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In Silico Discovery of β-Secretase Inhibitors
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Exhaustive docking of molecular fragments with electrostatic solvation
inferredcites →https://doi.org/10.1002/1097-0134(20010201)42:2<256::aid-prot130>3.0.co;2-4openalex-snapshot
Efficient electrostatic solvation model for protein-fragment docking
inferredcites →https://doi.org/10.1002/jcc.10384openalex-snapshot
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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Validation of the general purpose QUANTA ®3.2/CHARMm® force field
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Calculation of the electric potential in the active site cleft due to α-helix dipoles
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An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
inferredcites →https://doi.org/10.1016/j.jmb.2004.08.018openalex-snapshot
Apo and Inhibitor Complex Structures of BACE (β-secretase)
inferredcites →https://doi.org/10.1016/j.str.2005.06.015openalex-snapshot
Functional Plasticity in the Substrate Binding Site of β-Secretase
inferredcites →https://doi.org/10.1016/j.tips.2003.12.004openalex-snapshot
β-Secretase inhibition for the treatment of Alzheimer's disease – promise and challenge
inferredcites →https://doi.org/10.1016/s1359-6446(04)03364-1openalex-snapshot
Open-source software: not quite endsville
inferredcites →https://doi.org/10.1021/bi026232nopenalex-snapshot
Crystal Structure of Memapsin 2 (β-Secretase) in Complex with an Inhibitor OM00-3
inferredcites →https://doi.org/10.1021/cr00023a012openalex-snapshot
From atoms and bonds to three-dimensional atomic coordinates: automatic model builders
inferredcites →https://doi.org/10.1021/jm0101803openalex-snapshot
Structure-Based Design: Potent Inhibitors of Human Brain Memapsin 2 (β-Secretase)
inferredcites →https://doi.org/10.1021/jm049379gopenalex-snapshot
Structure-Based Design of Potent and Selective Cell-Permeable Inhibitors of Human β-Secretase (BACE-1)
inferredcites →https://doi.org/10.1021/jm049388popenalex-snapshot
Identification of a Small Molecule Nonpeptide Active Site β-Secretase Inhibitor That Displays a Nontraditional Binding Mode for Aspartyl Proteases
inferredcites →https://doi.org/10.1021/jm049817jopenalex-snapshot
Modeling the Protonation States of the Catalytic Aspartates in β-Secretase
inferredcites →https://doi.org/10.1021/jm050142+openalex-snapshot
Structure-Based Design, Synthesis, and Memapsin 2 (BACE) Inhibitory Activity of Carbocyclic and Heterocyclic Peptidomimetics
inferredcites →https://doi.org/10.1021/jm050463lopenalex-snapshot
Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/jm050499dopenalex-snapshot
Discovery of Cell-Permeable Non-Peptide Inhibitors of β-Secretase by High-Throughput Docking and Continuum Electrostatics Calculations
inferredcites →https://doi.org/10.1021/jp9714227openalex-snapshot
Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
inferredcites →https://doi.org/10.1023/b:jcam.0000021882.99270.4copenalex-snapshot
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
inferredcites →https://doi.org/10.1038/399a023openalex-snapshot
Translating cell biology into therapeutic advances in Alzheimer's disease
inferredcites →https://doi.org/10.1074/jbc.274.29.20499openalex-snapshot
Rank-Order of Potencies for Inhibition of the Secretion of Aβ40 and Aβ42 Suggests That Both Are Generated by a Single γ-Secretase
inferredcites →https://doi.org/10.1074/jbc.m109266200openalex-snapshot
Substrate and Inhibitor Profile of BACE (β-Secretase) and Comparison with Other Mammalian Aspartic Proteases
inferredcites →https://doi.org/10.1074/jbc.m501519200openalex-snapshot
X-ray Structure of Plasmepsin II Complexed with a Potent Achiral Inhibitor
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
A new method for predicting binding affinity in computer-aided drug design
inferredcites →https://doi.org/10.1093/protein/8.11.1137openalex-snapshot
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
inferredcites →https://doi.org/10.1097/00001756-199308000-00011openalex-snapshot
Cells with a familial Alzheimerʼs disease mutation produce authentic β-peptide
inferredcites →https://doi.org/10.1107/s0567739476001873openalex-snapshot
A solution for the best rotation to relate two sets of vectors
inferredcites →https://doi.org/10.1126/science.1105416openalex-snapshot
Semaphorin 3E and Plexin-D1 Control Vascular Pattern Independently of Neuropilins
inferredcites →https://doi.org/10.1126/science.1105850openalex-snapshot
Self-Propagating, Molecular-Level Polymorphism in Alzheimer's ß-Amyloid Fibrils
inferredcites →https://doi.org/10.1126/science.290.5489.150openalex-snapshot
Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor
inferredcites →https://doi.org/10.1515/bc.2001.168openalex-snapshot
Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
inferredcites →https://doi.org/10.1515/bc.2004.056openalex-snapshot
Searching for the most effective screening system to identify cell-active inhibitors of β-secretase
inferredcites →https://doi.org/10.2174/1568026024607490openalex-snapshot
Inhibition of BACE, a Promising Approach to Alzheimers Disease Therapy
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9780470495018.ch7openalex-snapshot
Development of Small‐Molecule Ligands and Inhibitors
inferred← citeshttps://doi.org/10.1002/9780470594087.ch5openalex-snapshot
Fragment‐Based Approaches for Identification of BACE Inhibitors
inferred← citeshttps://doi.org/10.1002/9783527335855.marprod004openalex-snapshot
Basic Marine Pharmacology
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Nonpeptide BACE1 Inhibitors: Design and Synthesis
inferred← citeshttps://doi.org/10.1002/9783527633326.ch17openalex-snapshot
Fragment‐Based Approaches in Virtual Screening
inferred← citeshttps://doi.org/10.1002/ange.201206673openalex-snapshot
Monitoring β‐Secretase Activity in Living Cells with a Membrane‐Anchored FRET Probe
inferred← citeshttps://doi.org/10.1002/anie.201206673openalex-snapshot
Monitoring β‐Secretase Activity in Living Cells with a Membrane‐Anchored FRET Probe
inferred← citeshttps://doi.org/10.1002/cmdc.200900078openalex-snapshot
Discovery of Plasmepsin Inhibitors by Fragment‐Based Docking and Consensus Scoring
inferred← citeshttps://doi.org/10.1002/ddr.20291openalex-snapshot
Structure and modeling in the design of β‐ and γ‐secretase inhibitors
inferred← citeshttps://doi.org/10.1002/jcc.21816openalex-snapshot
SwissParam: A fast force field generation tool for small organic molecules
inferred← citeshttps://doi.org/10.1002/jmr.981openalex-snapshot
Library screening by fragment‐based docking
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Structure‐based tailoring of compound libraries for high‐throughput screening: Discovery of novel EphB4 kinase inhibitors
inferred← citeshttps://doi.org/10.1007/978-1-0716-4232-0_2openalex-snapshot
BACE-1 Inhibition for the Treatment of Neurodegenerative Diseases: Rationale, Assay Methodologies, and Reference Compounds
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Protocol for Fragment Hopping
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Virtual Screening in the Search of New and Potent Anti-Alzheimer Agents
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Computational inhibitor design against malaria plasmepsins
inferred← citeshttps://doi.org/10.1007/s00044-011-9885-9openalex-snapshot
Pharmacopore hypothesis generation of BACE-1 inhibitors and pharmacophore-driven identification of potent multi-target neuroprotective agents
inferred← citeshttps://doi.org/10.1007/s00044-012-0204-xopenalex-snapshot
Ligand-based pharmacophore exploration and QSAR analysis of transition state analogues followed by in silico screening guide the discovery of new sub-micromolar β-secreatase inhibitors
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Beta-secretase as a target for Alzheimer’s disease drug discovery: an overview of in vitro methods for characterization of inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-013-9653-7openalex-snapshot
Effect of pH and ligand charge state on BACE-1 fragment docking performance
inferred← citeshttps://doi.org/10.1007/s11030-009-9139-7openalex-snapshot
Comparative molecular field analysis and comparative molecular similarity indices analysis of hydroxyethylamine derivatives as selective human BACE-1 inhibitor
inferred← citeshttps://doi.org/10.1007/s11064-009-0054-1openalex-snapshot
BACE and γ-Secretase Characterization and Their Sorting as Therapeutic Targets to Reduce Amyloidogenesis
inferred← citeshttps://doi.org/10.1007/s12539-013-0157-xopenalex-snapshot
High throughput virtual screening and E-pharmacophore filtering in the discovery of new BACE-1 inhibitors
inferred← citeshttps://doi.org/10.1016/j.bioorg.2017.07.014openalex-snapshot
Synthesis and biological evaluation of quinazolinone-based hydrazones with potential use in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1016/j.bioorg.2020.103997openalex-snapshot
Synthesis of furocoumarin–stilbene hybrids as potential multifunctional drugs against multiple biochemical targets associated with Alzheimer’s disease
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Enhanced sampling techniques in biomolecular simulations
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Elaborate ligand-based pharmacophore exploration and QSAR analysis guide the synthesis of novel pyridinium-based potent β-secretase inhibitory leads
inferred← citeshttps://doi.org/10.1016/j.bmc.2022.116879openalex-snapshot
Fragment hopping protocol for the design of small-molecule protein–protein interaction inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2006.11.003openalex-snapshot
β-Secretase (BACE-1) inhibitors: Accounting for 10s loop flexibility using rigid active sites
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Design and synthesis of aminohydantoins as potent and selective human β-secretase (BACE1) inhibitors with enhanced brain permeability
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Molecular dynamics in drug design
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In silico fragment-based drug design with SEED
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Development of a liquid chromatographic system with fluorescent detection for β-secretase immobilized enzyme reactor on-line enzymatic studies
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Neurosecretases provide strategies to treat sporadic and familial Alzheimer disorders
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Protein structure-based drug design: from docking to molecular dynamics
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Navigating large chemical spaces in early-phase drug discovery
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Chapter 6.3 Triazines, tetrazines and fused ring polyaza systems
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Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking
inferred← citeshttps://doi.org/10.1021/bi100637nopenalex-snapshot
Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1
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Fragment-Based High-Throughput Docking and Library Tailoring
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Postprocessing of Protein−Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors
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Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy
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Data Management System for Distributed Virtual Screening
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(−)-Cytisine and Derivatives: Synthesis, Reactivity, and Applications
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Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method
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Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity
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Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
inferred← citeshttps://doi.org/10.1021/jm070654jopenalex-snapshot
Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model
inferred← citeshttps://doi.org/10.1021/jm301127xopenalex-snapshot
Discovery of Biphenylacetamide-Derived Inhibitors of BACE1 Using de Novo Structure-Based Molecular Design
inferred← citeshttps://doi.org/10.1021/jm7012198openalex-snapshot
Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase
inferred← citeshttps://doi.org/10.1021/jm800242qopenalex-snapshot
Is Quantum Mechanics Necessary for Predicting Binding Free Energy?
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Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics
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Aminoimidazoles as Potent and Selective Human β-Secretase (BACE1) Inhibitors
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Structure-Based Optimization of Potent and Selective Inhibitors of the Tyrosine Kinase Erythropoietin Producing Human Hepatocellular Carcinoma Receptor B4 (EphB4)
inferred← citeshttps://doi.org/10.1021/jm901414eopenalex-snapshot
Design and Synthesis of 5,5′-Disubstituted Aminohydantoins as Potent and Selective Human β-Secretase (BACE1) Inhibitors
inferred← citeshttps://doi.org/10.1039/c3cs60460hopenalex-snapshot
BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease
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A peptide–WS 2 nanosheet based biosensing platform for determination of β-secretase and screening of its inhibitors
inferred← citeshttps://doi.org/10.1074/jbc.m112.411686openalex-snapshot
Structure-based Discovery of Antagonists of Nuclear Receptor LRH-1
inferred← citeshttps://doi.org/10.1080/07391102.2016.1276477openalex-snapshot
Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property
inferred← citeshttps://doi.org/10.1080/07391102.2017.1337590openalex-snapshot
Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads
inferred← citeshttps://doi.org/10.1093/brain/awl251openalex-snapshot
Alzheimer's centennial legacy: prospects for rational therapeutic intervention targeting the A amyloid pathway
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SwissDock, a protein-small molecule docking web service based on EADock DSS
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A double‐headed cathepsin B inhibitor devoid of warhead
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The Discovery of Novel β‐Secretase Inhibitors: Pharmacophore Modeling, Virtual Screening, and Docking Studies
inferred← citeshttps://doi.org/10.1186/1472-6807-12-21openalex-snapshot
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)
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Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking
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Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)
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Recent progress in the drug discovery of non-peptidic BACE1 inhibitors
inferred← citeshttps://doi.org/10.1517/17460441.2013.784267openalex-snapshot
Advances in the identification of β-secretase inhibitors
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Estimation of the Binding Free Energy by Linear Interaction Energy Models
inferred← citeshttps://doi.org/10.2174/156802609789207091openalex-snapshot
Docking Screens: Right for the Right Reasons?
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Novel Iodinated Hydrazide-hydrazones and their Analogues as Acetyl- and Butyrylcholinesterase Inhibitors
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Drug Discovery to Drug Development of BACE1 Inhibitor as Antialzheimer’s: A Review
inferred← citeshttps://doi.org/10.2174/1570159x15666171030142108openalex-snapshot
Combining in vitro and in silico Approaches to Find New Candidate Drugs Targeting the Pathological Proteins Related to the Alzheimer's Disease
inferred← citeshttps://doi.org/10.2174/1570159x16666180315141643openalex-snapshot
Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design
inferred← citeshttps://doi.org/10.3233/jad-2012-121537openalex-snapshot
Cognitive Enhancers (Nootropics). Part 2: Drugs Interacting with Enzymes
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A new insight into computational molecular design: A case study on BACE-1 inhibitors
inferred← citeshttps://doi.org/10.3389/fmolb.2017.00065openalex-snapshot
A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain
inferred← citeshttps://doi.org/10.3389/fmolb.2022.981020openalex-snapshot
In-silico probing of AML related RUNX1 cancer-associated missense mutations: Predicted relationships to DNA binding and drug interactions
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1,3,5-Triazine: A Promising Molecular Scaffold for Novel Agents for the Treatment of Alzheimer’s Disease
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Computational Medicinal Chemistry in Fragment-Based Drug Discovery: What, How and When
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