DNA methyltransferase 1 transition state structure and uses thereof
Methods and systems for obtaining inhibitors of human DNA methyltransferase 1 (DNMT1) are disclosed where the methods involve designing compounds that resemble the DNMT1 transition state.
1. A method of detecting, screening for or designing an inhibitor of human DNA methyltransferase 1 (DNMT1), the method comprising the steps of:
(i) measuring kinetic isotope effects on DNMT1-catalyzed methylation of hemimethylated DNA to obtain the DNMT1 transition state structure,
wherein the DNMT1 transition state comprises the structure
(ii) determining the molecular electrostatic potential at the van der Waals surface computed from a wave function of the DNMT1 transition state and a geometric atomic volume of the DNMT1 transition state;
(iii) obtaining a chemically stable compound that resembles the molecular electrostatic potential at the van der Waals surface computed from the wave function of the DNMT1 transition state and the geometric atomic volume of the DNMT1 transition state; and
(iv) testing the compound for inhibitory activity to DNMT1 by determining if the compound inhibits DNMT1-catalyzed methylation of hemimethylated DNA;
wherein the compound that inhibits DNMT1-catalyzed methylation of hemimethylated DNA is an inhibitor of DNMT1;
thereby detecting, screening for or designing an inhibitor of human DNA methyltransferase 1 (DNMT1).
2. The method of claim 1 , wherein step (i) comprises measuring 14 C and 3 H radiation levels of mononucleosides digested from the DNA after the DNMT1-catalyzed methylation.
3. The method of claim 1 , wherein step (i) comprises measuring 14 C and 3 H labelled and unreacted SAM substrate after the DNMT1-catalyzed methylation.
4. The method of claim 1 , wherein step (i) comprises reacting 14 C—and 3 H-labeled hemimethylated DNA and nonlabeled SAM for the DNMT1-catalyzed methylation.
5. A computer-implemented method performed using a system comprising a non-transitory computer-readable medium coupled to one or more data processing apparatus having instructions stored thereon, the method comprising:
(i) determining a molecular electrostatic potential at the van der Waals surface computed from a wave function of a DNMT1 transition state and a geometric atomic volume of the DNMT1 transition state,
wherein the DNMT1 transition state comprises the structure
(ii) identifying from a library of compounds a chemically stable compound that resembles the molecular electrostatic potential at the van der Waals surface computed from the wave function of the DNMT1 transition state and the geometric atomic volume of the DNMT1 transition state;
wherein the chemically stable compound that resembles the molecular electrostatic potential at the van der Waals surface computed from the wave function of the DNMT1 transition state and the geometric atomic volume of the DNMT1 transition state is a putative inhibitor of DNMT1;
(iii) testing the putative inhibitor for inhibitory activity to DNMT1 by determining if the a putative inhibitor inhibits DNMT1-catalyzed methylation of hemimethylated DNA;
wherein the putative inhibitor that inhibits DNMT1-catalyzed methylation of hemimethylated DNA is an inhibitor of DNMT1.