title: Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.
abstract: Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.
authors.affiliation: Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Luis Fernando Saraiva Macedo
authors.initials: LF
authors.lastname: Timmers
authors.forename: Rafael Andrade
authors.initials: RA
authors.lastname: Caceres
authors.forename: Ana Luiza
authors.initials: AL
authors.lastname: Vivan
authors.forename: Lisandra Marques
authors.initials: LM
authors.lastname: Gava
authors.forename: Raquel
authors.initials: R
authors.lastname: Dias
authors.forename: Rodrigo Gay
authors.initials: RG
authors.lastname: Ducati
authors.forename: Luiz Augusto
authors.initials: LA
authors.lastname: Basso
authors.forename: Diogenes Santiago
authors.initials: DS
authors.lastname: Santos
authors.forename: Walter Filgueira
authors.initials: WF
authors.lastname: de Azevedo
mesh_terms: D001051:Apoenzymes / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D004795:Enzyme Stability; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011683:Purine-Nucleoside Phosphorylase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D052999:Quinazolinones / Q000737:chemistry / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D015203:Reproducibility of Results; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship; D017356:Synchrotrons; D017186:Titrimetry; D014961:X-Ray Diffraction
chemical_list: C533051:2-mercapto-4(3H)-quinazolinone; D001051:Apoenzymes; D008024:Ligands; D052999:Quinazolinones; D011994:Recombinant Proteins; D011683:Purine-Nucleoside Phosphorylase