Review
Biochemistry & Molecular Biology
Laura L. Kiessling, Roger C. Diehl
Summary: The text discusses how proteins recognize sugars through CH-π interactions, highlighting the importance of electron-rich aromatic residues in glycan binding.
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Michio Yamada
Summary: This article summarizes recent advances in experimental and theoretical efforts to characterize the nature and strength of non-covalent interactions on fullerene surfaces. The studies include host-guest chemistry based on various macrocycles, catalyst chemistry based on conjugated molecular catalysts, and conformational isomerism analyses using fullerene-based molecular torsion balances and computational chemistry. These studies have provided a comprehensive evaluation of the contributions of electrostatic, dispersion, and polar interactions on the surface of fullerenes.
Article
Chemistry, Multidisciplinary
Muhammad Naeem Ahmed, Maheen Akhtar, Hina Andleeb, Muhammad Adnan Bashir, Mahmoud A. A. Ibrahim, Peter A. Sidhom, Ifzan Arshad, Muhammad Nawaz Tahir, Diego M. Gil, Rosa M. Gomila, Antonio Frontera
Summary: Three new 1,3,4-oxadiazoles were synthesized and their crystal structures were analyzed. The study focused on the weak noncovalent interactions between molecules, including hydrogen bonds and pi interactions. The properties and extent of these interactions were investigated using DFT calculations, QTAIM analysis, NCI plots, and MEP surface plots.
Article
Chemistry, Multidisciplinary
Yu Cao, Jian Yang, Dominik Eichin, Fangzhe Zhao, Dawei Qi, Laura Kahari, Chunman Jia, Markus Peurla, Jessica M. Rosenholm, Zhao Zhao, Sirpa Jalkanen, Jianwei Li
Summary: This study overcame the drawbacks of traditional nanocarriers using dynamic combinatorial chemistry, synthesizing a stable and highly responsive nanocarrier with increased drug loading capacity and enhanced drug potency to combat DOX resistance. Harnessing the interplay between synthesis and self-assembly in complex chemical systems can yield functional nanomaterials for advanced applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Rafael Santana Nunes, Diogo Vila-Vicosa, Paulo J. Costa
Summary: Halogen bonds (XBs) are noncovalent interactions in which halogen atoms act as electrophilic species interacting with Lewis bases. This type of interaction is relevant in biological membrane systems, influencing the pharmacological or toxicological activity of halogenated compounds. Molecular dynamics simulations provide evidence of the effects of XBs on ligands' membrane insertion profile and orientational preferences.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Yang Jiao, Haochuan Mao, Yunyan Qiu, Guangcheng Wu, Hongliang Chen, Long Zhang, Han Han, Xuesong Li, Xingang Zhao, Chun Tang, Xiao-Yang Chen, Yuanning Feng, Charlotte L. Stern, J. Fraser Stoddart, Michael R. Wasielewski
Summary: Molecular recognition based on noncovalent bonding is important in directing supramolecular phenomena. Weakly associated recognition motifs are challenging to identify and investigate. This study synthesized a [2]catenane compound to enhance weak interactions and reduce system complexity. By using this compound as a model, three possible binding modes between CBPQT and BIPY were discovered and characterized. These findings have potential applications in self-assembled materials and supramolecular catalysis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Huaichuan Duan, Kaixuan Hu, Dan Zheng, Yan Cheng, Zelan Zhang, Yueteng Wang, Li Liang, Jianping Hu, Ting Luo
Summary: In this study, the molecular recognition of hCNT3 with uridine was investigated using molecular docking and molecular dynamics simulations. Uridine derivatives with potentially high inhibitory activity were designed. The study revealed the molecular interactions between uridine and hCNT3 and provided potential lead compounds for anti-cancer drug development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Binzhou Lin, Hao Liu, Ishwor Karki, Erik C. Vik, Mark D. Smith, Perry J. Pellechia, Ken D. Shimizu
Summary: Stabilizing nitrogen pnictogen bond interactions were measured using molecular rotors. Intramolecular C=O···N interactions were formed in the bond rotation transition states which lowered the rotational barriers and increased the rates of rotation, as measured by EXSY NMR. The pnictogen interaction energies show a very strong correlation with the positive electrostatic potential on nitrogen, which was consistent with a strong electrostatic component. In contrast, the NBO perturbation and pyramidalization analyses show no correlation, suggesting that the orbital-orbital component is minor. The strongest C=O···N pnictogen interactions were comparable to C=O···C=O interactions and were stronger than C=O···Ph interactions, when measured using the same N-phenylimide rotor system. The ability of the nitrogen pnictogen interactions to stabilize transition states and enhance kinetic processes demonstrates their potential in catalysis and reaction design.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Natsuki Kishida, Yuya Tanaka, Michito Yoshizawa
Summary: In this study, selective binding of planar polyaromatics and effective isolation of planar metal complexes are achieved by utilizing multiple CH-pi interactions. The results demonstrate the predominance of multiple host-guest CH-pi interactions as the driving force for selectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Beatriz Suay-Garcia, Jose I. Bueso-Bordils, Antonio Falco, Gerardo M. Anton-Fos, Pedro A. Aleman-Lopez
Summary: Traditionally, drug development involved time-consuming and costly processes, but the application of virtual combinatorial chemistry and virtual screening can greatly accelerate the search and development of drugs, while saving costs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Boris Bartolec, Armin Kiani, Meagan A. A. Beatty, Meniz Altay, Guillermo Monreal Santiago, Sijbren Otto
Summary: The complex interplay between systems and their environment is crucial in self-assembly and evolution. Polymorphism, induced by environmental pressures, leads to various structural organizations. By combining covalent and non-covalent bond formation, three distinct polymorphs can be generated from the same molecular network, depending on the solvent environment.
Article
Biochemistry & Molecular Biology
Nicolas Foloppe, I-Jen Chen
Summary: This study utilized molecular dynamics simulations to comprehensively investigate the reorganization energy of compounds upon binding to proteins, revealing negative reorganization enthalpies and demonstrating that intramolecular interactions may not necessarily oppose binding, but could stabilize the bound state. The results indicated a redistribution of interactions upon binding, with occasional larger reorganization values observed, suggesting a qualitative compatibility with binding.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Luhan Zhai, Masayuki Nara, Yuko Otani, Tomohiko Ohwada
Summary: NH-pi and CH-pi interactions, which are weak in nature, are not easily detected in solution. However, a group of isolable short peptides with stable folds have been reported, in which these interactions can be identified using NMR and ATR-IR spectroscopy.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Masaaki Akamatsu, Koji Yamanaga, Kohei Tanaka, Yurina Kanehara, Masato Sumita, Kenichi Sakai, Hideki Sakai
Summary: Biological systems control ion binding through molecular interactions with membranes and proteins. However, anion recognition systems in highly polar media are limited. This study explored anion binding at air/water interfaces using amphiphilic NDI derivatives. The binding of anions was related to their electron density, and the packing of NDI derivatives influenced anion binding. These results provide insight into ion binding and have potential applications in sensing devices and semiconductor technologies.
Review
Chemistry, Multidisciplinary
Yufeng Huo, Zhenfeng He, Chao Wang, Lei Zhang, Qianyu Xuan, Suying Wei, Yanhong Wang, Duo Pan, Binbin Dong, Renbo Wei, Nithesh Naik, Zhanhu Guo
Summary: Supramolecular polymers, formed through multiple noncovalent interactions, have unique advantages and applications in various fields such as self-healing, drug delivery, and biomedicine.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Lucas Schaus, Anuvab Das, Anders M. Knight, Gonzalo Jimenez-Oses, K. N. Houk, Marc Garcia-Borras, Frances H. Arnold, Xiongyi Huang
Summary: It has been discovered that an engineered protoglobin from Aeropyrnum pernix (ApePgb) can catalyze the asymmetric synthesis of trans-CF3-CPAs, with yield and enantioselectivity depending on the substrate. Computational studies show that the steric environment in the active site of the protoglobin forces iron-carbenoid and substrates to adopt a pro-cis near-attack conformation. This study demonstrates the ability of enzyme catalysts to tackle challenging chemistry problems and expands the structural diversity of CF3-CPAs for drug discovery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Daniel Marcos-Atanes, Cristian Vidal, Claudio D. Navo, Francesca Peccati, Gonzalo Jimenez-Oses, Jose L. Mascarenas
Summary: Iridium-catalyzed borylations of aromatic C-H bonds allow for the synthesis of a wide variety of ortho-borylated derivatives. A subtle change in the bipyridine ligand, introducing a CF3 substituent at position 5, enables a complete change of regioselectivity in the borylation of aromatic amides. Computational studies suggest that this regio- and chemoselectivity is due to unusual outer-sphere interactions between the amide group of the substrate and the CF3-substituted aryl ring of the bipyridine ligand.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Francesco Milanesi, Luca Unione, Ana Arda, Cristina Nativi, Jesus Jimenez-Barbero, Stefano Roelens, Oscar Francesconi
Summary: Glycomics research has revealed the essential role of carbohydrates in biological systems and the importance of chemical tools in studying glycan function. While biomimetic receptors can selectively bind to simple saccharides, this study demonstrates the unprecedented recognition of a complex glycopeptide by a biomimetic receptor. The receptor shows high affinity for the core disaccharide of the N-glycan and has the potential for versatile applications in glycoscience.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Marta G. Lete, Antonio Franconetti, Sara Bertuzzi, Sandra Delgado, Mikel Azkargorta, Felix Elortza, Oscar Millet, Gonzalo Jimenez-Oses, Ana Arda, Jesus Jimenez-Barbero
Summary: Fluorine (F-19) incorporation into lectins has allowed monitoring of carbohydrate binding through NMR spectroscopy. Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were chosen. The presence of fluorine did not significantly affect glycan binding affinity, and allowed differentiation of binding events at different sites within the same lectin.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Nanoscience & Nanotechnology
Anna Blasi-Romero, Molly Angstrom, Antonio Franconetti, Taj Muhammad, Jesus Jimenez-Barbero, Ulf Goransson, Carlos Palo-Nieto, Natalia Ferraz
Summary: This study combines the wound-healing properties of KR-12 peptide with wood-derived cellulose nanofibrils (CNFs) to create bioactive materials for treating chronic wounds. Different coupling chemistries were used to covalently attach KR-12 derivatives onto CNFs, and the bioactivity of KR12-CNF conjugates was evaluated in terms of antibacterial activities and anti-inflammatory effects. The results showed that thiol-ene chemistry produced the most bioactive conjugates, attributed to favorable peptide conformation and accessibility. This study advances the development of CNF-based materials for chronic wound care and provides insights into the effect of conjugation chemistry on the bioactivity of host defense peptides.
ACS APPLIED MATERIALS & INTERFACES
(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, Multidisciplinary
Gean M. Dal Forno, Eloah Latocheski, Ana Beatriz Machado, Julie Becher, Lavinia Dunsmore, Albert L. St John, Bruno L. Oliveira, Claudio D. Navo, Gonzalo Jimenez-Oses, Rita Fior, Josiel B. Domingos, Goncalo J. L. Bernardes
Summary: The ability to control prodrug activation by transition metals has great potential for controlled drug release in cancer cells. However, current strategies are limited to cleavage of C-O or C-N bonds, hindering the use of drugs with amino or hydroxyl groups. This study presents a palladium-mediated C-C bond cleavage method for the activation of an ortho-quinone prodrug, expanding the range of drugs that can be used.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Matteo A. . Tallarida, Fabrizio Olivito, Claudio D. Navo, Vincenzo Algieri, Antonio Jiritano, Paola Costanzo, Ana Poveda, Maria J. Moure, Jesus Jimenez-Barbero, Loredana Maiuolo, Gonzalo Jimenez-Oses, Antonio De Nino
Summary: The synthesis of polysubstituted spirocyclopropyl oxindoles using rare-earth metal (REM) salts, particularly Sc(OTf)3, was achieved with high diastereoselectivity (<= 94:6:0:0) in a multicomponent reaction. Density functional theory calculations on the model reaction confirmed the observed selectivity and demonstrated that the coordinating capabilities and oxophilicity of the metal played a crucial role in inducing the formation of one main diastereoisomer.
Article
Multidisciplinary Sciences
Maria Pia Lenza, Leire Egia-Mendikute, Asier Antonana-Vildosola, Catia O. Soares, Helena Coelho, Francisco Corzana, Alexandre Bosch, Prodhi Manisha, Jon Imanol Quintana, Iker Oyenarte, Luca Unione, Maria Jesus Moure, Mikel Azkargorta, Unai Atxabal, Klaudia Sobczak, Felix Elortza, James D. Sutherland, Rosa Barrio, Filipa Marcelo, Jesus Jimenez-Barbero, Asis Palazon, June Ereno-Orbea
Summary: This study elucidates the structure and binding epitope of Siglec-15, providing insights into its mechanism of action and potential for cancer immunotherapy. The findings highlight the importance of glycosylation in controlling T cell responses and identify CD11b as a binding partner for Siglec-15 on human T cells.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Hans-Christian Siebert, Thomas Eckert, Anirban Bhunia, Nele Klatte, Marzieh Mohri, Simone Siebert, Anna Kozarova, John W. Hudson, Ruiyan Zhang, Ning Zhang, Lan Li, Konstantinos Gousias, Dimitrios Kanakis, Mingdi Yan, Jesus Jimenez-Barbero, Tibor Kozar, Nikolay E. Nifantiev, Christian Vollmer, Timo Brandenburger, Detlef Kindgen-Milles, Thomas Haak, Athanasios K. Petridis
Summary: The global outbreak of SARS-CoV-2/COVID-19 has provided an opportunity and challenge to accumulate a large amount of biomedical data and test new concepts and strategies to combat the pandemic. This study correlated clinical biomedical data with structural biology and biophysical data to evaluate new diagnostic and therapeutic approaches against SARS-CoV-2. The methods used were effective in identifying potential peptide sequences and carbohydrate moieties to protect the blood-brain barrier and develop new therapeutic approaches against long-COVID symptoms.
Article
Chemistry, Multidisciplinary
Yanira Mendez, Aldrin V. Vasco, Galway Ivey, Ana Laura Dias, Peter Gierth, Barbara B. Sousa, Claudio D. Navo, Angel Torres-Mozas, Tiago Rodrigues, Gonzalo Jimenez-Oses, Goncalo J. L. Bernardes
Summary: A novel multicomponent approach combining the isonitrile-tetrazine (4+1) cycloaddition and the Ugi four-component reaction was developed to generate pyrazole amide derivatives. The scope of the reaction and the mechanistic insights of the 4H-pyrazol-4-imine tautomerization were provided. This multicomponent process expands the chemical space of pyrazole amide derivatives and offers a tool for peptide modification and stapling.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Guang Yang, Young Ju Yun, Francesca Peccati, Abdelqader M. Jamhawi, Nareshbabu Kamatham, Steffen Jockusch, Gonzalo Jimenez-Oses, A. Jean-Luc Ayitou
Summary: This study reports the synthesis and characterization of novel QDM-based chromophores that exhibit unique photo-excited behavior and aromaticity. The results show that extending the aromatic core can modulate the optoelectronic properties of these chromophores, but aromaticity imbalance in some of them leads to relative instability. Local aromaticity is identified as the main driving force for populating the excited triplet state of these chromophores.
Article
Chemistry, Multidisciplinary
Giulio Fittolani, Theodore Tyrikos-Ergas, Ana Poveda, Yang Yu, Nishu Yadav, Peter H. Seeberger, Jesus Jimenez-Barbero, Martina Delbianco
Summary: This article introduces a synthetic glycan molecule that adopts a stable secondary structure not found in nature, called a glycan hairpin. The synthetic glycan is created by combining natural glycan motifs and utilizing unconventional hydrogen bonds and hydrophobic interactions. Nuclear magnetic resonance conformational analysis and long-range inter-residue nuclear Overhauser effects confirm the folded conformation of the synthetic glycan hairpin. The ability to control the 3D shape of glycans has the potential to provide more foldamer scaffolds with programmable properties and functions.
Article
Multidisciplinary Sciences
Beatriz Piniello, Javier Macias-Leon, Shun Miyazaki, Ana Garcia-Garcia, Ismael Companon, Mattia Ghirardello, Victor Taleb, Billy Veloz, Francisco Corzana, Atsushi Miyagawa, Carme Rovira, Ramon Hurtado-Guerrero
Summary: In this study, the structures of soluble HMW1C-like N-glycosyltransferases (NGTs) were reported, revealing a key dyad of basic/acidic residues that plays a crucial role in Asn catalysis. The study also found that UDP-galactose and UDP-glucose mimetics act as poor substrates and inhibitors, impeding catalysis. QM/MM simulations provide insight into the reaction mechanism of AaNGT. These findings are important for understanding the mechanism of NGTs and designing drugs.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Carlo Pifferi, Leire Aguinagalde, Ane Ruiz-de-Angulo, Nagore Sacristan, Priscila Tonon Baschirotto, Ana Poveda, Jesus Jimenez-Barbero, Juan Anguita, Alberto Fernandez-Tejada
Summary: The overexpression of aberrantly glycosylated tumor-associated mucin-1 (TA-MUC1) in human cancers makes it a major target for the development of anticancer vaccines derived from synthetic MUC1-(glyco)peptide antigens. However, glycopeptide-based subunit vaccines are weakly immunogenic, requiring adjuvants and/or additional immunopotentiating approaches to generate optimal immune responses.
