ArticleJournal of chemical information and modeling2014
Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- Structure-Activity Relationship Studies of Chalcones and Diarylpentanoids with Antitumor Activity: Potency and Selectivity Optimization.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches.Evidence-based complementary and alternative medicine : eCAM · 2022Review
- Synthesis, Biological Evaluation, and In Silico Studies of Novel Aminated Xanthones as Potential p53-Activating Agents.Molecules (Basel, Switzerland) · 2019Article
- An Efficient ABC_DE_Based Hybrid Algorithm for Protein-Ligand Docking.International journal of molecular sciences · 2018Article
- HIGA: A Running History Information Guided Genetic Algorithm for Protein-Ligand Docking.Molecules (Basel, Switzerland) · 2017Article
- In silico structure-based approaches to discover protein-protein interaction-targeting drugs.Methods (San Diego, Calif.) · 2017Review
- Genetic algorithm with a crossover elitist preservation mechanism for protein-ligand docking.AMB Express · 2017Article
- Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.Journal of molecular graphics & modelling · 2017Article
- Druggability and Binding Site Interaction Studies of Potential Metabolites Isolated from Marine Sponge Aurora globostellata against Human Epidermal Growth Factor Receptor-2.Bioinformation · 2017Article
- Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii.PloS one · 2017Article
- EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- Monitoring Ligand-Induced Protein Ordering in Drug Discovery.Journal of molecular biology · 2016Article
- Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.Journal of molecular modeling · 2015Article
- Identification of inhibitors of biological interactions involving intrinsically disordered proteins.International journal of molecular sciences · 2015Review
- Design, Synthesis and Evaluation of 2,5-Diketopiperazines as Inhibitors of the MDM2-p53 Interaction.PloS one · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The p53-binding domains of Mdm2 and Mdmx, two negative regulators of the tumor suppressor p53, are validated targets for cancer therapeutics, but correct binding poses of some proven inhibitors, particularly the nutlins, have been difficult to obtain with standard docking procedures. Virtual screening pipelines typically draw from a database of compounds represented with 1D or 2D structural information from which one or more 3D conformations must be generated. These conformations are then passed to a docking algorithm that searches for optimal binding poses on the target protein. This work tests alternative pipelines using several commonly used conformation generation programs (LigPrep, ConfGen, MacroModel, and Corina/Rotate) and docking programs (GOLD, Glide, MOE-dock, and AutoDock Vina) for their ability to reproduce known poses for a series of Mdmx and/or Mdm2 inhibitors, including several nutlins. Most combinations of these programs using default settings fail to find correct poses for the nutlins but succeed for all other compounds. Docking success for the nutlin class requires either computationally intensive conformational exploration or an "anchoring" procedure that incorporates knowledge of the orientation of the central imidazoline ring.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.