当前位置： SCI文献检索 > Journal of Chemical Information and Modeling期刊下所有文献 > Novel inhibitors of trihydroxynaphthalene reductase with antifungal activity identified by ligand-based and structure-based virtual screening.

Novel inhibitors of trihydroxynaphthalene reductase with antifungal activity identified by ligand-based and structure-based virtual screening.

Abstract：

:Curvularia lunata is a dark pigmented fungus that is the causative agent of several diseases in plants and in both immunodeficient and immunocompetent patients. 1,8-Dihydroxynaphthalene-melanin is found in the cell wall of C. lunata and is believed to be the important virulence factor of dematiaceous fungi. Trihydroxynaphthalene reductase is an enzyme of the 1,8-dihydroxynaphthalene-melanin biosynthetic pathway, and it thus represents an emerging target for the development of novel fungicides and antimycotics. In the present study, we describe novel inhibitors of trihydroxynaphthalene reductase from C. lunata. These inhibitors were identified by ligand-based three-dimensional similarity searching and docking to a homology-built model and by subsequent biochemical and antifungal evaluation. Discovery of competitive inhibitors with K(i) values in low micromolar and even nanomolar concentration range proves the aplicability of homology-built model of 3HNR for hit finding by virtual screening methods.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Brunskole Svegelj M,Turk S,Brus B,Lanisnik Rizner T,Stojan J,Gobec S

doi

10.1021/ci2001499

subject

Has Abstract

pub_date

2011-07-25 00:00:00

pages

1716-24

issue

7

eissn

1549-9596

issn

1549-960X

journal_volume

51

pub_type

杂志文章

相关文献

Journal of Chemical Information and Modeling文献大全
  • Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

    abstract：:Peptides that bind to ion channels have attracted much interest as potential lead molecules for the development of new drugs and insecticides. However, the structure determination of large peptide-channel complexes using experimental methods is challenging. Thus structural models are often derived from combining exper...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00529

    authors： Deplazes E,Davies J,Bonvin AM,King GF,Mark AE

    更新日期：2016-01-25 00:00:00

  • The molecular basis for the selectivity of tadalafil toward phosphodiesterase 5 and 6: a modeling study.

    abstract：:Great attention has been paid to the clinical significance of phosphodiesterase 5 (PDE5) inhibitors, such as sildenafil, tadalafil, and vardenafil widely used for erectile dysfunction. However, sildenafil causes side effects on visual functions since it shows similar potencies to inhibit PDE5 and PDE6, whereas tadalaf...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400458z

    authors： Huang YY,Li Z,Cai YH,Feng LJ,Wu Y,Li X,Luo HB

    更新日期：2013-11-25 00:00:00

  • Reaction site mapping of xenobiotic biotransformations.

    abstract：:Predictive metabolism methods can be used in drug discovery projects to enhance the understanding of structure-metabolism relationships. The present study uses data mining methods to exploit biotransformation data that have been recorded in the MDL Metabolite database. Reacting center fingerprints were derived from a ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci600376q

    authors： Boyer S,Arnby CH,Carlsson L,Smith J,Stein V,Glen RC

    更新日期：2007-03-01 00:00:00

  • Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization.

    abstract：:Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00063

    authors： Xu L,Shan S,Chen Y,Wang X,Nussinov R,Ma B

    更新日期：2015-06-22 00:00:00

  • Consensus QSAR models: do the benefits outweigh the complexity?

    abstract：:This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci700016d

    authors： Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

    更新日期：2007-07-01 00:00:00

  • Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators.

    abstract：:Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but h...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00624

    authors： Lautala S,Provenzani R,Koivuniemi A,Kulig W,Talman V,Róg T,Tuominen RK,Yli-Kauhaluoma J,Bunker A

    更新日期：2020-11-23 00:00:00

  • Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.

    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

    authors： Aldeghi M,Bodkin MJ,Knapp S,Biggin PC

    更新日期：2017-09-25 00:00:00

  • Improved Computation of Protein-Protein Relative Binding Energies with the Nwat-MMGBSA Method.

    abstract：:A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00196

    authors： Maffucci I,Contini A

    更新日期：2016-09-26 00:00:00

  • GESSE: Predicting Drug Side Effects from Drug-Target Relationships.

    abstract：:The in silico prediction of unwanted side effects (SEs) caused by the promiscuous behavior of drugs and their targets is highly relevant to the pharmaceutical industry. Considerable effort is now being put into computational and experimental screening of several suspected off-target proteins in the hope that SEs might...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00120

    authors： Pérez-Nueno VI,Souchet M,Karaboga AS,Ritchie DW

    更新日期：2015-09-28 00:00:00

  • Discovery of New SIRT2 Inhibitors by Utilizing a Consensus Docking/Scoring Strategy and Structure-Activity Relationship Analysis.

    abstract：:SIRT2, which is a NAD+ (nicotinamide adenine dinucleotide) dependent deacetylase, has been demonstrated to play an important role in the occurrence and development of a variety of diseases such as cancer, ischemia-reperfusion, and neurodegenerative diseases. Small molecule inhibitors of SIRT2 are thought to be potenti...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00714

    authors： Huang S,Song C,Wang X,Zhang G,Wang Y,Jiang X,Sun Q,Huang L,Xiang R,Hu Y,Li L,Yang S

    更新日期：2017-04-24 00:00:00

  • Critical Assessment of the Hildebrand and Hansen Solubility Parameters for Polymers.

    abstract：:Solubility parameter models are widely used to select suitable solvents/nonsolvents for polymers in a variety of processing and engineering applications. In this study, we focus on two well-established models, namely, the Hildebrand and Hansen solubility parameter models. Both models are built on the basis of the noti...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00656

    authors： Venkatram S,Kim C,Chandrasekaran A,Ramprasad R

    更新日期：2019-10-28 00:00:00

  • Sharing Data from Molecular Simulations.

    abstract：:Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00665

    authors： Abraham M,Apostolov R,Barnoud J,Bauer P,Blau C,Bonvin AMJJ,Chavent M,Chodera J,Čondić-Jurkić K,Delemotte L,Grubmüller H,Howard RJ,Jordan EJ,Lindahl E,Ollila OHS,Selent J,Smith DGA,Stansfeld PJ,Tiemann JKS,Trellet M

    更新日期：2019-10-28 00:00:00

  • Residue preference mapping of ligand fragments in the Protein Data Bank.

    abstract：:The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables u...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci100386y

    authors： Wang L,Xie Z,Wipf P,Xie XQ

    更新日期：2011-04-25 00:00:00

  • Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents.

    abstract：:Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a co...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00985

    authors： Shahraki A,Işbilir A,Dogan B,Lohse MJ,Durdagi S,Birgul-Iyison N

    更新日期：2021-01-21 00:00:00

  • TAMkin: a versatile package for vibrational analysis and chemical kinetics.

    abstract：:TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci100099g

    authors： Ghysels A,Verstraelen T,Hemelsoet K,Waroquier M,Van Speybroeck V

    更新日期：2010-09-27 00:00:00

  • Growth of ligand-target interaction data in ChEMBL is associated with increasing and activity measurement-dependent compound promiscuity.

    abstract：:Compounds with high-confidence target annotations and activity measurements in the original and current release of the ChEMBL database have been compared to better understand how the growth of compound activity data might influence the spectrum of ligand-target interactions and the degree of target promiscuity among a...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci3003304

    authors： Hu Y,Bajorath J

    更新日期：2012-10-22 00:00:00

  • QSAR Modeling of ToxCast Assays Relevant to the Molecular Initiating Events of AOPs Leading to Hepatic Steatosis.

    abstract：:Nonalcoholic hepatic steatosis is a worldwide epidemiological concern since it is among the most prominent hepatic diseases. Indeed, research in toxicology and epidemiology has gathered evidence that exposure to endocrine disruptors can perturb cellular homeostasis and cause this disease. Therefore, assessing the like...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00297

    authors： Gadaleta D,Manganelli S,Roncaglioni A,Toma C,Benfenati E,Mombelli E

    更新日期：2018-08-27 00:00:00

  • A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling.

    abstract：:FFAR4 has been considered as a potential target for metabolic diseases, including diabetes. Some compounds with biphenyl scaffold, represented by compound SR13 reported by our group, showed significant FFAR4 selectivity. However, the molecular basis for their selectivity has not been definitely disclosed. This study p...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00735

    authors： Zhang X,Sun H,Wen X,Yuan H

    更新日期：2019-10-28 00:00:00

  • Conformational determinants of the activity of antiproliferative factor glycopeptide.

    abstract：:The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400147s

    authors： Mallajosyula SS,Adams KM,Barchi JJ,MacKerell AD

    更新日期：2013-05-24 00:00:00

  • Scores of extended connectivity fingerprint as descriptors in QSPR study of melting point and aqueous solubility.

    abstract：:QSPR studies, using scores of SciTegic's extended connectivity fingerprint as raw descriptors, were extended to the prediction of melting points and aqueous solubility of organic compounds. Robust partial least-squares models were developed that perform as well as the best published QSPR models for structurally divers...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800024c

    authors： Zhou D,Alelyunas Y,Liu R

    更新日期：2008-05-01 00:00:00

  • Computational and conformational evaluation of FTase alternative substrates: insight into a novel enzyme binding pocket.

    abstract：:Protein farnesyltransferase (FTase) is an important anticancer drug target. In an effort to develop isoprenoid diphosphate-based FTase inhibitors, striking variations have been observed in the ability of conservatively modified analogues to bind to the enzyme. For example, 2Z-GGPP is an alternative substrate with high...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0496550

    authors： Henriksen BS,Zahn TJ,Evanseck JD,Firestine SM,Gibbs RA

    更新日期：2005-07-01 00:00:00

  • COSMOsar3D: molecular field analysis based on local COSMO σ-profiles.

    abstract：:The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have be...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300231t

    authors： Klamt A,Thormann M,Wichmann K,Tosco P

    更新日期：2012-08-27 00:00:00

  • Comparative analysis of binding energy of chymostatin with human cathepsin A and its homologous proteins by molecular orbital calculation.

    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

    authors： Yoshida T,Lepp Z,Kadota Y,Satoh Y,Itoh K,Chuman H

    更新日期：2006-09-01 00:00:00

  • Virtual drug screen schema based on multiview similarity integration and ranking aggregation.

    abstract：:The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci200481c

    authors： Kang H,Sheng Z,Zhu R,Huang Q,Liu Q,Cao Z

    更新日期：2012-03-26 00:00:00

  • Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes.

    abstract：:We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of mo...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.6b00493

    authors： Serafeim AP,Salamanos G,Patapati KK,Glykos NM

    更新日期：2016-10-24 00:00:00

  • Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case.

    abstract：:In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifica...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800313h

    authors： Yasuo K,Yamaotsu N,Gouda H,Tsujishita H,Hirono S

    更新日期：2009-04-01 00:00:00

  • FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space.

    abstract：:An essential feature of all practical de novo molecule generating programs is the ability to focus the potential combinatorial explosion of grown molecules on a desired chemical space. It is a daunting task to balance the generation of new molecules with limitations on growth that produce desired features such as stab...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci9000458

    authors： Kutchukian PS,Lou D,Shakhnovich EI

    更新日期：2009-07-01 00:00:00

  • Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways.

    abstract：:The roles of chemical compounds in biological systems are now systematically analyzed by high-throughput experimental technologies. To automate the processing and interpretation of large-scale data it is necessary to develop bioinformatics methods to extract information from the chemical structures of these small mole...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci700006f

    authors： Oh M,Yamada T,Hattori M,Goto S,Kanehisa M

    更新日期：2007-07-01 00:00:00

  • Evaluation of different virtual screening programs for docking in a charged binding pocket.

    abstract：:Virtual screening of small molecules against a protein target often identifies the correct pose, but the ranking in terms of binding energy remains a difficult problem, resulting in unacceptable numbers of false positives and negatives. To investigate this problem, the performance of three docking programs, FRED, QXP/...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800154w

    authors： Deng W,Verlinde CL

    更新日期：2008-10-01 00:00:00

  • Improving classical substructure-based virtual screening to handle extrapolation challenges.

    abstract：:Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for extrapolation, that is, for detecting molecules that are very different from those used for training. Herein, we evaluate the predictive power of...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci200472s

    authors： Biniashvili T,Schreiber E,Kliger Y

    更新日期：2012-03-26 00:00:00