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) approach to estimate the binding free energy relative to methotrexate (MTX) of three unreported inhibitors of DHFR. The validity of the calculation methodology was first proved by evaluating the relative binding free energy difference for two well-known anticancer agents aminopterin and methotrexate. The usefulness of the method in drug design has been demonstrated by the fact 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 pharmacological investigations.