Molecular modelling studies on the interactions of human DNA topoisomerase IB with pyridoxal-compounds.
Candida guilliermondii and human DNA topoisomerases I are inhibited by PL (pyridoxal), PLP (pyridoxal 5'-phosphate) and PLP-AMP (pyridoxal 5'-diphospho-5'-adenosine) (PL<PLP<PLP-AMP). We have recently shown that PLP acted as a competitive inhibitor of C. guilliermondii topoisomerase I, impeding the formation of the cleavable complex from a selective binding to an active site lysine. The targeted lysine in C. guilliermondii topoisomerase I occupies a position equivalent to that of lysine 532 (K(532)) in human topoisomerase I. K(532) acts as a general acid catalyst and is essential for the enzyme activity. This observation has suggested that, in the cell, PLP could down-regulate topoisomerases IB. We have proposed that PLP could be used as a new lead for anticancer drugs trapping the active site lysine (K(532)) and also as a tool to explore the enzyme dynamics required for catalysis. Now we explore the effects of PL, PLP and PLP-AMP on topoisomerases by a molecular modelling approach using the crystal structure of the human topoisomerase I active site and the conformation of K(39)-PLP moiety in Bacillus subtilis alanine racemase as templates. In the modified topoisomerase I several reactive atoms of the K(532)-PLP moiety are at close distance of the catalytic residues R(488), R(590), H(632) and Y(723,) suggesting that PLP develops disturbing interactions with these important residues. These interactions and the corresponding induced fit in the active site conformation are compared with the ones occurring with PL and PLP-AMP. The results could be useful in the search of topoisomerase I inhibitors related to the pyridoxal family.
Christmann-Franck
Serge
S
Département de Biologie et Pharmacologie Structurales, CNRS UMR 8113, Institut Gustave Roussy et ENS Cachan, 61 Avenue du Président Wilson, 94235 Cachan Cedex, France.
Fermandjian
Serge
S
Mirambeau
Gilles
G
Der Garabedian
P Arsène
PA
D001665:Binding Sites; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D011730:Pyridoxal / Q000378:metabolism*
D011730:Pyridoxal; D004264:DNA Topoisomerases, Type I