additionally, iron-manganese oxide modified biochar demonstrated better inhibitory effects on the phytotoxicity of DBP and DEHP in wheat grains compared to biochar.
Article
Biochemistry & Molecular Biology
Hye Ree Yoon, Chong Chul Chai, Cheol Hee Kim, Nam Sook Kang
Summary: This study evaluated the impact of atomic substitution on biological activity using both experimental and in silico methods, focusing on the interactions of PAK4 with compounds. Results showed differences in interaction energy between electron-withdrawing groups (EWGs) and electron-donating groups (EDGs) in the hinge region residues of PAK4 protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Respiratory System
Clarus Leung, Min Hyung Ryu, Anette Kocbach Bolling, Danay Maestre-Batlle, Christopher F. Rider, Anke Huls, Oscar Urtatiz, Julie L. MacIsaac, Kevin Soon-Keen Lau, David Tse Shen Lin, Michael S. Kobor, Chris Carlsten
Summary: This study investigates how SNPs in PPARG and oxidative stress genes modify the impact of DBP exposure on lung function and immune responses. The results suggest that variants in PPARG play a greater role in airway allergic responses to DBP than oxidative stress-related genes.
RESPIRATORY RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Hiroyuki Miyachi
Summary: Recent progress in understanding the structure and pharmacology of hPPAR gamma has allowed for investigation of various ligands and their effects on biological responses. These ligands serve as valuable tools for studying hPPAR gamma function and potential drugs for hPPAR gamma-related diseases. This review summarizes the medicinal chemistry research on the design, synthesis, and evaluation of hPPAR gamma antagonists based on the induction/inhibition concept of helix 12 (H12) and presents X-ray crystallographic analyses of their unique binding modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Sumit Kumar Mandal, Banoth Karan Kumar, Pankaj Kumar Sharma, Sankaranarayanan Murugesan, P. R. Deepa
Summary: Obesity is a disorder characterized by abnormal fat accumulation and has been linked to metabolic syndrome and various diseases. Nuclear receptors PPAR play a crucial role in metabolism and may be therapeutic targets in obesity. This study identified phytochemical ligands, such as rutin and quercetin, that showed high binding affinity with PPAR and demonstrated anti-obesity effects in experiments.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Environmental Sciences
Rong Wei, Weigao Zhang, Chunlin Pu, Qianchao Shao, Qian Xu, Peiqi Li, Xunan Zhao, Tingzhe Sun, Dan Weng
Summary: In this study, the potential adverse effects of DIBA on cellular homeostasis were evaluated using an integrated in silico and in vitro approach. The results showed that DIBA could disrupt lipid metabolism pathways by binding to PPAR gamma, leading to an increase in intracellular lipid content. This study demonstrates the utility of the integrated in silico and in vitro methodology for assessing the potential risk of environmental chemicals on human health.
ENVIRONMENTAL TOXICOLOGY
(2023)
Article
Engineering, Mechanical
S. N. Korobeynikov, V. V. Alyokhin, A. V. Babichev
Summary: The study utilized standard molecular mechanics (MM) method and molecular structural mechanics (MSM) method to investigate the quasi-static nonlinear buckling and post-buckling behavior of compressed graphene sheets, revealing that well-calibrated parameter sets yield similar buckling forces and post-buckling deformations. It also explored the effects of non-bonded van der Waals (vdW) forces on advanced post-buckling deformation modes, showing the theoretical possibility of post-buckling out-of-plane equilibrium configurations stabilized by attractive vdW forces.
INTERNATIONAL JOURNAL OF MECHANICAL SCIENCES
(2021)
Article
Chemistry, Physical
Yuting Sun, Ming Guo, Shengnan Hu, Xiaobo Fang, Zhicheng Jin, Ronghui Wu
Summary: In this study, a novel immobilized enzyme (MIP-HNTs@lipase) was successfully prepared by combining molecular imprinting and immobilized enzyme technology for the efficient degradation of PAEs. The MIP-HNTs@lipase showed good stability and high degradation efficiency towards DEHP. This research provides a new strategy for the industrial application of enzymes and the degradation of persistent pollutants.
MOLECULAR CATALYSIS
(2022)
Article
Chemistry, Multidisciplinary
Jun Koseki, Haruka Hirose, Masamitsu Konno, Teppei Shimamura
Summary: In this study, a strategy to predict the complex structure of DNA-binding proteins with arbitrary DNA and analyze the differences in their interactions was proposed. It was found that the binding affinity between the BCL-2-associated X sequence and the p53 tetramer is increased by the anticancer drug trifluoro-thymidine (FTD) incorporation, while in p53-binding sequences extracted from FTD-resistant cells, the binding affinity of DNA containing FTD was greatly reduced. This suggests that thymidine randomly substituted for FTD in resistant cells may acquire resistance by inhibiting binding to DNA-binding proteins. This versatile procedure, which considers energetics, will increase the importance of computational science in the life sciences.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Inorganic & Nuclear
Xiaoling Lai, Mengwei Hu, Yang Li
Summary: The mechanism of nickel-catalyzed intermolecular cycloaddition of diynes with methyleneaziridines to form substituted pyrroles has been investigated using DFT calculations. The results revealed that the preferred catalytic cycle is a combination of two mechanisms, involving four stages: oxidative addition, ligand substitution, alkyne insertion, and reductive elimination. Each alkyne moiety of the diyne substrate plays a crucial role in the reaction process, affecting the reaction rate and energy barrier.
DALTON TRANSACTIONS
(2021)
Article
Food Science & Technology
Xiaolan Lv, Zheng Jiang, Guofang Zeng, Sujuan Zhao, Na Li, Fengping Chen, Xiaojian Huang, Jia Yao, Xun Tuo
Summary: Phthalate esters are persistent organic pollutants that have adverse effects on human health. Through molecular docking and spectroscopic techniques, it was found that DCHP has higher binding affinity to HSA compared to MCHP, leading to changes in the protein's secondary structure and increased cytotoxicity. Understanding the binding affinity of PAEs with HSA may provide valuable insights for assessing their toxicity to organisms.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Tianchen Fu, Chongguang Zhao, Yanan Zhu, Pengfei Zhang, Yaowu He, Hong Meng
Summary: This article calculates the absorption spectra of phthalate derivatives under different conditions to understand the influences on the electrochromic properties by the electronic and steric effects. It is found that the carbonyl linking group can enhance absorption in the visible region and lower the driving voltage, offering potential for improving electrochromic materials.
ORGANIC ELECTRONICS
(2021)
Article
Public, Environmental & Occupational Health
Naoko Oya, Yuki Ito, Keisuke Hioki, Yuya Asai, Arisa Aoi, Yuka Sugiura, Jun Ueyama, Tomoko Oguri, Sayaka Kato, Takeshi Ebara, Michihiro Kamijima
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2017)
Article
Environmental Sciences
Machiko Minatoya, Atsuko Araki, Chihiro Miyashita, Seiko Sasaki, Yuko Goto, Tamie Nakajima, Reiko Kishi
SCIENCE OF THE TOTAL ENVIRONMENT
(2017)
Article
Nutrition & Dietetics
Yuan Yuan, Hisao Naito, Xiaofang Jia, Kazuya Kitamori, Tamie Nakajima
Article
Multidisciplinary Sciences
Husna Yetti, Hisao Naito, Yuan Yuan, Xiaofang Jia, Yumi Hayashi, Hazuki Tamada, Kazuya Kitamori, Katsumi Ikeda, Yukio Yamori, Tamie Nakajima
Article
Environmental Sciences
Yu Ait Bamai, Chihiro Miyashita, Atsuko Araki, Tamie Nakajima, Seiko Sasaki, Reiko Kishi
SCIENCE OF THE TOTAL ENVIRONMENT
(2018)
Article
Toxicology
Mio Miyake, Yuki Ito, Himiko Suzuki, Motohiro Tomizawa, Hirotaka Sato, Ming Liu, Ai Okamura, Tamie Nakajima, Katsumi Ohtani, Hisashi Takino, Hiroshi Inagaki, Michihiro Kamijima
TOXICOLOGY LETTERS
(2018)
Article
Multidisciplinary Sciences
Hirotaka Sato, Yuki Ito, Miho Inoue, Yuki Nakahira, Satoru Hashimoto, Tamie Nakajima, Michihiro Kamijima
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Hisao Naito, Yuki Yoshikawa-Bando, Yuan Yuan, Sayuki Hashimoto, Kazuya Kitamori, Hiroshi Yatsuya, Tamie Nakajima
SCIENTIFIC REPORTS
(2019)
Article
Environmental Sciences
Taro Matsuki, Takeshi Ebara, Hazuki Tamada, Yuki Ito, Yasuyuki Yamada, Hirohisa Kano, Takahiro Kurihara, Hirotaka Sato, Sayaka Kato, Shinji Saitoh, Mayumi Sugiura-Ogasawara, Michihiro Kamijima
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2020)
Article
Multidisciplinary Sciences
Yuan Yuan, Hisao Naito, Kazuya Kitamori, Sayuki Hashimoto, Tomomi Asano, Tamie Nakajima
Article
Reproductive Biology
Sumitaka Kobayashi, Fumihiro Sata, Chihiro Miyashita, Atsuko Ikeda-Araki, Houman Goudarzi, Tamie Nakajima, Reiko Kishi
Summary: This study investigated how the interaction between mono-(2-ethylhexyl) phthalate (MEHP) and maternal genotypes associated with nuclear receptors affect fatty acid levels during pregnancy. The results showed that the interaction between MEHP and maternal genotypes PPARGC1A (rs8192678) and LXRB (rs2303044) can decrease fatty acid levels in pregnant Japanese individuals.
REPRODUCTIVE TOXICOLOGY
(2022)
Article
Nutrition & Dietetics
Hazuki Tamada, Takeshi Ebara, Taro Matsuki, Sayaka Kato, Hirotaka Sato, Yuki Ito, Shinji Saitoh, Michihiro Kamijima, Mayumi Sugiura-Ogasawara
Summary: The consumption of processed food during pregnancy is associated with pregnancy outcomes, and frequent consumption of ready-meals and frozen meals may increase the risk of stillbirth.
Article
Toxicology
Tamie Nakajima, Hailan Wang, Yuan Yuan, Yuki Ito, Hisao Naito, Yoshiyuki Kawamoto, Kozue Takeda, Kiyoshi Sakai, Na Zhao, Hongling Li, Xinxiang Qiu, Lihua Xia, Jiabin Chen, Qifeng Wu, Laiyu Li, Hanlin Huang, Yukie Yanagiba, Hiroshi Yatsuya, Michihiro Kamijima
Summary: The study suggests that occupational exposure to TCE may lead to TCE-HS, and autoantibodies to CYP2E1 are primarily involved in the pathogenesis of this disorder.
ARCHIVES OF TOXICOLOGY
(2022)
Article
Nutrition & Dietetics
Hazuki Tamada, Yuki Ito, Takeshi Ebara, Sayaka Kato, Kayo Kaneko, Taro Matsuki, Mayumi Sugiura-Ogasawara, Shinji Saitoh, Michihiro Kamijima
Summary: The composition of human gut microbiota has a long-term impact on human health and disease. This study validated two methods for stool specimen collection and storage, and found them to be useful in large-scale epidemiological studies. However, these methods may alter the relative abundances of certain bacteria.
Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
