4.7 Article

Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations

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。
Review Chemistry, Multidisciplinary

Structure based virtual screening: Fast and slow

Alejandro Varela-Rial et al.

Summary: Virtual screening methods, such as molecular docking and physical-based molecular simulations, offer different advantages and limitations in drug discovery. While molecular docking provides fast results using approximations, physical-based simulations offer more accurate models but require expensive computing infrastructure. Both approaches are useful for solving different aspects of the drug discovery process.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2022)

Review Biochemical Research Methods

Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions

Debby D. Wang et al.

Summary: This paper reviews two classes of methods for accurately predicting protein-ligand binding affinities: free energy-based simulations and machine learning-based scoring functions. It follows thermodynamic cycles for the former and a feature-representation taxonomy for the latter. Additionally, recent deep learning-based predictions are also discussed, with comparisons of strengths, weaknesses, and future directions for improvements.

BRIEFINGS IN BIOINFORMATICS (2021)

Editorial Material Biochemistry & Molecular Biology

The Rise of Molecular Glues

Stuart L. Schreiber

Summary: The 30th anniversary of the discovery of cyclosporin A and FK506 marks a milestone in understanding their role as molecular glues that induce new protein-protein interactions. The emergence of new molecular-glue probes and medications has sparked interest in this field.
Article Multidisciplinary Sciences

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

David McMillan et al.

Summary: The authors characterized the inhibitor-bound TNF-receptor complex structurally and biochemically, demonstrating alterations in TNF-receptor binding stoichiometry and cluster formation, suggesting a new model for TNF signaling based on disrupted TNF-TNFR1 clusters by small molecule inhibitors.

NATURE COMMUNICATIONS (2021)

Review Pharmacology & Pharmacy

14-3-3 Proteins: Novel Pharmacological Targets in Neurodegenerative Diseases

F. Sanders Pair et al.

Summary: 14-3-3 proteins are a family of proteins expressed throughout the body that are involved in various diseases. Despite the challenges in targeting their interactions, recent advances have made it possible to develop compounds that target 14-3-3 interactions with therapeutic implications for neurodegenerative disorders. Challenges still remain in optimizing specificity and target engagement to avoid unintended negative consequences.

TRENDS IN PHARMACOLOGICAL SCIENCES (2021)

Article Chemistry, Medicinal

An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-κB-Utilizing a Reversible Covalent Tethering Approach

Madita Wolter et al.

Summary: This study describes the systematic bottom-up development of a reversible covalent PPI stabilizer and investigates how its chemical properties affect the structural changes in the ternary 14-3-3/p65/molecular glue complex, ultimately leading to increased stability and high cooperativity.

JOURNAL OF MEDICINAL CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions

Peter J. Cossar et al.

Summary: The study emphasizes the importance of considering the selectivity of stabilizer molecules in addition to their potency. Targeting the phosphorylated motifs on 14-3-3 hub proteins can lead to the stabilization of specific protein-protein interactions and drive selective PPI stabilization through cooperative complex formation.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Discovering protein-protein interaction stabilisers by native mass spectrometry

Jeddidiah Bellamy-Carter et al.

Summary: This study demonstrates the power of native mass spectrometry (MS) in rapidly searching for PPI stabilizers, providing insights into the dynamics of ternary complex formation. By focusing on three PPIs, the study showed that native MS can detect changes in stoichiometry and binding equilibrium, and serves as a screening tool for novel therapeutic PPI stabilizers.

CHEMICAL SCIENCE (2021)

Review Chemistry, Multidisciplinary

Computational prediction of protein-protein binding affinities

Till Siebenmorgen et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

Article Biochemistry & Molecular Biology

Analysis of Interactions Stabilized by Fusicoccin A Reveals an Expanded Suite of Potential 14-3-3 Binding Partners

Ananya Sengupta et al.

ACS CHEMICAL BIOLOGY (2020)

Review Chemistry, Multidisciplinary

Ligand binding free energy and kinetics calculation in 2020

Vittorio Limongelli

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

Article Chemistry, Multidisciplinary

Design of Drug-Like Protein-Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization

Francesco Bosica et al.

CHEMISTRY-A EUROPEAN JOURNAL (2020)

Article Chemistry, Medicinal

Fragment-based Differential Targeting of PPI Stabilizer Interfaces

Xavier Guillory et al.

JOURNAL OF MEDICINAL CHEMISTRY (2020)

Article Chemistry, Multidisciplinary

Selectivity via Cooperativity: Preferential Stabilization of the p65/14-3-3 Interaction with Semisynthetic Natural Products

Madita Wolter et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Multidisciplinary Sciences

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K

Mikolaj Slabicki et al.

NATURE (2020)

Article Multidisciplinary Sciences

Structure-based evolution of a promiscuous inhibitor to a selective stabilizer of protein-protein interactions

Eline Sijbesma et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

Tai-Sung Lee et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

Evolution of Alchemical Free Energy Methods in Drug Discovery

Lin Frank Song et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Biochemistry & Molecular Biology

Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers

Eline Sijbesma et al.

ACS CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Stabilization of Protein-Protein Interactions between CaMKK2 and 14-3-3 by Fusicoccins

Domenico Lentini Santo et al.

ACS CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Polypharmacological Perturbation of the 14-3-3 Adaptor Protein Interactome Stimulates Neurite Outgrowth

Andrew Kaplan et al.

CELL CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

Site-Directed Fragment-Based Screening for the Discovery of Protein-Protein Interaction Stabilizers

Eline Sijbesma et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Multidisciplinary Sciences

Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer

James O'Connell et al.

NATURE COMMUNICATIONS (2019)

Article Chemistry, Medicinal

Modulators of 14-3-3 Protein-Protein Interactions

Loes M. Stevers et al.

JOURNAL OF MEDICINAL CHEMISTRY (2018)

Article Chemistry, Medicinal

Free Energy Methods in Drug Design: Prospects of Alchemical Perturbation in Medicinal Chemistry

Billy J. Williams-Noonan et al.

JOURNAL OF MEDICINAL CHEMISTRY (2018)

Article Chemistry, Multidisciplinary

Rationally Designed Semisynthetic Natural Product Analogues for Stabilization of 14-3-3 Protein-Protein Interactions

Sebastian A. Andrei et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Biochemistry & Molecular Biology

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures

Hugues Ripoche et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Small-molecule stabilization of the p53-14-3-3 protein-protein interaction

Richard G. Doveston et al.

FEBS LETTERS (2017)

Article Chemistry, Medicinal

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

Zoe Cournia et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

Review Chemistry, Multidisciplinary

Advancing Drug Discovery through Enhanced Free Energy Calculations

Robert Abel et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

Review Chemistry, Multidisciplinary

Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions

Zhihai Liu et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

Review Biotechnology & Applied Microbiology

Small molecules, big targets: drug discovery faces the protein-protein interaction challenge

Duncan E. Scott et al.

NATURE REVIEWS DRUG DISCOVERY (2016)

Article Multidisciplinary Sciences

Characterization and small- molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR

Loes M. Stevers et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Biochemistry & Molecular Biology

Stabilization of Physical RAF/14-3-3 Interaction by Cotylenin A as Treatment Strategy for RAS Mutant Cancers

Manuela Molzan et al.

ACS CHEMICAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Impaired Binding of 14-3-3 to C-RAF in Noonan Syndrome Suggests New Approaches in Diseases with Increased Ras Signaling

Manuela Molzan et al.

MOLECULAR AND CELLULAR BIOLOGY (2010)

Review Biochemistry & Molecular Biology

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

James R. Perkins et al.

STRUCTURE (2010)

Review Biochemical Research Methods

Peptide-mediated interactions in biological systems: new discoveries and applications

Evangelia Petsalaki et al.

CURRENT OPINION IN BIOTECHNOLOGY (2008)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Review Chemistry, Multidisciplinary

Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models

PA Kollman et al.

ACCOUNTS OF CHEMICAL RESEARCH (2000)