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Which Three-Dimensional Characteristics Make Efficient Inhibitors of Protein–Protein Interactions?

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Molecular Descriptors for Chemoinformatics

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Drugs Targeting Protein–Protein Interactions

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On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects

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Bioactive Molecules: Perfectly Shaped for Their Target?

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Blind prediction of interfacial water positions in CAPRI

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Sample size calculation for the Wilcoxon–Mann–Whitney test adjusting for ties

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Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)

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Topography-biased compound library design: the shape of things to come?

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Predicting druggable binding sites at the protein–protein interface

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The impact of aromatic ring count on compound developability – are too many aromatic rings a liability in drug design?

inferredcites →https://doi.org/10.1016/j.drudis.2009.11.007openalex-snapshot

Rationalizing the chemical space of protein–protein interaction inhibitors

inferredcites →https://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

inferredcites →https://doi.org/10.1016/j.drudis.2011.03.003openalex-snapshot

Learning lessons from drugs that have recently entered the market

inferredcites →https://doi.org/10.1016/j.drudis.2013.05.003openalex-snapshot

iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein–protein interactions

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The importance of discerning shape in molecular pharmacology

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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

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VolSurf: a new tool for the pharmacokinetic optimization of lead compounds

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Discovery of Highly Potent p53-MDM2 Antagonists and Structural Basis for Anti-Acute Myeloid Leukemia Activities

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Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds

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Molecular Shape Profiles

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Using CONCORD to construct a large database of three-dimensional coordinates from connection tables

inferredcites →https://doi.org/10.1021/jm011051popenalex-snapshot

Surface Descriptors for Protein−Ligand Affinity Prediction

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm070533jopenalex-snapshot

Prediction of Protein−Protein Interaction Inhibitors by Chemoinformatics and Machine Learning Methods

inferredcites →https://doi.org/10.1021/jm401144zopenalex-snapshot

Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD) and Drug Repositioning: Discovery of Raloxifene and Bazedoxifene as Novel Inhibitors of IL-6/GP130 Interface

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How many drug targets are there?

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The influence of drug-like concepts on decision-making in medicinal chemistry

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Probing the links between in vitro potency, ADMET and physicochemical parameters

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The role of ligand efficiency metrics in drug discovery

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The druggable genome

inferredcites →https://doi.org/10.1039/c1md00017aopenalex-snapshot

Molecular obesity, potency and other addictions in drug discovery

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Constructing Confidence Sets Using Rank Statistics

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e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design

inferredcites →https://doi.org/10.1093/database/bat039openalex-snapshot

TIMBAL v2: update of a database holding small molecules modulating protein–protein interactions

inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.1093/nar/gkq325openalex-snapshot

Frog2: Efficient 3D conformation ensemble generator for small compounds

inferredcites →https://doi.org/10.1093/nar/gkq471openalex-snapshot

DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions

inferredcites →https://doi.org/10.1093/nar/gks1002openalex-snapshot

2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions

inferredcites →https://doi.org/10.1093/nar/gks1231openalex-snapshot

PrePPI: a structure-informed database of protein–protein interactions

inferredcites →https://doi.org/10.1371/journal.pcbi.1000695openalex-snapshot

Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

inferredcites →https://doi.org/10.2174/138161212802651571openalex-snapshot

A Leap into the Chemical Space of Protein-Protein Interaction Inhibitors

inferredcites →https://doi.org/10.2174/138920308784533989openalex-snapshot

Drug-Like Inhibitors of Protein-Protein Interactions: A Structural Examination of Effective Protein Mimicry

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A Step toward NRF2‐DNA Interaction Inhibitors by Fragment‐Based NMR Methods

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Protein–Protein Interaction Inhibitors in Cancer

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Protein-protein interaction inhibitors in cancer

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Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions

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Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions

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Targeting intrinsically disordered proteins at the edge of chaos

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Investigation of the molecular characteristics of bisindole inhibitors as HIV-1 glycoprotein-41 fusion inhibitors

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An optimised series of substituted N-phenylpyrrolamides as DNA gyrase B inhibitors

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Flexibility and small pockets at protein–protein interfaces: New insights into druggability

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In silico design of low molecular weight protein–protein interaction inhibitors: Overall concept and recent advances

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Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation

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The impact of in silico screening in the discovery of novel and safer drug candidates

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In silico structure-based approaches to discover protein-protein interaction-targeting drugs

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Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein–Protein Interfaces

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00607openalex-snapshot

Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01135openalex-snapshot

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein–Protein Interaction Inhibitors

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00435openalex-snapshot

Privileged Substructures to Modulate Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1021/acs.joc.8b00397openalex-snapshot

Rhodium-Catalyzed [4 + 1] Cyclization via C–H Activation for the Synthesis of Divergent Heterocycles Bearing a Quaternary Carbon

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Access to a Structurally Complex Compound Collection via Ring Distortion of the Alkaloid Sinomenine

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Fr-PPIChem: An Academic Compound Library Dedicated to Protein–Protein Interactions

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Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen

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Predictive compound accumulation rules yield a broad-spectrum antibiotic

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New machine learning and physics-based scoring functions for drug discovery

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An Intriguing Correlation Based on the Superimposition of Residue Pairs with Inhibitors that Target Protein-Protein Interfaces

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Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors

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Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors

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Analysis of physicochemical properties of protein–protein interaction modulators suggests stronger alignment with the “rule of five”

inferred← citeshttps://doi.org/10.1051/medsci/20153103017openalex-snapshot

Les chimiothèques ciblant les interactions protéine-protéine

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iPPI-DB: an online database of modulators of protein–protein interactions

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Benchmark of 3D conformer generation and molecular property calculation for medium-sized molecules

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Structure- and Ligand-Based Virtual Screening Identifies New Scaffolds for Inhibitors of the Oncoprotein MDM2

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Modulation of protein : protein interactions in inflammatory diseases

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Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

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Drug Repurposing Uncovers New Chemical Scaffolds as Potent Urease Inhibitors: A Comprehensive Computational Study

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Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

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Identification of a Quinone Derivative as a YAP/TEAD Activity Modulator from a Repurposing Library

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Facile and diastereoselective arylation of the privileged 1,4-dihydroisoquinolin-3(2 H )-one scaffold

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Unusual highly diastereoselective Rh(II)-catalyzed dimerization of 3-diazo-2-arylidenesuccinimides provides access to a new dibenzazulene scaffold

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Nouvelles données structurales sur l’Interleukine-15 par simulations de Dynamique Moléculaire : vers la mise au point rationnelle d’inhibiteurs spécifiques

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Développement d'outils pour l'étude des interactions protéine-protéine

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