Table of Contents:
Today, 34 million people worldwide are infected with the human immunodeficiency virus (HIV), which is the causative agent of the acquired immunodeficiency syndrome (AIDS). The development of numerous antiretroviral drugs, 26 of which are currently approved for treatment of HIV infection, has led to a substantial progress in the combat against HIV and AIDS. However, the development of resistance and the strong adverse effects of the marketed drugs still pose a challenge to drug research.
HIV protease is a viral enzyme essential for the replication of HIV and thus constitutes an important target for antiretroviral drugs. Currently, 10 HIV protease inhibitors are available on the market. To solve the steadily increasing problems of resistance and adverse effects of these approved inhibitors, intense academic as well as industrial research efforts are required to further pursue the search for novel, improved HIV protease inhibitors.
Since HIV protease represents with over 600 structures deposited in the PDB (Protein Data Bank) one of the crystallographically best studied enzymes with medical relevance, structure-based drug design is a promising tool to find new HIV protease inhibitors.
The aim of this thesis was to develop novel HIV protease inhibitors in an iterative process of structure-based design, synthesis, and affinity determination. The most promising compounds were additionally selected for a cytoprotection assay.
In addition to the Ki-value, the ligand efficiency was used to assess the synthesised inhibitors, since this measure allows a good comparability of entities of different molecular weight. For a drug-like compound, the desired value for the ligand efficiency is -0.29 kcal/mol, which corresponds to a 10 nM inhibitor with a molecular weight of around 500 g/mol.
Starting from the potent but relatively large HIV protease inhibitor AB111, smaller inhibitors with improved ligand efficiency were to be designed, synthesized, and tested for their enzyme affinity within the present thesis.
The first approach was to synthesize pyrrolidine-based inhibitors equipped with three substituents addressing the protease’s specificity pockets. These inhibitors address the catalytic dyad of the protease with two protonable amino functions. Through optimisation, the ligand efficiency could be improved compared to the starting compound of this series; however, the best compound with a Ki of 0.9 µM displayed only a moderate enzyme affinity.
Additionally, the SAR of this compound class proved to be non-additive and could also not be predicted in docking experiments.
In a second approach, pyrrolidino-oxalamides were developed, which possess a rigid core to address the catalytic dyad as well as the flap region of the enzyme and turned out to be a much more efficient scaffold.
Even though the inhibitors of the first series only address two of the four specificity pockets, they show largely improved ligand efficiencies, with the best compound displaying a value of -0.27 kcal/mol. These promising results are probably mainly due to the rigid core of the novel scaffold, which most likely leads to an advantageous entropic contribution to the binding affinity.
The following optimization cycle resulted in bicyclic inhibitors decorated with three or four substituents addressing the remaining specificity pockets of HIV protease. Three of the synthesized compounds reached or exceeded the target value of -0.29 kcal/mol for the ligand efficiency, displaying a molecular weight under 500 g/mol and a Ki in the low nM range thus depicting the desired properties for a putative drug.
Unfortunately, these potent bicyclic compounds displayed no cellular activity. Therefore a prodrug approach was utilized to improve the apparently low cell permeability. Carbamate prodrugs of the pyrrolidine-based bicyclic compounds were synthesized, hence lacking the positively charged nitrogen, which were therefore supposed to better penetrate cell membranes. The carbamates were then envisaged to be cleaved by intracellular esterases to reestablish the active free amino functionality.
The cellularly most active compound of the present thesis represents a methylcarbamate prodrug of a bis-benzhydryl-substituted bicyclic inhibitor with a cell activity of 42 % at 10 µM.