The emergence of multi-drug resistance and failure of HAART therapy, which targets primarily the RT and PR, to eliminate HIV from patient demand inhibition of other steps essential for viral survival and replication. In this regard, HIV-1 IN, which is crucial enzyme for viral replication, has emerged as a promising target for the
development of anti-retroviral drugs.
Although highly promising IN inhibitors have been developed, raltegravir is the only IN inhibitor approved by the FDA. Emergence of resistance against raltegravir and the clinically advanced drug candidate, elvitegravir necessitates the development of novel scaffolds targeting IN. In this study, covered in Chapter 3, a novel series of 3-keto
salicylic acid chalcones with diverse structural features were synthesized and biologically evaluated as promising integrase inhibitors. Few analogs of the series showed good activities against ST in in vitro enzymatic assay and were also equally potent against HIV-1 replication in cell cultures.
In Chapter 4, the chalcone scaffold was modified to a structurally related amide to synthesize a new series of compounds. A vast majority of potent IN inhibitors, including raltegravir, have an amide functionality which gives a conformationally favorable orientation to the halo benzyl group present in these compounds. In this study, 10 new amide analogs were synthesized and evaluated as HIV-1 integrase inhibitors. A couple of amide derivatives showed good in vitro potencies against ST step and displayed moderate anti-viral activities in cell cultures. These compounds hold promise for further
optimization to obtain more potent HIV-1 IN inhibitors. In the search of novel scaffolds for integrase inhibition, some structurally diverse compounds containing metal chelating atoms were also synthesized and tested for IN inhibitory activity.
ȕ-Diketo acid analogs were the first representative compounds that entered clinical trials. Previously, our laboratory has reported 5(H)-phenanthridin-6-one diketo acid as a new class of HIV-1 integrase inhibitors. In Chapter 5, 10 analogs of this series having electron withdrawing groups on the phenanthrene ring were synthesized and tested as HIV-1 integrase inhibitors. Most of the analogs showed good in vitro ST and 3ƍ-P activities and selected compounds when tested for their antiviral activity, showed moderate inhibition of HIV-1 replication. Modeling studies, described in Chapter 6, suggest that these compounds could be investigated against viral mutants resistant to currently available IN inhibitors.
Computational Studies on HIV-1 Integrase Inhibitors
Despite two decades of tremendous effort leading to promising IN inhibitors their binding modes, until recently, remained elusive. The absence of a complete DNA-bound
crystal structure has presented significant challenge to the structure-based design of IN inhibitors. Although X-ray structures of individual human HIV domains and their combinations have been reported, the absence of a 3D structure of HIV-1 IN and viral DNA along with the two-divalent metals in the active site make the structural information hitherto available limited and far from reality. To address this limitation, a homology model of HIV-1 integrase in complex with the viral DNA was constructed, by our collaborators at the Oak Ridge National Laboratory. The homology model was built based on the recently reported crystal structure of the foamy virus IN-DNA complex (PDB 3L2T and 3L2U).
In Chapter 6, a detailed computational study was undertaken to elucidate the binding modes of approved IN inhibitor raltegravir, elvitegravir, and our synthesized IN inhibitors. To determine the stereo-electronic features important for ligand binding, in the absence of a crystal structure of a full-length HIV-1 IN-DNA complex, a ligand-based approach was first employed. A PHASE pharmacophore model of the synthesized chalcone and amide derivatives was developed to determine their bio-active
conformations which were then used for deriving 3D-QSAR CoMFA and CoMSIA models. The resulting QSAR models had limited predictive ability probably because of the narrow range of activities of compounds in the dataset. Next, with the goal of developing a statistically significant and predictive model capable of estimating potent compounds, a comprehensive 3D-QSAR CoMFA and CoMSIA study was undertaken. A data set of 103 compounds including our synthesized chalcone and structurally related amide IN inhibitors, raltegravir and elvitegravir and their analogs reported in literature were used for the 3D-QSAR study. Atom-fit alignments and MM-GBSA validated docking-based conformations were used for the 3D-QSAR modeling. This study has yielded statistically significant models that could be further optimized to predict the activities of novel related HIV-1 IN inhibitors. Binding free energies of the inhibitors were also derived using the Linear Interaction Approximation (LIA) calculations, and the energy parameters were then used for building a LIA QSAR model. The resulting energy contributions were also studied to gain insights into the binding modes of raltegravir and elvitegravir and to validate the binding conformations of our synthesized IN inhibitors. Another objective of the computational studies was to use structure-based design to rationally guide the synthesis of potential 3-ketosalicylic acid amides IN inhibitors. RACHEL, a drug optimization module was used to design compounds with an aim of having desired interaction with the enzyme. Finally, to determine the binding modes of our synthesized phenanthrene derivatives, docking studies were performed and their poses evaluated.
CHAPTER 3. SYNTHESIS AND BIOLOGICAL EVALUATION OF 3-KETO