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Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods

https://doi.org/10.1021/ci100250z
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/anie.200351179openalex-snapshot
Benzoxazoles as Transthyretin Amyloid Fibril Inhibitors: Synthesis, Evaluation, and Mechanism of Action
inferredcites →https://doi.org/10.1002/bip.10207openalex-snapshot
Gaussian docking functions
inferredcites →https://doi.org/10.1002/prot.20123openalex-snapshot
Towards a structural classification of phosphate binding sites in protein–nucleotide complexes: An automated all‐against‐all structural comparison using geometric matching
inferredcites →https://doi.org/10.1002/prot.20588openalex-snapshot
General and targeted statistical potentials for protein–ligand interactions
inferredcites →https://doi.org/10.1006/gcen.2000.7520openalex-snapshot
Evolution of the Thyroid Hormone-Binding Protein, Transthyretin
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1007/bf00134183openalex-snapshot
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
inferredcites →https://doi.org/10.1007/s00018-009-0109-0openalex-snapshot
Transthyretin: the servant of many masters
inferredcites →https://doi.org/10.1007/s10822-008-9170-2openalex-snapshot
What do we know and when do we know it?
inferredcites →https://doi.org/10.1016/0263-7855(90)80070-vopenalex-snapshot
WHAT IF: A molecular modeling and drug design program
inferredcites →https://doi.org/10.1016/j.bmc.2006.10.013openalex-snapshot
3D pharmacophore based virtual screening of T-type calcium channel blockers
inferredcites →https://doi.org/10.1016/j.chembiol.2004.10.009openalex-snapshot
Hydroxylated Polychlorinated Biphenyls Selectively Bind Transthyretin in Blood and Inhibit Amyloidogenesis: Rationalizing Rodent PCB Toxicity
inferredcites →https://doi.org/10.1016/j.drudis.2006.10.005openalex-snapshot
Similarity-based virtual screening using 2D fingerprints
inferredcites →https://doi.org/10.1016/j.jmgm.2006.06.002openalex-snapshot
eHiTS: A new fast, exhaustive flexible ligand docking system
inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot
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
inferredcites →https://doi.org/10.1016/s0169-409x(96)00423-1openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
inferredcites →https://doi.org/10.1016/s0960-894x(98)00696-9openalex-snapshot
Synthesis and evaluation of anthranilic acid-based transthyretin amyloid fibril inhibitors
inferredcites →https://doi.org/10.1016/s0968-0004(98)01253-5openalex-snapshot
PQS: a protein quaternary structure file server
inferredcites →https://doi.org/10.1016/s0968-0896(00)00229-7openalex-snapshot
2,4-Disubstituted oxazoles and thiazoles as latent pharmacophores for diacylhydrazine of SC-51089, a potent PGE2 antagonist
inferredcites →https://doi.org/10.1016/s0968-0896(98)00130-8openalex-snapshot
Discovering transthyretin amyloid fibril inhibitors by limited screening
inferredcites →https://doi.org/10.1016/s0968-0896(99)00066-8openalex-snapshot
Synthesis and evaluation of inhibitors of transthyretin amyloid formation based on the non-steroidal anti-inflammatory drug, flufenamic acid
inferredcites →https://doi.org/10.1016/s1093-3263(02)00204-8openalex-snapshot
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
inferredcites →https://doi.org/10.1021/bi00619a020openalex-snapshot
Thyroxine-induced conformational changes in prealbumin
inferredcites →https://doi.org/10.1021/bi049621lopenalex-snapshot
Transthyretin Aggregation under Partially Denaturing Conditions Is a Downhill Polymerization
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci600303bopenalex-snapshot
Design and Evaluation of a Novel Class-Directed 2D Fingerprint to Search for Structurally Diverse Active Compounds
inferredcites →https://doi.org/10.1021/ci8004226openalex-snapshot
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information
inferredcites →https://doi.org/10.1021/ci900204yopenalex-snapshot
LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening
inferredcites →https://doi.org/10.1021/ja042929fopenalex-snapshot
Kinetic Stabilization of an Oligomeric Protein by a Single Ligand Binding Event
inferredcites →https://doi.org/10.1021/ja044351fopenalex-snapshot
Potent and Selective Structure-Based Dibenzofuran Inhibitors of Transthyretin Amyloidogenesis: Kinetic Stabilization of the Native State
inferredcites →https://doi.org/10.1021/ja908562qopenalex-snapshot
A Substructure Combination Strategy To Create Potent and Selective Transthyretin Kinetic Stabilizers That Prevent Amyloidogenesis and Cytotoxicity
inferredcites →https://doi.org/10.1021/jm000292eopenalex-snapshot
Prediction of Drug Absorption Using Multivariate Statistics
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm010257nopenalex-snapshot
Synthesis, Structure, and Activity of Diclofenac Analogues as Transthyretin Amyloid Fibril Formation Inhibitors
inferredcites →https://doi.org/10.1021/jm020017nopenalex-snapshot
Molecular Properties That Influence the Oral Bioavailability of Drug Candidates
inferredcites →https://doi.org/10.1021/jm030191ropenalex-snapshot
Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs
inferredcites →https://doi.org/10.1021/jm030266ropenalex-snapshot
A Specific Mechanism of Nonspecific Inhibition
inferredcites →https://doi.org/10.1021/jm030347nopenalex-snapshot
Diflunisal Analogues Stabilize the Native State of Transthyretin. Potent Inhibition of Amyloidogenesis
inferredcites →https://doi.org/10.1021/jm040163oopenalex-snapshot
A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction
inferredcites →https://doi.org/10.1021/jm0492002openalex-snapshot
A Bioavailability Score
inferredcites →https://doi.org/10.1021/jm049274dopenalex-snapshot
Bisaryloxime Ethers as Potent Inhibitors of Transthyretin Amyloid Fibril Formation
inferredcites →https://doi.org/10.1021/jm050090oopenalex-snapshot
Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm0708735openalex-snapshot
Biochemical and Structural Evaluation of Highly Selective 2-Arylbenzoxazole-Based Transthyretin Amyloidogenesis Inhibitors
inferredcites →https://doi.org/10.1021/jm801347sopenalex-snapshot
Toward Optimization of the Second Aryl Substructure Common to Transthyretin Amyloidogenesis Inhibitors Using Biochemical and Structural Studies
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1008158231558openalex-snapshot
Deciphering common failures in molecular docking of ligand-protein complexes
inferredcites →https://doi.org/10.1023/a:1015040217741openalex-snapshot
Polar Molecular Surface as a Dominating Determinant for Oral Absorption and Brain Penetration of Drugs
inferredcites →https://doi.org/10.1038/74082openalex-snapshot
Rational design of potent human transthyretin amyloid disease inhibitors.
inferredcites →https://doi.org/10.1038/nchembio.281openalex-snapshot
Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma
inferredcites →https://doi.org/10.1073/pnas.202495199openalex-snapshot
Sequence-dependent denaturation energetics: A major determinant in amyloid disease diversity
inferredcites →https://doi.org/10.1073/pnas.79.12.3754openalex-snapshot
Electrostatic potential molecular surfaces.
inferredcites →https://doi.org/10.1073/pnas.93.26.15051openalex-snapshot
Inhibiting transthyretin amyloid fibril formation via protein stabilization
inferredcites →https://doi.org/10.1074/jbc.m101024200openalex-snapshot
Tetramer Dissociation and Monomer Partial Unfolding Precedes Protofibril Formation in Amyloidogenic Transthyretin Variants
inferredcites →https://doi.org/10.1107/s0021889892009944openalex-snapshot
PROCHECK: a program to check the stereochemical quality of protein structures
inferredcites →https://doi.org/10.1107/s0907444996003046openalex-snapshot
Structures of Human Transthyretin Complexed with Thyroxine at 2.0 Å Resolution and 3',5'-Dinitro-N-acetyl- L -thyronine at 2.2 Å Resolution
inferredcites →https://doi.org/10.1126/science.1079589openalex-snapshot
Prevention of Transthyretin Amyloid Disease by Changing Protein Misfolding Energetics
inferredcites →https://doi.org/10.1210/jcem-68-6-1141openalex-snapshot
Drug Competition for Thyroxine Binding to Transthyretin (Prealbumin): Comparison with Effects on Thyroxine-Binding Globulin*
inferredcites →https://doi.org/10.1385/mb:31:1:055openalex-snapshot
Data Clustering in Life Sciences
inferredcites →https://doi.org/10.2174/0929867043455549openalex-snapshot
Pharmaceutical Strategies Against Amyloidosis: Old and New Drugs in Targeting a “Protein Misfolding Disease”
inferredcites →https://doi.org/10.2174/1568013033483230openalex-snapshot
Amyloid Formation by Transthyretin: From Protein Stability to Protein Aggregation

What points at this work

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

inferred← citeshttps://doi.org/10.1002/cmdc.201700051openalex-snapshot
Identification of Transthyretin Fibril Formation Inhibitors Using Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1007/978-3-030-62226-8_16openalex-snapshot
Key Aspects for Achieving Hits by Virtual Screening Studies
inferred← citeshttps://doi.org/10.1007/978-94-007-5416-4_21openalex-snapshot
Familial Amyloidotic Polyneuropathy and Transthyretin
inferred← citeshttps://doi.org/10.1016/j.cbpa.2011.02.021openalex-snapshot
The role of computational methods in the identification of bioactive compounds
inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.01.056openalex-snapshot
Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach
inferred← citeshttps://doi.org/10.1016/j.ejmech.2016.02.074openalex-snapshot
A novel bis-furan scaffold for transthyretin stabilization and amyloid inhibition
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113847openalex-snapshot
Targeting transthyretin in Alzheimer's disease: Drug discovery of small-molecule chaperones as disease-modifying drug candidates for Alzheimer's disease
inferred← citeshttps://doi.org/10.1021/acs.est.6b02771openalex-snapshot
Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin
inferred← citeshttps://doi.org/10.1021/acschemneuro.9b00059openalex-snapshot
Therapeutic Potential of Polyamidoamine Dendrimer for Amyloidogenic Transthyretin Amyloidosis
inferred← citeshttps://doi.org/10.1021/ci200562popenalex-snapshot
Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors
inferred← citeshttps://doi.org/10.1039/c1cc12380gopenalex-snapshot
Determination of relative binding affinities of labeling molecules with amino acids by using scanning tunneling microscopy
inferred← citeshttps://doi.org/10.2174/092986712800269281openalex-snapshot
Methods to Evaluate the Inhibition of TTR Fibrillogenesis Induced by Small Ligands
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