In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel.

Abstract:

:The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in silico. The appearance of several important hydrogen-bond networks has been discovered, as the addition of negatively charged lipid palmitoyloleoyl phosphatidylglycerol (POPG) and cholesterol reduces membrane fluidity and augments membrane rigidity. A more rigid membrane environment is beneficial to expand the channel, allow more water to enter the channel, promote channel hydration, and then even affect the proton conduction facilitated by the hydrated channel. Thus, membrane environment could be identified as an important influence factor of conformation and hydration of BM2. These findings can provide a unique perspective for understanding the mechanism of membrane lipid composition regulating conformation and hydration of BM2 and have important significance to the further study of anti-influenza virus B drugs.

journal_name

J Chem Inf Model

authors

Zhang Y,Zhang HX,Zheng QC

doi

10.1021/acs.jcim.0c00329

subject

Has Abstract

pub_date

2020-07-27 00:00:00

pages

3603-3615

issue

7

eissn

1549-9596

issn

1549-960X

journal_volume

60

pub_type

杂志文章
  • GalaxyDock: protein-ligand docking with flexible protein side-chains.

    abstract::An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of receptor flexibility using an ensemble of precompiled receptor conformations or by employing an effectively enlarged binding pocket has been reported to be useful. However, direct consideration ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300342z

    authors: Shin WH,Seok C

    更新日期:2012-12-21 00:00:00

  • First Multitarget Chemo-Bioinformatic Model To Enable the Discovery of Antibacterial Peptides against Multiple Gram-Positive Pathogens.

    abstract::Antimicrobial peptides (AMPs) have emerged as promising therapeutic alternatives to fight against the diverse infections caused by different pathogenic microorganisms. In this context, theoretical approaches in bioinformatics have paved the way toward the creation of several in silico models capable of predicting anti...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00630

    authors: Speck-Planche A,Kleandrova VV,Ruso JM,Cordeiro MN

    更新日期:2016-03-28 00:00:00

  • RASA: a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules.

    abstract::In this account, a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules, called RASA (Retrosynthesis-based Assessment of Synthetic Accessibility) is devised. RASA first constructs a synthesis tree for the target molecule based on retrosynthetic analysis; in thi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100216g

    authors: Huang Q,Li LL,Yang SY

    更新日期:2011-10-24 00:00:00

  • Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries.

    abstract::The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200078f

    authors: Li L,Wang B,Meroueh SO

    更新日期:2011-09-26 00:00:00

  • Algorithm for reaction classification.

    abstract::Reaction classification has important applications, and many approaches to classification have been applied. Our own algorithm tests all maximum common substructures (MCS) between all reactant and product molecules in order to find an atom mapping containing the minimum chemical distance (MCD). Recent publications hav...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400442f

    authors: Kraut H,Eiblmaier J,Grethe G,Löw P,Matuszczyk H,Saller H

    更新日期:2013-11-25 00:00:00

  • In silico renal clearance model using classical Volsurf approach.

    abstract::A data set of 130 diverse compounds containing both central nervous system (CNS) and non-CNS drugs was used to generate a renal clearance model using a classical Volsurf approach. Percentage renal clearance data was used as a biological input. The score plots obtained from principal component analysis and partial leas...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503309

    authors: Doddareddy MR,Cho YS,Koh HY,Kim DH,Pae AN

    更新日期:2006-05-01 00:00:00

  • OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.

    abstract::Side-chain modeling is critical for protein structure prediction since the uniqueness of the protein structure is largely determined by its side-chain packing conformation. In this paper, differing from most approaches that rely on rotamer library sampling, we first propose a novel side-chain rotamer prediction method...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00951

    authors: Xu G,Wang Q,Ma J

    更新日期:2020-12-28 00:00:00

  • Development of a computational tool to rival experts in the prediction of sites of metabolism of xenobiotics by p450s.

    abstract::The metabolism of xenobiotics--and more specifically drugs--in the liver is a critical process controlling their half-life. Although there exist experimental methods, which measure the metabolic stability of xenobiotics and identify their metabolites, developing higher throughput predictive methods is an avenue of res...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3003073

    authors: Campagna-Slater V,Pottel J,Therrien E,Cantin LD,Moitessier N

    更新日期:2012-09-24 00:00:00

  • Delineation of agonist binding to the human histamine H4 receptor using mutational analysis, homology modeling, and ab initio calculations.

    abstract::A three-dimensional homology model of the human histamine H 4 receptor was developed to investigate the binding mode of a series of structurally diverse H 4-agonists, i.e. histamine, clozapine, and the recently described selective, nonimidazole agonist VUF 8430. Mutagenesis studies and docking of these ligands in a rh...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700474a

    authors: Jongejan A,Lim HD,Smits RA,de Esch IJ,Haaksma E,Leurs R

    更新日期:2008-07-01 00:00:00

  • An Analysis of Different Components of a High-Throughput Screening Library.

    abstract::Since many projects at pharmaceutical organizations get their start from a high-throughput screening (HTS) campaign, improving the quality of the HTS deck can improve the likelihood of discovering a high-quality lead molecule that can be progressed to a drug candidate. Over the past decade, Janssen has implemented sev...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00258

    authors: Saha A,Varghese T,Liu A,Allen SJ,Mirzadegan T,Hack MD

    更新日期:2018-10-22 00:00:00

  • Combined 3D-QSAR modeling and molecular docking study on indolinone derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1.

    abstract::3-Phosphoinositide-dependent protein kinase-1 (PDK1) is a promising target for developing novel anticancer drugs. In order to understand the structure-activity correlation of indolinone-based PDK1 inhibitors, we have carried out a combined molecular docking and three-dimensional quantitative structure-activity relatio...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800147v

    authors: AbdulHameed MD,Hamza A,Liu J,Zhan CG

    更新日期:2008-09-01 00:00:00

  • Tertiary Element Interaction in HIV-1 TAR.

    abstract::HIV-1 replication requires binding to occur between Trans-activation Response Element (TAR) RNA and the TAT protein. This TAR-TAT binding depends on the conformation of TAR, and therapeutic development has attempted to exploit this dynamic behavior. Here we simulate TAR dynamics in the context of mutations inhibiting ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00152

    authors: Krawczyk K,Sim AY,Knapp B,Deane CM,Minary P

    更新日期:2016-09-26 00:00:00

  • Hidden active information in a random compound library: extraction using a pseudo-structure-activity relationship model.

    abstract::We propose a hypothesis that "a model of active compound can be provided by integrating information of compounds high-ranked by docking simulation of a random compound library". In our hypothesis, the inclusion of true active compounds in the high-ranked compound is not necessary. We regard the high-ranked compounds a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci7003384

    authors: Fukunishi H,Teramoto R,Shimada J

    更新日期:2008-03-01 00:00:00

  • Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions.

    abstract::Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Curren...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00310

    authors: Ashtawy HM,Mahapatra NR

    更新日期:2018-01-22 00:00:00

  • Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein.

    abstract::Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacter...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00702

    authors: Husen P,Nielsen C,Martino CF,Solov'yov IA

    更新日期:2019-11-25 00:00:00

  • Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface.

    abstract::The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemica...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00332

    authors: Sameera WMC,Maseras F

    更新日期:2018-09-24 00:00:00

  • Standardizing and simplifying analysis of peptide library data.

    abstract::Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, w...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300484q

    authors: White AD,Keefe AJ,Nowinski AK,Shao Q,Caldwell K,Jiang S

    更新日期:2013-02-25 00:00:00

  • Identification of ligand templates using local structure alignment for structure-based drug design.

    abstract::With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300178e

    authors: Lee HS,Im W

    更新日期:2012-10-22 00:00:00

  • Rapid evaluation of synthetic and molecular complexity for in silico chemistry.

    abstract::Methods that rapidly evaluate molecular complexity and synthetic feasibility are becoming increasingly important for in silico chemistry. We propose a new metric based on relative atomic electronegativities and bond parameters that evaluate both synthetic and molecular complexity (SMCM) starting from chemical structur...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0501387

    authors: Allu TK,Oprea TI

    更新日期:2005-09-01 00:00:00

  • Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.

    abstract::Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new hete...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00363

    authors: Greene D,Qi R,Nguyen R,Qiu T,Luo R

    更新日期:2019-06-24 00:00:00

  • Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors.

    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

    authors: Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

    更新日期:2014-02-24 00:00:00

  • Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles.

    abstract::Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation proc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00641

    authors: Jafari M,Doustdar F,Mehrnejad F

    更新日期:2019-01-28 00:00:00

  • Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.

    abstract::Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguis...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00057

    authors: Guterres H,Im W

    更新日期:2020-04-27 00:00:00

  • Searching for coordinated activity cliffs using particle swarm optimization.

    abstract::Activity cliffs are formed by structurally similar compounds having large potency differences. Coordinated activity cliffs evolve when compounds within groups of structural neighbors form multiple cliffs with different partners, giving rise to local networks of cliffs in a data set. Using particle swarm optimization, ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3000503

    authors: Namasivayam V,Bajorath J

    更新日期:2012-04-23 00:00:00

  • Drug effect prediction by polypharmacology-based interaction profiling.

    abstract::Most drugs exert their effects via multitarget interactions, as hypothesized by polypharmacology. While these multitarget interactions are responsible for the clinical effect profiles of drugs, current methods have failed to uncover the complex relationships between them. Here, we introduce an approach which is able t...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci2002022

    authors: Simon Z,Peragovics A,Vigh-Smeller M,Csukly G,Tombor L,Yang Z,Zahoránszky-Kohalmi G,Végner L,Jelinek B,Hári P,Hetényi C,Bitter I,Czobor P,Málnási-Csizmadia A

    更新日期:2012-01-23 00:00:00

  • Ligand-based virtual screening approach using a new scoring function.

    abstract::In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200617d

    authors: Hamza A,Wei NN,Zhan CG

    更新日期:2012-04-23 00:00:00

  • Molecular Simulation of αvβ6 Integrin Inhibitors.

    abstract::The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dynamics (MD) simulations of αvβ6 in complex with its natural ligand, pr...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00254

    authors: Guest EE,Oatley SA,Macdonald SJF,Hirst JD

    更新日期:2020-11-23 00:00:00

  • Applicability Domain ANalysis (ADAN): a robust method for assessing the reliability of drug property predictions.

    abstract::We report a novel method called ADAN (Applicability Domain ANalysis) for assessing the reliability of drug property predictions obtained by in silico methods. The assessment provided by ADAN is based on the comparison of the query compound with the training set, using six diverse similarity criteria. For every criteri...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500172z

    authors: Carrió P,Pinto M,Ecker G,Sanz F,Pastor M

    更新日期:2014-05-27 00:00:00

  • Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models.

    abstract::Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are th...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01178

    authors: Gong W,Liu Y,Zhao Y,Wang S,Han Z,Li C

    更新日期:2021-01-26 00:00:00

  • Machine Learning Enhanced Spectrum Recognition Based on Computer Vision (SRCV) for Intelligent NMR Data Extraction.

    abstract::A machine learning enhanced spectrum recognition system called spectrum recognition based on computer vision (SRCV) for data extraction from previously analyzed 13C and 1H NMR spectra has been developed. The intelligent system was designed with four function modules to extract data from three areas of NMR images, incl...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01046

    authors: Jia W,Yang Z,Yang M,Cheng L,Lei Z,Wang X

    更新日期:2021-01-25 00:00:00