Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.
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.
Timmers
Luis Fernando Saraiva Macedo
LF
Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
Caceres
Rafael Andrade
RA
Vivan
Ana Luiza
AL
Gava
Lisandra Marques
LM
Dias
Raquel
R
Ducati
Rodrigo Gay
RG
Basso
Luiz Augusto
LA
Santos
Diogenes Santiago
DS
de Azevedo
Walter Filgueira
WF
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
C533051:2-mercapto-4(3H)-quinazolinone; D001051:Apoenzymes; D008024:Ligands; D052999:Quinazolinones; D011994:Recombinant Proteins; D011683:Purine-Nucleoside Phosphorylase