Screening potential inhibitors for cancer target LSD1 from natural products by steered molecular dynamics

Thai, Nguyen Quoc; Nguyen, Ngan Quy; Nguyen, Chuong; Nguyen, Truong Quy; Ho, Kiet; Nguyen, Trung Tin; Li, Mai Suan

doi:10.1080/08927022.2017.1380802

Cited by 8 publications

(4 citation statements)

References 42 publications

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“…Recent works have used this technique to study the following targets: focal adhesion kinase, 220 the cancer target LSD1, 221 neuraminidase, 222 FK506 binding protein together with trypsin and cyclin-dependent kinase 2, 223 xylose permease, 224 and enzyme 5-enolpyruvylshikimate 3 phosphate synthase. 225 Summarizing this section, absolute binding energy computations are now computationally feasible, up to the accuracy limit of existing force fields, and of finite sampling of the relevant phase space.…”

Section: Chemical Reviewsmentioning

confidence: 99%

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Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

2020

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Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation’s role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.

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Section: Chemical Reviewsmentioning

confidence: 99%

“…Recent works have used this technique to study the following targets: focal adhesion kinase, the cancer target LSD1, neuraminidase, FK506 binding protein together with trypsin and cyclin-dependent kinase 2, xylose permease, and enzyme 5-enolpyruvylshikimate 3 phosphate synthase …”

Section: Applicationsmentioning

confidence: 99%

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

2020

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“…In 2018, Thai et al [125] conducted a virtual screening of 2000 drug-like compounds from the TCM database (https://tcm.cmu.edu.tw, accessed on 15 February 2017) [126] with potential inhibitory effects on LSD1. Employing Lipinski's rule, they selected the top 50 compounds based on favorable docking scores through molecular docking.…”

Section: Other Natural Productsmentioning

confidence: 99%

Lysine-Specific Demethylase 1 Inhibitors: A Comprehensive Review Utilizing Computer-Aided Drug Design Technologies

Han,

Lu,

Fan

et al. 2024

Molecules

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Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising therapeutic target for treating various cancers (such as breast cancer, liver cancer, etc.) and other diseases (blood diseases, cardiovascular diseases, etc.), owing to its observed overexpression, thereby presenting significant opportunities in drug development. Since its discovery in 2004, extensive research has been conducted on LSD1 inhibitors, with notable contributions from computational approaches. This review systematically summarizes LSD1 inhibitors investigated through computer-aided drug design (CADD) technologies since 2010, showcasing a diverse range of chemical scaffolds, including phenelzine derivatives, tranylcypromine (abbreviated as TCP or 2-PCPA) derivatives, nitrogen-containing heterocyclic (pyridine, pyrimidine, azole, thieno[3,2-b]pyrrole, indole, quinoline and benzoxazole) derivatives, natural products (including sanguinarine, phenolic compounds and resveratrol derivatives, flavonoids and other natural products) and others (including thiourea compounds, Fenoldopam and Raloxifene, (4-cyanophenyl)glycine derivatives, propargylamine and benzohydrazide derivatives and inhibitors discovered through AI techniques). Computational techniques, such as virtual screening, molecular docking and 3D-QSAR models, have played a pivotal role in elucidating the interactions between these inhibitors and LSD1. Moreover, the integration of cutting-edge technologies such as artificial intelligence holds promise in facilitating the discovery of novel LSD1 inhibitors. The comprehensive insights presented in this review aim to provide valuable information for advancing further research on LSD1 inhibitors.

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“…A força de ruptura, definida como a força máxima que a mola impõe sobre o complexo durante a simulação dirigida (Fig. 10), tem sido usada recentemente como um estimador de afinidade relativa altamente correlacionado com ΔG interação experimentalmente observado [122][123][124] .…”

Section: Força De Rupturaunclassified

Mecanismos moleculares de reconhecimento das glicosilações do envelope do vírus da Dengue pelas lectinas tipo-C e seus potenciais inibidores

Bortot¹,

Caliri²

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Farmacêuticas pelo suporte ao longo do doutorado. À FAPESP pelo apoio financeiro através do projeto regular de doutorado (processo 2013/00927-7) e pela bolsa BEPE (processo 2016/04958-2), possibilitando minha dedicação intensa à pesquisa ao longo do doutorado. Ao Professor David van der Spoel por ter me recebido gentilmente em seu grupo de pesquisa na Universidade de Uppsala, Suécia, e aos antigos colegas de grupo durante pouco menos de 1 ano pelo ambiente amigável e estimulante:

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Screening potential inhibitors for cancer target LSD1 from natural products by steered molecular dynamics

Cited by 8 publications

References 42 publications

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Lysine-Specific Demethylase 1 Inhibitors: A Comprehensive Review Utilizing Computer-Aided Drug Design Technologies

Mecanismos moleculares de reconhecimento das glicosilações do envelope do vírus da Dengue pelas lectinas tipo-C e seus potenciais inibidores

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