Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors

Abstract

Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (<300 Da) screened using primarily biophysical assays. FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs.

Targeting HIV-1 Reverse Transcriptase Using a Fragment-Based Approach

“…Table 1 shows RT inhibition and SPR dissociation constants for Series 1. The hit compound B-1 for the NNRTI Adjacent site was found to have a lower potency when tested in the DNA-dependent DNA polymerase (DDDP) activity assay used in this study compared to data from Bauman et al which used an assay that detects inhibition of both DNA polymerase and RNase H activity [ 6 ]. Substitution at some sites on the pyridine greatly reduced inhibition.…”

“…Binding efficiency can be quantified by the ligand efficiency (LE) metric [ 21 ]. LE is the free energy of binding of a ligand (ΔG) divided by the number of non-hydrogen (heavy) atoms (N) where ΔG is calculated using the equation ΔG = −RTlnK i [ 6 ]. Using the RT inhibition (IC 50 ), LE can be calculated using the equation LE = −1.4(logIC 50 )/N [ 22 ].…”

“…One relatively recent approach to discovering new druggable sites and compounds is fragment-based drug discovery (FBDD). FBDD aims to develop small molecule drugs with good pharmaceutical properties starting with chemical building blocks of drugs that are subsequently elaborated into larger more potent inhibitors [ 5 , 6 ]. In FBDD, libraries of low molecular weight chemical compounds, typically 300 Da or less, are screened using biophysical methods for binding to the protein target, with the notion that smaller molecules can make efficient binding interactions [ 7 ].…”

Molecular dissection of an inhibitor targeting the HIV integrase dependent preintegration complex nuclear import

“…Mapping the residues that showed significant (>0.02 ppm) perturbation from the Apo (unbound) IN spectra, onto the crystal structure of the IN core domain (Figure b, blue residues) highlighted the ability of budesonide to perturb residues mapping to and around an α‐helix located directly adjacent to the Impα/β1‐recognised NLS of IN (Figure b, core residues highlighted in pink), which is located directly adjacent to the binding site on IN for the critical host‐cell co‐factor LEDGF/p75 (lens epithelial derived growth factor; Berthoux, Sebastian, Muesing, & Luban, ; Hou et al, ; Latham, la, Tinetti, Chalmers, & Tachedjian, ; Peat, Dolezal, Newman, Mobley, & Deadman, ); residue 186 of the NLS is also known to contribute to IN multimerisation (Berthoux et al, ). Similarly, mifepristone impacted residues adjacent to the NLS on the opposite side of IN to budesonide, including those within a pocket known to be highly active for compound binding in fragment‐based drug discovery trials (the IN fragment binding pocket; see Latham et al, ; Peat et al, ; Wielens et al, ). These results clearly indicate direct binding of both budesonide and mifepristone to different sites on IN, both of which would appear to impact NLS‐recognition by Impα/β1.…”

Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example

“…Interestingly, this strategy has been largely applied in discovering several classes of pharmacological ligands, including enzyme inhibitors, receptor antagonists and, more recently, also allosteric (positive and negative) modulators [ 2 , 3 , 4 , 5 ]. In particular, allosteric modulation of G protein-coupled receptors (GPCRs) has stimulated an intensive campaign to identify new classes of hit-candidates different from conventional agonists and antagonists, in particular considering the breakthroughs coming from GPCR crystallographic determination that has resulted in a fast-growing number of structures obtained as complexes with allosteric modulators.…”