Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Pharmaceutical Sciences

Research Advisor

John K. Buolamwini, Ph.D.


Isaac O. Donkor, Ph.D. Richard E. Lee, Ph.D. Duane D. Miller, Ph.D. Abby L. Parrill, Ph.D.


HIV-1 integrase (IN) is essential for viral replication and offers a promising target for the development of anti-retroviral drugs. Two decades of extensive research has lead to the recent approval of raltegravir as the first IN inhibitor. Advancement of drug candidate elvitegravir, which is currently in Phase III clinical trial, has furthermore accelerated efforts against this potential target for combating HIV. However, the emergence of resistance against raltegravir and elvitegravir demands exploration of novel chemical scaffolds that could circumvent resistance against currently used HIV-1 IN inhibitors. With the goal of discovering new agents targeting HIV, a novel structural class of HIV-IN inhibitors have been designed and synthesized. Substantial computational studies were also performed that could aid the design and development of potent HIV IN inhibitors. A part of this dissertation research, covered in Chapter 3, details the design, synthesis, and biological evaluation of 3-keto salicylic acid chalcones as novel HIV-1 IN inhibitors. In the chalcone series, the most active compound, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichloro-phenyl)- acryloyl]-2-hydroxybenzoic acid (96) was selectively active against IN strand transfer (ST) with IC50 of 3.7 µM. While most of the compounds exhibit ST selectivity, a few were nonselective, such as 5-bromo-3-[3-(4-bromo-phenyl)-acryloyl]-2-hydroxybenzoic acid (86), which was active against both 3!-processing (3!-P) and ST with IC50 values of 11 ± 4 and 5 ± 2 "M, respectively. The compounds also inhibited HIV-1 replication with potencies comparable to their integrase inhibitory activities. Thus, compounds 96 and 86 inhibited HIV-1 replication with EC50 values of 7.3 and 8.7 "M, respectively. Chapter 4 describes the synthesis of structurally related amide derivatives which were designed by modification of the chalcone moiety. In the amide series, the most active compound, 5-bromo-3-[(3-chloro-2,4-difluoro benzyl)- carbamoyl]-2-hydroxybenzoic acid (151), inhibited ST with an IC50 of 4 µM. Chapter 5 discloses the synthesis, and biological studies of halogenated phenanthrene #-diketo acids as novel HIV-1 IN inhibitors. The two most active compounds of the series, 4-(8-chlorophenanthren-3-yl)-2,4-dioxobutanoic acid (179) and 4-(6-chlorophenanthren-2-yl)-2,4-dioxobutanoic acid (177) had ST IC50 values of 1.2 and 1.3 "M, respectively, and corresponding 3!-P values of 11.0 and 5.0 "M. In the last section of the dissertation detailed in Chapter 6, computational studies were conducted with the aim of exploring the possible binding modes of potent IN inhibitors and evaluating the structural requirements for IN inhibition. To determine the physicochemical parameters important for ligand binding, in the first part of this chapter, a PHASE pharmacophore hypothesis was developed and used for molecular alignments in the initial comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) 3D-quantitative structure activity relationship (3D-QSAR) modeling of the chalcone derivatives. A recent breakthrough in the field of anti-HIV research was achieved with the crystallization and 3D structure determination of a complete foamy virus IN-DNA complex. To take advantage of the power of structure-based drug design, in the second part of the computational studies, homology models of HIV-1 IN-DNA were constructed based on the foamy virus IN-DNA complex X-ray crystal structure as template through collaboration with the Oak Ridge National Laboratory. The binding modes of raltegravir and elvitegravir in our homology models were in accordance with their binding modes in their complexes with the foamy virus structure. The homology model was then used for docking and 3D-QSAR studies on our synthesized inhibitors and other integrase inhibitors including the clinically available raltegravir and elvitegravir. Free energy calculations using Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) methods were carried out to rescore and validate the binding modes of HIV-1 integrase inhibitors. 3D-QSAR models derived from this study provided detailed insights into the structural requirements for IN inhibition and established predictive tools to guide further inhibitor design. Linear interaction energy (LIE) calculations were also performed to derive energy parameters contributing to the binding free energies of the IN inhibitors in the data set. These energy parameters were also analyzed to gain insight into the binding modes of raltegravir and elvitegravir as well as to validate the conformations of our synthesized chalcone and amide derivatives. The energy terms were then used as descriptors to develop a linear interaction approximation (LIA) activity model for the inhibition of integration catalytic step. In the next section of the chapter, lead optimization was attempted using structure- and ligand-based drug design tools. RACHEL, a drug optimization software, was used to design an inhibitor with desired binding interactions with the IN active site residues. The hit obtained from RACHEL was used to design a structurally related compound (157), the synthesis and activity testing of which has been described in Chapter 4. Docking studies were also performed on the phenanthrene derivatives synthesized in Chapter 5. The docking studies predominantly revealed two binding poses that were distinct from the possible binding modes of clinically used raltegravir and advanced IN inhibitor elvitegravir and, moreover, do not interact significantly with some of the key amino acids (Q148 and N155) implicated in viral resistance. Therefore, this series of compounds can further be investigated as IN inhibitors to circumvent resistance associated with current clinically used HIV-1 IN inhibitors.