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Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery

https://doi.org/10.1007/128_2011_265

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Electrostatic complementarity at protein/protein interfaces 1 1Edited by B. Honig

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Fragment Screening Using X-Ray Crystallography

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Introduction to Fragment-Based Drug Discovery

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Combining NMR and X-ray Crystallography in Fragment-Based Drug Discovery: Discovery of Highly Potent and Selective BACE-1 Inhibitors

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Principles of Fluorescence Spectroscopy

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Principles of Fluorescence Spectroscopy

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Small Molecule Inhibitors of Protein–Protein Interactions

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The Hydrophobic Effect: Formation of Micelles and Biological Membranes

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Structural and thermodynamic analysis of the packing of two α-helices in bacteriophage T4 lysozyme

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Surface electrostatic interactions contribute little to stability of barnase

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Structure-based drug design

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Fragment Screening Purely with Protein Crystallography

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A fluorescence correlation spectroscopy-based assay for fragment screening of slowly inhibiting protein–peptide interaction inhibitors

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β-Peptides with improved affinity for hDM2 and hDMX

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Drugging challenging targets using fragment-based approaches

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Highly Discriminating Protein–Protein Interaction Specificities in the Context of a Conserved Binding Energy Hotspot

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Protein–Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking

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Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

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Higher throughput calorimetry: opportunities, approaches and challenges

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

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How Hofmeister ion interactions affect protein stability

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Temperature, stability, and the hydrophobic interaction

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Free Energy Landscapes of Encounter Complexes in Protein-Protein Association

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Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors

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Some Factors in the Interpretation of Protein Denaturation

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Electrostatic aspects of protein–protein interactions

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Unraveling hot spots in binding interfaces: progress and challenges

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Minimized proteins

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Design of a synthetic Mdm2-binding mini protein that activates the p53 response in vivo

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Structure-based drug design: progress, results and challenges

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Wet and dry interfaces: the role of solvent in protein–protein and protein–DNA recognition

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Morphology of protein–protein interfaces

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Crystal Structure of ARF1•Sec7 Complexed with Brefeldin A and Its Implications for the Guanine Nucleotide Exchange Mechanism

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Structure-based screening of low-affinity compounds

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Protein-interaction networks: from experiments to analysis

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Ligand efficiency: a useful metric for lead selection

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Keynote review: Structural biology and drug discovery

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Predicting protein druggability

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Small-molecule antagonists of the oncogenic Tcf/β-catenin protein complex

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NMR-based screening in drug discovery

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Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering

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Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-.ANG. resolution

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Contribution of long-range electrostatic interactions to the stabilization of the catalytic transition state of the serine protease subtilisin BPN'

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Surface Salt Bridges, Double-Mutant Cycles, and Protein Stability: an Experimental and Computational Analysis of the Interaction of the Asp 23 Side Chain with the N-Terminus of the N-Terminal Domain of the Ribosomal Protein L9

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Prevention of MKK6-Dependent Activation by Binding to p38α MAP Kinase

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Contribution of Cation−π Interactions to Protein Stability

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A Mutational Analysis of Binding Interactions in an Antigen−Antibody Protein−Protein Complex

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Effects of Core Mutations on the Folding of a β-Sheet Protein: Implications for Backbone Organization in the I-State

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Contribution of Surface Salt Bridges to Protein Stability,

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Using Small Molecules and Chemical Genetics To Interrogate Signaling Networks

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Fundamental Aspects of Protein−Protein Association Kinetics

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Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis

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Toward Proteomimetics: Terphenyl Derivatives as Structural and Functional Mimics of Extended Regions of an α-Helix

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A Novel Approach for Characterizing Protein Ligand Complexes: Molecular Basis for Specificity of Small-Molecule Bcl-2 Inhibitors

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Synthesis of a Negatively Charged Dibenzofuran-Based β-Turn Mimetic and Its Incorporation into the WW Miniprotein-Enhanced Solubility without a Loss of Thermodynamic Stability

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Protein Prosthesis: A Semisynthetic Enzyme with a β-Peptide Reverse Turn

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Discovery of a Potent Small Molecule IL-2 Inhibitor through Fragment Assembly

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Cross-Linking Strategy for Molecular Recognition and Fluorescent Sensing of a Multi-phosphorylated Peptide in Aqueous Solution

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Free Energy, Entropy, and Induced Fit in Host−Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm

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Structure-Based Design of Potent Non-Peptide MDM2 Inhibitors

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Monitoring the Effects of Antagonists on Protein−Protein Interactions with NMR Spectroscopy

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Inhibiting HIV Fusion with a β-Peptide Foldamer

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(α/β+α)-Peptide Antagonists of BH3 Domain/Bcl-xL Recognition: Toward General Strategies for Foldamer-Based Inhibition of Protein−Protein Interactions

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Surface Recognition and Fluorescence Sensing of Histone by Dansyl-Appended Cyclophane-Based Resorcinarene Trimer

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Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis

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Discovery of Potent Nonpeptide Inhibitors of Stromelysin Using SAR by NMR

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Identification of a Small Molecule Inhibitor of the IL-2/IL-2Rα Receptor Interaction Which Binds to IL-2

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Identification of Potent and Selective Small-Molecule Inhibitors of Caspase-3 through the Use of Extended Tethering and Structure-Based Drug Design

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Druggability Indices for Protein Targets Derived from NMR-Based Screening Data

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Fragment-Based Lead Discovery Using X-ray Crystallography

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Integrating Fragment Assembly and Biophysical Methods in the Chemical Advancement of Small-Molecule Antagonists of IL-2: An Approach for Inhibiting Protein−Protein Interactions

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Discovery of a Potent Inhibitor of the Antiapoptotic Protein Bcl-x L from NMR and Parallel Synthesis

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Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

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Structure-Based Design of Spiro-oxindoles as Potent, Specific Small-Molecule Inhibitors of the MDM2−p53 Interaction

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Surface Plasmon Resonance Biosensor Based Fragment Screening Using Acetylcholine Binding Protein Identifies Ligand Efficiency Hot Spots (LE Hot Spots) by Deconstruction of Nicotinic Acetylcholine Receptor α7 Ligands

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Surface Plasmon Resonance Based Assay for the Detection and Characterization of Promiscuous Inhibitors

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Identification of MMP-12 Inhibitors by Using Biosensor-Based Screening of a Fragment Library

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An Orally Bioavailable Pyrrolinone Inhibitor of HIV-1 Protease: Computational Analysis and X-ray Crystal Structure of the Enzyme Complex

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WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability

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The consequences of translational and rotational entropy lost by small molecules on binding to proteins

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Hydrophobic bonding and accessible surface area in proteins

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Hydrogen bonding and biological specificity analysed by protein engineering

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Identification of small-molecule inhibitors of interaction between the BH3 domain and Bcl-xL

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Design of GFB-111, a platelet-derived growth factor binding molecule with antiangiogenic and anticancer activity against human tumors in mice

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Discovering novel ligands for macromolecules using X-ray crystallographic screening

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A network of protein–protein interactions in yeast

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Tissue specificity and the human protein interaction network

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Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

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Large drugs outdo small

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A small molecule–kinase interaction map for clinical kinase inhibitors

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In situ assembly of enzyme inhibitors using extended tethering

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Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery

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Between a rock and a hard place?

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Integrated network analysis platform for protein-protein interactions

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Literature-curated protein interaction datasets

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Recurated protein interaction datasets

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The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability

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Fragment-based lead discovery

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How many drug targets are there?

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The productivity crisis in pharmaceutical R&D

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High-throughput crystallography for lead discovery in drug design

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Allosteric binding sites on cell-surface receptors: novel targets for drug discovery

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Specific versus non-specific contacts in protein crystals

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Apoptosis-based therapies and drug targets

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Electrostatic interactions affecting the active site of class Sigma glutathione S-transferase

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α-Helix mimetics as inhibitors of protein–protein interactions

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Stability and folding of the protein complexes of barnase

inferredcites →https://doi.org/10.1073/pnas.0607058103openalex-snapshot

Hot-spot mimicry of a cytokine receptor by a small molecule

inferredcites →https://doi.org/10.1073/pnas.0610494104openalex-snapshot

Ligand configurational entropy and protein binding

inferredcites →https://doi.org/10.1073/pnas.0700773104openalex-snapshot

Structure-based discovery of an inhibitor of Arf activation by Sec7 domains through targeting of protein–protein complexes

inferredcites →https://doi.org/10.1073/pnas.232566599openalex-snapshot

Short constrained peptides that inhibit HIV-1 entry

inferredcites →https://doi.org/10.1073/pnas.252756299openalex-snapshot

Binding of small molecules to an adaptive protein–protein interface

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A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor.

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Identification of a direct interaction between interleukin 2 and the p64 interleukin 2 receptor gamma chain.

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Measurement of the binding of tyrosyl phosphopeptides to SH2 domains: a reappraisal.

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Binding in the growth hormone receptor complex.

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Principles of protein-protein interactions.

inferredcites →https://doi.org/10.1073/pnas.97.10.5050openalex-snapshot

Selective disruption of protein aggregation by cyclodextrin dimers

inferredcites →https://doi.org/10.1073/pnas.97.4.1506openalex-snapshot

Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry

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Inhibition of Human Papillomavirus DNA Replication by Small Molecule Antagonists of the E1-E2 Protein Interaction

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ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions

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APID2NET: unified interactome graphic analyzer

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On the number of protein-protein interactions in the yeast proteome

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MINT: the Molecular INTeraction database

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The IntAct molecular interaction database in 2010

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MINT, the molecular interaction database: 2009 update

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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

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Hydrogen bonds and salt bridges across protein-protein interfaces

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An analysis of conformational changes on protein–protein association: implications for predictive docking

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The price of lost freedom: entropy of bimolecular complex formation

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In vitro display technologies reveal novel biopharmaceutics

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Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery

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Subcellular localization of the yeast proteome

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BindingDB Entry 50007648: Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase.

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