Drug repurposing for ligand-induced rearrangement of Sirt2 active site-based inhibitors via molecular modeling and quantum mechanics calculations

Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinases

(2020) Shiv Bharadwaj et al.   JOURNAL OF MOLECULAR LIQUIDS

SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1

(2020) Nicolás G. Simonet et al.   Science Advances

Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro

(2020) Shiv Bharadwaj et al.   BRIEFINGS IN BIOINFORMATICS

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

(2019) Katarina Roos et al.   Journal of Chemical Theory and Computation

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Computational aided mechanistic understanding of Camellia sinensis bioactive compounds against co-chaperone p23 as potential anticancer agent

(2019) Shiv Bharadwaj et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

QSAR Classification Models for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer’s Disease

(2019) Ignacio Ponzoni et al.   Scientific Reports

A Glycoconjugated SIRT2 Inhibitor with Aqueous Solubility Allows Structure-Based Design of SIRT2 Inhibitors

(2019) Jun Young Hong et al.   ACS Chemical Biology

Sirtuins as regulators of the cellular stress response and metabolism in marine ectotherms

(2019) M. Christina Vasquez et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Unraveling the Unbinding Pathways of Products Formed in Catalytic Reactions Involved in SIRT1–3: A Random Acceleration Molecular Dynamics Simulation Study

(2019) Charuvaka Muvva et al.   Journal of Chemical Information and Modeling

X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells

(2018) Ling-Ling Yang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Integrating molecular probes and molecular dynamics to reveal binding modes of GLUT5 activatory and inhibitory ligands

(2018) Jon Ainsley et al.   CHEMICAL COMMUNICATIONS

The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy

(2017) Rafał Kurczab   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

A SIRT2-Selective Inhibitor Promotes c-Myc Oncoprotein Degradation and Exhibits Broad Anticancer Activity

(2016) Hui Jing et al.   CANCER CELL

Using mitochondrial sirtuins as drug targets: disease implications and available compounds

(2016) Melanie Gertz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors

(2016) Yajing Fang et al.   Scientific Reports

Structure Based Docking and Molecular Dynamic Studies of Plasmodial Cysteine Proteases against a South African Natural Compound and its Analogs

(2016) Thommas M. Musyoka et al.   Scientific Reports

The chemical biology of sirtuins

(2015) Bing Chen et al.   CHEMICAL SOCIETY REVIEWS

Synthesis, QSAR and anticandidal evaluation of 1,2,3-triazoles derived from naturally bioactive scaffolds

(2015) Mohammad Irfan et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

(2015) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Selective Sirt2 inhibition by ligand-induced rearrangement of the active site

(2015) Tobias Rumpf et al.   Nature Communications

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

(2015) Karel Mena-Ulecia et al.   PLoS One

Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling

(2014) Daniel Cappel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of Potent and Selective Sirtuin 2 (SIRT2) Inhibitors Using a Fragment-Based Approach

(2014) Huaqing Cui et al.   JOURNAL OF MEDICINAL CHEMISTRY

Insights into activity enhancement of 4-aminoquinoline-based hybrids using atom-based and field-based QSAR studies

(2014) K. Kranthi Raj et al.   MEDICINAL CHEMISTRY RESEARCH

Recent Advances in Multidimensional QSAR (4D-6D): A Critical Review

(2014) Manoj Damale et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

The growing landscape of lysine acetylation links metabolism and cell signalling

(2014) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Building on a solid foundation: SAR and QSAR as a fundamental strategy to reduce animal testing

(2014) K.M. Sullivan et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

The NAD-dependent deacetylase sirtuin 2 is a suppressor of microglial activation and brain inflammation

(2013) Teresa Faria Pais et al.   EMBO JOURNAL

SIRT1 and SIRT2: emerging targets in neurodegeneration

(2013) Gizem Donmez et al.   EMBO Molecular Medicine

The tumor suppressor SirT2 regulates cell cycle progression and genome stability by modulating the mitotic deposition of H4K20 methylation

(2013) L. Serrano et al.   GENES & DEVELOPMENT

A Novel Sirtuin 2 (SIRT2) Inhibitor with p53-dependent Pro-apoptotic Activity in Non-small Cell Lung Cancer

(2013) Gesine Hoffmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Activation of the Protein Deacetylase SIRT6 by Long-chain Fatty Acids and Widespread Deacylation by Mammalian Sirtuins

(2013) Jessica L. Feldman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pharmacophore and 3D-QSAR Characterization of 6-Arylquinazolin-4-amines as Cdc2-like Kinase 4 (Clk4) and Dual Specificity Tyrosine-phosphorylation-regulated Kinase 1A (Dyrk1A) Inhibitors

(2013) Yongmei Pan et al.   Journal of Chemical Information and Modeling

The sirtuin family’s role in aging and age-associated pathologies

(2013) Jessica A. Hall et al.   JOURNAL OF CLINICAL INVESTIGATION

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Crystal structure analysis of human Sirt2 and its ADP-ribose complex

(2013) Sébastien Moniot et al.   JOURNAL OF STRUCTURAL BIOLOGY

SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine

(2013) Hong Jiang et al.   NATURE

How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials

(2012) Xuben Hou et al.   Journal of Chemical Information and Modeling

Design, Synthesis, and Biological Activity of a Novel Series of Human Sirtuin-2-Selective Inhibitors

(2012) Takayoshi Suzuki et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5

(2012) Bruce G. Szczepankiewicz et al.   JOURNAL OF ORGANIC CHEMISTRY

Are sirtuins viable targets for improving healthspan and lifespan?

(2012) Joseph A. Baur et al.   NATURE REVIEWS DRUG DISCOVERY

Essential dynamics: foundation and applications

(2012) Isabella Daidone et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

SIRT2 Maintains Genome Integrity and Suppresses Tumorigenesis through Regulating APC/C Activity

(2011) Hyun-Seok Kim et al.   CANCER CELL

Structure and Biochemical Functions of SIRT6

(2011) Patricia W. Pan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

(2011) Juan Du et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Sir-two-homolog 2 (Sirt2) modulates peripheral myelination through polarity protein Par-3/atypical protein kinase C (aPKC) signaling

(2011) B. Beirowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sirt5 Is a NAD-Dependent Protein Lysine Demalonylase and Desuccinylase

(2011) J. Du et al.   SCIENCE

3D-QSAR in Drug Design - A Review

(2010) Jitender Verma et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Accuracy Assessment of Protein-Based Docking Programs against RNA Targets

(2010) Yaozong Li et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

2D and 3D QSAR studies of the receptor binding affinity of progestins

(2010) Lea da Silva Veras et al.   JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY

Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations

(2010) Weihua Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Investigating the ADP-ribosyltransferase Activity of Sirtuins with NAD Analogues and32P-NAD†

(2009) Jintang Du et al.   BIOCHEMISTRY

Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease

(2009) Pedro Fong et al.   Journal of Chemical Information and Modeling

Pharmacophore generation and atom-based 3D-QSAR of novel 2-(4-methylsulfonylphenyl)pyrimidines as COX-2 inhibitors

(2009) Ujashkumar A. Shah et al.   MOLECULAR DIVERSITY