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.

Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications.

Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR-145. Manually verifying reagent identities in 36 recent miR-145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR-145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non-verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803, and MGC-823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities.

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 Aß 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.

Tricyclic heterocycles display diverse sensitivity to the A147T TSPO polymorphism.

The 18 kDa translocator protein (TSPO) is a target for the development of imaging agents to detect neuroinflammation. The clinical utility of second-generation TSPO ligands has been hindered by the presence of a polymorphism, rs6971, which causes a non-conservative substitution of alanine for threonine at amino acid residue 147 (TSPO A147T). Given the complex nature of TSPO binding, and the lack of non-discriminating high-affinity ligands at both wild type and A147T forms of TSPO, a series of novel TSPO ligands containing various heterocyclic scaffolds was developed to explore the pharmacophoric drivers of affinity loss at TSPO A147T. In general, N-benzyl-N-methyl-substituted amide ligands showed increased affinity at TSPO A147T, and a pyrazolopyrimidine acetamide containing this motif displayed low nanomolar binding affinities to both TSPO forms.

An overview of late-stage functionalization in today's drug discovery.

Introduction: Late-stage functionalization (LSF) can introduce important chemical groups in the very last steps of the synthesis. LSF has the potential to speed up the preparation of novel chemical entities and diverse chemical libraries and have a major impact on drug discovery. Functional group tolerance and mild conditions allows access to new molecules not easily accessible by conventional approaches without the need for laborious de novo chemical synthesis. Areas Covered: A historical overview of late-stage functionalization and its applicability to drug discovery is provided. Pioneering methodologies that laid the foundations for the field are briefly covered and archetypal examples of their application to drug discovery are discussed. Novel methodologies reported in the past few years mainly stemming from the recent renaissances of photoredox catalysis and radical chemistry are reviewed and their application to drug discovery considered. Expert opinion: It is envisioned that late-stage functionalization will improve the efficiency and efficacy of drug discovery. There is evidence of the widespread uptake of LSF by the medicinal chemistry community and it is expected that the recent and continuing endeavors of many academic laboratories and pharmaceutical companies will soon have an impact on drug development.

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.

Braiding a molecular knot with eight crossings.

Knots may ultimately prove just as versatile and useful at the nanoscale as at the macroscale. However, the lack of synthetic routes to all but the simplest molecular knots currently prevents systematic investigation of the influence of knotting at the molecular level. We found that it is possible to assemble four building blocks into three braided ligand strands. Octahedral iron(II) ions control the relative positions of the three strands at each crossing point in a circular triple helicate, while structural constraints on the ligands determine the braiding connections. This approach enables two-step assembly of a molecular 819 knot featuring eight nonalternating crossings in a 192-atom closed loop ~20 nanometers in length. The resolved metal-free 819 knot enantiomers have pronounced features in their circular dichroism spectra resulting solely from topological chirality.

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.