Structure-Based Drug Design for TSPO: Challenges and Opportunities

The translocator protein 18 kDa (TSPO) is an evolutionarily conserved mitochondrial transmembrane protein implicated in various neuropathologies and inflammatory conditions, making it a longstanding diagnostic and therapeutic target of interest. Despite the development of various classes of TSPO ligand chemotypes, and the elucidation of bacterial and non-human mammalian experimental structures, many unknowns exist surrounding its differential structural and functional features in health and disease. There are several limitations associated with currently used computational methodologies for modelling the native structure and ligand-binding behaviour of this enigmatic protein. In this perspective, we provide a critical analysis of the developments in the uses of these methods, outlining their uses, inherent limitations, and continuing challenges. We offer suggestions of unexplored opportunities that exist in the use of computational methodologies which offer promise for enhancing our understanding of the TSPO.

Glial reactivity in a mouse model of beta-amyloid deposition assessed by PET imaging of P2X7 receptor and TSPO using [11C]SMW139 and [18F]F-DPA

BACKGROUND

P2X7 receptor has emerged as a potentially superior PET imaging marker to TSPO, the gold standard for imaging glial reactivity. [11C]SMW139 is the most recently developed radiotracer to image P2X7 receptor. The aim of this study was to image reactive glia in the APP/PS1-21 transgenic (TG) mouse model of Aβ deposition longitudinally using [11C]SMW139 targeting P2X7 receptor and to compare tracer uptake to that of [18F]F-DPA targeting TSPO at the final imaging time point. TG and wild type (WT) mice underwent longitudinal in vivo PET imaging using [11C]SMW139 at 5, 8, 11, and 14 months, followed by [18F]F-DPA PET scan only at 14 months. In vivo imaging results were verified by ex vivo brain autoradiography, immunohistochemical staining, and analysis of [11C]SMW139 unmetabolized fraction in TG and WT mice.

RESULTS

Longitudinal change in [11C]SMW139 standardized uptake values (SUVs) showed no statistically significant increase in the neocortex and hippocampus of TG or WT mice, which was consistent with findings from ex vivo brain autoradiography. Significantly higher [18F]F-DPA SUVs were observed in brain regions of TG compared to WT mice. Quantified P2X7-positive staining in the cortex and thalamus of TG mice showed a minor increase in receptor expression with ageing, while TSPO-positive staining in the same regions showed a more robust increase in expression in TG mice as they aged. [11C]SMW139 was rapidly metabolized in mice, with 33% of unmetabolized fraction in plasma and 29% in brain homogenates 30 min after injection.

CONCLUSIONS

[11C]SMW139, which has a lower affinity for the rodent P2X7 receptor than the human version of the receptor, was unable to image the low expression of P2X7 receptor in the APP/PS1-21 mouse model. Additionally, the rapid metabolism of [11C]SMW139 in mice and the presence of several brain-penetrating radiometabolites significantly impacted the analysis of in vivo PET signal of the tracer. Finally, [18F]F-DPA targeting TSPO was more suitable for imaging reactive glia and neuroinflammatory processes in the APP/PS1-21 mouse model, based on the findings presented in this study and previous studies with this mouse model.

Late-stage Functionalization for Improving Drug-like Molecular Properties

The development of late-stage functionalization (LSF) methodologies, particularly C-H functionalization, has revolutionized the field of organic synthesis. Over the past decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, allowing for the drug discovery process to become more efficient. Most reported applications of late-stage C-H functionalization of drugs and drug-like molecules have been to rapidly diversify screening libraries to explore structure-activity relationships. However, there has been a growing trend toward the use of LSF methodologies as an efficient tool for improving drug-like molecular properties of promising drug candidates. In this review, we have comprehensively reviewed recent progress in this emerging area. Particular emphasis is placed on case studies where multiple LSF techniques were implemented to generate a library of novel analogues with improved drug-like properties. We have critically analyzed the current scope of LSF strategies to improve drug-like properties and commented on how we believe LSF can transform drug discovery in the future. Overall, we aim to provide a comprehensive survey of LSF techniques as tools for efficiently improving drug-like molecular properties, anticipating its continued uptake in drug discovery programs.

An update on late-stage functionalization in today's drug discovery

INTRODUCTION

Late-stage functionalization (LSF) allows for the introduction of new chemical groups toward the end of a synthetic sequence, which means new molecules can be rapidly accessed without laborious de novo chemical synthesis. Over the last decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, affording benefits such as efficient access to diverse libraries to explore structure-activity relationships and the improvement of physicochemical and pharmacokinetic properties.

AREAS COVERED

An overview of the key advancements in LSF methodology development from 2019 to 2022 and their applicability to drug discovery is provided. In addition, several examples from both academia and industry where LSF methodologies have been applied by medicinal chemists to their drug discovery programs are presented.

EXPERT OPINION

Utilization of LSF by medicinal chemists is on the rise, both in academia and in industry. The maturation of the LSF field to produce methodologies bearing increased regioselectivity, scope, and functional group tolerance is envisaged to narrow the gap between methodology development and medicinal chemistry research. The authors predict that the sheer versatility of these techniques in facilitating challenging chemical transformations of bioactive molecules will continue to increase the efficiency of the drug discovery process.

Understanding In Vitro Pathways to Drug Discovery for TDP-43 Proteinopathies

The use of cellular models is a common means to investigate the potency of therapeutics in pre-clinical drug discovery. However, there is currently no consensus on which model most accurately replicates key aspects of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) pathology, such as accumulation of insoluble, cytoplasmic transactive response DNA-binding protein (TDP-43) and the formation of insoluble stress granules. Given this, we characterised two TDP-43 proteinopathy cellular models that were based on different aetiologies of disease. The first was a sodium arsenite-induced chronic oxidative stress model and the second expressed a disease-relevant TDP-43 mutation (TDP-43 M337V). The sodium arsenite model displayed most aspects of TDP-43, stress granule and ubiquitin pathology seen in human ALS/FTD donor tissue, whereas the mutant cell line only modelled some aspects. When these two cellular models were exposed to small molecule chemical probes, different effects were observed across the two models. For example, a previously disclosed sulfonamide compound decreased cytoplasmic TDP-43 and increased soluble levels of stress granule marker TIA-1 in the cellular stress model without impacting these levels in the mutant cell line. This study highlights the challenges of using cellular models in lead development during drug discovery for ALS and FTD and reinforces the need to perform assessments of novel therapeutics across a variety of cell lines and aetiological models.

Recent Scaffold Hopping Applications in Central Nervous System Drug Discovery

The concept of bioisosterism and the implementation of bioisosteric replacement is fundamental to medicinal chemistry. The exploration of bioisosteres is often used to probe key structural features of candidate pharmacophores and enhance pharmacokinetic properties. As the understanding of bioisosterism has evolved, capabilities to undertake more ambitious bioisosteric replacements have emerged. Scaffold hopping is a broadly used term in the literature referring to a variety of different bioisosteric replacement strategies, ranging from simple heterocyclic replacements to topological structural overhauls. In this work, we have highlighted recent applications of scaffold hopping in the central nervous system drug discovery space. While we have highlighted the benefits of using scaffold hopping approaches in central nervous system drug discovery, these are also widely applicable to other medicinal chemistry fields. We also recommend a shift toward the use of more refined and meaningful terminology within the realm of scaffold hopping.

Strategies for targeting the P2Y12 receptor in the central nervous system

The purinergic 2Y type 12 receptor (P2Y₁₂R) is a well-known biological target for anti-thrombotic drugs due to its role in platelet aggregation and blood clotting. While the importance of the P2Y₁₂R in the periphery has been known for decades, much less is known about its expression and roles in the central nervous system (CNS), where it is expressed exclusively on microglia - the first responders to brain insults and neurodegeneration. Several seminal studies have shown that P2Y₁₂ is a robust, translatable biomarker for anti-inflammatory and neuroprotective microglial phenotypes in models of degenerative diseases such as multiple sclerosis and Alzheimer's disease. An enduring problem for studying this receptor in vivo, however, is the lack of selective, high-affinity small molecule ligands that can bypass the blood-brain barrier and accumulate in the CNS. In this Digest, we discuss previous attempts by researchers to target the P2Y₁₂R in the CNS and opine on strategies that may be employed to design and assess the suitability of novel P2Y₁₂ ligands for this purpose going forward.

A molecular endless (74) knot

Current strategies for the synthesis of molecular knots focus on twisting, folding and/or threading molecular building blocks. Here we report that Zn(II) or Fe(II) ions can be used to weave ligand strands to form a woven 3 × 3 molecular grid. We found that the process requires tetrafluoroborate anions to template the assembly of the interwoven grid by binding within the square cavities formed between the metal-coordinated criss-crossed ligands. The strand ends of the grid can subsequently be joined through within-grid alkene metathesis reactions to form a topologically trivial macrocycle (unknot), a doubly interlocked [2]catenane (Solomon link) and a knot with seven crossings in a 258-atom-long closed loop. This 7₄ knot topology corresponds to that of an endless knot, which is a basic motif of Celtic interlace, the smallest Chinese knot and one of the eight auspicious symbols of Buddhism and Hinduism. The weaving of molecular strands within a discrete layer by anion-template metal-ion coordination opens the way for the synthesis of other molecular knot topologies and to woven polymer materials.

Adventures in Translocation: Studies of the Translocator Protein (TSPO) 18 kDa

The 18 kDa translocator protein (TSPO) is an evolutionarily conserved transmembrane protein found embedded in the outer mitochondrial membrane. A secondary target for the benzodiazepine diazepam, TSPO has been a protein of interest for researchers for decades, particularly owing to its well-established links to inflammatory conditions in the central and peripheral nervous systems. It has become a key biomarker for assessing microglial activation using positron emission tomography (PET) imaging in patients with diseases ranging from atherosclerosis to Alzheimer’s disease. This Account describes research published by our group over the past 15 years surrounding the development of TSPO ligands and their use in probing the function of this high-value target.

O-GlcNAc Modification Protects against Protein Misfolding and Aggregation in Neurodegenerative Disease

Post-translational modifications (PTMs) of proteins are becoming the focus of intense research due to their implications in a broad spectrum of neurodegenerative diseases. Various PTMs have been identified to alter the toxic profiles of proteins which play critical roles in disease etiology. In Alzheimer's disease (AD), dysregulated phosphorylation is reported to promote pathogenic processing of the microtubule-associated tau protein. Among the PTMs, the enzymatic addition of N-acetyl-d-glucosamine (GlcNAc) residues to Ser/Thr residues is reported to deliver protective effects against the pathogenic processing of both amyloid precursor protein (APP) and tau. Modification of tau with as few as one single O-GlcNAc residue inhibits its toxic self-assembly. This modification also has the same effect on the assembly of the Parkinson's disease (PD) associated α-synuclein (ASyn) protein. In fact, O-GlcNAcylation ( O-linked GlcNAc modification) affects the processing of numerous proteins implicated in AD, PD, amyotrophic lateral sclerosis (ALS), and Huntington's disease (HD) in a similar manner. As such, manipulation of a protein's O-GlcNAcylation status has been proposed to offer therapeutic routes toward addressing multiple neurodegenerative pathologies. Here we review the various effects that O-GlcNAc modification, and its modulated expression, have on pathogenically significant proteins involved in neurodegenerative disease.

A Six-Crossing Doubly Interlocked [2]Catenane with Twisted Rings, and a Molecular Granny Knot

A molecular 6 2 3 link (a six crossing, doubly interlocked, [2]catenane with twisted rings) and a 31 #31 granny knot (a composite knot made up of two trefoil tangles of the same handedness) were constructed by ring-closing olefin metathesis of an iron(II)-coordinated 2×2 interwoven grid. The connections were directed by pendant phenyl groups to be between proximal ligand ends on the same faces of the grid. The 6 2 3 link was separated from the topoisomeric granny knot by recycling size-exclusion chromatography. The identity of each topoisomer was determined by tandem mass spectrometry and the structure of the 6 2 3 link confirmed by X-ray crystallography, which revealed two 82-membered macrocycles, each in figure-of-eight conformations, linked through both pairs of loops.

N@a and N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces

The α-helical coiled coil is one of the best-studied protein-protein interaction motifs. As a result, sequence-to-structure relationships are available for the prediction of natural coiled-coil sequences and the de novo design of new ones. However, coiled coils adopt a wide range of oligomeric states and topologies, and our understanding of the specification of these and the discrimination between them remains incomplete. Gaps in our knowledge assume more importance as coiled coils are used increasingly to construct biomimetic systems of higher complexity; for this, coiled-coil components need to be robust, orthogonal, and transferable between contexts. Here, we explore how the polar side chain asparagine (Asn, N) is tolerated within otherwise hydrophobic helix-helix interfaces of coiled coils. The long-held view is that Asn placed at certain sites of the coiled-coil sequence repeat selects one oligomer state over others, which is rationalized by the ability of the side chain to make hydrogen bonds, or interactions with chelated ions within the coiled-coil interior of the favored state. We test this with experiments on de novo peptide sequences traditionally considered as directing parallel dimers and trimers, and more widely through bioinformatics analysis of natural coiled-coil sequences and structures. We find that when located centrally, rather than near the termini of such coiled-coil sequences, Asn does exert the anticipated oligomer-specifying influence. However, outside of these bounds, Asn is observed less frequently in the natural sequences, and the synthetic peptides are hyperthermostable and lose oligomer-state specificity. These findings highlight that not all regions of coiled-coil repeat sequences are equivalent, and that care is needed when designing coiled-coil interfaces.

Triply Threaded [4]Rotaxanes

[4]Rotaxanes featuring three axles threaded through a single ring have been prepared through active metal template synthesis. Nickel-catalyzed sp(3)-sp(3) homocouplings of alkyl bromide "half-threads" through 37- and 38-membered 2,2':6',2″-terpyridyl macrocycles generate triply threaded [4]rotaxanes in up to 11% yield. An analogous 39-membered macrocycle produced no rotaxane products under similar conditions. The constitutions of the [4]rotaxanes were determined by NMR spectroscopy and mass spectrometry. Doubly threaded [3]rotaxanes were also obtained from the reactions but no [2]rotaxanes were isolated, suggesting that upon demetalation the axle of a singly threaded rotaxane can slip through a macrocycle that is sufficiently large to accommodate three threads.

A Solomon link through an interwoven molecular grid

A molecular Solomon link was synthesized through the assembly of an interwoven molecular grid consisting of four bis(benzimidazolepyridyl)benzthiazolo[5,4-d]thiazole ligands and four zinc(II), iron(II), or cobalt(II) cations, followed by ring-closing olefin metathesis. NMR spectroscopy, mass spectrometry, and X-ray crystallography confirmed the doubly interlocked topology, and subsequent demetalation afforded the wholly organic Solomon link. The synthesis, in which each metal ion defines the crossing point of two ligand strands, suggests that interwoven molecular grids should be useful scaffolds for the rational construction of other topologically complex structures.