Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

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dc.contributor.authorPena Neshich, Izabella Agostinho
dc.contributor.authorNishimura, Leticia
dc.contributor.authorMoraes, Fabio Rogerio de [UNESP]
dc.contributor.authorSalim, Jose Augusto
dc.contributor.authorVillalta-Romero, Fabian
dc.contributor.authorBorro, Luiz
dc.contributor.authorYano, Inacio Henrique
dc.contributor.authorMazoni, Ivan
dc.contributor.authorTasic, Ljubica
dc.contributor.authorJardine, Jose Gilberto
dc.contributor.authorNeshich, Goran
dc.contributor.institutionUniversidade Estadual de Campinas (UNICAMP)
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.date.accessioned2018-11-26T15:27:50Z
dc.date.available2018-11-26T15:27:50Z
dc.date.issued2015-01-01
dc.description.abstractThe term agrochemicals is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A drug on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally, we also briefly describe a workflow which might be useful when research requires that model structures of target proteins are firstly generated (starting from genome sequences), followed by identification of ligand-target sites at the surface of those modeled structures, then application of procedures that adequately prepare both protein and ligand structures (the latter also involving filtration that satisfies acceptable adsorption/desorption/metabolism/excretion/toxicity [ADMET] parameters) for virtual high throughput screening (involving docking of ligands to indicated sites) and terminating by ranking of best pairs: target protein with selected ligand.en
dc.description.affiliationUniv Estadual Campinas, Campinas, SP, Brazil
dc.description.affiliationUniv Sao Paulo, IQSC, Sao Carlos, SP, Brazil
dc.description.affiliationUNESP, Sao Jose Do Rio Preto, Brazil
dc.description.affiliationUniv Estadual Campinas, Inst Chem, Dept Organ Chem, Chem Biol Lab, Campinas, SP, Brazil
dc.description.affiliationEmbrapa Agr Informat, Campinas, SP, Brazil
dc.description.affiliationUnespUNESP, Sao Jose Do Rio Preto, Brazil
dc.format.extent701-717
dc.identifierhttp://dx.doi.org/10.2174/1389203716666150505234923
dc.identifier.citationCurrent Protein & Peptide Science. Sharjah: Bentham Science Publ Ltd, v. 16, n. 8, p. 701-717, 2015.
dc.identifier.doi10.2174/1389203716666150505234923
dc.identifier.issn1389-2037
dc.identifier.urihttp://hdl.handle.net/11449/158483
dc.identifier.wosWOS:000360697100004
dc.language.isoeng
dc.publisherBentham Science Publ Ltd
dc.relation.ispartofCurrent Protein & Peptide Science
dc.relation.ispartofsjr0,858
dc.rights.accessRightsAcesso restrito
dc.sourceWeb of Science
dc.subjectProtein-ligand interactions
dc.subjectinteraction nanoenvironment
dc.subjectSTING structure-function descriptors
dc.subjectagrochemicals
dc.subjectligand docking
dc.titleComputational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Designen
dc.typeResenha
dcterms.rightsHolderBentham Science Publ Ltd
unesp.author.orcid0000-0003-2930-7332[9]

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