4.6 Article

Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents

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。
Review Pharmacology & Pharmacy

Docking and scoring for nucleic acid-ligand interactions: Principles and current status

Yuyu Feng et al.

Summary: Nucleic acid-ligand interactions play crucial roles in cellular processes and have attracted significant interest in drug discovery. However, traditional docking algorithms and scoring functions for protein-ligand interactions may not be applicable to nucleic acid-ligand docking due to the differences in their properties. This review discusses the current status, challenges, and limitations of docking algorithms and scoring functions for DNA/RNA-ligand interactions.

DRUG DISCOVERY TODAY (2022)

Review Chemistry, Multidisciplinary

RNA-ligand molecular docking: Advances and challenges

Yuanzhe Zhou et al.

Summary: The rapid advancement in computer algorithms and hardware has drastically accelerated the selection of potent small molecule drug candidates through fast and accurate virtual screening. Computational modeling of RNA-small molecule interactions is essential for RNA-targeted drug discovery, with a focus on docking-and-scoring methods. Challenges in accurate docking and scoring include addressing issues like the flexibility of ligands and RNA, efficient sampling of binding sites and poses, and accurate scoring of different binding modes. Additionally, the complexity of predicting ligand binding to RNA, a negatively charged polymer, is further complicated by factors such as metal ion effects.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2022)

Article Chemistry, Multidisciplinary

Synthesis and Biological Evaluation of 3-(Pyridine-3-yl)-2-Oxazolidinone Derivatives as Antibacterial Agents

Bo Jin et al.

Summary: A series of 3-(pyridine-3-yl)-2-oxazolidinone derivatives were synthesized and evaluated for antibacterial activity, with some compounds showing strong activity against Gram-positive bacteria. Possible modes of action were predicted through molecular docking. Additionally, some compounds exhibited antibiofilm activity and low drug resistance.

FRONTIERS IN CHEMISTRY (2022)

Article Chemistry, Medicinal

Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch

Elisabeth Kallert et al.

Summary: This study reveals the potential of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to distinguish known binders from decoys. A prospective virtual screening experiment demonstrates the feasibility of this approach.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

Article Biochemistry & Molecular Biology

Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA

Jonathan Dickerhoff et al.

Summary: G-quadruplexes are important secondary structures of nucleic acids, with MycG4 being a commonly studied small-molecule target. The study found that the docking program DOCK 6 with GB/SA rescoring performs better than others, indicating that docking accuracy is mainly limited by scoring functions. Caution should be exercised when using current docking programs to predict G4 DNA-small molecule binding modes.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemical Research Methods

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

Filip Stefaniak et al.

Summary: RNA is a promising target for new small molecule drugs, with computational modeling aiding in the design of active compounds. AnnapuRNA is a knowledge-based scoring function developed to evaluate RNA-ligand complex structures, addressing the inadequacy of existing methods when applied to RNA-ligand systems. Factors such as the ligand's starting conformer, docking program, and scoring function can influence structure prediction.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Chemistry, Medicinal

NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes

Yuyu Feng et al.

Summary: Nucleic acid-ligand interactions play a crucial role in cellular processes, making nucleic acids important drug targets. The developed NLDock algorithm demonstrated superior performance in binding mode predictions and computational efficiency.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Medicinal

Current Landscape and Future Perspective of Oxazolidinone Scaffolds Containing Antibacterial Drugs

Qianqian Zhao et al.

Summary: The widespread use of antibiotics has led to a serious problem of bacterial resistance, making the study of new drug-resistant bacteria the main focus of antibacterial drug research. Oxazolidinone antibacterial drugs, such as linezolid and tedizolid, have good pharmacokinetic and pharmacodynamic characteristics, unique antibacterial mechanisms, and sensitivity to resistant bacteria.

JOURNAL OF MEDICINAL CHEMISTRY (2021)

Article Biochemical Research Methods

Investigation of radezolid interaction with non-canonical chloramphenicol binding site by molecular dynamics simulations

G. Makarov et al.

Summary: Radezolid is a promising antibiotic from the oxazolidinone family that can overcome some linezolid resistance mechanisms in bacterial ribosomes. Through molecular dynamics simulations, it is suggested that Radezolid may bind to an alternative binding site in the ribosome.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2021)

Article Biochemistry & Molecular Biology

A noncanonical binding site of linezolid revealed via molecular dynamics simulations

G. I. Makarov et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)

Article Chemistry, Physical

RNAPosers: Machine Learning Classifiers for Ribonucleic Acid-Ligand Poses

Sahil Chhabra et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Biochemical Research Methods

The HDOCK server for integrated protein-protein docking

Yumeng Yan et al.

NATURE PROTOCOLS (2020)

Article Biochemistry & Molecular Biology

Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors

Eric D. Boittier et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Chemistry, Physical

RLDOCK: A New Method for Predicting RNA-Ligand Interactions

Li-Zhen Sun et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Medicinal

ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions

Yuyu Feng et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM

Alexander Wright et al.

ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE (2020)

Review Biochemistry & Molecular Biology

Machine Learning Methods in Drug Discovery

Lauv Patel et al.

MOLECULES (2020)

Article Chemistry, Medicinal

cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria

Matthew J. Belousoff et al.

CHEMMEDCHEM (2019)

Article Chemistry, Medicinal

Challenges and current status of computational methods for docking small molecules to nucleic acids

Jiaying Luo et al.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2019)

Article Biochemistry & Molecular Biology

HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures

Jiahua He et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic

Alain Scaiola et al.

SCIENTIFIC REPORTS (2019)

Article Chemistry, Medicinal

Synthesis and antibacterial evaluation of novel oxazolidinone derivatives containing a piperidinyl moiety

Yunlei Hou et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2019)

Article Biochemistry & Molecular Biology

SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity

Zhiqiang Yan et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

NPDock: a web server for protein-nucleic acid docking

Irina Tuszynska et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Zohar Eyal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemical Research Methods

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Sergio Ruiz-Carmona et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Determinants of the species selectivity of oxazolidinone antibiotics targeting the large ribosomal subunit

Jagmohan S. Saini et al.

BIOLOGICAL CHEMISTRY (2013)

Article Biochemistry & Molecular Biology

LigandRNA: computational predictor of RNA-ligand interactions

Anna Philips et al.

Review Microbiology

Resistance to Linezolid Caused by Modifications at Its Binding Site on the Ribosome

Katherine S. Long et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2012)

Article Biology

Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?

Harold S. Bernhardt et al.

BIOLOGY DIRECT (2012)

Article Chemistry, Medicinal

Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery

Lu Chen et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Medicinal

Synthesis and Stereospecificity of 4,5-Disubstituted Oxazolidinone Ligands Binding to T-box Riboswitch RNA

Crina M. Orac et al.

JOURNAL OF MEDICINAL CHEMISTRY (2011)

Review Microbiology

How antibiotics kill bacteria: from targets to networks

Michael A. Kohanski et al.

NATURE REVIEWS MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

Revisiting the structures of several antibiotics bound to the bacterial ribosome

David Bulkley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Chemistry, Medicinal

Linezolid Resistance in Staphylococci

Stefania Stefani et al.

PHARMACEUTICALS (2010)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

DOCK 6: Combining techniques to model RNA-small molecule complexes

P. Therese Lang et al.

Article Chemistry, Multidisciplinary

Combining docking with pharmacophore filtering for improved virtual screening

Megan L. Peach et al.

JOURNAL OF CHEMINFORMATICS (2009)

Article Chemistry, Medicinal

Design at the atomic level: Design of biaryloxazolidinones as potent orally active antibiotics

Jiacheng Zhou et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2008)

Article Chemistry, Medicinal

Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit

Joseph A. Ippolito et al.

JOURNAL OF MEDICINAL CHEMISTRY (2008)

Article Biochemical Research Methods

Pharao: Pharmacophore alignment and optimization

Jonatan Taminau et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2008)

Article Multidisciplinary Sciences

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

Daniel N. Wilson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding

Adam W. Barb et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Medicinal

DrugScoreRNA -: Knowledge-based scoring function to predict RNA-ligand interactions

Patrick Pfeffer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Article Biochemistry & Molecular Biology

The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria

Karen L. Leach et al.

MOLECULAR CELL (2007)

Article Chemistry, Medicinal

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0

Christopher R. Corbeil et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Article Chemistry, Medicinal

3D QSAR studies of N-4-arylacryloylpiperazin-1-yl-phenyloxazolidinones:: A novel class of antibacterial agents

BB Lohray et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2006)

Article Pharmacology & Pharmacy

Structure-based drug design meets the ribosome

F Franceschi et al.

BIOCHEMICAL PHARMACOLOGY (2006)

Article Chemistry, Medicinal

Docking of Aminoglycosides to hydrated and flexible RNA

N Moitessier et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

Article Chemistry, Medicinal

Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

RA Friesner et al.

JOURNAL OF MEDICINAL CHEMISTRY (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Review Chemistry, Multidisciplinary

Oxazolidinone structure-activity relationships leading to linezolid

MR Barbachyn et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2003)

Review Chemistry, Multidisciplinary

Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models

PA Kollman et al.

ACCOUNTS OF CHEMICAL RESEARCH (2000)