4.6 Article

Machine Learning-Guided Computational Screening of New Candidate Reactions with High Bioorthogonal Click Potential

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Reaction profiles for quantum chemistry-computed [3+2] cycloaddition reactions

Thijs Stuyver et al.

Summary: Bio-orthogonal click chemistry has had a significant impact on biochemistry, and identifying new candidate reactions is crucial. This study used an automated workflow to compute over 5000 reaction profiles for [3 + 2] cycloadditions, providing valuable information for screening and predicting chemical reactivity. The B3LYP-D3(BJ)/def2-TZVP//B3LYP-D3(BJ)/def2-SVP level of theory was selected for the calculations, and standard conditions and a SMD model were used to mimic physiological conditions.

SCIENTIFIC DATA (2023)

Article Chemistry, Physical

Quantum chemistry-augmented neural networks for reactivity prediction: Performance, generalizability, and explainability

Thijs Stuyver et al.

Summary: This study investigates the performance, generalizability, and explainability of structure-based and descriptor-based molecular representations for predictive chemistry tasks. The quantum mechanics-augmented graph neural network (ml-QM-GNN) architecture is introduced, which combines structure-based representations with quantum mechanics descriptors to improve predictive accuracy and generalization to unseen compounds.

JOURNAL OF CHEMICAL PHYSICS (2022)

Review Chemistry, Multidisciplinary

Learning molecular potentials with neural networks

Hatice Gokcan et al.

Summary: The choice of computational approach for calculating molecular energy is challenging due to cost and reliability concerns, particularly for large molecules. On the other hand, neural network potentials have proven to accurately predict chemical properties with a cost similar to molecular mechanics calculations, making them attractive for researchers. This review outlines the current status of neural network potentials, strategies for improvement, and discusses challenges and future directions for their development and applications.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2022)

Review Chemistry, Multidisciplinary

Bioorthogonal Reactions Utilizing Nitrones as Versatile Dipoles in Cycloaddition Reactions

Didier A. Bilodeau et al.

Summary: Bioorthogonal chemical reactions involving nitrones have been optimized for efficient incorporation of unnatural functionality into living systems, with fast reaction rates. These reactions provide versatile tools for probing biological systems and have potential applications in biology.

CHEMICAL REVIEWS (2021)

Review Chemistry, Multidisciplinary

Click and Bio-Orthogonal Reactions with Mesoionic Compounds

Karine Porte et al.

Summary: Click chemistry and bio-orthogonal reactions are primarily based on cycloaddition reactions, especially 1,3-dipolar cycloadditions. Mesoionic compounds have recently emerged as attractive dipole partners due to their ability to be derivatized and have their reactivity tuned towards cycloaddition reactions. Some compounds from the mesoionic family can also undergo click-and-release reactions, showing interesting applications in cells and animals.

CHEMICAL REVIEWS (2021)

Article Chemistry, Multidisciplinary

Promotion Energy Analysis Predicts Reaction Modes: Nucleophilic and Electrophilic Aromatic Substitution Reactions

Thijs Stuyver et al.

Summary: This research develops an approach to predict major reaction modes associated with a chemical system based on reactant properties from the valence bond perspective. By analyzing promotion energies, predictive information about potential transition states and products can be obtained, and insight into the impact of environmental effects on mechanistic landscapes can be provided.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Medicinal

MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network

Xiaolin Pan et al.

Summary: pK(a) is a crucial property in lead optimization and drug discovery processes, and MolGpKa is a web server that utilizes a graph-convolutional neural network model for pK(a) prediction. The model shows better performance than machine learning models with human-engineered fingerprints, and it effectively learns the substitution effect on pK(a). MolGpKa is a convenient tool for rapid estimation of pK(a) during ligand design.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Multidisciplinary

Regio-selectivity prediction with a machine-learned reaction representation and on-the-fly quantum mechanical descriptors

Yanfei Guan et al.

Summary: Accurate and rapid evaluation of whether substrates can undergo the desired the transformation is crucial and challenging for both human knowledge and computer predictions. The proposed method combines machine-learned reaction representation with selected quantum mechanical descriptors to predict regio-selectivity in general substitution reactions. The method enhances the performance for selectivity predictions, enables learning from small datasets, and is generally applicable to a diverse range of chemical spaces.

CHEMICAL SCIENCE (2021)

Article Chemistry, Multidisciplinary

Predictive Multivariate Models for Bioorthogonal Inverse-Electron Demand Diels-Alder Reactions

Joao M. J. M. Ravasco et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Review Chemistry, Multidisciplinary

The Huisgen Reaction: Milestones of the 1,3-Dipolar Cycloaddition

Martin Breugst et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Review Chemistry, Multidisciplinary

Developing bioorthogonal probes to span a spectrum of reactivities

Sean S. Nguyen et al.

NATURE REVIEWS CHEMISTRY (2020)

Review Materials Science, Biomaterials

Recent advances in bio-orthogonal and dynamic crosslinking of biomimetic hydrogels

Matthew R. Arkenberg et al.

JOURNAL OF MATERIALS CHEMISTRY B (2020)

Article Multidisciplinary Sciences

Double-slit photoelectron interference in strong-field ionization of the neon dimer

Maksim Kunitski et al.

NATURE COMMUNICATIONS (2019)

Review Chemistry, Multidisciplinary

Bio-orthogonal Click Chemistry for In Vivo Bioimaging

Kenry et al.

TRENDS IN CHEMISTRY (2019)

Article Chemistry, Multidisciplinary

Exploitation of Environment-Sensitive Luminophores in the Design of Sydnone-Based Bioorthogonal Imaging Reagents

Lawrence Cho-Cheung Lee et al.

CHEMISTRY-A EUROPEAN JOURNAL (2018)

Article Chemistry, Multidisciplinary

The Future of Bioorthogonal Chemistry

Neal K. Devaraj

ACS CENTRAL SCIENCE (2018)

Article Chemistry, Multidisciplinary

Sydnone-alkyne cycloaddition: applications in synthesis and bioconjugation

Elodie Decuypere et al.

CHEMICAL COMMUNICATIONS (2017)

Review Chemistry, Multidisciplinary

Inverse electron demand Diels-Alder reactions in chemical biology

B. L. Oliveira et al.

CHEMICAL SOCIETY REVIEWS (2017)

Article Chemistry, Multidisciplinary

Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening

Maruthi Kumar Narayanam et al.

CHEMICAL SCIENCE (2016)

Article Chemistry, Multidisciplinary

A Bioorthogonal Reaction of N-Oxide and Boron Reagents

Justin Kim et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Chemistry, Multidisciplinary

Diazo Groups Endure Metabolism and Enable Chemoselectivity in Cellulo

Kristen A. Andersen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Review Chemistry, Multidisciplinary

Inverse electron demand Diels-Alder (iEDDA)-initiated conjugation: a (high) potential click chemistry scheme

Astrid-Caroline Knall et al.

CHEMICAL SOCIETY REVIEWS (2013)

Article Chemistry, Multidisciplinary

A Bioorthogonal Quadricyclane Ligation

Ellen M. Sletten et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Chemistry, Multidisciplinary

The electrostatic potential: an overview

Jane S. Murray et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)

Article Chemistry, Multidisciplinary

Readily Accessible Bicyclononynes for Bioorthogonal Labeling and Three-Dimensional Imaging of Living Cells

Jan Dommerholt et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Review Chemistry, Multidisciplinary

Cu-free click cycloaddition reactions in chemical biology

John C. Jewett et al.

CHEMICAL SOCIETY REVIEWS (2010)

Review Chemistry, Multidisciplinary

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

Ellen M. Sletten et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2009)

Article Oncology

Growing Applications of Click Chemistry for Bioconjugation in Contemporary Biomedical Research

Kido Nwe et al.

CANCER BIOTHERAPY AND RADIOPHARMACEUTICALS (2009)

Review Chemistry, Multidisciplinary

Chemoselective Ligation and Modification Strategies for Peptides and Proteins

Christian P. R. Hackenberger et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)

Article Biochemical Research Methods

Tetrazine-Based Cycloadditions: Application to Pretargeted Live Cell Imaging

Neal K. Devaraj et al.

BIOCONJUGATE CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Tetrazine ligation: Fast bioconjugation based on inverse-electron-demand Diels-Alder reactivity

Melissa L. Blackman et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Biochemistry & Molecular Biology

Metal-free triazole formation as a tool for bioconjugation

Sander S. van Berkel et al.

CHEMBIOCHEM (2007)

Article Chemistry, Multidisciplinary

Semiempirical GGA-type density functional constructed with a long-range dispersion correction

Stefan Grimme

JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)

Review Biochemistry & Molecular Biology

Chemistry in living systems

JA Prescher et al.

NATURE CHEMICAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Chemical remodelling of cell surfaces in living animals

JA Prescher et al.

NATURE (2004)

Article Chemistry, Multidisciplinary

A strain-promoted [3+2] azide-alkyne cycloaddition for covalent modification of blomolecules in living systems

NJ Agard et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Multidisciplinary Sciences

A metabolic labeling approach toward proteomic analysis of mucin-type O-linked glycosylation

HC Hang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Review Chemistry, Multidisciplinary

Conceptual density functional theory

P Geerlings et al.

CHEMICAL REVIEWS (2003)

Article Multidisciplinary Sciences

Cell surface engineering by a modified Staudinger reaction

E Saxon et al.

SCIENCE (2000)