Article
Chemistry, Multidisciplinary
Sebastian Dengler, Ryan T. Howard, Vasily Morozov, Christos Tsiamantas, Wei-En Huang, Zhiwei Liu, Christopher Dobrzanski, Vojislava Pophristic, Sophie Brameyer, Celine Douat, Hiroaki Suga, Ivan Huc
Summary: Expanding the chemical diversity of peptide macrocycle libraries through the inclusion of a large aromatic helical foldamer has been implemented. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected, and its crystal structure and molecular dynamics simulations revealed an intriguing reciprocal helical folding of the peptide and foldamer. The results represent a significant extension in the chemical space amenable to display selection and highlight the potential benefits of incorporating an aromatic foldamer into a peptide macrocycle for protein recognition.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Materials Science, Biomaterials
Ketav Kulkarni, Jenisi Kelderman, Harold Coleman, Marie-Isabel Aguilar, Helena Parkington, Mark Del Borgo
Summary: Researchers have successfully synthesized a novel beta-amino acid to allow for the self-assembly of a trifunctional beta-tripeptide, which acts as a bioactive neuronal scaffold, showing promise for studies involving neuronal cell growth and development.
JOURNAL OF MATERIALS CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Takahito Ito, Hidetomo Yokoo, Takuma Kato, Mitsunobu Doi, Yosuke Demizu
Summary: In this study, a new cyclic peptide with a different amino acid arrangement was designed, leading to a change in the molecular conformation. The study demonstrates the potential to obtain diverse conformations by manipulating the arrangement of amino acids, providing a direction for developing new applications.
Article
Chemistry, Multidisciplinary
DRGKoppalu Puneeth R. Kumar, Zahid Manzoor Bhat, Sanjit Dey, Souvik Roy, Souvik Panda Mahapatra, Saikat Pahan, Musthafa Ottakam Thotiyl, Hosahudya N. Gopi
Summary: The development of miniaturized lab-on-chip devices for the detection of small molecule-protein interactions at low concentrations is of great importance in drug discovery and biomedicine. In this study, label-free detection of small molecule-protein interactions was achieved using nanoscale capacitance and impedance spectroscopy on surface functionalizable nanotubes of α, γ-hybrid peptide helical foldamers. The functionalizable hybrid peptide nanotubes enabled the label-free detection of various small molecule-protein interactions at very low concentrations.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Samapan Sikdar, Garima Rani, Satyavani Vemparala
Summary: Understanding the role of lipid packing defects in the detection and partitioning of antimicrobial agents into bacterial membranes is crucial for understanding antimicrobial mechanisms. In this study, we investigate the effects of different functional groups in antimicrobial polymers on lipid packing defects in model bacterial membranes. Our findings suggest that the insertion of different polymers leads to different packing defects in the membrane. We provide evidence that the insertion of antimicrobial polymers is preceded by sensing of interfacial lipid packing defects.
Article
Computer Science, Software Engineering
Andras Wacha, Tamas Beke-Somfai
Summary: Beta-peptides are peptide-mimetics widely used in biomedical and biotechnological applications, known for their ability to fold into unique secondary structures and enhance enzymatic stability. The additional methylene group in their backbone makes them incompatible with established algorithms for alpha-peptides and proteins. An extension to PyMOL v2.x is introduced for rapid graphical visualization and simplified model building for computational studies of beta-peptides, highlighting the direct formation of diverse folding states.
Article
Chemistry, Organic
Pablo Tovillas, Claudio D. Navo, Paula Oroz, Alberto Avenoza, Francisco Corzana, Maria M. Zurbano, Gonzalo Jimenez-Oses, Jesus H. Busto, Jesus Peregrina
Summary: Chiral bicyclic N,O-acetal isoserine derivatives have been synthesized using acid-catalyzed reactions, which have significant applications in peptidomimetic and medicinal chemistry.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Bibhuti Bhusana Palai, Nagendra K. Sharma
Summary: This study demonstrates the significant influence of the troponyl group on the structure and conformation of short peptides, confirmed through various experimental methods.
Review
Biochemistry & Molecular Biology
Pavel V. Ershov, Yuri V. Mezentsev, Alexis S. Ivanov
Summary: The identification of disease-related protein-protein interactions (PPIs) allows for objective modulation of these interactions. Recent progress in interfacial peptide design has overcome specific challenges associated with targeted delivery and binding to cellular targets, leading to promising therapeutic formulations that are currently being investigated in clinical trials.
Article
Chemistry, Multidisciplinary
Sinead McCann, William E. Roe, Hannah E. Agnew, Peter C. Knipe
Summary: To imitate the dynamic molecules in biological systems, foldamers need to possess stimulus-responsive behavior. In this study, we present a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is prevented via a copper-catalyzed coupling protocol. The native conformation of the compounds is initially investigated in both solid and solution states. The foldamers can be solubilized in DMSO and pH 9.5 buffer while retaining conformational control. Furthermore, dynamic switching is demonstrated through acid treatment, resulting in stimulus-responsive sidechain reconfiguration.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Friedericke S. Menke, Barbara Wicher, Lars Allmendinger, Victor Maurizot, Ivan Huc
Summary: Through the synthesis of four helically folded aromatic oligoamide sequences, it was found that the 2-(2-aminophenoxy)-propionic acid unit can quantitatively bias helix handedness in chloroform and dichloromethane. Helix handedness control was achieved by introducing an N-terminal (1H)-camphanyl group or a 2-(2-aminophenoxy)-propionic acid unit in specific helical segments. The formation of stable helix-turn-helix tertiary folds was observed in some cases.
Article
Chemistry, Analytical
Xiaohan Chen, Youwen Zhang, Pearl Arora, Xiyun Guan
Summary: Different species can be detected using nanopores engineered with various recognition sites based on non-covalent interactions. This strategy allows for differentiation between species, making it potentially useful for molecular detection in medical and environmental applications.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
David T. J. Morris, Steven M. Wales, David P. Tilly, Elliot H. E. Farrar, Matthew N. Grayson, John W. Ward, Jonathan Clayden
Summary: A class of oligomers has been discovered that can communicate information through a global reversal of polarity by utilizing coherent reversals of directionality in hydrogen-bonded chains. By detecting local information and transmitting it as a directionality switch in the hydrogen-bond chain to a remote polarity-sensitive fluorophore, these oligomers offer a new mechanism for molecular communication.
Review
Chemistry, Applied
Hisashi Masui, Shinichiro Fuse
Summary: Peptides have gained increasing importance as drugs and drug candidates. Microflow synthesis, with an inner tube diameter of <=1 mm, offers advantages such as precise control of reaction time and temperature, as well as easy scale-up. The combination of microflow technology, automated synthesis, and online monitoring has improved synthetic efficiency and provided reliable data for machine learning models.
ORGANIC PROCESS RESEARCH & DEVELOPMENT
(2022)
Article
Chemistry, Multidisciplinary
Yusuke Takashima, Yuki Komoto, Takahito Ohshiro, Kazuhiko Nakatani, Masateru Taniguchi
Summary: Chemical properties have been determined using statistical averages, but the lack of suitable counting methods for single molecules has been a challenge. This study presents a new approach using single-molecule electrical measurements and AI to quantify important parameters like binding selectivity and microscopic hydrogen bonds. The results provide insights into the nature of DNA and its interaction with small molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biotechnology & Applied Microbiology
M. Orth, T. Fritz, J. Stutz, C. Scheuer, B. Ganse, Y. Bullinger, J. S. Lee, W. L. Murphy, M. W. Laschke, M. D. Menger, T. Pohlemann
Summary: MCM + VB, loaded with VEGF and BMP-2, improves bone healing in atrophic non-unions by promoting angiogenesis and osteogenesis, as well as reducing early osteoclast activity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nicholas J. Rettko, Judith Campisi, James A. Wells
Summary: In this study, antibodies targeting p16 MHC-peptide complexes were developed using antibody technology, which can recognize and activate cells expressing these peptide complexes. These tools provide a platform for studying the surface of senescent cells and offer a novel strategy for senescent cell clearance.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jiani Niu, Annika J. Cederstrand, Geoffrey A. Eddinger, Boyu Yin, James W. Checco, Craig A. Bingman, Victor K. Outlaw, Samuel H. Gellman
Summary: This study investigates the mechanism of an anti-inflammatory drug by regulating the binding relationship between the monomeric and trimeric forms of tumor necrosis factor-alpha (TNFα), thereby inhibiting cell death.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Md Shadman Ridwan Abid, Haowen Qiu, Bridget A. Tripp, Aline de Lima Leite, Heidi E. Roth, Jiri Adamec, Robert Powers, James W. Checco
Summary: This study aims to investigate the profile of endogenous peptides in urine samples from IC/BPS patients, in order to identify potential peptide biomarkers. The results show a general increase in the abundance of urinary peptides in IC/BPS patients, consistent with increased inflammation and protease activity. Additionally, five urinary peptides were found to reliably differentiate IC/BPS from healthy controls. However, the utility of the APF peptide as a sole biomarker for IC/BPS may be limited.
SCIENTIFIC REPORTS
(2022)
Article
Engineering, Biomedical
Andrew S. Khalil, Daniel Hellenbrand, Kaitlyn Reichl, Jennifer Umhoefer, Mallory Filipp, Joshua Choe, Amgad Hanna, William L. Murphy
Summary: Spinal cord injuries often have devastating consequences and limited therapeutic options. This study utilizes mineral-coated microparticles as efficient non-viral gene delivery vehicles to produce exogenous ChABC in spinal cord injuries, reducing CSPG deposition and improving motor function recovery.
ADVANCED HEALTHCARE MATERIALS
(2022)
Article
Multidisciplinary Sciences
Lauren E. Stopfer, Nicholas J. Rettko, Owen Leddy, Joshua M. Mesfin, Eric Brown, Shannon Winski, Bryan Bryson, James A. Wells, Forest M. White
Summary: Combining multiple therapeutic strategies may improve survival benefits for NRAS/BRAF mutant melanoma patients. This study utilized immunopeptidomics to measure the impact of MEK inhibition on anti-tumor immunity and identified enhanced expression of specific tumor antigens following therapy. Targeting these upregulated tumor antigens can enhance cell killing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Md Shahadat Hossan, Ethan Samuel Lin, Eleanor Riedl, Austin Stram, Eric Mehlhaff, Luke Koeppel, Jamie Warner, Inem Uko, Lori Mankowski Gettle, Sam Lubner, Stephanie M. McGregor, Wei Zhang, William Murphy, Jeremy D. Kratz
Summary: To accurately predict therapeutic responses in pancreatic and ampullary cancers, researchers have developed a low-volume screening assay and an automated alignment algorithm. By comparing the oligoclonal growth response with validated markers of response, subclonal populations and their relationship with treatment sensitivity were identified. This study is of great significance for utilizing cancer organoid models as biomarkers and advancing novel therapeutic development across different cancer types.
BIOENGINEERING-BASEL
(2023)
Article
Multidisciplinary Sciences
Baba M. Yussif, Cole V. Blasing, James W. Checco
Summary: This article reports that the Aplysia allatotropin-related peptide (ATRP) signaling system utilizes L- to D-amino acid residue isomerization to modulate selectivity between two distinct receptors. The study characterizes the stereoselectivity of the receptors for different isomers and reveals dual signaling pathways in the ATRP system. These findings provide insights into a novel mechanism by which nature regulates intercellular communication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Biochemistry & Molecular Biology
James W. Checco
Summary: Peptidomics is an underutilized method that uses mass spectrometry to identify and measure endogenous peptides, which play crucial biological roles and have potential as biomarkers. This article serves as a brief introduction to peptidomics, aiming to raise awareness and encourage its application among researchers interested in studying endogenous peptides.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Matthew T. Andrews, James W. Checco
Summary: During winter, hibernating mammals undergo extreme physiological changes, such as decreased metabolism, near-freezing body temperatures, and reduced heart rate, allowing them to survive without food for several months. The neurochemical basis of this regulation is largely unknown. This study used a peptidomics approach to examine the changes in endogenous peptides in the hypothalamus and pituitary of a hibernating mammal, the thirteen-lined ground squirrel. The results provide critical insight into the molecular basis of hibernation and have potential implications for organ preservation, obesity treatment, and stroke treatment.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Frazer I. Heinis, Eric C. Bredahl, Md Shadman Ridwan Abid, Ashley D. Clifton, Matthew T. Andrews, James W. Checco
Summary: This study investigated the effects of the commonly used anesthetics isoflurane and sodium pentobarbital on the peptide profile in the rodent hypothalamus and cerebral cortex. The results showed that acute anesthetic administration does not greatly affect the measured peptide profiles.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Engineering, Biomedical
Junsu Yun, Samantha Robertson, Chanul Kim, Masatoshi Suzuki, William L. Murphy, Padma Gopalan
Summary: Decellularized plant scaffolds with innate uniaxial micropatterned topography were biofunctionalized with a copolymer to enable cell adhesion, growth, and alignment. Human muscle cells cultured on this biofunctionalized leaf scaffold showed aligned cell orientation and formation of muscle-like myotube structures, demonstrating potential for tissue engineering applications.
ACTA BIOMATERIALIA
(2023)
Article
Chemistry, Multidisciplinary
Tzong-Hsien Lee, James W. Checco, Tess Malcolm, Chelcie H. Eller, Ronald T. Raines, Samuel H. Gellman, Erinna F. Lee, W. Douglas Fairlie, Marie-Isabel Aguilar
Summary: The Bcl-2 family of proteins regulates the intrinsic pathway of apoptosis. Inhibition of the antiapoptotic members is a strategy to induce apoptotic cell death in cancer cells. This study measured the membrane binding properties of modified peptides designed to be more permeable and have enhanced access to engage with Bcl-2 family members. The results showed that these modified peptides have increased affinity for the mitochondrial membrane and can significantly alter its structure, providing insights into selective membrane targeting of peptides.
AUSTRALIAN JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Frazer I. Heinis, Md Shadman Ridwan Abid, Matthew T. Andrews, James W. Checco
Summary: The study evaluated the impact of short-term anesthetic administration on the abundance of cell-cell signaling peptides and found that isoflurane administration changed the levels of a small number of peptides, while sodium pentobarbital administration had negligible impact on peptide abundance.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Materials Science, Biomaterials
Jae Sung Lee, Ping Guo, Katarina Klett, MacGregor Hall, Krishna Sinha, Sudheer Ravuri, Johnny Huard, William L. Murphy
Summary: Autologous platelet-rich plasma (PRP) is a popular treatment for musculoskeletal tissue injuries due to its favorable safety profile and cost-effectiveness. However, the therapeutic efficacy of PRP for osteoarthritis and damaged cartilage has been inconsistent. In this study, the researchers developed a method to enhance the efficacy of PRP treatment by attenuating a growth factor known to inhibit cartilage repair. The results showed that VEGF-attenuated PRP significantly improved healing of rat OA cartilage compared to conventional PRP treatment or control group. This study provides a new PRP customization method that can be applied to various tissue repair processes.
BIOMATERIALS SCIENCE
(2022)