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Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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A semiempirical free energy force field with charge‐based desolvation
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Boom in the development of non‐peptidic β‐secretase (BACE1) inhibitors for the treatment of Alzheimer's disease
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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Very fast empirical prediction and rationalization of protein pK a values
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Very fast prediction and rationalization of pKa values for protein–ligand complexes
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Outstanding challenges in protein–ligand docking and structure‐based virtual screening
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Identification of a Novel Aspartic Protease (Asp 2) as β-Secretase
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X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases
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Amyloid deposition as the central event in the aetiology of Alzheimer's disease
inferredcites →https://doi.org/10.1016/j.bmcl.2006.04.076openalex-snapshot
BACE-1 inhibition by a series of ψ[CH2NH] reduced amide isosteres
inferredcites →https://doi.org/10.1016/j.bmcl.2007.10.116openalex-snapshot
Potent pyrrolidine- and piperidine-based BACE-1 inhibitors
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Second generation of BACE-1 inhibitors part 3: Towards non hydroxyethylamine transition state mimetics
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β-Secretase as a Therapeutic Target for Alzheimer's Disease
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HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential
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Gene action in the aging brain: an evolutionary biological perspective
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Emerging Alzheimer’s disease therapies: inhibition of β-secretase
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Soluble Alzheimers β-amyloid constricts the cerebral vasculature in vivo
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Follow the Protons: A Low-Barrier Hydrogen Bond Unifies the Mechanisms of the Aspartic Proteases
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Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
inferredcites →https://doi.org/10.1021/bi060131yopenalex-snapshot
Catalysis and Linear Free Energy Relationships in Aspartic Proteases
inferredcites →https://doi.org/10.1021/bi100637nopenalex-snapshot
Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1
inferredcites →https://doi.org/10.1021/bi200081hopenalex-snapshot
Computational Modeling of Substrate Specificity and Catalysis of the β-Secretase (BACE1) Enzyme
inferredcites →https://doi.org/10.1021/bi900017qopenalex-snapshot
Fragment-Based Discovery of Nonpeptidic BACE-1 Inhibitors Using Tethering
inferredcites →https://doi.org/10.1021/bi901061aopenalex-snapshot
Fragment-Based Discovery of BACE1 Inhibitors Using Functional Assays
inferredcites →https://doi.org/10.1021/ci900345hopenalex-snapshot
Ligand−Protein Cross-Docking with Water Molecules
inferredcites →https://doi.org/10.1021/ci970005oopenalex-snapshot
Constructing Protein Models for Ligand−Receptor Binding Thermodynamic Simulations: An Application to a Set of Peptidometic Renin Inhibitors
inferredcites →https://doi.org/10.1021/ct0600060openalex-snapshot
Assigning the Protonation States of the Key Aspartates in β-Secretase Using QM/MM X-ray Structure Refinement
inferredcites →https://doi.org/10.1021/ct100578zopenalex-snapshot
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions
inferredcites →https://doi.org/10.1021/ct200133yopenalex-snapshot
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values
inferredcites →https://doi.org/10.1021/ja00063a005openalex-snapshot
Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation
inferredcites →https://doi.org/10.1021/ja00102a057openalex-snapshot
NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor
inferredcites →https://doi.org/10.1021/ja0304493openalex-snapshot
Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design
inferredcites →https://doi.org/10.1021/ja044608+openalex-snapshot
Evolutionarily Conserved Functional Mechanics across Pepsin-like and Retroviral Aspartic Proteases
inferredcites →https://doi.org/10.1021/ja801269xopenalex-snapshot
The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-ray Diffraction
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
inferredcites →https://doi.org/10.1021/jm049133bopenalex-snapshot
Virtual Screening for β-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228
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/jm0509142openalex-snapshot
Aminoethylenes: A Tetrahedral Intermediate Isostere Yielding Potent Inhibitors of the Aspartyl Protease BACE-1
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm061046ropenalex-snapshot
Discovery of Oxadiazoyl Tertiary Carbinamine Inhibitors of β-Secretase (BACE-1)
inferredcites →https://doi.org/10.1021/jm061338sopenalex-snapshot
Design, Synthesis, and X-ray Structure of Potent Memapsin 2 (β-Secretase) Inhibitors with Isophthalamide Derivatives as the P2-P3-Ligands
inferredcites →https://doi.org/10.1021/jm101568yopenalex-snapshot
On a Possible Neutral Charge State for the Catalytic Dyad in β-Secretase When Bound to Hydroxyethylene Transition State Analogue Inhibitors
inferredcites →https://doi.org/10.1021/jm200544qopenalex-snapshot
From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1)
inferredcites →https://doi.org/10.1021/jp037651copenalex-snapshot
Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations
inferredcites →https://doi.org/10.1021/jp811154wopenalex-snapshot
Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42)
inferredcites →https://doi.org/10.1038/337576a0openalex-snapshot
Crystal structure of a retroviral protease proves relationship to aspartic protease family
inferredcites →https://doi.org/10.1038/399a023openalex-snapshot
Translating cell biology into therapeutic advances in Alzheimer's disease
inferredcites →https://doi.org/10.1038/85059openalex-snapshot
Mice deficient in BACE1, the Alzheimer's β-secretase, have normal phenotype and abolished β-amyloid generation
inferredcites →https://doi.org/10.1038/85064openalex-snapshot
BACE1 is the major β-secretase for generation of Aβ peptides by neurons
inferredcites →https://doi.org/10.1038/990107openalex-snapshot
Membrane-anchored aspartyl protease with Alzheimer's disease β-secretase activity
inferredcites →https://doi.org/10.1038/990114openalex-snapshot
Purification and cloning of amyloid precursor protein β-secretase from human brain
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The Nonfibrillar Amyloid β‐Peptide Induces Apoptotic Neuronal Cell Death
inferredcites →https://doi.org/10.1073/pnas.0810631106openalex-snapshot
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
inferredcites →https://doi.org/10.1073/pnas.84.20.7009openalex-snapshot
Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
inferredcites →https://doi.org/10.1074/jbc.m111.260471openalex-snapshot
Loss of Cleavage at β′-Site Contributes to Apparent Increase in β-Amyloid Peptide (Aβ) Secretion by β-Secretase (BACE1)-Glycosylphosphatidylinositol (GPI) Processing of Amyloid Precursor Protein
inferredcites →https://doi.org/10.1074/jbc.r800019200openalex-snapshot
Amyloid Precursor Protein Trafficking, Processing, and Function
inferredcites →https://doi.org/10.1093/bioinformatics/18.2.315openalex-snapshot
Models@Home: distributed computing in bioinformatics using a screensaver based approach
inferredcites →https://doi.org/10.1110/ps.03372304openalex-snapshot
The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV‐1 protease
inferredcites →https://doi.org/10.1126/science.1072994openalex-snapshot
The Amyloid Hypothesis of Alzheimer's Disease: Progress and Problems on the Road to Therapeutics
inferredcites →https://doi.org/10.1126/science.286.5440.735openalex-snapshot
β-Secretase Cleavage of Alzheimer's Amyloid Precursor Protein by the Transmembrane Aspartic Protease BACE
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/10.1146/annurev.bb.19.060190.001201openalex-snapshot
The Structure and Function of the Aspartic Proteinases
inferredcites →https://doi.org/10.1523/jneurosci.3647-11.2011openalex-snapshot
Robust Central Reduction of Amyloid-β in Humans with an Orally Available, Non-Peptidic β-Secretase Inhibitor
inferredcites →https://doi.org/10.2174/1570180043485581openalex-snapshot
Grid-Based Hydrogen Bond Potentials with Improved Directionality

What points at this work

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

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Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations
inferred← citeshttps://doi.org/10.1002/qua.24854openalex-snapshot
Molecular insight into the interaction mechanisms of amino-2 H -imidazole derivatives with BACE1 protease: A QM/MM and QTAIM study
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Effect of pH and ligand charge state on BACE-1 fragment docking performance
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Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches
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Design, synthesis, in silico and in vitro screening of 1,2,4-thiadiazole analogues as non-peptide inhibitors of beta-secretase
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Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment
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The potential of natural product vs neurodegenerative disorders: In silico study of artoflavanocoumarin as BACE-1 inhibitor
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Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations
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Edaravone N-benzyl pyridinium derivatives: BACE-1 inhibition, kinetics and in silico binding pose determination
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Potent BACE1 inhibitory and neuroprotective activities of three lignans, styraxlignolide A, masutakeside I, and egonol, isolated from Styrax japonica
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Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study
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A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds
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Computational insights into the protonation states of catalytic dyad in BACE1–acyl guanidine based inhibitor complex
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A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process
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G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket
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Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
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BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c04085openalex-snapshot
Selective Protonation of Catalytic Dyad for γ-Secretase-Mediated Hydrolysis Revealed by Multiscale Simulations
inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00234openalex-snapshot
Effects of Disulfide Bonds on Binding of Inhibitors to β-Amyloid Cleaving Enzyme 1 Decoded by Multiple Replica Accelerated Molecular Dynamics Simulations
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Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations
inferred← citeshttps://doi.org/10.1021/bi5000977openalex-snapshot
Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1
inferred← citeshttps://doi.org/10.1039/c5mb00088bopenalex-snapshot
Target specific proteochemometric model development for BACE1 – protein flexibility and structural water are critical in virtual screening
inferred← citeshttps://doi.org/10.1080/07391102.2017.1393461openalex-snapshot
Population density analysis for determining the protonation state of the catalytic dyad in BACE1-tertiary carbinamine-based inhibitor complex
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New substituted aminopyrimidine derivatives as BACE1 inhibitors: in silico design, synthesis and biological assays
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Molecular mechanism underlying effect of D93 and D289 protonation states on inhibitor-BACE1 binding: exploration from multiple independent Gaussian accelerated molecular dynamics and deep learning
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Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad ofβ-Secretase
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Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization
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High-Order Perturbation Theory Models of Drug-Target Interactomes for Proteins Expressed on Networks of Hippocampus Brain Region of Alzheimer Disease Patients
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Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria
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On the Active Site Protonation State in Aspartic Proteases: Implications for Drug Design
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BACE-1 Inhibitors Targeting Alzheimer's Disease
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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
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Biological and computational evaluation of resveratrol inhibitors against Alzheimer’s disease
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Dual Inhibitors of AChE and BACE-1 for Reducing Aβ in Alzheimer’s Disease: From In Silico to In Vivo
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