Article
Chemistry, Multidisciplinary
Antonella Ciancetta, Amandeep Kaur Gill, Tianyi Ding, Dmitry S. Karlov, George Chalhoub, Peter J. McCormick, Irina G. Tikhonova
Summary: This study developed a probe confined dynamic mapping protocol to predict allosteric sites on GPCRs, demonstrating the advantage of specific probes derived from GPCR allosteric ligand structures over commonly used cosolvents in allosteric site mapping. The protocol was successfully validated retrospectively on selected receptors and prospectively on the D-2 dopamine receptor, confirming the prediction through subsequent mutagenesis. It provides a fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins, aiding in the design of allosteric modulators based on protein structure.
ACS CENTRAL SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Prashant Donthamsetti, David B. Konrad, Belinda Hetzler, Zhu Fu, Dirk Trauner, Ehud Y. Isacoff
Summary: G protein-coupled receptors (GPCRs) are common drug discovery targets, but the complexity of in vivo receptor activation has hindered drug development. Photopharmacology offers the potential to control drug action using light. Recent advances include a photoswitchable allosteric agonist that selectively activates receptors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Janik B. Hedderich, Margherita Persechino, Katharina Becker, Franziska M. Heydenreich, Torben Gutermuth, Michel Bouvier, Moritz Buenemann, Peter Kolb
Summary: Researchers computationally describe alternative allosteric pockets in G-protein-coupled receptors, identifying nine previously untargeted sites for synthetic ligands. They further investigate the potential of modulating receptor function through ligand binding to these sites.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Faisal Malik, Zhijun Li
Summary: Analyzing over 100 representative human GPCR structures, a common allosteric site has been identified in the intracellular region below the middle of the transmembrane domain. This site is druggable for 89% of GPCRs and shows variation in physico-chemical properties and amino acid composition within and among different GPCR classes, suggesting it as a potential target for structure-based allosteric drug design.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Review
Oncology
Kayla E. Kroning, Wenjing Wang
Summary: This review discusses the design and application of sensors for real-time detection of GPCR agonists in vivo, as well as methods for integrating these agonist signals into quantifiable marks. It also explores the potential of using real-time and integrator sensors together to study the spatiotemporal dynamics of GPCR agonist release.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Felix Sigmund, Oleksandr Berezin, Sofia Beliakova, Bernhard Magerl, Martin Drawitsch, Alberto Piovesan, Filipa Goncalves, Silviu-Vasile Bodea, Stefanie Winkler, Zoe Bousraou, Martin Grosshauser, Eleni Samara, Jesus Pujol-Marti, Sebastian Schaedler, Chun So, Stephan Irsen, Axel Walch, Florian Kofler, Marie Piraud, Joergen Kornfeld, Kevin Briggman, Gil Gregor Westmeyer
Summary: By incorporating metal-interacting moieties into encapsulin nanocompartments, researchers created a suite of electron microscopy-readable barcodes called EMcapsulins. These barcodes can be automatically segmented and differentiated, and their coding capacity can be increased by arranging them into distinct patterns. EMcapsulins are compatible with different types of electron microscopy techniques and can provide multiplexed gene expression maps. They have been successfully applied to brain imaging.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Hsin-Yung Yen, Idlir Liko, Wanling Song, Parth Kapoor, Fernando Almeida, Joanna Toporowska, Karolina Gherbi, Jonathan T. S. Hopper, Steven J. Charlton, Argyris Politis, Mark S. P. Sansom, Ali Jazayeri, Carol Robinson
Summary: This study presents a mass spectrometry-based approach to investigate the biased signaling and allosteric modulation of the beta(1)-adrenergic receptor in response to different ligands. The researchers discovered that isoprenaline can act as a biased agonist and that endogenous zinc ions enhance the binding between the receptor and G(s) proteins.
Article
Biotechnology & Applied Microbiology
Kanuj Mishra, Juan Pablo Fuenzalida-Werner, Francesca Pennacchietti, Robert Janowski, Andriy Chmyrov, Yuanhui Huang, Christian Zakian, Uwe Klemm, Ilaria Testa, Dierk Niessing, Vasilis Ntziachristos, Andre C. Stiel
Summary: Reversibly photo-switchable proteins have been utilized for super-resolution and optoacoustic imaging methods, and in this study, a prototype of a photo-switchable Ca2+ sensor was constructed based on GCaMP5G. The molecular mechanisms of the sensor were described at the structural level, demonstrating the ability to image calcium and other analytes at super-resolution and in vivo.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shanshan Li, Nanxi Wang, Bingchen Yu, Wei Sun, Lei Wang
Summary: Protein-carbohydrate interactions are important in biological processes but challenging to study. This study engineered covalent linkages between proteins and carbohydrates, offering a solution to overcome the low affinity and weak strength of these interactions.
Article
Chemistry, Analytical
Yan Peng, Linjuan Shu, Xiongfei Deng, Xin Huang, Xianming Mo, Feng Du, Zhuo Tang
Summary: We developed a genetically encoded sensor for sensitive imaging and tracking of endogenous RNA in living cells. This sensor can specifically recognize target RNAs and induce structural changes to enable fluorescence imaging. We successfully demonstrated its application in monitoring mRNA expression and confirming RNA distribution in cancer cells and zebrafish embryos, respectively. This study provides an effective molecular tool for RNA imaging and has potential applications in disease diagnosis and treatment evaluation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Hongxia Zhao, Chao Liu, Wenlong Ding, Ling Tang, Yu Fang, Yulin Chen, Linzhen Hu, Ying Yuan, Dong Fang, Shixian Lin
Summary: This study reports an approach to greatly increase the binding energy of cation-pi interactions by replacing Trp in the aromatic box with an electron-rich Trp derivative. By using this approach, the binding affinity between histone H3K4me3 and its reader can be significantly enhanced, and a high-affinity H3K4me3 Super-Reader can be constructed.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Endocrinology & Metabolism
Siyuan Shen, Chang Zhao, Chao Wu, Suyue Sun, Ziyan Li, Wei Yan, Zhenhua Shao
Summary: GPCRs, as the largest family of transmembrane proteins, regulate various physiological processes. However, their complicated signal transduction pathways and difficulties in drug development have presented challenges. By identifying new ligands that bind to allosteric sites, safer drugs for treating various diseases can be designed.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Wei Sun, Nanxi Wang, Hongjiang Liu, Bingchen Yu, Ling Jin, Xingjie Ren, Yin Shen, Lei Wang
Summary: Protein-RNA interactions play a crucial role in regulating the fate and function of RNA. This study demonstrates a novel approach, using genetically encoded unnatural amino acids, to crosslink proteins with bound RNA and analyze their interactions. The technique allows for the identification of specific RNA molecules and the discovery of unknown chemical modifications in cells. This research is highly significant in advancing our understanding of protein-RNA interactions in biological processes.
Article
Chemistry, Multidisciplinary
Li Wang, Jia Zhang, Ming-Jie Han, Lu Zhang, Chao Chen, Aiping Huang, Ruipei Xie, Guosheng Wang, Jiangrui Zhu, Yuchuan Wang, Xiaohong Liu, Wei Zhuang, Yunliang Li, Jiangyun Wang
Summary: The genetic incorporation of a novel 2D-IR probe, N3Y, in the active site of DddK enzyme demonstrates potential application in investigating enzyme dynamics. Results indicate that oxidation of active-site iron to Fe-III and addition of denaturation reagents result in significant decrease in enzyme activity and active-site water motion confinement, highlighting the importance of tyrosine residues in enzyme function.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Augustine George, Mohan Indhu, Sundarapandian Ashokraj, Ganesh Shanmugam, Ponesakki Ganesan, Numbi Ramudu Kamini, Niraikulam Ayyadurai
Summary: Genetic code engineering is used to modify proteins for enhanced biological availability, with the addition of 3,4-dihydroxy-L-phenylalanine through tyrosinase catalysis. This method allows for selective cell labeling and improved sensitivity for protein-based fluorescence labeling.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Review
Biophysics
Karim Fahmy, Thomas P. Sakmar
Summary: The centenary of H. Gobind Khorana's birth provides an opportunity to review the origins and evolution of biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary collaboration in the Khorana laboratory led to significant advances in the biophysical study of membrane proteins, particularly in understanding the molecular mechanisms of energy transduction by bacteriorhodopsin and signal transduction by rhodopsin. This review focuses on the application of molecular genetics approaches to engineer alterations in membrane protein structures, enabling detailed studies of membrane proteins.
BIOPHYSICAL REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Kinga Ostrowska, Anna Lesniak, Weronika Gryczka, Lukasz Dobrzycki, Magdalena Bujalska-Zadrozny, Bartosz Trzaskowski
Summary: A series of piperazine-containing derivatives of 6-acetyl-7-hydroxy-4-methylcoumarin were designed and synthesized to study their affinity for serotonin receptors. Compounds 4 and 7 exhibited excellent activity for 5-HT1A receptors with Ki values comparable to 8-OH-DPAT. The tested compounds showed differential intrinsic activities in agonist and antagonist modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pharmacology & Pharmacy
Ilana B. Kotliar, Emily Lorenzen, Jochen M. Schwenk, Debbie L. Hay, Thomas P. Sakmar
Summary: G protein-coupled receptors (GPCRs) interact with a variety of membrane proteins, but the extent and mechanisms of these interactions are not well understood. RAMPs, a class of GPCR-interacting proteins, have been extensively studied. Recent research suggests that GPCR-RAMP interactions may be more widespread than previously thought. This review summarizes the latest techniques for discovering GPCR-RAMP interactions and their functional consequences, and discusses future research prospects.
PHARMACOLOGICAL REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Jordan M. Mattheisen, Jaina S. Wollowitz, Thomas Huber, Thomas P. Sakmar
Summary: We developed a luciferase-based reporter assay for site-specific bioorthogonal labeling of expressed G protein-coupled receptors (GPCRs) in live cells. The assay compared amber codon suppression efficiency, receptor functionality, and efficiency of different bioorthogonal labeling chemistries. We used three different noncanonical amino acids to incorporate into a GPCR, resulting in successful labeling and functional assessment of the engineered mutants in live cells.
Article
Chemistry, Inorganic & Nuclear
Katarzyna Gajda, Adrian Sytniczuk, Laure Vendier, Bartosz Trzaskowski, Noel Lugan, Anna Kajetanowicz, Stephanie Bastin, Karol Grela, Vincent Cesar
Summary: Three Hoveyda-Grubbs complexes supported by N-(9-alkylfluorenyl)imidazol-2-ylidene ligands were synthesized. The C(sp(3))-H activation of the dangling alkyl group was studied for generating cyclometalated (C,C-NHC) ruthenium complexes for Z-selective olefin metathesis. The methyl derivative led to the expected cyclometalated complex, while no C(sp(2))-H activation of the fluorenyl moiety and no evolution/transformation were observed for the ethyl and benzyl derivatives, respectively. The cyclometalated complex exhibited Z/E stereoselectivity up to 94/6, despite its fragility under catalytic conditions. An unprecedented insertion of the alkylidene moiety into the Ru-C-NHC bond leading to ruthenium N-heterocyclic olefin complexes was also observed and supported by calculations of the corresponding reaction pathway.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Olga Michalak, Marcin Cybulski, Wojciech Szymanowski, Agnieszka Gornowicz, Marek Kubiszewski, Kinga Ostrowska, Piotr Krzeczynski, Krzysztof Bielawski, Bartosz Trzaskowski, Anna Bielawska
Summary: A series of new derivatives of ursolic acid (UA) were designed and synthesized by substituting various amino acids (AAs) or dipeptides (DP) at the C-3 position of the steroid skeleton. These conjugates exhibited cytotoxic activity against hormone-dependent and triple-negative breast cancer cells. Mechanistic studies revealed the activation of apoptotic pathways for some compounds and the induction of autophagy for others. Additionally, the synthesized compounds showed potential as anticancer agents based on their ADME properties and molecular docking to the estrogen receptor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ilana B. Kotliar, Emilie Ceraudo, Kevin Kemelmakher-Liben, Deena A. Oren, Emily Lorenzen, Tea Dodig-Crnkovic, Mizuho Horioka-Duplix, Thomas Huber, Jochen M. Schwenk, Thomas P. Sakmar
Summary: The interaction between MRGPRX4 and RAMP2 can regulate the signaling pathway and cell surface expression of cholestatic itch, suggesting potential therapeutic implications for future drug development in treating cholestatic itch.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Jordan M. Mattheisen, Chris Limberakis, Roger B. Ruggeri, Matthew S. Dowling, Christopher W. am Ende, Emilie Ceraudo, Thomas Huber, Christopher L. McClendon, Thomas P. Sakmar
Summary: We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Piotr Krzeczynski, Malgorzata Dutkiewicz, Oliwia Zegrocka-Stendel, Bartosz Trzaskowski, Katarzyna Koziak
Summary: Chronic overproduction of IL-15 is involved in various inflammatory and autoimmune disorders. Inhibiting IL-15 signaling by targeting its specific high affinity subunit alpha of the IL-15 receptor (IL-15R alpha) shows potential as a therapeutic approach to alleviate IL-15-related diseases. This study explored the structure-activity relationship of known IL-15R alpha inhibitors and identified new molecules that efficiently reduced IL-15-dependent cell proliferation and cytokine secretion. The rational design of IL-15 inhibitors holds promise in the development of safe and effective therapeutic agents.
Article
Chemistry, Inorganic & Nuclear
Anna Marczyk, Bartosz Trzaskowski
Summary: Despite efforts, synthesizing ruthenium metathesis catalysts with anionic N-heterocyclic carbenes has not been successful. Computational studies show that the previously synthesized anionic N-heterocyclic carbenes are generally too weak to replace chloride ions in common ruthenium metathesis catalysts. Transmetalation from silver or copper complexes is not feasible due to the strong affinity of anionic N-heterocyclic carbenes for these transition metals compared to ruthenium. Additionally, the heterobimetallic Ag/Ru and Cu/Ru complexes formed during transmetalation are unlikely to catalyze olefin metathesis but may have potential as other catalysts.
Article
Multidisciplinary Sciences
Leo Dahl, Ilana B. Kotliar, Annika Bendes, Tea Dodig-Crnkovic, Samuel Fromm, Arne Elofsson, Mathias Uhlen, Thomas P. Sakmar, Jochen M. Schwenk
Summary: A multiplexed immunoassay was developed to test the selectivity of over 400 anti-GPCR antibodies. The results showed that about 61% of the antibodies were selective, 11% bound off-target, and 28% did not bind to any GPCR. It was also found that on-target antibodies had longer, more disordered antigens and were less buried in the interior of GPCR proteins compared to other antibodies.
Article
Biophysics
Adrian Koterwa, Mattia Pierpaoli, Bozena Nejman-Falenczyk, Sylwia Bloch, Artur Zielinski, Wioletta Adamus-Bialek, Zofia Jeleniewska, Bartosz Trzaskowski, Robert Bogdanowicz, Grzegorz Wegrzyn, Pawel Niedzialkowski, Jacek Ryl
Summary: This manuscript presents a novel approach using multiparametric impedance discriminant analysis (MIDA) to address the challenges of electrode fouling and highly complex electrode nanoarchitecture in biosensors operating in real environments. Real-time monitoring combined with singular value decomposition and partial least squares discriminant analysis enables selective identification of the analyte from raw impedance data without the use of electric equivalent circuits. The proposed approach offers a limit of detection of 11.3 CFU/mL for detecting uropathogenic Escherichia coli in real human urine.
BIOSENSORS & BIOELECTRONICS
(2023)
