Article
Multidisciplinary Sciences
Yan Zhang, Nikolay A. Aleksashin, Dorota Klepacki, Caleb Anderson, Nora Vazquez-Laslop, Carol A. Gross, Alexander S. Mankin
Summary: Kasugamycin (KSG) is a small ribosomal subunit-targeting antibiotic that interferes with translation in different stages. It inhibits protein synthesis by blocking the binding of canonical messenger RNA (mRNA) and initiator transfer RNA (tRNA) to the small ribosomal subunit. Even after the formation of the 70S initiation complex, KSG can still interfere with translation to a certain extent. However, it does not completely abolish translation and allows for the expression of certain proteins. The effectiveness of KSG depends on the nature of the mRNA residue preceding the start codon and is attenuated by translational coupling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Apurva Panjla, Grace Kaul, Abdul Akhir, Deepanshi Saxena, Saurabh Joshi, Chandrima Modak, Dipti Kumari, Alok Jain, Sidharth Chopra, Sandeep Verma
Summary: Antimicrobial resistance is a significant public health risk, and there is a need for novel antimicrobial compounds. In this study, cationic chlorpromazine peptide conjugates were found to effectively target multidrug-resistant bacteria, particularly MDR S. aureus. The most potent compound, CPWL, showed promising antibacterial activity without cytotoxicity. Molecular docking and MD simulation studies confirmed that CPWL specifically targeted S. aureus enoyl reductase (saFabI). These findings highlight cationic chlorpromazine as a promising scaffold for the development of saFabI inhibitors for severe staphylococcal infections.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Infectious Diseases
Derek C. K. Chan, Lori L. Burrows
Summary: Thiopeptides were previously thought to be inactive against Gram-negative bacteria due to their inability to cross the outer membrane, but recent research has shown that some thiopeptides, such as thiostrepton, exhibit antimicrobial activity against Pseudomonas aeruginosa. This highlights the potential for thiopeptides as antipseudomonal antibiotics.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Chemistry, Medicinal
G. Ian Gallicano, Jiayu Fu, Samiksha Mahapatra, Michael V. R. Sharma, Conor Dillon, Claire Deng, Maliha Zahid
Summary: Research has shown that miRNA106a can target genes that cause hypertrophy and heart failure, reversing the disease. By using a cardiac targeting peptide reversibly linked to miRNA106a, delivery specific to cardiomyocytes has been demonstrated.
Article
Multidisciplinary Sciences
Gerhard Koenig, Pandian Sokkar, Niclas Pryk, Sascha Heinrich, David Moeller, Giuseppe Cimicata, Donna Matzov, Pascal Dietze, Walter Thiel, Anat Bashan, Julia Elisabeth Bandow, Johannes Zuegg, Ada Yonath, Frank Schulz, Elsa Sanchez-Garcia
Summary: Antibiotic resistance poses a major threat to global health, but computational methods can aid in the development of new antibacterial agents and provide rapid decision-making. The best-designed compounds exhibit excellent activity in both in vitro and in vivo experiments, showing promising inhibitory effects against priority pathogens identified by the World Health Organization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Pooja Srinivas, Kenneth C. Keiler, Christine M. Dunham
Summary: Bacteria use trans-translation to rescue stalled ribosomes and target incomplete proteins. New structural and biochemical data reveal important differences between trans-translation and traditional translation processes. These differences provide insights into the fundamental nature of trans-translation and guide the development of new antibiotics that specifically target bacteria.
Article
Infectious Diseases
Artemis Tsirogianni, Georgia G. Kournoutou, Anthony Bougas, Eleni Poulou-Sidiropoulou, George Dinos, Constantinos M. Athanassopoulos
Summary: By chemically modifying a known antibiotic, we developed new pharmacophores with high antimicrobial activity, particularly the bis-dichloroacetyl derivative of ornithine. This compound showed the highest antimicrobial activity both in vivo and in vitro, indicating potential for further modification and development.
Article
Chemistry, Organic
Yassin M. Elbatrawi, Taylor Gerrein, Avraz Anwar, Kamlesh M. Makwana, David Degen, Richard H. Ebright, Juan R. Del Valle
Summary: We have achieved the total synthesis and configurational assignment of pargamicin A, a highly oxidized nonribosomal peptide that effectively inhibits the growth of drug-resistant bacteria. Our synthetic strategy involves late-stage piperazine ring formation and careful selection of condensation reagents to assemble the densely substituted hexapeptide backbone. This work facilitates the synthesis of pargamicin derivatives for structure-activity relationship studies and provides insights into accessing other piperazic acid-containing natural products with steric congestion.
Article
Microbiology
Rodrigo Campos-Silva, Gaetano D'Urso, Olivier Delalande, Emmanuel Giudice, Alexandre Jose Macedo, Reynald Gillet
Summary: Finding new antibiotics is crucial due to increasing multidrug resistance in microorganisms. Translation is a fundamental process that uses a significant amount of cellular energy, and the ribosome is a major target for antibiotics. Trans-translation is a quality control mechanism in bacteria that solves the problem of ribosomal stalling.
Article
Biochemistry & Molecular Biology
Alireza Japoni Nejad, Nader Shahrokhi, Peter E. Nielsen
Summary: In this study, a series of PNA-BPP conjugates targeting CRAB strains were designed and synthesized. These compounds demonstrated potent antimicrobial activity against CRAB, exhibiting complete growth inhibition at 1-2x MIC and sensitivity in 12 isolates. Additionally, the conjugates showed no bacterial membrane disruption activity and no cellular toxicity in HepG2 cells, indicating potential as precision designer antibiotics for specific treatment of CRAB infections.
Review
Microbiology
Jose Arcadio Farias-Rico, Carlos Michel Mourra-Diaz
Summary: Proteins have been crucial throughout the evolution of all organisms, and the origin of life from prebiotic chemistry is still a fascinating question. It is widely accepted that amino acids were available on early Earth, allowing for the formation of peptides. Peptides likely coevolved with ancestral forms of RNA, leading to the development of the ribosome, a complex nanomachine involved in protein synthesis.
Article
Biochemistry & Molecular Biology
Vera A. Alferova, Tinashe P. Maviza, Mikhail V. Biryukov, Yuliya V. Zakalyukina, Vladimir I. Polshakov, Petr V. Sergiev, Vladimir A. Korshun, Ilya A. Osterman
Summary: Recently discovered aromatic polyketide tetracenomycins are potent inhibitors of protein synthesis, with a unique binding site located within the tunnel of the large ribosomal subunit. We report the isolation and structure elucidation of a novel tetracenomycin congener, O4-Me-tetracenomycin C, which is isomeric to tetracenomycin X. However, unlike tetracenomycin X, O4-Me-tetracenomycin C showed no antimicrobial activity and failed to inhibit protein synthesis in vitro. Structural alignment of tetracenomycins revealed the crucial role of the 4-hydroxyl group. These findings are important for the development of semi-synthetic tetracenomycins as potential antibacterials.
Article
Chemistry, Multidisciplinary
Prabhakara R. Tharra, Andrey A. Mikhaylov, Jiri Svejkar, Marina Gysin, Sven N. Hobbie, Jakub Svenda
Summary: We report a concise synthesis method for the naturally occurring protein synthesis inhibitor (+)-actinobolin. The complex molecular structure of 1 was assembled using (-)-quinic acid, L-threonine, and L-alanine. Our simplified synthesis route, consisting of 9 steps with 18% overall yield, has practical applications for analog preparation, as shown in this study.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Lidia Orea-Ordonez, Susana Masia, Jeronimo Bravo
Summary: Ribosome biogenesis is considered a crucial factor in the addiction of cancer cells and has the potential for cancer therapy. Initial research suggests that inhibiting ribosome production can more effectively impact cancer cells without harming normal cells, but there are still limitations in the development of RNA Pol I inhibitors.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Infectious Diseases
Merce Espona, Daniel Echeverria-Esnal, Sergi Hernandez, Alexander Almendral, Silvia Gomez-Zorrilla, Enric Limon, Olivia Ferrandez, Santiago Grau
Summary: The introduction of generic antimicrobials may lead to an increase in consumption of broad-spectrum molecules and a potential rise in resistance, which could dilute the economic benefits of generic antibiotics. Antimicrobial stewardship should continue to monitor these molecules despite generic entry.
Article
Biochemical Research Methods
Philipp T. Kaulich, Konrad Winkels, Tobias B. Kaulich, Christian Treitz, Liam Cassidy, Andreas Tholey
Summary: Top-down proteomics analyzes intact proteoforms with all modifications and splice variants. MSTopDiff is a software tool that allows the detection of protein modifications without a database search. It is useful for quality control and parameter evaluation in top-down proteomics research.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Laura Hobohm, Tomas Koudelka, Fenja H. Bahr, Jule Truberg, Sebastian Kapell, Sarah-Sophie Schacht, Daniel Meisinger, Marion Mengel, Alexander Jochimsen, Anna Hofmann, Lukas Heintz, Andreas Tholey, Matthias Voss
Summary: This study identifies more than 20 substrates of the intramembrane protease SPPL3 and demonstrates its significant role in Golgi enzyme turnover, secretion, and regulation of global glycosylation pathways.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Cell Biology
Julia Bar, Yannes Popp, Tomas Koudelka, Andreas Tholey, Marina Mikhaylova
Summary: This study reveals that intracellular Ca2+ is necessary for efficient microtubule detyrosination and that calpains can regulate this process. The identification of the calpain-regulated pathway for microtubule detyrosination is of significant importance for basic and clinical research.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ludwig Werny, Antonia Grogro, Kira Bickenbach, Cynthia Bulck, Fred Armbrust, Tomas Koudelka, Kriti Pathak, Franka Scharfenberg, Martin Sammel, Farah Sheikhouny, Andreas Tholey, Stefan Linder, Christoph Becker-Pauly
Summary: This study investigated the interaction between membrane-type-I matrix metalloproteinase (MT1-MMP) and meprin beta, revealing a potential regulatory connection between the two enzymes.
Article
Biochemical Research Methods
Max K. Steinbach, Jan Leipert, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: This study demonstrates a highly sensitive sample preparation workflow using digital microfluidics and high-resolution mass spectrometry for nanoproteomics research.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Konrad Winkels, Tomas Koudelka, Philipp T. Kaulich, Matthias Leippe, Andreas Tholey
Summary: Top-down proteomics (TDP) can provide additional information about post-translational modifications and C-termini. In this study, TDP workflows were used to analyze the proteome of Caenorhabditis elegans, and the identified proteoforms were validated using a bottom-up proteomics (BUP) approach. The results showed low overlap between the two methods, with caveats in both workflows contributing to this. The study also demonstrated the applicability of reductive dimethylation in TDP to confirm biological N-termini.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Jerome Genth, Patrick Kaleja, Christian Treitz, Kathrin Schaefer, Simon Graspeutner, Jan Rupp, Andreas Tholey
Summary: In this study, the proteome response of B. thetaiotaomicron cultivated on different carbon sources was analyzed. The results showed that the bacterium maintains its intracellular proteome upon change of the carbohydrates, with major changes observed in the machinery necessary to use the carbon sources provided. These findings contribute to the understanding of how different carbohydrates shape bacterial community in the gut microbiome.
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Liam Cassidy, Philipp T. Kaulich, Andreas Tholey
Summary: Microproteins and SEPs can undergo various posttranslational modifications like other proteins. However, traditional proteomic methods face challenges in identifying, quantifying and characterizing proteoforms. Top-down proteomics, in contrast, allows for direct identification of intact proteoforms. This article provides an overview of modified microproteins and SEPs, introduces proteoform terminology, and compares the advantages and disadvantages of traditional bottom-up and top-down proteomic workflows. It also discusses future developments in top-down proteomics for proteoform-centric analysis of microproteins and SEPs.
Article
Chemistry, Multidisciplinary
Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: Researchers have developed a sample preparation method based on protein aggregation and acidic elution, allowing for sensitive protein identification analysis of single nematodes on a digital microfluidics device. Compared to in-tube sample preparation, this method increases proteoform identifications by 46%. Label-free quantification also reveals changes in proteoform abundance that cannot be distinguished by bottom-up proteomics. This workflow facilitates proteoform-focused analysis on limited availability samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Johanna Rueter, Gerald Rimbach, Christian Treitz, Anke Schloesser, Kai Lueersen, Andreas Tholey, Patricia Huebbe
Summary: The study identified protein-protein interactions of APOE with BCKDHA and VDAC1, suggesting a possible involvement of APOE in mitochondrial processes and adaptation to hepatic energy demands. The activity of the BCKD enzyme complex was higher in obese APOE4 mice, while the interaction with VDAC1 was induced upon dietary restriction.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemical Research Methods
Philipp T. Kaulich, Liam Cassidy, Andreas Tholey
Summary: Efficient proteoform separation is crucial for top-down (TD) proteomics. A two-dimensional low pH/low pH reversed-phase liquid chromatography separation scheme was developed. The optimized separation scheme led to the identification of more than 4900 proteoforms from 1250 protein groups in Caco-2 cells. The low/low pH separation strategy resulted in a higher number of proteoform identifications below 20 kDa compared to the previously published high pH/low pH strategy.
Article
Biochemical Research Methods
Ayako Takemori, Philipp T. Kaulich, Ryo Konno, Yusuke Kawashima, Yuto Hamazaki, Ayuko Hoshino, Andreas Tholey, Nobuaki Takemori
Summary: Middle-down proteomics (MDP) is an analytical method that uses proteases to generate large peptides for mass spectrometry analysis. It is particularly useful for studying high-molecular-weight proteins. In this study, we applied a multidimensional separation workflow combining gel-based prefractionation with LC-FAIMS MS for deep MDP. By improving the digestion conditions and implementing size fractionation and additional ion mobility fractionation, we were able to increase the detectable peptide length and explore proteoform information not covered by conventional top-down proteomics.
Article
Microbiology
Jerome Genth, Kathrin Schaefer, Liam Cassidy, Simon Graspeuntner, Jan Rupp, Andreas Tholey
Summary: Short open reading frames (sORFs) can encode small proteins called sORF-encoded peptides (SEP) that play important roles in various physiological processes. Using proteomics techniques, researchers identified 45 novel and previously reported SEPs in single cultures of Blautia producta under different growth conditions and stress exposure. The results suggest that the biosynthesis of specific SEPs is not limited to bacterial interactions within the microbiome but is influenced by growth and environmental conditions during cultivation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Kyowon Jeong, Philipp T. Kaulich, Wonhyeuk Jung, Jihyung Kim, Andreas Tholey, Oliver Kohlbacher
Summary: Top-down proteomics provides more comprehensive proteoform-level information, but reliable data analysis remains challenging. The conventional FDR estimation method may not work at the proteoform level, and the precursor deconvolution error rate should be taken into account.