Abstract：
:The study of chromatographic retention of natural products can be used to increase their identification speed in complex biological matrices. In this work, six variables were used to study the retention behavior in reversed phase liquid chromatography of 39 sesquiterpene lactones (SL) from an in-house database using chemoinformatics tools. To evaluate the retention of the SL, retention parameters on an ODS C-18 column in two different solvent systems were experimentally obtained, namely, MeOH-H2O 55:45 and MeCN-H2O 35:75. The chemoinformatics approach involved three descriptor type sets (one 2D and two 3D) comprising three groups of each (four, five, and six descriptors), two different training and test sets, four algorithms for variable selection (best first, linear forward, greedy stepwise, and genetic algorithm), and two modeling methods (partial least-squares regression and back-propagation artificial neural network). The influence of the six variables used in this study was assessed in a holistic context, and influences on the best model for each solvent system were analyzed. The best set for MeOH-H2O showed acceptable correlation statistics with training R(2) = 0.91, cross-validation Q(2) = 0.88, and external validation P(2) = 0.80, and the best MeCN-H2O model showed much higher correlation statistics with training R(2) = 0.96, cross-validation Q(2) = 0.92, and external validation P(2) = 0.91. Consensus models were built for each chromatographic system, and although all of them showed an improved statistical performance, only one for the MeCN-H2O system was able to separate isomers as well as to improve the performance. The approach described herein can therefore be used to generate reproducible and robust models for QSRR studies of natural products as well as an aid for dereplication of complex biological matrices using plant metabolomics-based techniques.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Oliveira TB,Gobbo-Neto L,Schmidt TJ,Da Costa FBdoi
10.1021/ci500581qsubject
Has Abstractpub_date
2015-01-26 00:00:00pages
26-38issue
1eissn
1549-9596issn
1549-960Xjournal_volume
55pub_type
杂志文章abstract：:How well do different classification methods perform in selecting the ligands of a protein target out of large compound collections not used to train the model? Support vector machines, random forest, artificial neural networks, k-nearest-neighbor classification with genetic-algorithm-optimized feature selection, tren...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050519k
更新日期：2006-05-01 00:00:00
abstract：:Class II fructose-1,6-bisphosphate aldolases (FBA-II) are attractive new targets for the discovery of drugs to combat invasive fungal infection, because they are absent in animals and higher plants. Although several FBA-II inhibitors have been reported, none of these inhibitors exhibit antifungal effect so far. In thi...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00763
更新日期：2017-06-26 00:00:00
abstract：:In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc molecular dynamics protocols in a novel and task-oriented environment; as a notebook, BiKi (acronym of Binding Kinetics) keeps memory of any activity together with dependencies among...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00680
更新日期：2018-02-26 00:00:00
abstract：:Reversible covalent inhibitors have drawn increasing attention in drug design, as they are likely more potent than noncovalent inhibitors and less toxic than covalent inhibitors. Despite those advantages, the computational prediction of reversible covalent binding presents a formidable challenge because the binding pr...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00959
更新日期：2019-05-28 00:00:00
abstract：:The chronic toxicity is fundamental for toxicological risk assessment, but its correlation with the chemical structures has been studied only little. This is partly due to the complexity of such an experimental test that embraces a plethora of different biological effects and mechanisms of action, making (Q)SAR studie...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci8001974
更新日期：2008-10-01 00:00:00
abstract：:Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coord...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300430v
更新日期：2013-02-25 00:00:00
abstract：:We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published cryst...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050142i
更新日期：2006-07-01 00:00:00
abstract：:Mapping the chemical space of small organic molecules is approached from a theoretical graph theory viewpoint, in an effort to begin the systematic exploration of molecular topologies. We present an algorithm for exhaustive generation of scaffold topologies with up to eight rings and an efficient comparison method for...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci7003412
更新日期：2008-07-01 00:00:00
abstract：:Maltose-binding protein is a periplasmic binding protein responsible for transport of maltooligosaccarides through the periplasmic space of Gram-negative bacteria, as a part of the ABC transport system. The molecular mechanisms of the initial ligand binding and induced large scale motion of the protein's domains still...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci500520q
更新日期：2015-02-23 00:00:00
abstract：:Interfacial hydration strongly influences interactions between biomolecules. For example, drug-target complexes are often stabilized by hydration networks formed between hydrophilic residues and water molecules at the interface. Exhaustive exploration of hydration networks is challenging for experimental as well as th...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.5b00638
更新日期：2016-01-25 00:00:00
abstract：:Protein-protein interactions are central to many biological processes, from intracellular communication to cytoskeleton assembly, and therefore represent an important class of targets for new therapeutics. The most common secondary structure in natural proteins is an α-helix. Small molecules seem to be attractive cand...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci200424a
更新日期：2012-02-27 00:00:00
abstract：:New hits against HIV-1 wild-type and Y181C drug-resistant reverse transcriptases were predicted taking into account the possibility of some of the known metabolism interactions. In silico hits against a set of antitargets (i.e., proteins or nucleic acids that are off-targets from the desired pharmaceutical target obje...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci200203h
更新日期：2011-10-24 00:00:00
abstract：:The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In th...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00148
更新日期：2018-06-25 00:00:00
abstract：:In this study, we have developed a two model system to mimic the active and inactive states of a G-protein coupled receptor specifically the alpha1A adrenergic receptor. We have docked two agonists, epinephrine (phenylamine type) and oxymetazoline (imidazoline type), as well as two antagonists, prazosin and 5-methylur...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci700026v
更新日期：2007-09-01 00:00:00
abstract：:The α2a adrenoceptor is a medically relevant subtype of the G protein-coupled receptor family. Unfortunately, high-throughput techniques aimed at producing novel drug leads for this receptor have been largely unsuccessful because of the complex pharmacology of adrenergic receptors. As such, cutting-edge in silico liga...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c01019
更新日期：2021-01-25 00:00:00
abstract：:Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular a...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b00020
更新日期：2019-02-25 00:00:00
abstract：:The efficiency of automated compound screening is heavily influenced by the design and the quality of the screening libraries used. We recently reported on the assembly of one diverse and one target-focused lead-like screening library. Using data from 15 enzyme-based screenings conducted using these libraries, their p...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300382f
更新日期：2013-03-25 00:00:00
abstract：:Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00235
更新日期：2017-07-24 00:00:00
abstract：:A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci600427x
更新日期：2007-01-01 00:00:00
abstract：:Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its h...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00287
更新日期：2017-11-27 00:00:00
abstract：:Scoring the activity of compounds in phenotypic high-throughput assays presents a unique challenge because of the limited resolution and inherent measurement error of these assays. Techniques that leverage the structural similarity of compounds within an assay can be used to improve the hit-recovery rate from screenin...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050087d
更新日期：2005-11-01 00:00:00
abstract：:Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c00877
更新日期：2020-12-28 00:00:00
abstract：:Thermoplastic polyurethanes (TPUs) are designed using a large variety of basic building blocks but are only synthesized in a limited number of solvent systems. Understanding the behavior of the copolymers in a selected solvent system is of particular interest to tune the intricate balance of microphase separation/mixi...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00781
更新日期：2019-05-28 00:00:00
abstract：:Structure-based computational target prediction methods identify potential targets for a bioactive compound. Methods based on protein-ligand docking so far face many challenges, where the greatest probably is the ranking of true targets in a large data set of protein structures. Currently, no standard data sets for ev...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci500131x
更新日期：2014-08-25 00:00:00
abstract：:The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to char...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci900452z
更新日期：2010-04-26 00:00:00
abstract：:We present a succession of structural changes involved in hormone peptide activation of a prototypical GPCR. Microsecond molecular dynamics simulation generated conformational ensembles reveal propagation of structural changes through key "microswitches" within human AT1R bound to native hormone. The endocrine octa-pe...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00583
更新日期：2019-01-28 00:00:00
abstract：:Cathepsin A is a mammalian lysosomal enzyme that catalyzes the hydrolysis of the carboxy-terminal amino acids of polypeptides and also regulates beta-galactosidase and neuraminidase-1 activities through the formation of a multienzymic complex in lysosomes. Human cathepsin A (hCathA), yeast carboxypeptidase (CPY), and ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci060093p
更新日期：2006-09-01 00:00:00
abstract：:Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explore...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00347
更新日期：2017-09-25 00:00:00
abstract：:Different forms of synaptic plasticity in the cerebellum expressed at the synapses onto Purkinje cells (PCs) are mediated by membrane metabotropic glutamate receptors (mGluRs). There are three main mGluR groups with a total of 8 subtypes. Although mGluRs are also found at the climbing fiber (CF) to PC synapses, the di...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050161s
更新日期：2005-11-01 00:00:00
abstract：:The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci400644r
更新日期：2014-02-24 00:00:00
