Date of Award


Document Type

On-Campus Dissertation

Degree Name

Doctor of Philosophy (PhD)


Pharmaceutical Sciences

Research Advisor

Duane D. Miller


Bob M. Moore II Dominic M. Desiderio Richard W. Kriwacki James T. Dalton


androgen receptor, non-steroidal, homology modeling, molecular dynamics, SAR, drug design, nuclear receptor, OWFEG, AMBER, free energy perturbation, docking, flutamide, casodex


Ligands for the androgen receptor (AR), androgens and antiandrogens alike, have therapeutic value in the treatment of various androgen-dependent conditions, from regulation of male fertility to prostate cancer. Nonsteroidal AR ligands have advantages over their steroidal counterparts with respect to specificity, tolerability, and pharmacokinetic attributes. The purpose of the work described herein was to initiate and integrate a structure-based approach toward the goal of the development of novel nonsteroidal AR ligands.

We developed homology models of the human AR ligand-binding domain (LBD) in the agonist- and antagonist-bound forms. These models of the AR were based on the crystal structure of the human progesterone receptor LBD bound to progesterone, or the estrogen receptor LBD bound to raloxifene, respectively. The initial homology-modeled LBDs were refined using the new approach of multiple molecular dynamics simulations (MMDS). Key H-bonding partners with the 17-hydroxy group and 3-keto group of testosterone are Asn705 and Thr877; and Gln711 and Arg752, respectively. These models also show the presence of a unique unoccupied sub-pocket within the AR binding pocket that may be valuable in the development of novel selective AR modulators. We show that the MMDS approach to homology model refinement offers advantages over minimal energy-based methods.

The binding modes of several hydroxyflutamide-like nonsteroidal ligands for the AR were investigated. These nonsteroidal ligands were docked into one of our AR models with FlexX, followed by refinement of the initial AR-ligand complexes with molecular dynamics simulations. Asn705 is indicated as an important determinant in binding hydroxyflutamide and its derivatives by participating in H-bonding with the £\-hydroxyl moiety within these ligands. In addition, the nitro functionality mimics the 3-keto group of the testosterone and is involved in H-bonding interactions with Gln711 and Arg752. We were able to rationalize the observed SAR for a broad set of hydroxyflutamide derivatives based on these AR-ligand complexes. The hAR LBD agonist-bound model and the thermodynamic integration method was used to calculate the relative binding free-energies between hydroxyflutamide and two high affinity ligands synthesized in our laboratories. The calculated relative binding free-energies for one of these ligand pairs was calculated correctly, whereas the relative binding free-energies for the other ligand pairs was not calculated correctly, due to problems with sampling conformational space.

Toward the goal of structure-based design of AR ligands, the OWFEG approximate freeenergy method was used to design several novel AR ligands. The OWFEG method was successful at predicting where new atoms could be added to the parent compound; all ligands designed using the OWFEG contours displayed higher affinity for the AR than the parent compound.

Finally, a traditional medicinal chemistry approach was applied to the search for metabolically stable nonsteroidal AR ligands based on bicaluatmide. The majority of these ligands displayed a high affinity for the AR; however, no clear structure activity relationships could be ascertained. We docked these ligands in the ligand-binding site of one of the agonistbound AR models to try to gain insights to the rank order of binding for this series of compounds.