Article
Biochemistry & Molecular Biology
Luying Jiang, Quancheng Sun, Li Li, Fuping Lu, Fufeng Liu
Summary: GV971 components inhibit the conformational transition of A beta 42 monomer by preventing the conversion from α-helix to β-sheet and the hydrophobic collapse. Both electrostatic and van der Waals interactions are beneficial for the binding of GV971 components to A beta 42 monomer, with electrostatic interactions playing a dominant role. GV971 components mainly interact with charged residues D1, R5, K16, and K28 through salt bridges and hydrogen bonds, specifically binding to the N-terminal region of A beta 42.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Yehong Gong, Chendi Zhan, Yu Zou, Zhenyu Qian, Guanghong Wei, Qingwen Zhang
Summary: This study revealed that serotonin and melatonin can disrupt the structure of Aβ(42) protofibril through different modes of action, with melatonin exhibiting greater binding capacity. The findings provide valuable information for the design of potential drug candidates against Alzheimer's disease.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Pavan Krishna Kanchi, Ashok Kumar Dasmahapatra
Summary: Alzheimer's disease is a major cause of dementia in the elderly population with no current cure. Experimental studies have shown that THC molecules may reduce the fibril content in neurotoxic plaques. Research suggests that THC molecules could be considered for therapy in treating Alzheimer's disease.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Engineering, Environmental
Samal Kaumbekova, Mehdi Amouei Torkmahalleh, Naoya Sakaguchi, Masakazu Umezawa, Dhawal Shah
Summary: Recent studies have found a correlation between environmental pollutants like PAHs and the progression of neurodegenerative disorders. This study revealed that organic pollutants may affect the structure of protein molecules and contribute to the progression of Alzheimer's disease.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Pavan Krishna Kanchi, Ashok Kumar Dasmahapatra
Summary: A designed peptide KLVFFP5 was shown to bind to protofibrils in the brain, reducing beta-sheet content significantly and disrupting hydrogen bonding network and salt bridges. This peptide is considered an effective beta-sheet disruptor and may have potential in Alzheimer's disease therapy.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Biochemistry & Molecular Biology
Shivani Gupta, Ashok Kumar Dasmahapatra
Summary: The omega-3 polyunsaturated fatty acids EPA and HXA have shown potential to destabilize A beta fibrils, the pathological hallmark of Alzheimer's disease, making them promising drug leads for AD treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Rajdeep Kaur, Rajneet Kaur Saini, Pritpal Singh, Bhupesh Goyal
Summary: The study investigated the inhibitory mechanism of the peptidomimetic compound C1 against Aβ(42) aggregation and disassembly of S-shaped protofibril structure through molecular docking and molecular dynamics simulations. Results showed that C1 disrupted the salt bridge interaction within Aβ(42) monomer and destabilized the protofibril structure, leading to lower binding affinity between chains and destabilization of the overall structure. These findings provide insight into the design of potential inhibitors to combat Aβ(42) aggregation and disassembly.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Rayala Swetha, Anjali Sharma, Ravi Singh, Ankit Ganeshpurkar, Devendra Kumar, Ashok Kumar, Sushil K. Singh
Summary: The PDE9 enzyme plays an important role in AD drug discovery as its inhibition can enhance synaptic plasticity and stabilization by increasing cGMP levels and enhancing NMDA signaling. This study used a pharmacophoric approach to identify potential PDE9 inhibitors and successfully identified two compounds with promising inhibitory activity.
MOLECULAR DIVERSITY
(2022)
Article
Biochemistry & Molecular Biology
Na Shi, Qingchuan Zheng, Hongxing Zhang
Summary: This study investigated the recognition and binding mechanism of CYP46A1 with cholesterol using molecular docking and simulations. The study identified key factors affecting their interaction and provided insights for drug design and understanding the structure-function relationship of CYP46A1.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemical Research Methods
Mei Fang, Kehe Su, Xin Wang, Ping Guan, Xiaoling Hu
Summary: In this study, it was found through molecular dynamics simulations that two licochalcones can disrupt the configuration of Aβ(1-42) protofibrils and form stable interactions with them. The presence of licochalcone A or licochalcone B leads to a reduction in the β-sheet structure and an increase in the random coil structure of the Aβ(1-42) protofibrils. Van der Waals interactions and electrostatic interactions play important roles in the binding between licochalcones and Aβ(1-42) protofibrils. This research is significant for the development of new drug candidates against Aβ protofibrils.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Biochemistry & Molecular Biology
Noopur Khare, Sanjiv Kumar Maheshwari, Abhimanyu Kumar Jha
Summary: The study explores the potential of using compounds like Dihydroquercetin as inhibitors for Alzheimer's Disease by targeting Acetylcholinesterase and Butyrylcholinesterase. Molecular docking and dynamics simulations show promising binding patterns and stability, suggesting Dihydroquercetin as a good candidate for further therapeutic studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Hubert Santuz, Phuong H. Nguyen, Fabio Sterpone, Philippe Derreumaux
Summary: This study explores the early aggregation steps of A beta 42 using the deep learning method AlphaFold2 and provides insights into the structure determination of A beta 42 monomers up to hexamers.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Elena Ermakova, Olga Makshakova, Yuriy Zuev, Igor Sedov
Summary: The study utilized accelerated molecular dynamics technique to investigate the unfolding process of hen egg-white lysozyme at elevated temperatures, revealing the potential presence of β-enriched intermediates before the aggregation process. Additionally, the influence of disulfide bonds on conformational dynamics and the energy landscape of denaturation process was considered.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Ravi Singh, Ankit Vyankatrao Pokle, Powsali Ghosh, Ankit Ganeshpurkar, Rayala Swetha, Sushil Kumar Singh, Ashok Kumar
Summary: LIM kinases play a crucial role in the regulation of actin dynamics. In this study, ligand-based drug design and molecular modelling were used to identify potential compounds that can inhibit LIMKs. Through comprehensive docking and molecular dynamics simulation, three virtual hits with optimal binding properties were discovered. These hits have the potential to be developed into drugs for targeting LIMKs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shuheng Huang, Hu Mei, Linxin Chen, Tingting Shi, Zuyin Kuang, Yu Heng, Yonghong Zhang, Laichun Lu
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2020)
Article
Pharmacology & Pharmacy
Hong Wang, Jianchun Luo, Yonghong Zhang, Dan He, Rong Jiang, Xuemei Xie, Qiang Yang, Kailing Li, Jiaxi Xie, Jingqing Zhang
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2020)
Article
Biochemistry & Molecular Biology
Zhenhua Li, Sathishkumar Chinnasamy, Yonghong Zhang, Dong-Qing Wei
Summary: Microcins are small bacterial inhibitory molecules produced by ribosomes, with Microcin J25 having a unique lasso-like structure. The binding of Microcin J25 to its target receptor FhuA is essential for its inhibitory function, with specific amino acid mutations affecting the binding energy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Nanoscience & Nanotechnology
Jing Gu, Yongjia Huang, Zijun Yan, Dan He, Yonghong Zhang, Jingyu Xu, Yao Li, Xuemei Xie, Jiaxi Xie, Da Shi, Ruben Abagyan, Jingqing Zhang, Qunyou Tan
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Nanoscience & Nanotechnology
Xiaoqian He, Jiao Feng, Shenglei Yan, Yonghong Zhang, Cailing Zhong, Yuying Liu, Da Shi, Ruben Abagyan, Tingxiu Xiang, Jingqing Zhang
Summary: A novel biomimetic nanovesicle-loaded supramolecular enzyme-based therapeutic has been developed, utilizing various technologies to combine multiple functional motifs for effective transport of arginine deiminase (ADI) to hepatic tumor cells. The antitumor effects were enhanced by the unique combination of enzyme treatment and components like TPGS within the nanovesicle.
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
(2021)
Article
Chemistry, Applied
Pei Pu, Xin Zheng, Linna Jiao, Lang Chen, Han Yang, Yonghong Zhang, Guizhao Liang
Summary: This study investigated the noncovalent mechanism of inhibiting the antigenicity of beta-LG by six flavonoids, with EGCG showing the highest antigenic inhibition rate. The flavonoids induced conformational changes in beta-LG and bound to specific antigen epitopes to decrease protein antigenicity.
Article
Biochemical Research Methods
Hong Wang, Jingqing Zhang, Zhigang Lu, Weina Dai, Chuanjiang Ma, Yun Xiang, Yonghong Zhang
Summary: This study developed useful drug repurposing tools based on data-driven modeling and network pharmacology. Hub proteins important in the onset and development of COVID-19 were identified as potential targets for repurposing approved drugs. The study also predicted the therapeutic effects of bioactive herbal ingredients and chemicals using network distance metrics in the protein-protein interaction network. The method proves to be advantageous in feasibility analysis of drug repurposing or drug screening during pandemic outbreaks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Juan Huang, Qin Xu, Zhuo Liu, Nitin Jain, Madhusudan Tyagi, Dong-Qing Wei, Liang Hong
Summary: This study found that the high density of salt bridges in CYP450 proteins reduces structural flexibility, affecting substrate selection and catalytic activity. By making slight chemical changes, the CYP450 superfamily can regulate the structural flexibility of its member proteins to differentiate substrate specificities.
Article
Biochemistry & Molecular Biology
Lei Wang, Xia Mu, Wenjin Li, Qin Xu, Ping Xu, Liyun Zhang, Yuebin Zhang, Geng Wu
Summary: This study provides a comprehensive structural, mechanistic, and functional investigation of the molybdenum hydroxylase Kdh in the nicotine degradation pathway of Arthrobacter nicotinovorans. Through crystal structure analysis, molecular docking, molecular dynamics simulations, and enzymatic activity assays, the catalytic mechanism of Kdh was elucidated. Additionally, electrochemical results demonstrated electron transfer among the various cofactors of Kdh.
Article
Food Science & Technology
Wei Luo, Hui Huang, Yonghong Zhang, Faxiang Wang, Jian Yu, Yongle Liu, Xianghong Li
Summary: This study investigated the complex coacervation of rice glutelin and gum arabic under different conditions and found that the formation of maximum complex occurred at specific mass ratios, NaCl concentrations, and in the presence of urea, indicating different structures and interactions between the biopolymers. The molecular docking analysis revealed that hydrogen bonding and hydrophobic interaction, in addition to electrostatic interaction, were the main driving forces for the formation of the RG-GA complex coacervation, providing valuable theoretical and methodological information for the use of rice protein in food products.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zheng Cheng, Yonghong Zhang, Yang Zhuo, Jie Fan, Ying Xu, Mengmeng Li, Hao Chen, Li Zhou
Summary: This study found that the rs2327433 site in lncRNA TARID was associated with the risk of coronary artery disease (CAD) and the severity of the disease in the Chinese Han population. Further analysis showed that the rs2327433 site may affect the expression of the atherosclerosis-related transcription factor TCF21 regulated by lncRNA TARID. The study revealed a new mechanism of lncRNA-mediated cell proliferation.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Chemistry, Physical
Hui-Yuan Zhang, Qin Xu, Dong-Qing Wei
Summary: Charge plays a key role in passive permeation of small molecules, and simulations on water and sulfide molecules reveal distinct characteristics in their permeation processes, with free energy highly correlated with the hydrophilic shell.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemical Research Methods
Tiantian Tang, Xiaofeng Gan, Li Zhou, Kexue Pu, Hong Wang, Weina Dai, Bo Zhou, Lingyun Mo, Yonghong Zhang
Summary: A novel method based on network strategies and machine learning algorithms has been developed to explore the drug-induced liver injury (DILI). The method provides a new approach to predict the hepatotoxicity of drugs and understand the mechanism behind DILI.
CURRENT BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Weizhi Chen, Rui Liu, Yamei Yu, Dongqing Wei, Qiang Chen, Qin Xu
Summary: This study uncovers the molecular mechanisms of cancer-causing mutations in DCLK1 by analyzing its crystal structure and performing molecular dynamics simulations. The disruption of the assembly of the autoinhibitory domain leads to exposure of a key residue in the kinase domain. The researchers conducted a screening process and evaluated the binding affinity of potential inhibitors to DCLK1.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yongjia Huang, Jing Gu, Zijun Yan, Xueyuan Hu, Dan He, Yonghong Zhang, Yao Li, Cailing Zhong, Jie Yang, Da Shi, Ruben Abagyan, Qunyou Tan, Jingqing Zhang