4.7 Article Data Paper

AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

New potentiators of ineffective antibiotics: Targeting the Gram-negative outer membrane to overcome intrinsic resistance

Kristina Klobucar et al.

Summary: With the rise of antibiotic resistance and the dwindling pipeline of effective antibiotics, it is crucial to find ways to revitalize existing drugs. Perturbing the outer membrane to enhance the susceptibility of Gram-negative bacteria to antibiotics has recently gained increased attention in the field, offering a potential new avenue for combating antibiotic resistance.

CURRENT OPINION IN CHEMICAL BIOLOGY (2022)

Article Multidisciplinary Sciences

QMugs, quantum mechanical properties of drug-like molecules

Clemens Isert et al.

Summary: The QMugs dataset, with over 665k molecules of biological and pharmacological relevance, provides quantum mechanical properties and facilitates development of models for drug discovery and machine learning.

SCIENTIFIC DATA (2022)

Article Microbiology

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Jitender Mehla et al.

Summary: Efflux pump avoidance and inhibition are crucial properties for optimizing antibacterial activities against Gram-negative bacteria. This study identified molecular determinants and predictive models that can help researchers discover and optimize antibacterial agents suitable for treating P. aeruginosa infections. The developed predictive models are based on physicochemical predictors such as molecular shape, amphiphilicity, aromaticity, and partition coefficient, which can be applied to compounds with unrelated chemical scaffolds.
Review Engineering, Chemical

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Outi M. H. Salo-Ahen et al.

Summary: This review provides a comprehensive overview of the current applications of MD in the drug development process, covering target validation, lead discovery, lead optimization, and pharmaceutical formulation development. The importance of MD in providing insights into drug targets, evaluating ligand-receptor interactions, and considering lipid bilayer environments in membrane protein simulations is highlighted. Additionally, the emerging role of MD in studying crystalline and amorphous solids, drug-polymer formulations, drug solubility, and nano-particle simulations is discussed.

PROCESSES (2021)

Review Chemistry, Multidisciplinary

Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors

Helen Zgurskaya et al.

Summary: Antibiotics are effective against infectious bacterial diseases, but antibiotic-resistant bacteria present a challenge to modern medicine. Gram-negative bacteria, with their outer membrane acting as a permeability barrier, rely on active efflux and low permeability to resist antibiotics. Efforts to overcome this resistance include enhancing antibiotic penetration and inhibiting efflux pumps, offering potential for novel therapeutic strategies.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

Review Pharmacology & Pharmacy

Mastering the Gram-negative bacterial barrier ? Chemical approaches to increase bacterial bioavailability of antibiotics q

Henni-Karoliina Ropponen et al.

Summary: The article emphasizes the importance of understanding the uptake, distribution, metabolic, and efflux pathways of antibiotics in Gram-negative bacteria for anti-infective activity and drug discovery. It points out the lack of a sufficiently accurate holistic approach in studying these mechanisms and anticipates that new findings on Gram-negative bacterial bioavailability will guide future research on anti-infectives.

ADVANCED DRUG DELIVERY REVIEWS (2021)

Review Chemistry, Multidisciplinary

Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria

Ilyas Alav et al.

Summary: Tripartite efflux pumps and related type 1 secretion systems in Gram-negative organisms exhibit diverse functions, energization, and structural organization. This review highlights the role of periplasmic adaptor proteins (PAPs) in providing a common architectural scaffold and proposes a new integrated model of PAP-mediated communication within these systems.

CHEMICAL REVIEWS (2021)

Review Biochemistry & Molecular Biology

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

Andrzej Bak

Summary: A key question for computational chemists is the preferred ligand geometry that fits into the receptor pocket, with 4D-QSAR schemes offering higher model abstraction for examining multiple molecular conformations, orientations, and representations. The current interest in this method appears to be experiencing a promising revival.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Chemistry, Medicinal

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields

Joao Morado et al.

Summary: The quality of force field parameterization plays a crucial role in determining the accuracy of observable properties computed from molecular mechanics simulations. ParaMol is a Python package focused on parameterizing bonded and nonbonded terms of druglike molecules by fitting to ab initio data. Through case studies, ParaMol demonstrates the ability to derive near-ideal parameters within the constraints of the functional form, while also discussing best practices and weighting methods for parameterization routes.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Biochemistry & Molecular Biology

Novel 1,2,4-oxadiazole-chalcone/oxime hybrids as potential antibacterial DNA gyrase inhibitors: Design, synthesis, ADMET prediction and molecular docking study

Tarek S. Ibrahim et al.

Summary: New antibacterial drugs are urgently needed to combat the rise in multi-drug resistant bacteria. In this study, a novel series of 1,2,4-oxadiazole-chalcone/oxime compounds were synthesized and evaluated for their in-vitro antimicrobial activity, with some compounds showing potent activity against both Gram-positive and Gram-negative organisms, particularly E. coli. The study also revealed promising DNA gyrase inhibitory activity for specific compounds, which may serve as lead candidates for future antibacterial drug development.

BIOORGANIC CHEMISTRY (2021)

Review Microbiology

Bacterial efflux transporters' polyspecificity-a gift and a curse?

Helen Zgurskaya et al.

Summary: This article reviews the mechanisms underlying the biochemical versatility of RND transporters in reducing intracellular accumulation of toxins and antibiotics. The discussion also touches on the implications of the polyspecificity of RND transporters for bacterial survival and the development of efflux pump inhibitors effective in clinics.

CURRENT OPINION IN MICROBIOLOGY (2021)

Review Biochemistry & Molecular Biology

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds

Samson Olaitan Oselusi et al.

Summary: The increasing antimicrobial resistance highlights the urgent need for novel antimicrobial agents from non-conventional sources. Some natural products have shown promising in vitro activities against multidrug-resistant pathogens.

MOLECULES (2021)

Article Multidisciplinary Sciences

Rational design of a new antibiotic class for drug-resistant infections

Thomas F. Durand-Reville et al.

Summary: The study presents a rational design strategy for developing new antibiotics to combat infections caused by drug-resistant Gram-negative pathogens. The inhibitors are able to overcome multiple mechanisms of resistance and show potential clinical efficacy against superbugs.

NATURE (2021)

Review Chemistry, Multidisciplinary

Towards the sustainable discovery and development of new antibiotics

Marcus Miethke et al.

Summary: There is a growing demand for novel antimicrobials to treat infections caused by multidrug-resistant bacterial pathogens, but there is currently a lack of investment in this field. New agents with innovative chemistry and modes of action are urgently needed to combat the public health threat posed by antimicrobial resistance. The consortium proposes short-term and long-term solutions to overcome urgent limitations in research and funding, aiming to bridge the gap between academic, industrial, and political stakeholders to improve the ability to discover and develop new antibiotics.

NATURE REVIEWS CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge

Nandan Haloi et al.

Summary: The introduction of a primary amine can enhance the permeability of bacterial outer membranes in certain contexts, as shown through molecular dynamics simulations and free energy calculations. The amine facilitates antibiotic permeation by aligning the antibiotic molecule's dipole with the protein channel's electric field and forming favorable electrostatic interactions with specific residues. This study provides insights into the importance of primary amines in antibiotic permeation and offers a new computational approach for calculating free energy in processes where relevant molecular conformations cannot be efficiently captured.

CHEMICAL SCIENCE (2021)

Review Biochemistry & Molecular Biology

A review on machine learning approaches and trends in drug discovery

Paula Carracedo-Reboredo et al.

Summary: In recent years, machine learning techniques have been widely used in drug discovery to improve efficiency and reduce costs. To achieve the goals set by the Precision Medicine initiative, higher requirements have been proposed for the robustness, standardization, and reproducibility of computational methods.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Chemistry, Physical

Molecular insights into the Patched1 drug efflux inhibitory activity of panicein A hydroquinone: a computational study

Sandra Kovachka et al.

Summary: This study identified the first PTCH1 efflux inhibitor through screening of natural compounds and combined different computational techniques to gain insights into its inhibitory activity.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2021)

Article Biochemistry & Molecular Biology

PubChem in 2021: new data content and improved web interfaces

Sunghwan Kim et al.

Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.

NUCLEIC ACIDS RESEARCH (2021)

Review Chemistry, Physical

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age

Wonpil Im et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 71 (2020)

Article Biochemistry & Molecular Biology

A Deep Learning Approach to Antibiotic Discovery

Jonathan M. Stokes et al.

Article Biochemistry & Molecular Biology

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

Mehtap Isik et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)

Review Biotechnology & Applied Microbiology

Rethinking drug design in the artificial intelligence era

Petra Schneider et al.

NATURE REVIEWS DRUG DISCOVERY (2020)

Review Biochemistry & Molecular Biology

The Science of Antibiotic Discovery

Kim Lewis

Review Biochemistry & Molecular Biology

Resistance of Gram-Negative Bacteria to Current Antibacterial Agents and Approaches to Resolve It

Zeinab Breijyeh et al.

MOLECULES (2020)

Editorial Material Chemistry, Medicinal

How to Stimulate and Facilitate Early Stage Antibiotic Discovery

Johannes Zuegg et al.

ACS INFECTIOUS DISEASES (2020)

Article Chemistry, Medicinal

Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict?

Phyo Phyo Kyaw Zin et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates

Carmen Esposito et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Physical

Exploring the Conformational Landscape of Bioactive Small Molecules

Sanja Zivanovic et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Editorial Material Multidisciplinary Sciences

Machine learning for chemical discovery

Alexandre Tkatchenko

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Discovery of Prenyltransferase Inhibitors with In Vitro and In Vivo Antibacterial Activity

Junfeng Song et al.

ACS INFECTIOUS DISEASES (2020)

Article Biochemistry & Molecular Biology

Defining new chemical space for drug penetration into Gram-negative bacteria

Shibin Zhao et al.

NATURE CHEMICAL BIOLOGY (2020)

Review Microbiology

Drug repurposing for antimicrobial discovery

Maya A. Farha et al.

NATURE MICROBIOLOGY (2019)

Review Biochemistry & Molecular Biology

β-Lactamases and β-Lactamase Inhibitors in the 21st Century

Catherine L. Tooke et al.

JOURNAL OF MOLECULAR BIOLOGY (2019)

Review Pharmacology & Pharmacy

4D-quantitative structure-activity relationship modeling: making a comeback

Denis Fourches et al.

EXPERT OPINION ON DRUG DISCOVERY (2019)

Article Multidisciplinary Sciences

The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model

Lucile Moynie et al.

NATURE COMMUNICATIONS (2019)

Review Infectious Diseases

Epidemiology and Mechanisms of Resistance of Extensively Drug Resistant Gram-Negative Bacteria

Emily M. Eichenberger et al.

ANTIBIOTICS-BASEL (2019)

Article Chemistry, Medicinal

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Matteo Rossi Sebastiano et al.

JOURNAL OF MEDICINAL CHEMISTRY (2018)

Review Microbiology

Mobile Genetic Elements Associated with Antimicrobial Resistance

Sally R. Partridge et al.

CLINICAL MICROBIOLOGY REVIEWS (2018)

Article Biochemistry & Molecular Biology

The ChEMBL database in 2017

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Medicinal

Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories

Jeremy Ash et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

Article Multidisciplinary Sciences

Predictive compound accumulation rules yield a broad - spectrum antibiotic

Michelle F. Richter et al.

NATURE (2017)

Article Chemistry, Medicinal

Probabilistic Approach to Generating MPOs and Its Application as a Scoring Function for CNS Drugs

Hakan Gunaydin

ACS MEDICINAL CHEMISTRY LETTERS (2016)

Article Pharmacology & Pharmacy

Solubility, lipophilicity and membrane permeability of some fluoroquinolone antimicrobials

Svetlana V. Blokhina et al.

EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES (2016)

Article Chemistry, Medicinal

MCPB.py: A Python Based Metal Center Parameter Builder

Pengfei Li et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Biochemistry & Molecular Biology

Predicting bioactive conformations and binding modes of macrocycles

Andrew Anighoro et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2016)

Article Mathematics, Interdisciplinary Applications

Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

Giuliano Malloci et al.

COMPUTATION (2016)

Article Chemistry, Medicinal

Cheminformatic comparison of approved drugs from natural product versus synthetic origins

Christopher F. Stratton et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2015)

Article Chemistry, Medicinal

ZINC 15-Ligand Discovery for Everyone

Teague Sterling et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

Article Biochemistry & Molecular Biology

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

Giuliano Malloci et al.

MOLECULES (2015)

Editorial Material Chemistry, Medicinal

Helping Chemists Discover New Antibiotics

Mark A. T. Blaskovich et al.

ACS INFECTIOUS DISEASES (2015)

Article Biochemistry & Molecular Biology

General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

Tony D. Davis et al.

ACS CHEMICAL BIOLOGY (2014)

Review Chemistry, Physical

Molecular Recognition and Ligand Association

Riccardo Baron et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 64 (2013)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Physics, Multidisciplinary

Machine learning of molecular electronic properties in chemical compound space

Gregoire Montavon et al.

NEW JOURNAL OF PHYSICS (2013)

Article Chemistry, Medicinal

Freely Available Conformer Generation Methods: How Good Are They?

Jean-Paul Ebejer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Medicinal

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

K. Vanommeslaeghe et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Multidisciplinary

Open Babel: An open chemical toolbox

Noel M. O'Boyle et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Chemistry, Analytical

Electrochemical Investigation and Determination of the Antibacterial Loracarbef by Voltammetric Methods

Burcu Dogan Topal et al.

ANALYTICAL LETTERS (2009)

Article Computer Science, Interdisciplinary Applications

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Massimiliano Bonomi et al.

COMPUTER PHYSICS COMMUNICATIONS (2009)

Article Biochemistry & Molecular Biology

The role of dynamic conformational ensembles in biomolecular recognition

David D. Boehr et al.

NATURE CHEMICAL BIOLOGY (2009)

Article Chemistry, Medicinal

Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns

Jens Auer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)

Article Chemistry, Physical

Performance of B3LYP density functional methods for a large set of organic molecules

Julian Tirado-Rives et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Multidisciplinary

cclib: A library for package-independent computational chemistry algorithms

Noel M. O'Boyle et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (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, Medicinal

Physicochemical properties of antibacterial compounds: Implications for drug discovery

Rosemarie O'Shea et al.

JOURNAL OF MEDICINAL CHEMISTRY (2008)

Article Microbiology

Rifampin

TUBERCULOSIS (2008)

Article Biochemistry & Molecular Biology

REDDB: A database for RESP and ESP atomic charges, and force field libraries

Francois-Yves Dupradeau et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Chemistry, Analytical

Determination of pKa values of active pharmaceutical ingredients

Sandra Babic et al.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2007)

Review Chemistry, Physical

Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms

Jianyin Shao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Chemistry, Medicinal

Computation of octanol-water partition coefficients by guiding an additive model with knowledge

Tiejun Cheng et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Article Biochemistry & Molecular Biology

Mechanism of the inhibitory effect of zwitterionic drugs (levofloxacin and grepafloxacin) on carnitine transporter (OCTN2) in Caco-2 cells

Takeshi Hirano et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2006)

Article Biochemical Research Methods

Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Article Biochemistry & Molecular Biology

DrugBank: a comprehensive resource for in silico drug discovery and exploration

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2006)

Review Chemistry, Multidisciplinary

Quantum mechanical continuum solvation models

J Tomasi et al.

CHEMICAL REVIEWS (2005)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

An isocratic separation of underivatized gentamicin components, 1H NMR assignment and protonation pattern

W Lesniak et al.

CARBOHYDRATE RESEARCH (2003)

Article Chemistry, Multidisciplinary

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

A Jakalian et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)