Article
Biochemistry & Molecular Biology
Jie Liu, Tangbing Cui
Summary: Leucyl-aminopeptidase (LAP), an important metallopeptidase, hydrolyses amino acid residues from the N-terminus of polypeptides and proteins. A new leucyl-aminopeptidase, bcLAP, was found in Bacillus cereus CZ, and it showed moderate thermostability and alkaline pH adaptation range. Molecular docking results suggested the involvement of specific residues in hydrogen bonding with ligands and zinc ions, and two different catalytic mechanisms may exist in bcLAP.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Tingjunhong Ni, Zichao Ding, Fei Xie, Yumeng Hao, Junhe Bao, Jingxiang Zhang, Shichong Yu, Yuanying Jiang, Dazhi Zhang
Summary: In this study, a series of triazole derivatives with good antifungal activities were designed and synthesized. Compound 6c showed excellent in vitro and in vivo activities against various fungal strains, making it a promising candidate for further investigation.
Article
Biochemistry & Molecular Biology
Preeti Jha, Shubhra Chaturvedi, Ruchika Bhat, Nidhi Jain, Anil K. Mishra
Summary: The 5HT1A receptor is crucial in the treatment of depression and anxiety disorders, and the developed homology model shows promise in designing high-affinity probes for these neurological disorders.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Entomology
Yuting Yang, Liang Luo, Lixia Tian, Changwei Zhao, Hongli Niu, Yifeng Hu, Caihua Shi, Wen Xie, Youjun Zhang
Summary: The study reveals the olfactory function of BodoOBP8 in recognizing plant volatiles and sex pheromones, providing insights into new approaches for controlling B. odoriphaga. Real-time PCR analysis confirms the importance of BodoOBP8 in the olfactory process, laying the theoretical foundation for the development of novel ways to control B. odoriphaga.
Article
Biochemistry & Molecular Biology
Anica Dadwal, Vishal Singh, Shilpa Sharma, Tulasi Satyanarayana
Summary: This study analyzed the structure of a cellulase enzyme from a thermophilic fungus using computational methods. The study provided insights into the structural characteristics of the enzyme and predicted its binding sites and tolerance to different sugars.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Bhrugesh Pravinchandra Joshi, Vishwambhar Vishnu Bhandare, Prittesh Patel, Abhishek Sharma, Rajesh Patel, Ramar Krishnamurthy
Summary: This study aims to investigate the structure and function of DLL3 using molecular modeling techniques, providing more insights into the treatment of neuroendocrine differentiated prostate cancer. Several potential DLL3 inhibitors were identified through virtual screening and affinity calculations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Entomology
Yang Yuting, Hua Dengke, Shi Caihua, Xie Wen, Zhang Youjun
Summary: In this study, a full-length cDNA sequence of BodoOBP5 was cloned from the insect pest Bradysia odoriphaga, and its expression patterns in different developmental stages and tissues were investigated. The results demonstrated that BodoOBP5 strongly binds to two sulfur compounds and specific amino acid residues are crucial for this interaction.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mustapha Abdullahi, Adamu Uzairu, Gideon Adamu Shallangwa, Paul Andrew Mamza, Muhammad Tukur Ibrahim, Anshuman Chandra, Vijay Kumar Goel
Summary: Using molecular modelling strategies and quantitative structure-activity relationship studies, substituted indole molecules with anti-IAV activity were identified, and new molecules with enhanced activity were designed. The developed models and contour maps illustrate the relationship between molecular fields and inhibitory effects, and molecular dynamics simulations confirmed the binding stability of the designed molecules with the NA protein.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Environmental Sciences
Wei-hao Yao, Ling-yun Mo, Liu-sen Fang, Li-tang Qin
Summary: A large number of antibiotics have been extensively used in various industries in recent years, which may lead to pollution in the aquatic environment and pose a threat to human health. This study aims to investigate the toxicity mechanism of five antibiotics on luciferase. Through a combination of toxicity testing, molecular docking, molecular dynamics, and binding free energy analysis, the researchers found that the toxicity and binding energy of the antibiotics were correlated. The shape compensation and specific interactions between the antibiotics and luciferase were identified as important factors in their toxicity. This research provides insights into the toxicity mechanisms of antibiotics and contributes to the risk assessment of antibiotic contaminants in the aquatic environment.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Pharmacology & Pharmacy
M. Pooja, Gangavaram Jyothi Reddy, Kanipakam Hema, Sujatha Dodoala, Bharathi Koganti
Summary: The COVID-19 pandemic has prompted the search for effective drug candidates due to the lack of vaccines and drugs. This study focused on the TMPRSS2 enzyme as a potential pharmacological target and identified eight high affinity drug candidates through modeling and molecular docking studies.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhaochen Wu, Guozhen Wang, Borui Zhang, Tan Dai, Anyu Gu, Xiaolin Li, Xingkai Cheng, Pengfei Liu, Jianjun Hao, Xili Liu
Summary: Probenazole fungicide is used to control rice blast by inducing disease resistance in plants. Treatment with probenazole significantly impacted the metabolic profile of rice seedlings, with specific metabolites up-regulated and others down-regulated. The study revealed a metabolic pathway of rice seedlings induced by probenazole treatment.
Article
Plant Sciences
Nagaraju Jhansirani, Venkatappa Devappa, Chittarada Gopal Sangeetha, Shankarappa Sridhara, Kodegandlu Subbanna Shankarappa, Mooventhiran Mohanraj
Summary: Through homology modeling and docking analysis, it was found that phytochemicals from cucumber, antimicrobial compounds from botanical sources, and chemically synthesized compounds can interact with proteins linked to cucumber downy mildew, showing potential antifungal activity.
Article
Biochemistry & Molecular Biology
Pavel A. Montero-Dominguez, Sergio Mares-Samano, Ramon Garduno-Juarez
Summary: Discrepin is a toxin extracted from the venom of Venezuelan scorpion Tityus discrepans, which inhibits ionic transit in voltage-dependent potassium channels (Kv) of A-type current. The specific residues affecting the IC50 between Discrepin and Kv4.3 have been known, but the molecular details of the toxin-channel interaction remain unclear. In this study, interaction models between Discrepin and two peptide variants on the pore-forming domain of Kv4.3 channel were proposed using homology, docking, and molecular dynamics modeling techniques. The free energy calculations in these models are consistent with the experimentally determined IC50 values. Our findings highlight the importance of the K13 residue in blocking the Kv4.3 selectivity filter and the significance of the V6K mutation in the approach and stabilization of toxin-channel complex interactions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Vinay Kumar Singh, Arvind M. Kayastha
Summary: This study determined the three-dimensional structure of fenugreek α-amylase using homology modeling and analyzed its molecular basis and mode of action through molecular dynamics simulations and molecular docking. The study identified functional groupings and binding interactions between the enzyme and its substrate maltose. The research provides valuable insights into the atomic-level molecular underpinnings of α-amylase interaction with maltose.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Entomology
Qingtai Wang, Kui Fang, Lizhong Qi, Xiao Wang, Yu Pan, Yunshuo Li, Jinghui Xi, Juhong Zhang
Summary: This study identified and cloned a trehalase gene (LoTRE1) in rice water weevil and investigated its expression levels in different tissues. The study found that LoTRE1 plays a crucial role in the development of the rice water weevil, which could be valuable for future pest control efforts.
Article
Environmental Sciences
Jingnan Jin, Jun Yao, Wenjuan Liu, Qingye Zhang, Jianli Liu
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Bangqiang Mao, Min Gao, Changshui Chen, Zhijun Li, Hong-Yu Zhang, Qingye Zhang
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Bo-Min Lv, Xin-Yu Tong, Yuan Quan, Meng-Yuan Liu, Qing-Ye Zhang, Yun-Feng Song, Hong-Yu Zhang
Article
Chemistry, Medicinal
Xuan Liao, Qing-Ye Zhang, Lei Xu, Hong-Yu Zhang
Article
Biochemistry & Molecular Biology
Ze-Jia Cui, Wei-Tong Zhang, Qiang Zhu, Qing-Ye Zhang, Hong-Yu Zhang
PROTEIN AND PEPTIDE LETTERS
(2020)
Article
Environmental Sciences
Xiao-Long Liang, Zhan-Min Liang, Shuo Wang, Xiao-Hui Chen, Yao Ruan, Qing-Ye Zhang, Hong-Yu Zhang
JOURNAL OF ENVIRONMENTAL SCIENCES
(2020)
Article
Genetics & Heredity
Yuan Quan, Qing-Ye Zhang, Bo-Min Lv, Rui-Feng Xu, Hong-Yu Zhang
MOLECULAR GENETICS & GENOMIC MEDICINE
(2020)
Article
Clinical Neurology
Hui Wang, David A. Bennett, Philip L. De Jager, Qing-Ye Zhang, Hong-Yu Zhang
Summary: This study conducted a genome-wide epistasis analysis to identify novel genetic interactions potentially involved in Alzheimer's disease, and developed a new method to assess the genetic risk of AD. The findings suggest that Epistasis Risk Scores (ERS) can serve as an indicator for genetic risk of AD.
ALZHEIMERS RESEARCH & THERAPY
(2021)
Article
Chemistry, Medicinal
Min-Hui Cao, Bao-He Tang, Yao Ruan, Xiao-Long Liang, Xin-Yi Chu, Zhan-Min Liang, Qing-Ye Zhang, Hong-Yu Zhang
Summary: The study introduced a specific bactericidal design strategy by optimizing antibacterial agents with exogenous metabolites, resulting in improved antibacterial activity and selectivity.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Virology
Xuan Xu, Qing-Ye Zhang, Xin-Yi Chu, Yuan Quan, Bo-Min Lv, Hong-Yu Zhang
Summary: The article summarizes the genetic, subcellular location, and evolutionary features of human genes that have been successfully used as antiviral targets. These features are then used to screen novel druggable antiviral targets and find potential antiviral drugs, aiming to promote the discovery of new antiviral drugs.
Article
Biochemistry & Molecular Biology
Yao Ruan, Xiao-Hui Chen, Feng Jiang, Yan-Guang Liu, Xiao-Long Liang, Bo-Min Lv, Hong-Yu Zhang, Qing-Ye Zhang
Summary: The study used a network module-based method for drug repositioning, clustering drugs with similar pharmacology based on differential metabolic flux distribution, and identifying candidate drugs for inhibiting JEV infection. The findings provide new insights into drug repositioning strategies and their mechanisms of action.
Article
Biochemistry & Molecular Biology
Xuan Xu, Hui Wang, David A. Bennett, Qing-Ye Zhang, Gang Wang, Hong-Yu Zhang
Summary: Using systems genetics methods, mitochondrial-associated nuclear genes involved in the pathogenesis of AD were identified and AD risk prediction models were constructed.
Article
Biochemistry & Molecular Biology
Hao Tang, Yanguang Liu, Yao Ruan, Lingqiao Ge, Qingye Zhang
Summary: This study reveals the adaptive metabolic changes in peripheral blood mononuclear cells (PBMCs) in severe COVID-19 patients and identifies potential therapeutic targets, providing reference for immune cell metabolism-targeting therapy against COVID-19.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xin-Yu Tong, Xuan Liao, Min Gao, Bo-Min Lv, Xiao-Hui Chen, Xin-Yi Chu, Qing-Ye Zhang, Hong-Yu Zhang
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Article
Mathematics, Applied
Qingye Zhang, Bin Xu
ELECTRONIC JOURNAL OF QUALITATIVE THEORY OF DIFFERENTIAL EQUATIONS
(2017)