Review
Biochemistry & Molecular Biology
Lin Han, Pamela V. Chang
Summary: Activity-based protein profiling (ABPP) is a powerful chemical method to investigate protein function and enzymatic activity in complex biological systems. It utilizes activity-based probes to bind specific proteins or amino acid residues through a reactivity-based warhead. Mass spectrometry-based proteomic platforms are then employed to identify protein function and enzymatic activity. ABPP has played a crucial role in deciphering bacterial biological processes, discovering new antibiotics, and characterizing host-microbe interactions. This review focuses on recent advances and applications of ABPP in bacteria and complex microbial communities.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Organic
Camille Metier, Jennifer Dow, Hayley Wootton, Steven Lynham, Brendan Wren, Gerd K. Wagner
Summary: In this study, covalent probes based on anomerically pure d-galactosamine and d-glucosamine scaffolds were used to profile Haemophilus influenzae strain R2866, resulting in predominant labeling of nucleotide-binding proteins. The difference in labeling patterns between lysates and intact cells indicates the probes can penetrate the periplasm but not the cytoplasm of H. influenzae, providing insight into bacterial pathogenicity determination.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Chemistry, Analytical
Xuanwen Li, Divya Chandra, Simon Letarte, Gregory C. Adam, Jonathan Welch, Rong-Sheng Yang, Shannon Rivera, Smaranda Bodea, Alex Dow, An Chi, Christopher A. Strulson, Douglas D. Richardson
Summary: Polysorbate is widely used in pharmaceutical formulation development to maintain the stability of biotherapeutic proteins, but its degradation can cause particle formation in drug products, posing a major quality issue and patient risk factor. This study successfully identified and confirmed active host cell enzymes responsible for polysorbate degradation using an activity-based protein profiling (ABPP) approach, bridging the gap between lipase abundance and activity.
ANALYTICAL CHEMISTRY
(2021)
Article
Polymer Science
Jose M. Orts, Juan Parrado, Jose A. Pascual, Angel Orts, Jessica Cuartero, Manuel Tejada, Margarita Ros
Summary: In this study, Tenebrio molitor larvae were fed polyurethane foam and degraded the polymer by 35% in 17 days, resulting in a 14% weight loss in the mealworms. Changes in the gut bacterial community and diversity of T. molitor were observed, which may be associated with the colonization of species involved in polyurethane degradation. The physical and structural biodegradation of polyurethane by T. molitor was analyzed and compared to the original polymer using FTIR, TGA, and SEM.
Article
Chemistry, Multidisciplinary
Yurong Chen, Zachary Armstrong, Marta Artola, Bogdan Florea, Chi-Lin Kuo, Casper de Boer, Mikkel S. Rasmussen, Maher Abou Hachem, Gijsbert A. van der Marel, Jeroen D. C. Codee, Johannes M. F. G. Aerts, Gideon J. Davies, Herman S. Overkleeft
Summary: Amylases play a key role in starch processing across different kingdoms of life and have significant industrial biotechnological applications. Efficient assays are crucial for identifying new amylase inhibitors and microbial amylases with advantageous features. Activity-based protein profiling is a suitable method for developing such assays, as demonstrated in this study.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
News Item
Biochemistry & Molecular Biology
Supuni Thalalla Gamage, Jordan L. Meier
Summary: RNA modifications play a role in development and disease, and using a metabolic labeling approach with 5-fluorocytidine allows for profiling RNA-modifying enzymes and potential discovery of new RNA targets.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Immunology
Hui Hua, Cem Meydan, Evan E. Afshin, Loukia N. Lili, Christopher R. D'Adamo, Nate Rickard, Joel T. Dudley, Nathan D. Price, Bodi Zhang, Christopher E. Mason
Summary: This study introduces and validates a novel wipe-based approach for collecting and stabilizing fecal samples for metagenomics analysis. The results show that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens, with comparable performance to commercially available preservation kits and maintenance of taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ramiro Vilchez-Vargas, Franz Salm, Eva B. Znalesniak, Katharina Haupenthal, Denny Schanze, Martin Zenker, Alexander Link, Werner Hoffmann
Summary: This study examines the spatial distribution of bacterial flora in the murine alimentary tract and its correlation with Tff3 deficiency and colitis. The results show variations in bacterial species richness and community structure along different regions of the tract. Interestingly, while Tff3 deficiency is linked to increased colitis, it does not significantly affect the bacterial communities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Ting Lu, Congjian Ni
Summary: This study presents an individual-based, biophysical computational framework for simulating the spatiotemporal dynamics of microbial populations. The framework successfully validates single-cell chemotaxis simulations and reveals spatial patterns of different microbial populations. This study provides insights into microbial spatial ecology and offers a tool for designing spatial patterns in synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elias K. Zegeye, Natalie C. Sadler, Gerard X. Lomas, Isaac K. Attah, Janet K. Jansson, Kirsten S. Hofmockel, Christopher R. Anderton, Aaron T. Wright
Summary: The microbial catabolism of chitin plays a fundamental role in carbon and nitrogen cycles on land and in water. Despite the importance of this function, there is limited understanding of the synergy between various enzymes involved in chitin catabolism. Activity-based probes (ABPs) were used to target active chitinolytic enzymes and determine their complement in soil bacteria over time. The ABPs proved useful in identifying the synergy between different enzymes involved in chitin catabolism, providing insights into microbial roles in soil bio-geochemical cycling under changing climate conditions.
Article
Multidisciplinary Sciences
Fang Liu, Zong-sheng Yuan, Zhi-hao Zeng, Hui Pan
Summary: In this study, samples of bamboo rhizome, rhizome root, stem, leaf, rhizosphere soil, and non-rhizosphere soil were collected from high-yield and low-yield moso bamboo forests in Yong'an City and Jiangle County, Fujian Province, China. The genomic DNA of the samples was extracted, sequenced, and analyzed. The results showed that the main differences between the high-yield and low-yield forests were in the bacterial community compositions in the bamboo rhizome, rhizome root, and soil samples. The bacterial species and diversity in the rhizome root and rhizosphere soil of high-yield forests were lower than those of low-yield forests. The relative abundance of certain bacterial taxa differed between high-yield and low-yield forests. The bacterial community composition in the rhizome root system was found to be correlated with high bamboo yield. This study provides a theoretical basis for using microbes to enhance the yields of moso bamboo forests.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Weizhi Song, Shan Zhang, Torsten Thomas
Summary: This study developed a tool called MarkerMAG that links 16S rRNA genes to metagenome-assembled genomes (MAGs) using paired-end sequencing reads. Evaluation on multiple datasets showed that MarkerMAG significantly increases the number of MAGs with 16S rRNA genes and accurately assigns and estimates their copy number. MarkerMAG-improved MAGs also enhance the accuracy of functional prediction from 16S rRNA gene amplicon data.
Article
Immunology
Zhichao Ren, Qing Liu, Wenfeng Li, Xian Wu, Yanling Dong, Yusen Huang
Summary: The ocular surface microbiota may lead to bacterial keratitis, with high-throughput 16S rDNA sequencing showing higher identification rates compared to bacterial culture. Imbalances in ocular microbiota may contribute to susceptibility to bacterial keratitis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Giovanni Brandi, Silvia Turroni, Florencia McAllister, Giorgio Frega
Summary: Recent evidence suggests that microorganisms play a significant role in modulating responses to anticancer treatments and reshaping the tumor-immune microenvironment. Gut microbiota and intra-tumoral bacteria are recognized as crucial components in cancer development and treatment responses. These elements are likely to become important for early diagnosis and risk stratification in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Joshua J. Yim, Stefan Harmsen, Krzysztof Flisikowski, Tatiana Flisikowska, Hong Namkoong, Megan Garland, Nynke S. van den Berg, Jose G. Vilches-Moure, Angelika Schnieke, Dieter Saur, Sarah Glasl, Dimitris Gorpas, Aida Habtezion, Vasilis Ntziachristos, Christopher H. Contag, Sanjiv S. Gambhir, Matthew Bogyo, Stephan Rogalla
Summary: Fluorescently labeled probes show great potential for clinical application in highlighting gastrointestinal lesions, providing fluorescence-guided surveillance and enhancing histopathological analysis by highlighting areas of dysplasia as small as 400 microns, even in tissues with severe inflammation and ulceration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Medicinal
Kas Steuten, Heeyoung Kim, John C. Widen, Brett M. Babin, Ouma Onguka, Scott Lovell, Oguz Bolgi, Berati Cerikan, Christopher J. Neufeldt, Mirko Cortese, Ryan K. Muir, John M. Bennett, Ruth Geiss-Friedlander, Christoph Peters, Ralf Bartenschlager, Matthew Bogyo
Summary: Two proteases produced by the SARS-CoV-2 virus play essential roles in viral replication, but inhibitors may also affect host cells; careful assessment of the selectivity of protease inhibitors is needed during drug development to avoid unnecessary interference with redundant pathways for viral entry.
ACS INFECTIOUS DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Brett M. Babin, Gabriela Fernandez-Cuervo, Jessica Sheng, Ori Green, Alvaro A. Ordonez, Mitchell L. Turner, Laura J. Keller, Sanjay K. Jain, Doron Shabat, Matthew Bogyo
Summary: FLASH is a fast, luminescent, and affordable sensor developed for detecting and monitoring drug susceptibility of Mycobacterium tuberculosis (Mtb). It is selective for the Mtb protease Hip1 and can detect low amounts of Mtb cells with high sensitivity within minutes. FLASH can distinguish live from dead cells and has the potential to enhance TB diagnostics and drug resistance monitoring in resource-limited settings.
ACS CENTRAL SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Ryan K. Muir, Matteo Guerra, Matthew M. Bogyo
Summary: This review highlights recent methodologies employed in activity-based diagnostics for detecting various diseases by leveraging the dysregulated enzyme expression and activity. These methods exhibit exquisite signal sensitivity and specificity in complex biological systems, and some have advanced into clinical trials.
ACS CHEMICAL BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Markus Lakemeyer, Matthew Bogyo
Article
Oncology
Gregory T. Kennedy, David E. Holt, Feredun S. Azari, Elizabeth Bernstein, Bilal Nadeem, Ashley Chang, Neil T. Sullivan, Alix Segil, Charuhas Desphande, Eric Bensen, John T. Santini Jr, John C. Kucharczuk, Edward J. Delikatny, Matthew Bogyo, A. J. Matthew Egan, Charles W. Bradley, Evgeniy Eruslanov, Jason D. Lickliter, Gavin Wright, Sunil Singhal
Summary: This study successfully translated a cathepsin activity-based probe (VGT-309) for fluorescence-guided surgery and conducted human research. The results showed that VGT-309 has good specificity and feasibility, and it can successfully label tumors during tumor resection.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Ethan Walker, Daan G. J. Linders, Eric Abenojar, Xinning Wang, Hans Marten Hazelbag, Marieke E. Straver, Okker D. Bijlstra, Taryn L. March, Alexander L. Vahrmeijer, Agata Exner, Matthew Bogyo, James P. Basilion, Brian Straight
Summary: A formulation of a fluorescent molecular probe has been developed to enhance the resection quality for solid-tumor cancers. This formulation can be topically applied immediately after surgery and activates in the presence of residual cancer, providing a strong fluorescent signal to precisely delineate any remaining cancer cells. The utilization of this formulation has the potential to reduce re-excisions and improve patient quality of life.
Article
Chemistry, Analytical
Jim Nonomiya, Ke Sherry Li, Brett M. Babin, Melinda M. Mulvihill
Summary: Interest in covalent drug discovery has increased following the success of covalent inhibitors targeting BTK and KRAS G12C approved by the FDA. High-throughput screening by intact protein mass spectrometry is commonly used to identify lead compounds, but it does not provide binding site information. This article introduces CoMPAS, a new targeted mass spectrometry-based covalent screening method that provides binding site information in the initial screen and offers advantages such as higher sensitivity and reduced protein reagent requirements.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Laura J. Keller, Taylor H. Nguyen, Lawrence J. Liu, Brianna M. Hurysz, Markus Lakemeyer, Matteo Guerra, Danielle J. Gelsinger, Rachael Chanin, Nhi Ngo, Kenneth M. Lum, Franco Faucher, Phillip Ipock, Micah J. Niphakis, Ami S. Bhatt, Anthony J. O'Donoghue, Kerwyn Casey Huang, Matthew Bogyo
Summary: In this study, serine hydrolases specific to the Bacteroidetes phylum were identified in the gut commensal Bacteroides thetaiotaomicron. Two of them were predicted to be homologs of the human dipeptidyl peptidase 4 (hDPP4). Functional studies showed that BT4193 is a true homolog of hDPP4 and can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other one is a misannotated proline-specific triaminopeptidase. The results also indicated that BT4193 is important for envelope integrity and fitness of B. thetaiotaomicron in a diverse bacterial community, independent of its proteolytic activity.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Astrid Illigmann, Marie-Theres Vielberg, Markus Lakemeyer, Felix Wolf, Taulant Dema, Patrik Stange, Wolfgang Kuttenlochner, Elisa Liebhart, Andreas Kulik, Nicole D. Staudt, Imran Malik, Stephanie Grond, Stephan A. Sieber, Leonard Kaysser, Michael Groll, Heike Broetz-Oesterhelt
Summary: The caseinolytic protease, known as a crucial enzyme in protein homeostasis, shows promising potential as a target for antibacterial and anticancer drugs. The discovery of cystargolides as the first natural beta-lactone inhibitors of the proteolytic core ClpP opens up new possibilities for research in this field. The inhibition of ClpP by cystargolide A and B is demonstrated through different biochemical methods, and further experiments confirm the specificity of ClpP as a target in Staphylococcus aureus cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Brett M. Babin, Laura J. Keller, Yishay Pinto, Veronica L. Li, Andrew S. Eneim, Summer E. Vance, Stephanie M. Terrell, Ami S. Bhatt, Jonathan Z. Long, Matthew Bogyo
Summary: The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat. In this study, researchers screened a narrow-spectrum inhibitor that successfully suppressed the growth of Mycobacterium tuberculosis. Analyses revealed that the inhibition of SH enzymes was linked to defects in cell envelope biogenesis. It was also found that resistance was primarily developed through the synthesis of mycocerates rather than mutations to SH targets.
CELL CHEMICAL BIOLOGY
(2022)
