Article
Multidisciplinary Sciences
Jeffrey Y. K. Wong, Arunika I. Ekanayake, Serhii Kharchenko, Steven E. Kirberger, Ryan Qiu, Payam Kelich, Susmita Sarkar, Jianqian Li, Kleinberg X. Fernandez, Edgar R. Alvizo-Paez, Jiayuan Miao, Shiva Kalhor-Monfared, J. Dwyer John, Hongsuk Kang, Hwanho Choi, John M. Nuss, John C. Vederas, Yu-Shan Lin, Matthew S. Macauley, Lela Vukovic, William C. K. Pomerantz, Ratmir Derda
Summary: Peptide-based therapeutics with poor circulation half-life have been a challenge. In this study, researchers successfully selected albumin-binding macrocyclic peptides from genetically encoded libraries modified by specific chemistry. The selected peptides showed high affinity for human serum albumin and demonstrated longer in vivo circulation half-life, which is a promising starting point for developing compact macrocycles with extended half-life.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Akihiro Takamura, Peter S. Thuy-Boun, Seiya Kitamura, Zhen Han, Dennis W. Wolan
Summary: Folate and its derivatives play essential roles in the crosstalk between commensal organisms and hosts, with a folate-based probe designed to detect and quantify folate-binding proteins showing high selectivity for specific targets. The probe's ability to isolate low-abundance folate-dependent proteins has great potential in elucidating the roles of microbial folate-binding proteins in health and microbiome-related diseases.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Organic
Daniel Joaquin, Samuel A. Mansfield, Joseph C. Chanthakhoun, Austin K. LeSueur, Tiffani A. Blackburn, Steven L. Castle
Summary: Three new bulky cycloalkyl alpha, beta-dehydroamino acids have been synthesized, which enhance the rigidity of model peptides and their stability to proteolysis. Larger ring sizes have greater effects. Peptides containing these bulky cycloalkyl Delta AAs are inert to conjugate addition by a nucleophilic thiol, suggesting their potential as effective tools for improving the proteolytic stability of bioactive peptides.
Article
Multidisciplinary Sciences
Shang-Chuen Wu, Nourine A. Kamili, Marcelo Dias-Baruffi, Cassandra D. Josephson, Matthew F. Rathgeber, Melissa Y. Yeung, William J. Lane, Jianmei Wang, Hau-Ming Jan, Seth Rakoff-Nahoum, Richard D. Cummings, Sean R. Stowell, Connie M. Arthur
Summary: Adaptive immunity is regulated by tolerogenic mechanisms, but it faces challenges in combating microbes that mimic self-antigens. A study shows that the innate immune lectin Galectin-7 (Gal-7) can recognize various microbes that display blood group-like antigens, leading to their loss of viability without causing harm to host cells.
Article
Oncology
Mary J. van Helden, Seline A. Zwarthoff, Roel J. Arends, Inge M. J. Reinieren-Beeren, Marc C. B. C. Parade, Lilian Driessen-Engels, Karin de Laat-Arts, Desiree Damming, Ellen W. H. Santegoeds-Lenssen, Daphne W. J. van Kuppeveld, Imke Lodewijks, Hugo Olsman, Hanke L. Matlung, Katka Franke, Ellen Mattaar-Hepp, Marloes E. M. Stokman, Benny de Wit, Dirk H. R. F. Glaudemans, Danielle E. J. W. van Wijk, Lonnie Joosten-Stoffels, Jan Schouten, Paul J. Boersema, Monique van der Vleuten, Jorien W. H. Sanderink, Wendela A. Kappers, Diels van den Dobbelsteen, Marco Timmers, Ruud Ubink, Gerard J. A. Rouwendal, Gijs Verheijden, Miranda M. C. van der Lee, Wim H. A. Dokter, Timo K. van den Berg
Summary: This study describes a novel antibody called BYON4228, which recognizes both allelic variants of SIRP alpha and shows potential clinical applicability. BYON4228 blocks the binding of CD47 to SIRP alpha, enhancing the ability of macrophages and neutrophils to kill tumor cells. It has a unique profile compared to other SIRP alpha antibodies, making it a promising candidate for further preclinical and clinical studies.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Immunology
In-Young Chung, Bi-O Kim, Ju-Hyun Han, Jonggwan Park, Hee Kyoung Kang, Yoonkyung Park, You-Hee Cho
Summary: The study reveals a new method inspired by phages for antibacterial discovery. Critical residues in the bioactivity of the Tip protein were identified, and a synthetic 15-aa peptide P1 showed potential in inhibiting Pseudomonas aeruginosa infections.
Article
Microbiology
Keisuke Tonouchi, Yu Adachi, Tateki Suzuki, Daisuke Kuroda, Ayae Nishiyama, Kohei Yumoto, Haruko Takeyama, Tadaki Suzuki, Takao Hashiguchi, Yoshimasa Takahashi
Summary: This study analyzed human monoclonal antibodies against a stem-helix region in influenza virus hemagglutinin (HA), which is concealed in the native prefusion state but exposed in the postfusion state. The LAH31 antibody showed cross-group protection by targeting a unique kinked loop epitope in the postfusion state. Structural analysis revealed key contact sites responsible for the epitope specificity and cross-group breadth. This study uncovered a non-native epitope in the postfusion state, highlighting its potential for broadly protective antigen design.
Article
Engineering, Environmental
Zihao Wan, Yalu Chen, Senhua Hu, Qiaolian Chen, Yuxin Li, Xiuhua Chen, Wenfeng Tan, Yongjun Lin, Kenneth J. Shea, Mingming Liu
Summary: Monitoring transgenic crops is essential, but conventional antibody detection faces challenges with multiple protein variants engineered into important crops. A peptide epitope with high sequence similarity to certain proteins is identified, but lacks the necessary properties for practical applications. Conjugation of the peptide to a synthetic polymer creates a hybrid material that can be used for extraction and detection of transgenic protein variants from water and soil samples.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Cell Biology
Leerang Yang, Timothy M. Caradonna, Aaron G. Schmidt, Arup K. Chakraborty
Summary: By using a computational model, this study investigates antibody evolution through affinity maturation after immunization with two types of immunogens (a heterotrimeric chimerahemagglutinin enriched for the receptor-binding site epitope and a cocktail of non-epitope-enriched homotrimers). Experiments in mice demonstrate that the chimerahemagglutinin is more effective in eliciting receptor-binding site-specific antibodies compared to the cocktail. The results highlight the interplay between B cells, antigens, and diverse helper T cells in antibody evolution and emphasize the importance of immunogen design and T cell modulation in vaccination outcomes.
Article
Biochemistry & Molecular Biology
Roshny Prasad, Harikrishnan Ajith, Naveen Kumar Chandrakumaran, Pawan Dnyaneshwar Khangar, Anand Mohan, Shijulal Nelson-Sathi
Summary: Since December 2019, SARS-CoV-2 has diverged into multiple variants due to accumulated mutations in its genome. This study analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 on potential peptide inhibitors. The results showed that specific non-synonymous mutations correspond to key binding sites on the virus protein, and synthesized peptides have the ability to interact with these viral proteins. Molecular docking and simulation confirmed the potential inhibitory effects of these peptides.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Public, Environmental & Occupational Health
Shuai Yuan, Yingyu Wu
Summary: This study systematically assessed and compared the effectiveness and cost-effectiveness of GLP-1RAs approved in China for the treatment of type 2 diabetes. The results showed that the combination of loxenatide and metformin was the most cost-effective choice, and the use of these medications significantly reduced the disease burden.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Biochemistry & Molecular Biology
Rebecca Justiniano, Lohanna de Faria Lopes, Jessica Perer, Anh Hua, Sophia L. Park, Jana Jandova, Mauricio S. Baptista, Georg T. Wondrak
Summary: This study demonstrates the efficacy of FICZ as a nanomolar sensitizer for the photodynamic elimination of human melanoma and nonmelanoma skin cancer cells. The combination of solar simulated UVA and FICZ induces oxidative stress and cell death in vitro. The experimental FICZ/UVA photodynamic treatment regimen shows potential for blocking the progression of UV-induced tumorigenesis in mice, suggesting the feasibility of utilizing FICZ for the elimination of malignant cells in vivo.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Paulina K. Walencik
Summary: Colorectal cancer is the third most commonly diagnosed form of cancer worldwide. Recent studies have shown a strong correlation between microbial imbalance and the development of colorectal cancer. An abundance of the bacterium Fusobacterium nucleatum has been identified as a biomarker for colorectal cancer progression. Furthermore, binding copper ions to bacterial proteins has been found to promote the production of reactive oxygen species, leading to colorectal carcinogenesis. This study investigated the molecular relation of copper with a protein expressed by Fusobacterium nucleatum and found that conditional dissociation constants and electrochemical activity affect the stability of copper complexes.
DALTON TRANSACTIONS
(2022)
Article
Multidisciplinary Sciences
Siddhartha Kundu
Summary: The peptide loading complex (PLC) is a multi-protein complex of the endoplasmic reticulum (ER) that optimizes the export of high-affinity peptides mediated by major histocompatibility I (MHC1). A low-affinity peptide-driven (LAPD) model of MHC1-mediated high-affinity peptide export was formulated, implemented, analyzed, and simulated in this study. The results suggest that low-affinity peptides can bisect the export of high-affinity peptides into distinct early and late phases, with different contributions from retrograde and anterograde pathways.
Article
Ophthalmology
Hancheng Guan, Manunya Nuth, Vivian Lee, Chenyan Lin, Claire H. Mitchell, Wennan Lu, Richard W. Scott, Michael H. Parker, John L. Kulp, Allen B. Reitz, Robert P. Ricciardi
Summary: Research has shown that hydrocarbon stapled peptides mimicking the alpha-helix structure from the C-terminus of HSV-1 DNA polymerase can specifically block DNA synthesis and infection of HSV-1 in human primary corneal epithelial cells, providing a foundation for developing a topical therapeutic for treating human ocular Herpes Keratitis.
Article
Biochemical Research Methods
Camilla Restellini, Alessandro Cuomo, Michela Lupia, Marco Giordano, Tiziana Bonaldi, Roberta Noberini
PROTEOMICS CLINICAL APPLICATIONS
(2019)
Article
Oncology
Ramya Ramaswami, Thomas S. Uldrick, Mark N. Polizzotto, Kathleen M. Wyvill, Priscila Goncalves, Anaida Widell, Kathryn Lurain, Seth M. Steinberg, William Douglas Figg, Giovanna Tosato, Denise Whitby, Robert Yarchoan
CLINICAL CANCER RESEARCH
(2019)
Article
Biochemical Research Methods
Laura De Clerck, Sander Willems, Roberta Noberini, Camilla Restellini, Bart Van Puyvelde, Simon Daled, Tiziana Bonaldi, Dieter Deforce, Maarten Dhaenens
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Oncology
Michael DiPrima, Dunrui Wang, Alix Troester, Dragan Maric, Nekane Terrades-Garcia, Taekyu Ha, Hyeongil Kwak, David Sanchez-Martin, Denis Kudlinzki, Harald Schwalbe, Giovanna Tosato
MOLECULAR ONCOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Lisa Ritchey, Taekyu Ha, Atsushi Otsuka, Kenji Kabashima, Dunrui Wang, Yuyi Wang, Douglas R. Lowy, Giovanna Tosato
Article
Biochemical Research Methods
Roberta Noberini, Camilla Restellini, Evelyn Oliva Savoia, Tiziana Bonaldi
Article
Biochemistry & Molecular Biology
Roberta Noberini, Tiziana Bonaldi
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Wan Li, Qingxia Wang, Xiaoyu Qi, Yuanyuan Guo, Hongmei Lu, Yuheng Chen, Zhongmou Lu, Qin Yan, Xiaofei Zhu, Jae U. Jung, Giovanna Tosato, Shou-Jiang Gao, Chun Lu
Review
Biochemical Research Methods
Roberto Gasparri, Giulia Sedda, Roberta Noberini, Tiziana Bonaldi, Lorenzo Spaggiari
PROTEOMICS CLINICAL APPLICATIONS
(2020)
Review
Cell Biology
Nazzarena Labo, Hidetaka Ohnuki, Giovanna Tosato
Article
Biochemistry & Molecular Biology
Roberta Noberini, Morales Cristina Torres, Evelyn Oliva Savoia, Stefania Brandini, Maria Giovanna Jodice, Giovanni Bertalot, Giuseppina Bonizzi, Maria Capra, Giuseppe Diaferia, Paola Scaffidi, Tiziana Bonaldi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Review
Biochemistry & Molecular Biology
Roberta Noberini, Giulia Robusti, Tiziana Bonaldi
Summary: In the past 15 years, research has shown the potential of investigating histone post-translational modifications and variants in clinical samples for discovering biomarkers and therapeutic targets in cancer biology. Mass spectrometry has emerged as a powerful tool for unbiased, comprehensive, and quantitative investigation of histones in clinical samples, with recent advancements in technology expanding its application possibilities. The 'bottom-up' strategy of analyzing short proteolytic peptides has shown success in clinical sample analysis, offering a promising approach for histone PTM profiling.
Article
Biochemistry & Molecular Biology
Hidetaka Ohnuki, David J. Venzon, Alexei Lobanov, Giovanna Tosato
Summary: Gene expression in individual cells is regulated by various epigenetic mechanisms, but the predictive ability of epigenomic analysis for single cells is limited. A new method proposed in this study allows for the analysis of multiple components of the epigenome in the same single cell, enabling reanalysis and identification of reproduced reads. This method provides mechanistic insights for cellular phenotypes through multilayered epigenome analysis, with the ability to predict active signaling pathways in single cells.
Article
Medicine, Research & Experimental
Yuyi Wang, Ombretta Salvucci, Hidetaka Ohnuki, Andy D. Tran, Taekyu Ha, Jing-Xin Feng, Michael DiPrima, Hyeongil Kwak, Dunrui Wang, Yanlin Yu, Michael Kruhlak, Giovanna Tosato
Summary: SHP2 is essential for promoting endothelial cell survival and growth in tumor vasculature remodeling. Inhibiting SHP2 activity leads to reduced tumor growth and degeneration of tumor vasculature. Combination of SHP2 inhibitors with Ang2/TIE2 inhibitors shows promise in effectively targeting the tumor endothelium.
EMBO MOLECULAR MEDICINE
(2021)
Article
Cell Biology
Stefania Faletti, Daniela Osti, Elena Ceccacci, Cristina Richichi, Brunella Costanza, Luciano Nicosia, Roberta Noberini, Giulia Marotta, Laura Furia, Mario R. Faretta, Silvia Brambillasca, Micaela Quarto, Luca Bertero, Renzo Boldorini, Bianca Pollo, Sara Gandini, Davide Cora, Saverio Minucci, Ciro Mercurio, Mario Varasi, Tiziana Bonaldi, Giuliana Pelicci
Summary: Glioblastoma (GBM) is a deadly tumor with high aggressiveness, heterogeneity, poor blood-brain barrier penetration, and resistance to therapy, emphasizing the need for new treatment targets. Research shows that LSD1 inhibition can penetrate brain tissue, exhibit anti-tumor activity in GBM TICs, and disrupt stress responses in cells, thereby reducing tumor aggressiveness.
SCIENCE TRANSLATIONAL MEDICINE
(2021)