Amyloid Precursor Protein Secretases

Graph and Multi-Level Sequence Fusion Learning for Predicting the Molecular Activity of BACE-1 Inhibitors.

International journal of molecular sciences Feb 16, 2025

The development of BACE-1 (β-site amyloid precursor protein cleaving enzyme 1) inhibitors is a crucial focus in exploring early treatments for Alzheimer's disease (AD). Recently, graph neural networks (GNNs) have demonstrated significant advantages i...

Alzheimer Disease Enzyme Inhibitors Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Humans Neural Networks, Computer Machine Learning

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Enhanced prediction of beta-secretase inhibitory compounds with mol2vec technique and machine learning algorithms.

SAR and QSAR in environmental research Dec 20, 2024

A comprehensive computational strategy that combined QSAR modelling, molecular docking, and ADMET analysis was used to discover potential inhibitors for β-secretase 1 (BACE-1). A dataset of 1,138 compounds with established BACE-1 inhibitory activitie...

Amyloid Precursor Protein Secretases Molecular Docking Simulation Quantitative Structure-Activity Relationship Molecular Dynamics Simulation Enzyme Inhibitors Machine Learning Algorithms

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Natural compounds for Alzheimer's prevention and treatment: Integrating SELFormer-based computational screening with experimental validation.

Computers in biology and medicine Dec 9, 2024

BACKGROUND: This study aimed to develop and apply a novel computational pipeline combining SELFormer, a transformer architecture-based chemical language model, with advanced deep learning techniques to predict natural compounds (NCs) with potential i...

Humans Amyloid Precursor Protein Secretases Deep Learning Quantitative Structure-Activity Relationship Animals Biological Products Rats PC12 Cells Molecular Docking Simulation Alzheimer Disease Acetylcholinesterase

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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.

SAR and QSAR in environmental research Nov 8, 2024

BACE1 has been regarded as an essential drug design target for treating Alzheimer's disease (AD). Multiple independent Gaussian accelerated molecular dynamics simulations (GaMD), deep learning (DL), and molecular mechanics general Born surface area (...

Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Quantitative Structure-Activity Relationship Hydrogen Bonding Drug Design Deep Learning Molecular Dynamics Simulation Protons

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Classification of beta-site amyloid precursor protein cleaving enzyme 1 inhibitors by using machine learning methods.

Chemical biology & drug design Oct 11, 2021

The beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a transmembrane aspartyl-protease, that cleaves amyloid precursor protein (APP) at the β-site. The sequential proteolytic cleavage of APP, first by β-secretase and then by γ-secreta...

Aspartic Acid Endopeptidases Protease Inhibitors Databases, Pharmaceutical Molecular Structure Bayes Theorem Amyloid Precursor Protein Secretases Reproducibility of Results Models, Theoretical Humans Machine Learning

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Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

Journal of computer-aided molecular design Feb 1, 2020

Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secret...

Aspartic Acid Endopeptidases Macrocyclic Compounds Binding Sites Ligands Enzyme Inhibitors Humans Amyloid Precursor Protein Secretases Molecular Docking Simulation Neural Networks, Computer Drug Design Protein Binding

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MathDL: mathematical deep learning for D3R Grand Challenge 4.

Journal of computer-aided molecular design Feb 1, 2020

We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranki...

Molecular Docking Simulation Drug Design Deep Learning Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Protein Binding Ligands Humans Cathepsins Binding Sites Thermodynamics Small Molecule Libraries

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Comprehensive Exploration of Target-specific Ligands Using a Graph Convolution Neural Network.

Molecular informatics Jan 1, 2020

Machine learning approaches are widely used to evaluate ligand activities of chemical compounds toward potential target proteins. Especially, exploration of highly selective ligands is important for the development of new drugs with higher safety. On...

Algorithms Ligands Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Cathepsin D Humans Neural Networks, Computer

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[Effects of long non-coding RNA RP1-90L14.1 on the biological behaviors of cancer prostate LNCaP cells and its regulating mechanisms].

Zhonghua nan ke xue = National journal of andrology Mar 1, 2019

OBJECTIVE: To investigate the effects of long non-coding RNA RP1-90L14.1 on the proliferation, migration and invasion of prostate cancer LNCaP cells and the expressions of GRIN2A and BACE2.

Neoplasm Invasiveness Gene Expression Regulation, Neoplastic RNA, Long Noncoding Receptors, N-Methyl-D-Aspartate Prostatic Neoplasms Humans Transfection Cell Proliferation Male Amyloid Precursor Protein Secretases Cell Movement Cell Line, Tumor Aspartic Acid Endopeptidases

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A Dual Targeting Drug Delivery System for Penetrating Blood-Brain Barrier and Selectively Delivering siRNA to Neurons for Alzheimer's Disease Treatment.

Current pharmaceutical biotechnology Jan 1, 2017

BACKGROUND: Alzheimer's disease (AD) is one of most serious threats to human beings, however, the treatment is hindered by blood-brain barrier and poor intra-brain cell selectivity.

Drug Delivery Systems PC12 Cells Animals Gene Knockdown Techniques Nanoparticles Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Humans Molecular Targeted Therapy Blood-Brain Barrier RNA, Small Interfering Neurons Alzheimer Disease Rats Permeability Mice, Nude Drug Carriers

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Amyloid Precursor Protein Secretases

Graph and Multi-Level Sequence Fusion Learning for Predicting the Molecular Activity of BACE-1 Inhibitors.

Enhanced prediction of beta-secretase inhibitory compounds with mol2vec technique and machine learning algorithms.

Natural compounds for Alzheimer's prevention and treatment: Integrating SELFormer-based computational screening with experimental validation.

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.

Classification of beta-site amyloid precursor protein cleaving enzyme 1 inhibitors by using machine learning methods.

Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

MathDL: mathematical deep learning for D3R Grand Challenge 4.

Comprehensive Exploration of Target-specific Ligands Using a Graph Convolution Neural Network.

[Effects of long non-coding RNA RP1-90L14.1 on the biological behaviors of cancer prostate LNCaP cells and its regulating mechanisms].

A Dual Targeting Drug Delivery System for Penetrating Blood-Brain Barrier and Selectively Delivering siRNA to Neurons for Alzheimer's Disease Treatment.

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