4.7 Article

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

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 Chemistry, Multidisciplinary

Application of site-identification by ligand competitive saturation in computer-aided drug design

Himanshu Goel et al.

Summary: SILCS utilizes molecular simulation to obtain functional group affinity patterns for drug discovery, allowing for identification of novel ligand binding pockets, prediction of protein-ligand binding affinities, and other applications in computer-aided drug design. It represents a comprehensive approach to improve drug development processes through accuracy and throughput enhancements.

NEW JOURNAL OF CHEMISTRY (2022)

News Item Biotechnology & Applied Microbiology

First small-molecule drug targeting RNA gains momentum

Cormac Sheridan

NATURE BIOTECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Haley M. Wilt et al.

Summary: Effective gene regulation by the tetrahydrofolate riboswitch relies on both ligand affinity and binding kinetics, involving two cooperative binding sites. The crystal structure of the ligand-free THF riboswitch aptamer at 1.9-angstrom resolution reveals structural changes in the absence of ligand, with unwinding of the pseudoknot binding site. The second binding site at the three-way junction remains structurally conserved between apo and holo forms, suggesting a kinetic role in promoting regulatory pseudoknot site formation and ligand binding.

JOURNAL OF STRUCTURAL BIOLOGY (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

Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A

Anderson A. Gomes et al.

Summary: Second-generation ethanol production utilizes agricultural and forestry waste as feedstock, offering a more sustainable alternative to first-generation technology. The success of second-generation biorefineries depends on efficient processes and enzyme cocktails. Research shows that glucose-6-phosphate (G6P) acts as a positive allosteric modulator of Bacillus polymyxa beta-glucosidase A, improving efficiency and providing glucose tolerance.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Multidisciplinary

Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation

Himanshu Goel et al.

Summary: This study utilized SILCS methodology to predict protein-ligand binding affinities on eight target proteins, optimizing atomic free energy contributions using a Bayesian Markov chain Monte Carlo approach to improve prediction accuracy. The results validate the accuracy and computational efficiency of SILCS methodology for lead optimization and drug discovery.

CHEMICAL SCIENCE (2021)

Article Biochemistry & Molecular Biology

PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions

Herschel Mukherjee et al.

ACS CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister ribozyme

Abhishek A. Kognole et al.

Article Chemistry, Physical

RLDOCK: A New Method for Predicting RNA-Ligand Interactions

Li-Zhen Sun et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Review Pharmacology & Pharmacy

RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges

Ai-Ming Yu et al.

PHARMACOLOGICAL REVIEWS (2020)

Article Chemistry, Medicinal

Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations

Mandi Mousaei et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Review Pharmacology & Pharmacy

Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design

Marc O'Reilly et al.

DRUG DISCOVERY TODAY (2019)

Review Chemistry, Multidisciplinary

Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine

Matthew D. Disney

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Chemistry, Medicinal

Optimization and Evaluation of Site-Identification by Ligand Competitive. Saturation (SILCS) as a Tool for Target-Based Ligand Optimization

Vincent D. Ustach et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Multidisciplinary Sciences

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

Hung T. Nguyen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

R-BIND: An Interactive Database for Exploring and Developing RNA Targeted Chemical Probes

Brittany S. Morgan et al.

ACS CHEMICAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb

Matthew D. Shortridge et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Discovery of Selective RNA-Binding Small Molecules by Affinity Selection Mass Spectrometry

Noreen F. Rizvi et al.

ACS CHEMICAL BIOLOGY (2018)

Review Biophysics

Ensemble Docking in Drug Discovery

Rommie E. Amaro et al.

BIOPHYSICAL JOURNAL (2018)

Review Cell Biology

RNA-Targeted Therapeutics

Stanley T. Crooke et al.

CELL METABOLISM (2018)

Article Chemistry, Physical

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

Changsheng Zhang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Biotechnology & Applied Microbiology

Principles for targeting RNA with drug-like small molecules

Katherine Deigan Warner et al.

NATURE REVIEWS DRUG DISCOVERY (2018)

Article Biochemistry & Molecular Biology

Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch

Quentin Vicens et al.

ACS CHEMICAL BIOLOGY (2018)

Editorial Material Biotechnology & Applied Microbiology

Small molecules get the message

Justin Petrone et al.

NATURE BIOTECHNOLOGY (2018)

Article Chemistry, Multidisciplinary

Polarizable force field for RNA based on the classical drude oscillator

Justin A. Lemkul et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)

Article Multidisciplinary Sciences

HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry

Vincent V. Pham et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Physical

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

Asaminew H. Aytenfisu et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

News Item Biotechnology & Applied Microbiology

Small molecules against RNA targets attract big backers

Asher Mullard

NATURE REVIEWS DRUG DISCOVERY (2017)

Review Genetics & Heredity

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome

Ira W. Deveson et al.

TRENDS IN GENETICS (2017)

Article Biochemistry & Molecular Biology

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs

Matthew D. Disney et al.

ACS CHEMICAL BIOLOGY (2016)

Article Multidisciplinary Sciences

Structure of a low-population binding intermediate in protein-RNA recognition

Aditi N. Borkar et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Mathematical & Computational Biology

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Subodh Kumar Mishra et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Chemistry, Multidisciplinary

Characterization of Mg2+ Distributions around RNA in Solution

Justin A. Lemkul et al.

ACS OMEGA (2016)

Review Chemistry, Medicinal

Role of computer-aided drug design in modern drug discovery

Stephani Joy Y. Macalino et al.

ARCHIVES OF PHARMACAL RESEARCH (2015)

Article Biochemistry & Molecular Biology

Targeting Influenza A Virus RNA Promoter

Angel Bottini et al.

CHEMICAL BIOLOGY & DRUG DESIGN (2015)

Article Multidisciplinary Sciences

Selective small-molecule inhibition of an RNA structural element

John A. Howe et al.

NATURE (2015)

Article Chemistry, Multidisciplinary

A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication

Mi-Kyung Lee et al.

CHEMICAL COMMUNICATIONS (2014)

Article Biochemistry & Molecular Biology

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically

Katherine Deigan Warner et al.

CHEMISTRY & BIOLOGY (2014)

Article Biochemistry & Molecular Biology

SMMRNA: a database of small molecule modulators of RNA

Ankita Mehta et al.

NUCLEIC ACIDS RESEARCH (2014)

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)

Review Biochemistry & Molecular Biology

Folding of RNA Tertiary Structure: Linkages Between Backbone Phosphates, Ions, and Water

David E. Draper

BIOPOLYMERS (2013)

Article Chemistry, Medicinal

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

E. Prabhu Raman et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Review Chemistry, Medicinal

Structure-Based DNA-Targeting Strategies with Small Molecule Ligands for Drug Discovery

Jia Sheng et al.

MEDICINAL RESEARCH REVIEWS (2013)

Article Biochemistry & Molecular Biology

LigandRNA: computational predictor of RNA-ligand interactions

Anna Philips et al.

Article Chemistry, Medicinal

Potential and Limitations of Ensemble Docking

Oliver Korb et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Physical

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

Katarina Hart et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Review Biochemistry & Molecular Biology

Natural product DNA major groove binders

Paris L. Hamilton et al.

NATURAL PRODUCT REPORTS (2012)

Article Multidisciplinary Sciences

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

Huimin Chen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches

Sergey M. Dibrov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Chemistry, Multidisciplinary

Impact of 2′-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA

Elizabeth J. Denning et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

A Small-Molecule Probe Induces a Conformation in HIV TAR RNA Capable of Binding Drug-Like Fragments

Amy Davidson et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch

Olga Pikovskaya et al.

NATURE CHEMICAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

Andrew C. Stelzer et al.

NATURE CHEMICAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein

Amy Davidson et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

Lili Huang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Chemistry, Multidisciplinary

CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields

K. Vanommeslaeghe et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)

Article Multidisciplinary Sciences

Inhibitor-induced structural change in the HCV IRES domain IIa RNA

Ryan B. Paulsen et al.

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

Article Multidisciplinary Sciences

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

Alexander Serganov et al.

NATURE (2009)

Article Multidisciplinary Sciences

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein

Amy Davidson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

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

P. Therese Lang et al.

Article Biochemistry & Molecular Biology

Adaptive Ligand Binding by the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs

Sunny D. Gilbert et al.

STRUCTURE (2009)

Article Biochemical Research Methods

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Olgun Guvench et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

Structure of hepatitis C virus IRES subdomain IIa

Qiang Zhao et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2008)

Review Biophysics

RNA folding: Conformational statistics, folding kinetics, and ion electrostatics

Shi-Jie Chen

ANNUAL REVIEW OF BIOPHYSICS (2008)

Article Chemistry, Medicinal

Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets

Christophe Guilbert et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)

Article Chemistry, Multidisciplinary

Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

Sunhwan Jo et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch

Stephane Thore et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

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

HCV and CSFVIRES domain II mediate eIF2 release during 80S ribosome assembly

Nicolas Locker et al.

EMBO JOURNAL (2007)

Article Chemistry, Multidisciplinary

Functional architecture of HCVIRES domain II stabilized by divalent metal ions in the crystal and in solution

Sergey M. Dibrov et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2007)

Article Multidisciplinary Sciences

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

Alexander Serganov et al.

NATURE (2006)

Article Biochemistry & Molecular Biology

TAR RNA recognition by a cyclic peptidomimetic of Tat protein

TC Leeper et al.

BIOCHEMISTRY (2005)

Review Biochemistry & Molecular Biology

Metal ions and RNA folding: a highly charged topic with a dynamic future

SA Woodson

CURRENT OPINION IN CHEMICAL BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

SD Morley et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2004)

Review Biochemistry & Molecular Biology

A guide to ions and RNA structure

DE Draper

Article Biochemistry & Molecular Biology

Structure-based drug design targeting an inactive RNA conformation: Exploiting the flexibility of HIV-1 TAR RNA

AIH Murchie et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic hot spots

B Davis et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Physical

Grand canonical Monte Carlo simulations of water in protein environments

HJ Woo et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biochemistry & Molecular Biology

Structure of HCVIRES domain II determined by NMR

PJ Lukavsky et al.

NATURE STRUCTURAL BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation

AG Vitreschak et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Multidisciplinary Sciences

Structural features of an influenza virus promoter and their implications for viral RNA synthesis

SH Bae et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biochemistry & Molecular Biology

Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

C Faber et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2000)