PMID- 12614151 OWN - NLM STAT- MEDLINE DCOM- 20030616 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 9 DP - 2003 Mar 11 TI - Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds. PG - 2568-77 AB - Nucleoside analogue prodrugs are dependent on efficient intracellular stepwise phosphorylation to their triphosphate form to become therapeutically active. In many cases it is this activation pathway that largely determines the efficacy of the drug. To gain further understanding of the determinants for efficient conversion by the enzyme thymidylate kinase (TMPK) of clinically important thymidine monophosphate analogues to the corresponding diphosphates, we solved the crystal structures of the enzyme, with either ADP or the ATP analogue AppNHp at the phosphoryl donor site, in complex with TMP, AZTMP (previous work), NH2TMP, d4TMP, ddTMP, and FLTMP (this work) at the phosphoryl acceptor site. In conjunction with steady-state kinetic data, our structures shed light on the effect of 3'-substitutions in the nucleoside monophosphate (NMP) sugar moiety on the catalytic rate. We observe a direct correlation between the rate of phosphorylation of an NMP and its ability to induce a closing of the enzyme's phosphate-binding loop (P-loop). Our results show the drastic effects that slight modifications of the substrates exert on the enzyme's conformation and, hence, activity and suggest the type of substitutions that are compatible with efficient phosphorylation by TMPK. FAU - Ostermann, Nils AU - Ostermann N AD - Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany. FAU - Segura-Pena, Dario AU - Segura-Pena D FAU - Meier, Chris AU - Meier C FAU - Veit, Thomas AU - Veit T FAU - Monnerjahn, Christian AU - Monnerjahn C FAU - Konrad, Manfred AU - Konrad M FAU - Lavie, Arnon AU - Lavie A LA - eng SI - PDB/1NMX SI - PDB/1NMY SI - PDB/1NMZ SI - PDB/1NN0 SI - PDB/1NN1 SI - PDB/1NN3 SI - PDB/1NN5 GR - R01-AI46943/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (2',3'-dideoxy-2',3'-didehydrothymidine monophosphate) RN - 0 (Anti-HIV Agents) RN - 0 (Cyclosaligenyl-2',3'-didehydro-2',3'-dideoxythymidine monophosphate) RN - 0 (Dideoxynucleotides) RN - 0 (Macromolecular Substances) RN - 0 (Prodrugs) RN - 0 (Thymine Nucleotides) RN - 365-07-1 (Thymidine Monophosphate) RN - 42214-32-4 (3'-amino-3'-deoxythymidine 5'-monophosphate) RN - BO9LE4QFZF (Stavudine) RN - EC 2.7.4.4 (Nucleoside-Phosphate Kinase) RN - EC 2.7.4.9 (dTMP kinase) RN - VC2W18DGKR (Thymidine) SB - IM MH - Anti-HIV Agents/chemical synthesis/chemistry MH - Crystallography, X-Ray MH - Dideoxynucleotides MH - *Drug Design MH - Humans MH - Kinetics MH - Macromolecular Substances MH - Nucleoside-Phosphate Kinase/*chemistry MH - Prodrugs/chemical synthesis/*chemistry MH - Protein Conformation MH - Stavudine/*analogs & derivatives/chemistry MH - Structure-Activity Relationship MH - Substrate Specificity MH - Thymidine/*analogs & derivatives/chemistry MH - Thymidine Monophosphate/*analogs & derivatives/chemistry MH - Thymine Nucleotides EDAT- 2003/03/05 04:00 MHDA- 2003/06/17 05:00 CRDT- 2003/03/05 04:00 PHST- 2003/03/05 04:00 [pubmed] PHST- 2003/06/17 05:00 [medline] PHST- 2003/03/05 04:00 [entrez] AID - 10.1021/bi027302t [doi] PST - ppublish SO - Biochemistry. 2003 Mar 11;42(9):2568-77. doi: 10.1021/bi027302t.