Repurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson's disease: computational modelling studies

Review Cell Biology

Diabetes mellitus and Parkinson's disease: dangerous liaisons between insulin and dopamine

Angela De Iuliis et al.

Summary: This review reevaluates the dangerous liaison between diabetes mellitus and Parkinson's disease, highlighting the possible functional link between insulin and dopamine.

NEURAL REGENERATION RESEARCH (2022)

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Article Neurosciences

New therapeutic approaches to Parkinson's disease targeting GBA, LRRK2 and Parkin

Konstantin Senkevich et al.

Summary: Parkinson's disease is a complex disorder that may be a mixture of different diseases, with genes playing an important role in patient classification and drug development. GBA, LRRK2, and PRKN are key genes associated with PD, and targeting these genes could lead to novel therapeutic approaches.

NEUROPHARMACOLOGY (2022)

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Article Biochemistry & Molecular Biology

Novel Imidazole Phenoxyacetic Acids as Inhibitors of USP30 for Neuroprotection Implication via the Ubiquitin-Rho-110 Fluorometric Assay: Design, Synthesis, and In Silico and Biochemical Assays

Subhankar Mandal et al.

Summary: In this study, potential USP30 inhibitors were discovered from an imidazole series of ligands by understanding the structural requirements. Compound 3g and 3f showed inhibitory effects on USP30 and compound 3g also exhibited neuroprotective efficacy. These findings provide a new protocol for designing and developing ligands against USP30, offering a therapeutic strategy for conditions like kidney damage and neurodegenerative disorders, including Parkinson's disease.

ACS CHEMICAL NEUROSCIENCE (2022)

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Editorial Material Pharmacology & Pharmacy

Drug repurposing: An effective strategy to accelerate contemporary drug discovery

Peng Zhan et al.

DRUG DISCOVERY TODAY (2022)

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Review Biochemistry & Molecular Biology

How the ends signal the end: Regulation by E3 ubiquitin ligases recognizing protein termini

Dawafuti Sherpa et al.

Summary: E3 ubiquitin ligases interact with protein termini to intricately control protein quality and cellular signaling.

MOLECULAR CELL (2022)

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Review Pharmacology & Pharmacy

USP30: Structure, Emerging Physiological Role, and Target Inhibition

Feng Wang et al.

Summary: USP30 is a deubiquitinating enzyme localized in mitochondria and peroxisomes, playing essential roles in various cellular events. Dysregulation of USP30 is associated with physiological disorders, and research on USP30 inhibitors shows promise for potential therapeutic applications, especially in treating pulmonary disorders.

FRONTIERS IN PHARMACOLOGY (2022)

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Article Geriatrics & Gerontology

Correlation of matrix metalloproteinase 3 and matrix metalloproteinase 9 levels with non-motor symptoms in patients with Parkinson's disease

Chuan Ze Liu et al.

Summary: This study found that serum MMP3 levels were lower and MMP9 levels were higher in patients with Parkinson's disease (PD) compared to healthy controls. Serum MMP3 levels were correlated with non-motor symptoms and sleep disturbance in PD patients, while MMP9 levels were correlated with non-motor symptoms and cognitive function in PD patients.

FRONTIERS IN AGING NEUROSCIENCE (2022)

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Article Computer Science, Artificial Intelligence

A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism

Vanessa Lage-Rupprecht et al.

Summary: The high failure rate of pre-clinical and clinical studies for Alzheimer disease (AD) drugs highlights the need for reassessing existing strategies. In this study, a holistic approach combining computational analytics and experimental screening data was used to identify 77 druggable modifiers of tau phosphorylation (pTau), and 20 repurposing candidates were found through screening with 5,632 drugs. Four compounds were found to have links to AD-specific genes. This approach can be applied to discover more repurposing candidates for various AD-associated mechanisms.

PATTERNS (2022)

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Article Biochemistry & Molecular Biology

Investigation of USP30 inhibition to enhance Parkin-mediated mitophagy: tools and approaches

Eliona Tsefou et al.

Summary: Research suggests that inhibition of USP30 can enhance the mitophagy pathway, playing a crucial role in regulating mitochondrial function in cellular models relevant to Parkinson's disease.

BIOCHEMICAL JOURNAL (2021)

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Article Biochemistry & Molecular Biology

Targeting mitophagy in Parkinson's disease

Emily H. Clark et al.

Summary: The genetics and pathophysiology of Parkinson's disease strongly implicate mitochondria in disease development, with defects in mitophagy potentially playing a role in pathogenesis. Pharmacological enhancement of mitophagy is a promising therapeutic approach, but the full therapeutic potential of targeting mitophagy pathways requires further exploration.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Chemistry, Physical

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

Mario S. Valdes-Tresanco et al.

Summary: gmx_MMPBSA is a new tool for performing end-state free energy calculations from GROMACS molecular dynamics trajectories, offering various options including binding free energy calculations with different solvation models, stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Additionally, promising methodologies for calculating relative binding free energies have been implemented.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Integrated computational approach on sodium-glucose co-transporter 2 (SGLT2) Inhibitors for the development of novel antidiabetic agents

Sushanta Bhattacharya et al.

Summary: This study focused on computational analysis and drug design targeting SGLT2 to find potential molecules for treating diabetes and validated their contribution to the model. The construction of a structural model for SGLT2 and docking studies with potent inhibitors showed the active conformations and critical interactions involved in potential inhibition.

JOURNAL OF MOLECULAR STRUCTURE (2021)

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Article Biochemistry & Molecular Biology

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor

Negin Forouzesh et al.

Summary: The study introduces a new flavor of the generalized Born model for calculating binding affinity in protein-ligand complexes. It presents an efficient computational protocol and evaluates two options for representing dielectric boundaries, showing quantitative agreement with experimental values. Additionally, efficient entropy calculation strategies are proposed.

MOLECULES (2021)

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Review Biochemistry & Molecular Biology

Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response

Nathan A. Snyder et al.

Summary: Ubiquitin signaling is a dynamic process that impacts protein activity, localization, or stability. Deubiquitinating enzymes counteract this process by removing ubiquitin, playing a crucial role in physiological pathways. DUB activity is tightly regulated in dynamic environments and plays a significant role in oxidative stress conditions.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Clinical Neurology

Prediabetes, type 2 diabetes mellitus and risk of Parkinson's disease: A population-based cohort study

Almudena Sanchez-Gomez et al.

Summary: The study found that patients with type 2 diabetes and prediabetes have a higher risk of Parkinson's disease, especially in women and young individuals.

PARKINSONISM & RELATED DISORDERS (2021)

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Review Cell Biology

The potential roles of deubiquitinating enzymes in brain diseases

Key-Hwan Lim et al.

AGEING RESEARCH REVIEWS (2020)

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Review Chemistry, Medicinal

Matrix metalloproteinase-9 (MMP-9) and its inhibitors in cancer: A minireview

Subha Mondal et al.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2020)

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Article Biochemistry & Molecular Biology

Dynamic Regulation of Mitochondrial Import by the Ubiquitin System

Lilian Phu et al.

MOLECULAR CELL (2020)

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Article Biochemistry & Molecular Biology

Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling

Alban Ordureau et al.

MOLECULAR CELL (2020)

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Review Pharmacology & Pharmacy

Open access in silico tools to predict the ADMET profiling of drug candidates

Supratik Kar et al.

EXPERT OPINION ON DRUG DISCOVERY (2020)

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Article Multidisciplinary Sciences

Discovery of potent and specific inhibitors targeting the active site of MMP-9 from the engineered SPINK2 library

Hidenori Yano et al.

PLOS ONE (2020)

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Article Oncology

Repurposing Pimavanserin, an Anti-Parkinson Drug for Pancreatic Cancer Therapy

Sharavan Ramachandran et al.

MOLECULAR THERAPY-ONCOLYTICS (2020)

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Review Neurosciences

Multiple pathways for mitophagy: A neurodegenerative conundrum for Parkinson's disease

Charleen T. Chu

NEUROSCIENCE LETTERS (2019)

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Editorial Material Cardiac & Cardiovascular Systems

Class effect for SGLT-2 inhibitors: a tale of 9 drugs

Dario Giugliano et al.

CARDIOVASCULAR DIABETOLOGY (2019)

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Review Neurosciences

Therapeutic approaches to enhance PINK1/Parkin mediated mitophagy for the treatment of Parkinson's disease

Silke Miller et al.

NEUROSCIENCE LETTERS (2019)

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Article Biochemistry & Molecular Biology

The Michael J. Fox Foundation for Parkinson's Research Strategy to Advance Therapeutic Development of PINK1 and Parkin

Shalini Padmanabhan et al.

BIOMOLECULES (2019)

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Review Biochemistry & Molecular Biology

From Discovery to Bedside: Targeting the Ubiquitin System

Ingrid E. Wertz et al.

CELL CHEMICAL BIOLOGY (2019)

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Article Biochemistry & Molecular Biology

ADMET-score - a comprehensive scoring function for evaluation of chemical drug-likeness

Longfei Guan et al.

MEDCHEMCOMM (2019)

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Article Chemistry, Medicinal

Novel highly selective inhibitors of ubiquitin specific protease 30 (USP30) accelerate mitophagy

Arthur F. Kluge et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2018)

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Article Clinical Neurology

Diabetes mellitus and Parkinson disease

Gennaro Pagano et al.

NEUROLOGY (2018)

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Article Biochemistry & Molecular Biology

Mechanism and regulation of the Lys6-selective deubiquitinase USP30

Malte Gersch et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

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Review Neurosciences

Autophagy and Neurodegeneration: Pathogenic Mechanisms and Therapeutic Opportunities

Fiona M. Menzies et al.

NEURON (2017)

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Article Biochemistry & Molecular Biology

Mechanism and regulation of the Lys6-selective deubiquitinase USP30

Malte Gersch et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

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Review Neurosciences

Parkin and PINK1 functions in oxidative stress and neurodegeneration

Sandeep K. Barodia et al.

BRAIN RESEARCH BULLETIN (2017)

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Review Biochemistry & Molecular Biology

Mitochondria, autophagy and age-associated neurodegenerative diseases: New insights into a complex interplay

Eirini Lionaki et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2015)

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Review Neurosciences

The Roles of PINK1, Parkin, and Mitochondrial Fidelity in Parkinson's Disease

Alicia M. Pickrell et al.

NEURON (2015)

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Review Pharmacology & Pharmacy

SGLT2 inhibitors: a promising new therapeutic option for treatment of type 2 diabetes mellitus

Monika Misra

JOURNAL OF PHARMACY AND PHARMACOLOGY (2013)

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Article Multidisciplinary Sciences

Association Studies of MMP-9 in Parkinson's Disease and Amyotrophic Lateral Sclerosis

Xianghua He et al.

PLOS ONE (2013)

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Article Chemistry, Medicinal

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

Feixiong Cheng et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

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Article Chemistry, Multidisciplinary

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

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JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)

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Article Biochemistry & Molecular Biology

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Daniel Seeliger et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)

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Article Cell Biology

Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane

Nobuhiro Nakamura et al.

MOLECULAR BIOLOGY OF THE CELL (2008)

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Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

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JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

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Repurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson's disease: computational modelling studies

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