Article
Chemistry, Physical
Dan Zhao, Shijun Zhong
Summary: This study investigated the binding mechanisms of varic acid inhibitors on PTP1B using molecular docking, molecular dynamics simulation, and MM/GBSA binding free energy calculation. The research identified key structural characteristics in the ligand binding and designed novel varic acid derivatives for lead validation. The retained molecules showed more favorable binding free energy compared to the parent structure compound 6.
MOLECULAR SIMULATION
(2021)
Article
Biochemistry & Molecular Biology
Dao-Cuong To, Thanh Q. Bui, Nguyen Thi Ai Nhung, Quoc-Toan Tran, Thi-Thuy Do, Manh-Hung Tran, Phan-Phuoc Hien, Truong-Nhan Ngu, Phan-Tu Quy, The-Hung Nguyen, Huu-Tho Nguyen, Tien-Dung Nguyen, Phi-Hung Nguyen
Summary: Folk experiences suggest natural products in Tetradium ruticarpum can be effective inhibitors towards diabetes-related enzymes. Experimental studies isolate two natural products which demonstrate high potential in inhibiting PTP1B and alpha-glucosidase, suggesting potential alternatives for diabetes treatment. Computational methods confirm the stability of the ligands and their interaction with targeted proteins, correlating with experimental results.
Article
Spectroscopy
Bin Li, Ranran Fu, Hui Tan, Ye Zhang, Wei Teng, Zhiying Li, Jinlong Tian
Summary: Procyanidins PB1 and PB2 inhibit the activity of PTP1B in a mixed inhibition mode, leading to decreased enzyme activity and altered secondary structure. Hydrophobic interactions play a key role in the binding of procyanidins with PTP1B.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Multidisciplinary Sciences
Muhammad Shahab, Shahin Shah Khan, Maryam Zulfat, Yousef A. Bin Jardan, Amare Bitew Mekonnen, Mohammed Bourhia, Guojun Zheng
Summary: Cancer is a leading cause of death, with an estimated 9.6 million deaths in 2018, and around 500,000 deaths from cancer annually in the United States alone. The SHP2 enzyme plays a key role in cell regulation and its dysregulation is associated with oncogenesis. In this study, we designed peptide inhibitors against SHP2 mutant and identified mutations that enhanced binding affinity. Molecular dynamics simulations and energy calculations confirmed the stability and improved binding affinity of the mutated peptide. Our findings suggest that our proposed peptide may inhibit SHP2 and prevent cancer metastasis.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Mohd Saeed, Ambreen Shoaib, Munazzah Tasleem, Nadiyah M. Alabdallah, Md Jahoor Alam, Zeina El Asmar, Qazi Mohammad Sajid Jamal, Fevzi Bardakci, Saad S. Alqahtani, Irfan Ahmad Ansari, Riadh Badraoui
Summary: Diabetes mellitus is a major global public health issue, requiring the search for safe and effective drugs. Shikonin may serve as an anti-diabetic agent, showing competitive inhibitory effects on PTP1B, and has the potential to be a source for the production of preventive and therapeutic agents.
Review
Oncology
Pei-Jie Chen, Yun-Tian Zhang
Summary: Tyrosine phosphorylation is a reversible process regulated by protein tyrosine kinases and phosphatases. Abnormalities in these proteins, such as PTP1B, can contribute to the development of diseases including cancer. Recent studies have shown that PTP1B plays an important role in cancer initiation and progression, making it a potential target for cancer therapies. This review focuses on the functions and pharmacological effects of PTP1B in different types of cancer.
CURRENT CANCER DRUG TARGETS
(2022)
Review
Medicine, Research & Experimental
Tapan Behl, Amit Gupta, Aayush Sehgal, Ali Albarrati, Mohammed Albratty, Abdulkarim M. Meraya, Asim Najmi, Saurabh Bhatia, Simona Bungau
Summary: Type 2 diabetes is a widely spread metabolic disorder with limitations in conventional therapies. Protein tyrosine phosphatase is a promising therapeutic target, and various inhibitors have shown effectiveness in managing diabetes.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Chemistry, Physical
B. Manasa, Suman Manandhar, Gangadhar Hari, Keerthi Priya, B. Harish Kumar, K. Sreedhara Ranganath Pai
Summary: Neuroinflammation, a key feature in neurodegenerative diseases like Alzheimer's disease, leads to increased expression of PTP1B, promoting inflammation. Computational studies identified potential PTP1B inhibitors from a library of phytomolecules, with top compounds showing promising binding interactions and pharmacokinetic properties, warranting further experimental validation.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Medicinal
Ying Yang, Lei Zhang, Jinying Tian, Fei Ye, Zhiyan Xiao
Summary: A hierarchical virtual screening identified four potential PTP1B inhibitors with distinct structures, among which H3 and H9 showed selectivity to PTP1B. Key residues responsible for potent allosteric inhibition and excellent PTP selectivity were identified through molecular dynamics simulations and MM-GBSA calculations, aiding future molecular design of PTP1B allosteric inhibitors.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Orathai Saeting, Kasemsiri Chandarajoti, Angsuma Phongphisutthinan, Parichat Hongsprabhas, Sudathip Sae-tan
Summary: The study demonstrated that mungbean water extract increased cellular glucose uptake and improved insulin sensitivity of insulin-resistant HepG2 cells by inhibiting PTP-1B and modulating the expression of genes related to glucose metabolism. This suggests that mungbean water extract has the potential to be a functional ingredient for diabetes.
Article
Multidisciplinary Sciences
Hyunbum Jang, Iris Nira Smith, Charis Eng, Ruth Nussinov
Summary: The research used explicit solvent simulations to uncover how PTEN is localized on the cell membrane and inhibits cancer. By observing the interaction of PTEN with different components of the cell membrane, the study revealed its localization on signaling lipids and its effect on PIP3.
Article
Biochemistry & Molecular Biology
Miriam Diaz-Rojas, Huzefa Raja, Martin Gonzalez-Andrade, Jose Rivera-Chavez, Manuel Rangel-Grimaldo, Isabel Rivero-Cruz, Rachel Mata
Summary: Three undescribed compounds, named alboluteins A-C, were isolated from solid rice-based cultures of Malbranchea albolutea. These compounds showed inhibitory activity against PTP1B, with albolutein C behaving as a noncompetitive inhibitor. Docking and molecular dynamic studies indicated that the compounds prefer to bind at the allosteric site of the enzyme, providing insights into their mechanism of action.
Article
Chemistry, Physical
Antonios Kousaxidis, Anthi Petrou, Philippa Rouvim, Pavol Bodo, Milan Stefek, Ioannis Nicolaou, Athina Geronikaki
Summary: This study designed a series of novel benzothiazole-based 4-oxothiazolidin-2-yl-imino acetic acid derivatives as aldose reductase inhibitors. The compounds 5b and 5d showed potent inhibitory activity and optimal selectivity. Docking simulations were performed to explore the binding modes and the influence of fluorinated moieties on selectivity profiles.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biochemistry & Molecular Biology
Emanuele Bellacchio
Summary: The localization and activity of SHP2 tyrosine phosphatase are regulated by the binding of phosphotyrosine peptides to the tandem SH2 domains. The N-SH2 domain can inhibit the enzyme's activity by blocking the catalytic site, but this inhibition can be relieved by binding of phosphotyrosine peptides. A molecular dynamics simulation study reveals that the closed conformation of the self-inhibited phosphatase is stabilized by the interaction between the N-SH2 domain and a conserved peptide portion in PTPN11 exon 6.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Daopeng Tan, Jianmei Wang, Xianting Wang, Lin Qin, Yimei Du, Changkuo Zhao, Peijun Liu, Qianru Zhang, Feifei Ma, Jian Xie, Di Wu, Yuqi He
Summary: This study evaluated the inhibitory activity of five new and four known compounds isolated from Gynostemma pentaphyllum on PTP1B, a key factor and regulator of glucose and lipid metabolism. The results showed that all the compounds exhibited significant inhibitory activity against PTP1B. The structure-activity relationship indicated that the strength of PTP1B inhibitory activity was mainly related to the presence of an electron-donating group on its side chain.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
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)