Article
Multidisciplinary Sciences
Chun-Wei Chang, Mei-Huei Lin, Tsun-Yi Chiang, Chia-Hui Wu, Tzu-Chun Lin, Cheng-Chung Wang
Summary: The stereoselectivity of glycosidic bond formation poses a challenge in carbohydrate synthesis. This study analyzed the glycosylation mechanism and provided insights for building block tailoring and reaction condition optimization in carbohydrate synthesis.
Article
Chemistry, Organic
Yousra Hamdane, Pradeep S. Chauhan, Suresh Vutla, Mukandila Mulumba, Huy Ong, William D. Lubell
Summary: Fifteen N-aminoimidazolone (Nai) dipeptides with different 5-position side-chain groups were synthesized through regioselective proline-catalyzed reactions and acid-mediated dehydration. Introducing 5-aryl-Nai dipeptides into CD36 receptor peptide ligands provided insights into the conformation responsible for binding affinity and anti-inflammatory activity.
Article
Chemistry, Analytical
Diana Campos, Michael Girgis, Qiang Yang, Guanghui Zong, Radoslav Goldman, Lai-Xi Wang, Miloslav Sanda
Summary: Mass spectrometry can provide valuable insights into glycosylation analysis, but analyzing isobaric glycopeptide structures remains challenging. Modulating collision energy can improve structural elucidation, especially for qualitative purposes. Our research identified the potential for false-positive structure assignments and established a minimum intensity threshold to prevent misidentification of structure-specific fragments in glycoproteomics analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Joann Chongsaritsinsuk, Alexandra D. Steigmeyer, Keira E. Mahoney, Mia A. Rosenfeld, Taryn M. Lucas, Courtney M. Smith, Alice Li, Deniz Ince, Fiona L. Kearns, Alexandria S. Battison, Marie A. Hollenhorst, D. Judy Shon, Katherine H. Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R. Bertozzi, Michael J. Ferracane, Mark A. Lemmon, Rommie E. Amaro, Stacy A. Malaker
Summary: This study investigates the structure and function of mucin glycoproteins. By using the mucinase SmE for mass spectrometric analysis, the researchers successfully overcome the challenges associated with studying mucin domains. They also employ molecular dynamics simulations and binding assays to gain a deeper understanding of how glycosylation controls protein structure and function.
NATURE COMMUNICATIONS
(2023)
Article
Polymer Science
Michael Jacobs, Carlos G. Lopez, Andrey Dobrynin
Summary: The study implemented a scaling approach to evaluate properties of carboxymethylcellulose and polystyrene sulfonate solutions, showing that divalent ions have a significant impact on the excluded volume of polymers while their effect on the renormalization of the Kuhn length is weaker. These effects reduce chain stretching and promote chain disentanglement in solutions with divalent ions compared to solutions with monovalent ions.
Article
Chemistry, Organic
Pawel A. Wieczorkiewicz, Krzysztof K. Zborowski, Tadeusz M. Krygowski, Halina Szatylowicz
Summary: A computational study on amino- and nitro-substituted penta- and heptafulvenes reveals the interplay between aromaticity and the substituent effect. Ring substitution alone has little influence on aromaticity, but when combined with an exo substituent of opposite properties, it substantially enhances cyclic pi-electron delocalization. Despite the stronger substituent effect from beta substitution, only gamma substitution leads to higher aromaticity. The electron density of delocalized bonds (EDDB) method provides an explanation and proves to be a valuable tool for analyzing cyclic delocalization and the substituent effect.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Shuwei Lin, Qiyun Tong, Pan Jiang, Baozong Li, Yi Li, Yonggang Yang
Summary: This study on three dipeptides based on the Ala-Ala building block with different substituent positions of the dodecyloxy group on the benzoyl residue at the N terminus found that they formed different well-ordered structures with parallel beta-sheets, providing a theoretical basis for their different self-assembling behaviors.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Jifan Shi, Kazuyuki Aihara, Tiejun Li, Luonan Chen
Summary: This study establishes a landscape theory for cell differentiation with a proliferation effect, and identifies two energy landscapes U and V that collectively contribute to the establishment of non-equilibrium steady differentiation.
NATIONAL SCIENCE REVIEW
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Anoop Manjunath, Hongyu Li, Shuchen Song, Zhixing Zhang, Shu Liu, Nathan Kahrobai, Arya Gowda, Angelina Seffens, James Zou, Ishan Kumar
Summary: A citation map connecting patents to biomedical publications provides insights that can be used to better evaluate productivity, diversity, and translational impact.
NATURE BIOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Abigail L. L. Whittock, Adam M. M. Cowden, Martin Wills, Vasilios G. G. Stavros
Summary: In this study, four biomimetic molecules with varying substituents on the carbon ring were synthesized based on the natural UV filter mycosporine. The photoprotective properties of these molecules were investigated, and design guidelines were inferred, which may have an impact on the production of next generation UV filters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Prince Tiwari, Ri Wu, Jonas B. Metternich, Renato Zenobi
Summary: The study presented the first evidence of transition metal ion FRET in the gas phase and its application in measuring short biomolecular backbone distances. The distances estimated in the gas phase were consistently longer than in solution, suggesting an expanded structure and a potential loss of helicity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Ri Wu, Lukas R. Benzenberg, Despoina Svingou, Renato Zenobi
Summary: The recent research discovered that copper ions (Cu(II)) can alter the conformation and function of the cyclic neuropeptide somatostatin (SST), leading to self-aggregation and loss of biological function as a neurotransmitter. However, the precise impact of Cu(II) ions on the structure and function of SST remains unclear. In this study, transition metal ion Fo''rster resonance energy transfer (tmFRET) and native ion mobility mass spectrometry (IM-MS) were used to investigate the structures of well-defined gas-phase ions of SST and octreotide (OCT). The results indicate that Cu(II) ions bind to two specific sites in both native-like SST and OCT ions, either near the disulfide bond or complexed by two aromatic residues. These binding sites can initiate aggregation of SST and affect the essential motif for receptor binding, impairing the biological function of SST and OCT when bound to SST receptors. The study demonstrates the capability of tmFRET to locate transition metal ion binding sites in neuropeptides and provides structural insights into the self-aggregation mechanisms and overall biological functions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Development Studies
Stuti Haldar
Summary: In accordance with India's sustainable energy targets, the private sector plays a crucial role in promoting entrepreneurship in the renewable energy sector. Despite policy regulations aimed at promoting innovation and entrepreneurship in the RE industry, the profitability of RE entrepreneurs remains low.
SUSTAINABLE DEVELOPMENT
(2022)
Article
Polymer Science
Adam Mizera, Alina T. Dubis, Andrzej Lapinski
Summary: The electronic and vibrational structures of pyrrole oligomer and its derivatives were investigated using Density Functional Theory (DFT) and Time-dependent DFT (TD-DFT) computations. The influence of substituent groups on the optical and electronic properties of polypyrrole and polypyrrole derivatives, as well as the molecular structure and frontier molecular orbitals of neutral and ionized oligomers, were analyzed.
Article
Spectroscopy
Qi Li, Yu Wan, Qiao Zhou, You Li, Bo Li, Lixia Zhu, Yongfeng Wan, Hang Yin, Ying Shi
Summary: In this study, the mechanism behind the difference in quantum yields between 2-(4,4-Dimethyl-4,5-dihydrooxazol-2-yl)-3-hydroxybenzonitrile (1-CN) and 4-(4,4-Dimethyl-4,5-dihydrooxazol-2-yl)-3-hydroxybenzonitrile (3-CN) was explored. The calculation results showed that the fluorescence peaks of both molecules originated from keto* configuration. The comparison of emission oscillator strength suggested that neither radiative transition nor internal conversion process was the main reason for the difference in quantum yields. It was found that the intersystem crossing process was more prominent in 1-CN compared to 3-CN, providing direct evidence for the lower fluorescence quantum yield of 1-CN.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Xiaobo Sun, Thomas Hansen, Jordi Poater, Trevor A. Hamlin, Friedrich Matthias Bickelhaupt
Summary: By modulating the electronic or structural effects of iron catalysts, the reaction barrier for C-X bond activation can be significantly decreased.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Zhen Wang, Ana Gimeno, Marta G. Lete, Herman S. Overkleeft, Gijsbert A. van der Marel, Fabrizio Chiodo, Jesus Jimenez-Barbero, Jeroen D. C. Codee
Summary: We report the first total synthesis of the Streptococcus pneumoniae serotype 1 (Sp1) oligosaccharide, which is a zwitterionic capsular polysaccharide carrying unstable O-acetyl esters. The synthesis was achieved by assembling trisaccharide building blocks in a highly stereoselective manner, up to the 9-mer level. The structure investigation revealed that the oligomers adopt a right-handed helical structure, with the acetyl esters exposed on the periphery and in close proximity of the neighboring AAT residues.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Wouter A. A. Remmerswaal, Thomas Hansen, Trevor A. A. Hamlin, Jeroen D. C. Codee
Summary: Oxocarbenium ions play a key role in organic chemistry and their reactions with allyltrimethylsilane were investigated in this study. The researchers found that the preference for the chair conformation of the oxocarbenium ion influences the stereochemical outcome of the reaction. The introduction of alkoxy substituents on the ions also affects their conformational preference and stereoselectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Jacob M. A. van Hengst, Rik J. C. Hellemons, Wouter A. Remmerswaal, Koen N. A. van de Vrande, Thomas Hansen, Stefan van der Vorm, Hermen S. Overkleeft, Gijsbert A. van der Marel, Jeroen D. C. Codee
Summary: By systematically surveying 67 acceptor alcohols in glycosylation reactions, this study reveals how the reactivity of a carbohydrate acceptor depends on its configuration and substitution pattern, which greatly influences the yield and stereoselectivity of the reaction. The study demonstrates the influence of functional groups flanking the acceptor alcohol on its reactivity, highlighting the importance of both the nature and relative orientation. The empirical acceptor reactivity guidelines obtained will assist in the rational optimization of glycosylation reactions and serve as an important tool in oligosaccharide assembly.
Article
Chemistry, Multidisciplinary
Liangshen Duan, Qin Nie, Yongxin Hu, Liming Wang, Kaiyan Guo, Zhuoyi Zhou, Xu Song, Yuanhong Tu, Hui Liu, Thomas Hansen, Jian-song Sun, Qingju Zhang
Summary: In this study, we successfully synthesized the pentasaccharide and decasaccharide of A. baumannii ATCC 17961 O-antigen for the development of a synthetic carbohydrate-based vaccine against A. baumannii infection. We employed an organocatalytic glycosylation method to efficiently synthesize the rare sugar 2,3-diacetamido-glucuronate. We also discovered the improved beta-selectivity in glycosylations by the long-range levulinoyl group participation via a hydrogen bond, which solved the stereoselectivity problem of highly branched galactose acceptors. The proposed mechanism was supported by control experiments and DFT computations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Thomas Hansen, Pascal Vermeeren, Kim W. J. Zijderveld, F. Matthias Bickelhaupt, Trevor A. A. Hamlin
Summary: The influence of ring strain on the competition between the S(N)2 and E2 pathways has been studied using quantum chemical methods. It was found that increasing ring strain decreases the activation energy of the S(N)2 pathway but generally increases the activation energy of the E2 pathway. This results in a mechanistic switch in the preferred reaction pathway for strong Lewis bases, favoring S(N)2 for small cyclic substrates and E2 for large cyclic substrates.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Editorial Material
Chemistry, Organic
Sabine Flitsch, Suvarn Kulkarni, Jeroen D. C. Codee
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Organic
Tim P. Ofman, Gijsbert A. van Der Marel, Jeroen D. C. Codee, Hermen S. Overkleeft
Summary: Cyclophellitol aziridines are widely used as irreversible inhibitors of retaining glycosidases. In this study, different chemistries were explored to construct cyclitol aziridines with the aziridine electrophile attached in an exocyclic fashion, closer to an inverting glycosidase active site nucleophile. These newly synthesized cyclitol aziridines can be evaluated as inhibitors or inactivators of both alpha- and beta-glucosidases.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Zhen Wang, Ana Poveda, Qingju Zhang, Luca Unione, Herman S. Overkleeft, Gijsbert A. van der Marel, Jimenez-Barbero Jesus, Jeroen D. C. Codee
Summary: Researchers have successfully synthesized a series of polysaccharide fragments with a unique structure that can activate T cells and bind to specific receptors. Detailed structural studies have revealed the secondary structure of these fragments, providing a basis for further understanding their mode of action.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Jerre M. M. Madern, Jim Voorneveld, Johannes G. M. Rack, Hans A. V. Kistemaker, Ivan Ahel, Gijsbert A. A. van der Marel, Jeroen D. C. Codee, Dmitri V. V. Filippov
Summary: Adenosine diphosphate (ADP) ribosylation is an important post-translational modification (PTM) that affects various cellular processes. Synthetic analogues such as the 4-thioribosyl APRr peptide provide valuable tools for studying the enzymes involved in the establishment, recognition, and removal of this PTM. In this study, the 4-thioribosyl serine building block was synthesized using a stereoselective glycosylation reaction.
Article
Chemistry, Organic
Yongyong Wan, Meimei Zhou, Liming Wang, Kexin Hu, Deyong Liu, Hui Liu, Jian-Song Sun, Jeroen D. C. Codee, Qingju Zhang
Summary: Here, a unique organo-catalysis relay glycosylation method is described for the regio- and stereoselective synthesis of 2-amino-2-deoxy-dithioglycosides. This method exhibits excellent site- and stereoselectivity, good to excellent yields, mild reaction conditions, and broad substrate scope. The dithiolated O-antigen of E. coli serogroup 64 was successfully synthesized using this newly developed method.
Article
Chemistry, Medicinal
Merle A. van Gelder, Sabina Y. van der Zanden, Merijn B. L. Vriends, Roos A. Wagensveld, Gijsbert A. van der Marel, Jeroen D. C. Codee, Herman S. Overkleeft, Dennis P. A. Wander, Jacques J. C. Neefjes
Summary: Anthracycline anti-cancer drugs are widely used in the clinic to treat various cancers. They induce DNA double strand breaks and chromatin damage, which contribute to their reported side effects. Despite advancements in understanding the structure-activity relationship of anthracyclines, there are still many unexplored structural variations. This study prepared a diverse set of anthracyclines with variations in the sugar moiety, amine alkylation pattern, saccharide chain, and aglycone, and evaluated their cytotoxicity, DNA- and chromatin damage-inducing capacity in vitro. This work provides guidelines for anthracycline design and identifies novel and highly potent anthracyclines that may have improved patient tolerance.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Hugo Minnee, Hayley Chung, Johannes Gregor Matthias Rack, Gijsbert A. van der Marel, Herman S. Overkleeft, Jeroen D. C. Codee, Ivan Ahel, Dmitri V. Filippov
Summary: This article describes the synthesis of a series of triazole-isosteres of ADP-ribosylated histidine, which serve as probes for studying ADP-ribosylating enzymes. The synthesized structures mimic N(& tau;)- and N(& pi;)-ADP-ribosylated histidine and have been evaluated for their chemical and enzymatic stability.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
