Discovery, characterization, and lead optimization of 7-azaindolenon-nucleoside HIV-1 reverse transcriptase inhibitors Open Access

Stanton, Richard Allen (2016)

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Current antiretroviral therapy can effectively manage HIV infections, but often carries unwanted side effects and can select for resistant viral strains. Most pressingly, it cannot cure infected patients. In an effort to identify new drug candidates, a library of 585 compounds built off a novel 7-azaindole core was screened for anti-HIV activity. Ten hits emerged with submicromolar potency and little toxicity. Two of these selected mutations on the viral polymerase reverse transcriptase (RT), in the binding pocket of non-nucleoside reverse transcriptase inhibitors (NNRTI). NNRTI are a class of allosteric inhibitors of RT, five of which have been FDA approved for clinical use. Cell-free assays verified that three of the hit compounds directly inhibited the polymerase activity of RT in a manner consistent with that of other NNRTI. The most promising compound inhibited RT with submicromolar potency (IC50 = 0.73 μM). However, that is still several log fold less than existing NNRTI, necessitating further optimization of this compound. Unfortunately, optimization of NNRTI using rational design approaches remains difficult in spite of the availability of > 150 solved NNRTI-bound RT crystal structures. Because of the diversity of NNRTI, docking results vary largely between receptor structures. To address this problem, more than 40 chemical descriptors were evaluated for their ability to pre-select a best receptor for NNRTI cross-docking. The receptor selection was based on similarity scores between the bound- and target-ligands generated by each descriptor. The top descriptors were able to double the probability of cross-docking accuracy over random receptor selection. Additionally, recall of known NNRTI from a large library of similar decoys was increased using the same approach. Applying that method, the lead 7-azaindole and related analogs were docked and the resultant structures were used as a basis for free energy perturbation (FEP) calculations. FEP was used to explore potential modifications of the lead compound that could increase potency. Of the dozens analyzed, three compounds were chosen for synthesis and testing, one of which displayed a two-fold increase in potency against RT (IC50 = 0.36 μM). These results suggest that further optimization of the 7-azaindole NNRTI may produce more effective anti-HIV agents.

Table of Contents

Chapter 1: Introduction.....1

1.1 Treatment of HIV Infections.....2

1.2 Reverse Transcriptase.....6

1.3 RT-Targeting Compounds.....10

1.4 NNRTI Binding.....13

1.5 NNRTI Mechanisms of Action.....15

1.6 NNRTI Resistance.....22

1.7 Side Effects of NNRTI.....30

1.8 NNRTI and Viral Reservoirs.....32

1.9 Opportunities for NNRTI Development.....32

Chapter 2: Discovery and Characterization of 7-azaindole Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.....34

2.1 Abstract.....35

2.2 Introduction.....35

2.3 Results and Discussion.....38

2.4 Conclusions.....54

2.5 Materials and Methods.....55

Chapter 3: Ligand Similarity Guided Receptor Selection Enhances Docking Accuracy and Recall for Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.....58

3.1 Abstract.....59

3.2 Introduction.....59

3.3 Results and Discussion.....61

3.4 Conclusions.....93

3.5 Methods.....93

Chapter 4: Free Energy Perturbation Guided Lead Optimization of 7-azaindole Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.....98

4.1 Abstract.....99

4.2 Introduction.....99

4.3 Results and Discussion.....100

4.4 Conclusions.....121

4.5 Methods.....122

Chapter 5: Concluding Remarks.....123

5.1 Introduction.....124

5.2 Increasing Potency.....124

5.3 Activity Against Resistant Mutants.....129

5.4 Safety and Tolerability.....134

5.5 Penetration of Viral Reservoirs.....135

5.6 Concluding Statements.....135


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