4.7 Article

Structure-based virtual screening and molecular dynamics simulation for the identification of sphingosine kinase-2 inhibitors as potential analgesics

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Quantitative structure-activity relationships analysis, homology modeling, docking and molecular dynamics studies of triterpenoid saponins as Kirsten rat sarcoma inhibitors

Mourad Stitou et al.

Summary: Using computational methods and bioinformatics techniques, potential inhibitors targeting the KRAS mutated protein were screened using various analytical and simulation methods, and the accuracy and stability of the simulation results were validated.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Biochemistry & Molecular Biology

Natural Products for the Treatment of Pain: Chemistry and Pharmacology of Salvinorin A, Mitragynine, and Collybolide

Soumen Chakraborty et al.

Summary: Pain management has been a significant issue in medicine, with efforts focused on developing alternative opioids without side effects.

BIOCHEMISTRY (2021)

Article Biochemistry & Molecular Biology

Pharmacological Characterization of μ-Opioid Receptor Agonists with Biased G Protein or β-Arrestin Signaling, and Computational Study of Conformational Changes during Receptor Activation

Justyna Piekielna-Ciesielska et al.

Summary: This study investigates biased agonism at opioid receptors by analyzing the structural features and biased characteristics of two cyclopeptides in complex with MOP through experiments and simulations.

MOLECULES (2021)

Article Endocrinology & Metabolism

An Unanticipated Role for Sphingosine Kinase-2 in Bone and in the Anabolic Effect of Parathyroid Hormone

Joanne M. Walker et al.

Summary: SPHK2 plays an important role in both normal bone remodeling and the anabolic response to PTH.

ENDOCRINOLOGY (2021)

Article Biochemical Research Methods

Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children

Laurens F. M. Verscheijden et al.

Summary: The study developed a morphine PB-PK/PD model to predict brain drug disposition and analgesic effects in different age groups. In neonates, pharmacodynamic characteristics were altered compared to adults and older children, while brain drug disposition remained similar, potentially explaining reported differences in analgesic effects.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Chemistry, Medicinal

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations

Ercheng Wang et al.

Summary: The novel VAD-MM/GBSA, a version of MM/GBSA with machine-learning optimization, assigns variable dielectric constants to protein/ligand atoms for improved accuracy in binding affinity calculations. It outperforms prime MM/GBSA and shows remarkable predictive performance for specific protein targets, potentially replacing traditional MM/GBSA in AMBER software.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Medicinal

Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein-Protein Docking, Molecular Dynamics, and MM-GBSA Calculations

Alberto Ongaro et al.

Summary: Orf7a in SARS-CoV-2 structurally resembles members of the immunoglobulin superfamily and ICAMs, potentially contributing to virus infectivity and pathogenicity by forming a complex with LFA-1. The study utilized protein-protein docking, MD simulations, and MM-GBSA to provide refined models for insight into this macromolecular assembly.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Physical

Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?

Shuting Zhang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Clinical Neurology

FKBP51‐Hsp90 complex as a novel therapeutic target for Alzheimer’s disease

Lisha Wang et al.

Alzheimers & Dementia (2020)

Article Biochemistry & Molecular Biology

Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model

Benjamin Tam et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Chemistry, Medicinal

Computational Outlook of Marine Compounds as Anti-cancer Representatives Targeting BCL-2 and Survivin

Eram Shakeel et al.

CURRENT COMPUTER-AIDED DRUG DESIGN (2019)

Article Chemistry, Medicinal

Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization

Fernanda I. Saldivar-Gonzalez et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Multidisciplinary Sciences

A primer on natural product-based virtual screening

Eleni Koulouridi et al.

PHYSICAL SCIENCES REVIEWS (2019)

Article Multidisciplinary Sciences

Discovery of novel choline acetyltransferase inhibitors using structure-based virtual screening

Rajnish Kumar et al.

SCIENTIFIC REPORTS (2017)

Article Oncology

Targeting sphingosine kinase 2 (SphK2) by ABC294640 inhibits colorectal cancer cell growth in vitro and in vivo

Cai Xun et al.

JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH (2015)

Article Neurosciences

Sphingosine kinase 2-deficiency mediated changes in spinal pain processing

Jastrow Canlas et al.

FRONTIERS IN MOLECULAR NEUROSCIENCE (2015)

Article Biochemistry & Molecular Biology

Molecular Basis of Sphingosine Kinase 1 Substrate Recognition and Catalysis

Zhulun Wang et al.

STRUCTURE (2013)

Article Biochemical Research Methods

Template-based protein structure modeling using the RaptorX web server

Morten Kaellberg et al.

NATURE PROTOCOLS (2012)

Article Biochemical Research Methods

Protein structure homology modeling using SWISS-MODEL workspace

Lorenza Bordoli et al.

NATURE PROTOCOLS (2009)

Article Biochemistry & Molecular Biology

QMEAN server for protein model quality estimation

Pascal Benkert et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

The SWISS-MODEL Repository and associated resources

Florian Kiefer et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

QMEAN: A comprehensive scoring function for model quality assessment

Pascal Benkert et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Markus Wiederstein et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Chemistry, Multidisciplinary

GROMACS: Fast, flexible, and free

D Van der Spoel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

SWISS-MODEL: an automated protein homology-modeling server

T Schwede et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Structure validation by Cα geometry:: φ,ψ and Cβ deviation

SC Lovell et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)