Article
Chemistry, Medicinal
Renzo Carlucci, Maria-Natalia Lisa, Guillermo R. Labadie
Summary: This study demonstrates the diverse noncovalent interactions between the 1,2,3-triazole scaffold and amino acids in proteins, which contribute to protein-ligand binding and may have implications for drug development.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Francesca Peccati, Gonzalo Jimenez-Oses
Summary: This mini-review provides an overview of the enthalpy-entropy compensation phenomenon in biomacromolecular recognition simulations with emphasis on ligand binding. Examples are presented to illustrate different approaches to interpret and predict compensation phenomena at an atomistic level, moving beyond traditional textbook assumptions.
Article
Chemistry, Multidisciplinary
Zichao Wei, Chung-Hao Liu, Qiang Luo, Srinivas Thanneeru, Alfredo M. Angeles-Boza, Mu-Ping Nieh, Jie He
Summary: We investigated the hydrophobicity-enhanced reactivity of Cu2+ ions as an ester hydrolase. By varying the synthetic sequence of amphiphilic block copolymers, we controlled the location of the Cu2+ binding motif in polymer micelles. The hydrophobicity of Cu2+ sites significantly impacted their catalytic efficiency, with as much as 60 times more activity. Our findings highlight the importance of hydrophobic microenvironments in the design of bioinspired catalysts.
MATERIALS CHEMISTRY FRONTIERS
(2023)
Article
Physics, Multidisciplinary
Tomasz Skora, Mathijs Janssen, Andreas Carlson, Svyatoslav Kondrat
Summary: Macromolecular crowding can have significant impacts on various biophysical processes, including diffusion, gene expression, cell growth, and senescence. However, the effects of crowding on reactions, especially multivalent binding, are not fully understood. In this study, we used scaled particle theory and molecular simulation to investigate the binding of monovalent to divalent biomolecules. Our findings show that crowding can greatly enhance or reduce cooperativity, depending on the sizes of the involved molecular complexes. Furthermore, crowding can enable binding that would not occur otherwise.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Marta Meneghello, Ana Rita Oliveira, Aurore Jacq-Bailly, Ines A. C. Pereira, Christophe Leger, Vincent Fourmond
Summary: Mo/W formate dehydrogenases catalyze the reversible reduction of CO2 to formate, and it has been definitively demonstrated through an electrochemical method that the substrate is indeed CO2, not a hydrated species like HCO3-.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biology
Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei
Summary: A sequence-based virtual screening method utilizes natural language processing algorithms and optimized deep K-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. It outperforms current methods in multiple datasets and has significant potential in drug discovery and protein engineering.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ferran Esteve, Fidan Rahmatova, Jean-Marie Lehn
Summary: This study reveals the remarkable effect of supramolecular multivalency on increasing imine stability. By synthesizing a series of reactive aldehydes bearing supramolecularly-active sites, it was found that decreasing the degree of supramolecular multivalency significantly decreased imine yields. Preliminary results on protein bioconjugation demonstrated the ability to dynamically inhibit the activity of carbonic anhydrase and recover its initial activity with a suitable chemical effector.
Article
Chemistry, Physical
Navjeet Ahalawat, Jagannath Mondal
Summary: Computer simulation approaches have greatly advanced in biomolecular recognition processes, particularly through unbiased simulation and Markov state modeling methods. Enhanced sampling approaches are crucial in accelerating simulations of ligand recognition processes, but key issues such as force fields and sampling bottlenecks still need to be addressed to achieve quantitative reconstruction of experimental measurements. Adopting multiscale approaches and coarse-grained simulations may be a possible way forward for efficient elucidation of ligand binding kinetics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Cell Biology
Andrew S. Lyon, William B. Peeples, Michael K. Rosen
Summary: Biomolecular condensates are membraneless molecular assemblies formed via liquid-liquid phase separation, playing important roles in controlling biochemical reactions and regulating cell organization and function throughout eukaryotic cells.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Heba Abdelrasheed Allam, Mohamed E. Albakry, Walaa R. Mahmoud, Alessandro Bonardi, Shaimaa A. Moussa, Samy Mohamady, Hatem A. Abdel-Aziz, Claudiu T. Supuran, Hany S. Ibrahim
Summary: In this study, three novel series of aryl enaminones and pyrazole-linked compounds with sulphonamides, sulfaguanidine, or carboxylic acid functionalities were designed and synthesized as carbonic anhydrase inhibitors (CAIs). The synthesized compounds were evaluated for their inhibitory activity against human isoforms hCA I, II, IX, and XII. The results showed that the enaminone sulphonamide derivatives potently inhibited hCA IX and hCA XII, and one derivative (3c) exhibited cytotoxic activity against MCF-7 and MDA-MB-231 cancer cell lines, inducing apoptosis in MCF-7 cells.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Daniel J. Mueller, Andra C. Dumitru, Cristina Lo Giudice, Hermann E. Gaub, Peter Hinterdorfer, Gerhard Hummer, James J. De Yoreo, Yves F. Dufrene, David Alsteens
Summary: Over the past three decades, key technological improvements have transformed AFM into a nanoscopic laboratory for directly observing and chemically characterizing molecular and cell biological systems under physiological conditions. By customizing nanoscopic chemical laboratories and utilizing different AFM modes, it is possible to chemically image, sense, and manipulate biosystems at extremely small spatial and temporal resolutions. The combination of AFM with optical microscopy and spectroscopy shows great potential in addressing the complexity of biological systems and tackling fundamental challenges in life sciences.
Article
Spectroscopy
Xiaojuan Wang, Zhixiong Zhang, Zhenzhen Liu, Xiqi Ma, Qi Dai, Xiaoqiang Wang, Baosheng Ge, Hua He, Fang Huang
Summary: This study systematically investigated the interactions between ultrasmall graphene quantum dots (GQDs) and biomacromolecules using carbonic anhydrase (CA) as a model protein. The results showed that GQDs could quench the intrinsic fluorescence of CA in a static binding mode driven by van der Waal interactions and hydrogen bonding. Additionally, the binding of GQDs induced slight conformational changes of CA and resulted in the reduction of its biological functions.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Multidisciplinary Sciences
Joanna Xiuzhu Xu, Md Siddik Alom, Rahul Yadav, Nicholas C. Fitzkee
Summary: The authors develop a residue-based affinity scale to predict protein orientation on gold nanoparticles. The scale takes into account the steric considerations for hydrophobic residues and the electrostatic interactions for hydrophilic residues. Using this model, the accessibility of active sites on proteins on nanoparticles can be predicted.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Cristhian Molina-Fernandez, Ariane Peters, Damien P. Debecker, Patricia Luis
Summary: Poly(ionic liquid)s are interesting materials for CO2 separation due to their affinity towards CO2. Immobilizing carbonic anhydrase in poly(ionic liquid)s can enhance CO2 capture efficiency, although it may decrease the enzyme activity. The immobilized enzyme shows better storage stability compared to the free enzyme.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Chemistry, Inorganic & Nuclear
Priyaranjan Kumar, Prerana Singh, Sanjoy Saren, Sandip Pakira, Sri Sivakumar, Ashis K. Patra
Summary: In this study, six kinetically labile ruthenium(II) complexes containing saccharin and substituted terpyridines were designed, showing potential biological binding activity and drug release capability. These complexes demonstrated promising utility in Ru-assisted photoactivated chemotherapy, inducing apoptosis in breast cancer cells and cervical cancer cells. The complexes also exhibited reactivity in solvation kinetics and ligand-substitution reactions, providing insight into their potential applications as therapeutic agents.
DALTON TRANSACTIONS
(2021)
Article
Chemistry, Physical
Dmitrij Rappoport
Summary: Property-optimized Gaussian basis sets tailored for lanthanides with different oxidation states were developed and assessed for accuracy in atomic and molecular polarizability calculations using a test set. Extended basis sets were also provided for precise calculations of lanthanide atoms and neutral clusters. These basis sets were shown to accurately reproduce electronic absorption spectra of a series of LnCp3 complexes using time-dependent density functional theory.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Analytical
Tyler S. Larson, Gary L. Glish, Matthew R. Lockett
Summary: Paper-based cultures provide an emerging platform for preparing 3D tissue and tumor-like structures with defined cellular compositions and microenvironments. Spatially resolved quantification of cell viability and drug metabolism was achieved in a stacked structure using liquid chromatography-mass spectrometry. The study showed that cells at the bottom of the stack were more drug-resistant, similar to nutrient-poor center cells of a tumor being more resistant than rapidly dividing cells at the periphery.
ANALYTICA CHIMICA ACTA
(2021)
Review
Chemistry, Multidisciplinary
Antonella lenia Alfano, Heiko Lange, Margherita Brindisi
Summary: The formation of amide bonds is essential in organic and synthetic medicinal chemistry. In recent years, the application of flow chemistry in amide bond formation has shown significant advantages and potential for development. This review summarizes and compares various methods and discusses future needs and prospects for sustainable synthesis.
Article
Chemistry, Multidisciplinary
Anika Salanti, Marco Orlandi, Heiko Lange, Federica Ferruti, Luca Zoia
Summary: An analytical approach based on phenol fluorescence labeling was used to understand the phenolic group distribution in different lignin specimens. The method involved selective derivatization of lignin phenolic functionalities and analysis using gel permeation chromatography. The results provided insights into the distribution of phenolic groups in different lignins.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Chemistry, Analytical
Rachael M. Kenney, Maggie C. Lee, Matthew W. Boyce, Zachary R. Sitte, Matthew R. Lockett
Summary: Cellular invasion is a crucial step in metastasis, and invasion assays are used to study cell movement in the presence of chemokines or inhibitors. To improve physiological relevance, a new assay format was developed to track cellular movement in a uniform density of cells. Results showed that highly invasive cells persisted and continued to move, suggesting they may have stem-like properties, and their invasion distance was not affected by cell density or oxygen gradients.
ANALYTICAL CHEMISTRY
(2023)
Article
Agricultural Engineering
Elisabetta Alfonsi, Heiko Lange, Luc Zongo, Giovanna Poce, Massimo Sgarzi, Claudia Crestini
Summary: Salicylate and benzoate sunscreen agents were encapsulated in tannin microcapsules using a green, fast, and robust ultrasound technique. The microcapsules, obtained without cross linking agents, were fully characterized, including encapsulation efficiencies. The release kinetics of the microcapsules mimicked skin conditions and showed synergistic effects between sunscreen actives and natural tannin polyphenols, reducing the amount of synthetic sunscreens needed for sustainable and environmentally friendly UV-protection systems.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Dmitrij Rappoport, Samuel Bekoe, Luke Nambi Mohanam, Scott Le, Naje' George, Ziyue Shen, Filipp Furche
Summary: This article presents the design and implementation of libkrylov, an open-source library for solving matrix-free eigenvalue, linear, and shifted linear equations using Krylov subspace methods. The key features of libkrylov include flexible API design, modular structure, and integration with specialized matrix-vector evaluation engines.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Tyler S. Larson, Cameron D. Worthington, Matthew D. Verber, James E. Keating, Matthew R. Lockett, Gary L. Glish
Summary: The traditional data-dependent acquisition (DDA) approach for mass spectrometry selects precursor ions based on their absolute intensity, but may miss low-abundance species as biomarkers. This study proposes a new DDA approach called DiffN, which uses the relative differential intensity of ions between two samples to target species with large fold changes for analysis. The DiffN approach, coupled with a dual nano-electrospray (nESI) ionization source, showed promising results in quantifying lipid abundance differences in colorectal cancer cells.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Chemical
Sandro Stucki, Heiko Lange, Christopher H. Dreimol, Yves Weinand, Ingo Burgert
Summary: The moisture resistance of friction-welded wood joints can be improved by applying bio-based bonding additives. Kraft lignin showed significantly increased moisture stability after 24 h water immersion, with an average wet bond strength of 1.5 MPa. However, modification of kraft lignin through succinylation, acetylation or depolymerization did not further improve moisture stability, and depolymerized kraft lignin actually led to a higher delamination rate during water immersion. Structural and chemical analyses showed the impact of various lignin variations on thermal behavior and intermolecular interactions.
JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Medicinal
Dmitrij Rappoport, Adrian Jinich
Summary: This study constructs and evaluates three-dimensional feature representations of protein structures based on space-filling curves (SFCs), with the aim of accurately predicting protein properties and functions. SFCs, such as the Hilbert curve and the Morton curve, enable the encoding of three-dimensional molecular structures in a system-independent manner using a few adjustable parameters. The performance of the SFC-based feature representations is assessed in predicting enzyme substrate properties, yielding high accuracies and AUC values for the classification tasks.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Colin Schiltz, Dmitrij Rappoport, Vladimir A. Mandelshtam
Summary: The self-consistent phonon (SCP) method combines with ab initio (AI) potential energy evaluation to efficiently compute Gaussian averages of the AI potential energy and its derivatives. The SCP method allows for the inclusion of anharmonic effects in thermal equilibrium quantum systems, providing estimations of dynamic and static properties. The quasi-Monte Carlo method is used for efficient computation, with a further improvement in efficiency achieved through a perturbation theory-like approach when an approximation of the AI potential is available. Codes and scripts are provided.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Dmitrij Rappoport
Summary: Selection bias is inevitable in manually curated computational reaction databases. Quasireaction subgraphs are proposed as a discrete, graph-based representation of reaction mechanisms. A binary classification of feasible and infeasible reaction subgraphs must be applied. The construction, properties, and clustering of quasireaction subgraphs from CHO transition networks are explored.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Gabriel S. Phun, Dmitrij Rappoport, Filipp Furche, Tammie R. Gibson, Sergei Tretiak
Summary: In this study, we computationally investigated the protonation states, stereoisomers, chemical mechanism, and dynamics of the bioluminescence intermediate responsible for chemiexcitation in dinoflagellate luciferin. The study found that a 4-membered ring, dioxetanol compound that undergoes [2π + 2π] cycloreversion is likely responsible for chemiexcitation, and the cleaved structure is the biolumiphore. The simulated emission spectra and luciferase-dependent absorbance spectra supported the proposed mechanism and biolumiphore, and circular dichroism spectra of the intermediate's stereoisomers were computed to guide future experiments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Analytical
Zachary R. Sitte, Abel Andre Miranda Buzetta, Sarina J. Jones, Zhi-Wei Lin, Nathan Ashbrook Whitman, Matthew R. Lockett
Summary: This article introduces a paper-based culture platform for studying intercellular signaling between two cell types. By culturing breast cancer cells and fibroblasts in paper scaffolds and comparing the effects in different configurations, the researchers found that the presence, number, and proximity of fibroblasts can affect the transcriptional activation of estrogen receptors, and this is a result of intercellular signaling molecules.
ACS MEASUREMENT SCIENCE AU
(2023)
Article
Chemistry, Analytical
Zachary R. Sitte, Tyler S. Larson, Julie C. McIntosh, Melanie Sinanian, Matthew R. Lockett
Summary: Cellular viability measurements are used to assess the effects of drug candidates or toxins on cell proliferation and cytotoxicity. While direct viability measures provide accurate results, they can be challenging and time-consuming in 3D cell cultures. Indirect viability measures are less labor-intensive but less accurate due to the complex cell microenvironment. This study evaluates the analytical performance of five indirect viability assays in a paper-based cell culture platform, considering factors such as hypoxia and reproducibility.
