Article
Chemistry, Multidisciplinary
Michal Avital-Shmilovici, Xiaohe Liu, Thomas Shaler, Andrew Lowenthal, Pauline Bourbon, Janey Snider, Arlyn Tambo-Ong, Claire Repellin, Kenya Yniguez, Lidia Sambucetti, Peter B. Madrid, Nathan Collins
Summary: Combinatorial methods allow for the synthesis of large chemical libraries, but screening and sequencing remain challenging. This study developed a novel technology for efficient screening and sequencing of billion-compound synthetic libraries. The versatility and high-throughput of the platform were demonstrated through screening two libraries and finding hits with low nanomolar binding affinities.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Medicinal
Anna Pepanian, Furkan Ayberk Binbay, Suchismita Roy, Britta Nubbemeyer, Amritendu Koley, Curran A. Rhodes, Hermann Ammer, Dehua Pei, Pradipta Ghosh, Diana Imhof
Summary: Novel bicyclic peptides were identified through combinatorial library screening and showed prominent properties as molecular switch-on/off modulators of Gαi signaling, with GPM-3 being the first chemically identified GAP modulator with a high binding affinity for Gαi protein. Computational analyses assessed the structure of the peptides, ligand-protein interaction sites, and their impact on the nucleotide binding site. This approach may lead to the development of efficient chemical biological probes targeting Gαi protein modulation within a cellular context.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Alessandra Monti, Luigi Vitagliano, Andrea Caporale, Menotti Ruvo, Nunzianna Doti
Summary: Protein-protein interfaces play crucial roles in pathophysiological pathways and are important targets for therapeutic compounds. However, identifying binding sites on protein surfaces and developing modulators of protein-protein interactions remain challenging due to their dynamic nature. Various strategies, including structural, computational, and combinatorial approaches, have been developed to characterize PPIs. Peptides are particularly potent and selective for inhibiting PPIs. This review discusses the impact of chemical peptide libraries in medicinal chemistry, focusing on recent applications, and explores the role of this methodology in the era of predictive approaches based on artificial intelligence in structural biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Marianna Zanatelli, Simone Jacovaci Colleta, Luiz Henrique Alves Guerra, Fernanda Cristina Alcantara Santos, Rejane Maira Goes, Patricia Simone Leite Vilamaior, Sebastiao Roberto Taboga
Summary: The study reveals that prolactin has a strong influence on prostate morphology, acting in synergy with androgens in males and mainly with estrogens in females to sustain prostate cell activity. It also demonstrates that prolactin can assist in recovering from atrophic effects caused by castration.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Zhijie Chen, Zhenqin Wang, Yang Xu, Xiaochun Zhang, Boxue Tian, Jingwei Bai
Summary: The study presents a strategy to control peptide translocation through the MspA nanopore, achieving a read length of up to 17 amino acids and demonstrating the feasibility of distinguishing between different amino acid residues or phosphorylation sites. Further engineering of MspA-M2 may be required to improve resolution.
Article
Biochemical Research Methods
Fabian Gauch, Klaus Abraham, Bernhard H. Monien
Summary: This study developed a new method for simultaneous quantification of adducts of eight genotoxic substances in hemoglobin. The method is simple, sensitive, and accurate, and can be extended to other adducts.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Organic
YashoNandini Singh, Predrag Cudic, Mare Cudic
Summary: Fluorescently labelled alanine scan analogues of odorranalectin were used to screen for binding BSA-conjugated monosaccharides. Certain amino acid substitutions increased the binding affinities. The thermodynamics of binding with different molecules were evaluated, showing entropy-driven mechanism for one interaction and enthalpy-entropy compensation for another.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Peixiang Ma, Ping Ren, Chuyue Zhang, Jiaxing Tang, Zheng Yu, Xuekai Zhu, Kun Fan, Guanglei Li, Wei Zhu, Wei Sang, Chenyu Min, Wenzhang Chen, Xingxu Huang, Guang Yang, Richard A. Lerner
Summary: A novel approach using CAR-T cells with an avidity-based selection method has been proposed by scientists, achieving specific recognition of tumor cells with reduced off-tumor effects and retained antitumor efficacy.
Article
Biochemistry & Molecular Biology
Jennifer C. Mortensen, Jovan Damjanovic, Jiayuan Miao, Tiffani Hui, Yu-Shan Lin
Summary: This study introduces a new rotamer library (MEDFORD) created using explicit-solvent metadynamics simulations to assign side chain dihedral angles of amino acids in protein structures. The MEDFORD library has high coverage and accurately predicts side chain conformations in high-resolution protein crystal structures. This approach can also be applied to noncanonical amino acids.
Article
Chemistry, Applied
Xiao Sun, Lulu Zhu, Xin Qi, Hongwei Zhang, Ling Wu, Jinhua Wang, Hu Hou
Summary: The non-enzymatic degradation of ready-to-eat sea cucumber products is closely related to their quality, as indicated by decreased hardness, increased free water content, and higher levels of free hydroxyproline. Protein was found to break easily at specific sites, with certain peptide bonds being more susceptible to cleavage, while the relative free energies of specific steps determined the rate of peptide bond cleavage.
Article
Agriculture, Dairy & Animal Science
F. Sosa, A. T. Carmickle, L. J. Oliveira, M. Sagheer, M. Saleem, F. H. Yu, M. D. Altman, S. Dikmen, A. C. Denicol, T. S. Sonstegard, C. C. Larson, P. J. Hansen
Summary: This study suggests that the SLICK1 mutation does not alter the abundance of sweat glands in the skin, but it does modify the functional properties of the sweat glands.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Chemistry, Medicinal
Thomas Liphardt, Thomas Sander
Summary: We propose an efficient algorithm for substructure search in combinatorial libraries defined by synthons. Our method improves on existing approaches by introducing powerful heuristics and fast fingerprint screening. With this, we achieve quick response times for searches in large combinatorial libraries. We have also made the Java source code available under the BSD license and implemented tools for substructure search in custom combinatorial libraries.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Agriculture, Dairy & Animal Science
Froylan Sosa, Jose E. P. Santos, D. Owen Rae, Colleen C. Larson, Marissa Macchietto, Juan E. Abrahante, Thiago F. Amaral, Anna C. Denicol, Tad S. Sonstegard, Peter J. Hansen
Summary: The SLICK1 mutation in bovine PRLR results in a phenotype characterized by short hair coat and increased heat stress resistance. The mutation, a dominant allele affecting liver gene expression, can also potentially impact other physiological characteristics. Results suggest that inheritance of the SLICK1 allele can lead to functional changes beyond hair growth effects.
Article
Food Science & Technology
Nick Bergau, Uta M. Herfurth, Benjamin Sachse, Klaus Abraham, Bernhard H. Monien
Summary: Estragole and anethole are secondary metabolites found in commonly used herbs, with potential genotoxic and carcinogenic effects. Research has shown similarities in their metabolic pathways and bioactivation. Specific adducts were detected in human blood, indicating internal exposure to these compounds.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Article
Endocrinology & Metabolism
Zin Khant Aung, Ilona C. Kokay, David R. Grattan, Sharon R. Ladyman
Summary: Adaptive changes in glucose regulation during pregnancy involve proliferation of insulin-secreting beta-cells in the pancreas and increased sensitivity to glucose-stimulated insulin secretion. Maternal prolactin/placental lactogen concentrations play a role in these changes, with evidence suggesting the pancreas as the direct target of these actions.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xuewen Qin, Hongting Tang, Wenbing Cao, Zhen Dai, Liming Hu, Yujia Huang, Tao Liu
Editorial Material
Biochemistry & Molecular Biology
Vaishnavi Ananthanarayanan, Kausik Chattopadhyay, Lei Chen, Liang Cheng, Laura Edgington-Mitchell, Sandeep Eswarappa, Tanweer Hussain, Taiho Kambe, Seokhee Kim, Jun-Seok Lee, Mihye Lee, Xuechen Li, Mi Hee Lim, Sang Min Lim, Shixian Lin, Tao Liu, Radhakrishnan Mahalakshmi, Samir K. Maji, Athi N. Naganathan, Wataru Nomura, Toby Passioura, Yu Rao, Govardhan Reddy, Hyun-Woo Rhee, Ashok Sekhar, Jiwon Seo, Arun Kumar Shukla, Mahavir Singh, Woon Ju Song, Hongyan Sun, Tomonori Tamura, Chun Tang, Shinya Tsukiji, Cai-Guang Yang, Chengqi Yi, Peng Zou, Alanna Schepartz
Article
Chemistry, Multidisciplinary
Yong Wang, Xiaoxu Chen, Wenkang Cai, Linzhi Tan, Yutong Yu, Boyang Han, Yuxuan Li, Yuanzhe Xie, Yeyu Su, Xiaozhou Luo, Tao Liu
Summary: Incorporation of structurally novel noncanonical amino acids (ncAAs) into proteins was achieved through biosynthesis, with nearly 50 ncAAs synthesized from simple small-molecule precursors. Furthermore, bioorthogonal reactive groups could be incorporated into proteins with high yields for subsequent chemical conjugation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Wenbing Cao, Xuewen Qin, Yong Wang, Zhen Dai, Xianyin Dai, Haoyu Wang, Weimin Xuan, Yingming Zhang, Yu Liu, Tao Liu
Summary: A general host-guest molecular recognition approach involving modification of protein functional surfaces with genetically encoded unnatural amino acids has been developed in this study, which can reversibly regulate protein function through molecular recognition, providing valuable tools for studying protein functions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Editorial Material
Biochemistry & Molecular Biology
Wenbing Cao, Xuewen Qin, Tao Liu
Summary: Supramolecular chemistry is a promising approach for targeting proteins, utilizing genetic-code expansion and enzyme-mediated ligation to build guest recognition elements. This allows for supramolecular control of protein function and regulation.
Review
Biochemistry & Molecular Biology
Xuewen Qin, Tao Liu
Summary: Protein phosphorylation is a crucial posttranslational modification involved in cell signaling. The use of genetic code expansion has advanced the study of protein phosphorylation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xinyu Ling, Liying Chang, Heqi Chen, Xiaoqin Gao, Jianhang Yin, Yi Zuo, Yujia Huang, Bo Zhang, Jiazhi Hu, Tao Liu
Summary: Researchers have improved the genome editing efficiency of the Cas12a system by covalently linking CRISPR RNA and Cas12a, achieving high-efficiency gene editing and providing a new approach for engineering other low-efficiency Cas family members.
Article
Biochemistry & Molecular Biology
Chao Chen, Guiling Yu, Yujia Huang, Wenhui Cheng, Yuxuan Li, Yi Sun, Haifeng Ye, Tao Liu
Summary: The engineered NATS system allows for fast therapeutic protein expression triggered by noncanonical amino acids at the translational level, demonstrating potential for next-generation cell-based therapies with orally induced protein expression.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiaoyu Song, Fengrui Yang, Xu Liu, Peng Xia, Wu Yin, Zhikai Wang, Yong Wang, Xiao Yuan, Zhen Dou, Kai Jiang, Mingming Ma, Bing Hu, Rui Zhang, Chao Xu, Zhiyong Zhang, Ke Ruan, Ruijun Tian, Lin Li, Tao Liu, Donald L. Hill, Jianye Zang, Xing Liu, Jinsong Li, Jinke Cheng, Xuebiao Yao
Summary: This study identified a new mitosis-specific crotonylation-regulated astral microtubule-EB1-NuMA interaction that plays a crucial role in accurate spindle positioning. Real-time imaging of chromosome movements in HeLa cells expressing genetically encoded crotonylated EB1 demonstrated the importance of crotonylation dynamics for precise control of spindle orientation during metaphase-anaphase transition. These findings highlight a general signaling cascade that integrates protein crotonylation with accurate spindle positioning for chromosome stability in mitosis.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Dan Wu, Yunfeng Zhang, Zhiheng Tang, Xiaoxu Chen, Xinyu Ling, Longtu Li, Wenbing Cao, Wei Zheng, Jiale Wu, Hongting Tang, Xiaoyun Liu, Xiaozhou Luo, Tao Liu
Summary: This study investigates the functions and regulations of structurally diverse acylations as post-translational modifications (PTMs) on histone lysine residues. It introduces the concept of a lysine acylation analog, pyrrolysine, as a co-translational modification (CTM) through genetic encoding. By creating a model organism Saccharomyces cerevisiae with site-specific lysine CTMs at histone H3K56, the study demonstrates that acetylation of histone H3K56 provides a more favorable chromatin environment for DNA repair compared to crotonylation and crosstalk with other PTMs differently. This research provides a potentially universal approach to understanding the consequences of different histone lysine PTMs in eukaryotes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Editorial Material
Chemistry, Multidisciplinary
Xinyu Ling, Tao Liu
Summary: Wang and his team provide an elegant selection platform to identify the targets of a nonproliferative drug by linking transcription activation to a suicide gene.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dan Wu, Tao Liu
Summary: Understanding post-translational modifications is crucial for manipulating physiological processes in eukaryotes. Genetic code expansion technology has been used to investigate the roles of these modifications, and can be combined with synthetic biology to create genetically modified organisms. This article discusses the applications, limitations, and future perspectives of genetic code expansion technology for studying post-translational modifications, as well as the implications for genetically modified organisms.
Editorial Material
Biochemistry & Molecular Biology
Tao Liu
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemical Research Methods
Xinyu Ling, Liying Chang, Heqi Chen, Tao Liu
Summary: A system utilizing conjugated Cas12a and its CRISPR RNA is developed to efficiently edit human cells and precisely integrate CAR genes into the T cell genome.
Article
Chemistry, Multidisciplinary
Xinyu Ling, Xiaoqin Gao, Liying Chang, Heqi Chen, Xiaomeng Shi, Tao Liu
CHEMICAL COMMUNICATIONS
(2020)
