Calculation of relative binding free energy difference of DHFR inhibitors by a Finite Difference Thermodynamic Integration (FDTI) approach

We have implemented a Finite Difference Thermodynamic Integration (FDTI) ap proach to estimate the binding free energy relative to methotrexate (MTX) o f three unreported inhibitors of DHFR. The validity of the calculation meth odology was first proved by evaluating the relative binding free energy dif ference for two well-known anticancer agents aminopterin and methotrexate. The usefulness of the method in drug design has been demonstrated by the fa ct that inhibitor 5, designed by us was found to bind more tightly than MTX , by as much 7.5 kcal/mole and is a worthy candidate for further pharmacolo gical investigations.