Chemical probes and drug leads from advances in synthetic planning and methodology

Abstract

Screening of small-molecule libraries is a productive method for identifying both chemical probes of disease-related targets and potential starting points for drug discovery. In this article, we focus on strategies such as diversity-oriented synthesis that aim to explore novel areas of chemical space efficiently by populating small-molecule libraries with compounds containing structural features that are typically under-represented in commercially available screening collections. Drawing from more than a decade's worth of examples, we highlight how the design and synthesis of such libraries have been enabled by modern synthetic chemistry, and we illustrate the impact of the resultant chemical probes and drug leads in a wide range of diseases.

Figure 1 |. A selection of compounds generated by diversity-oriented synthesis and related strategies as probes for a wide range of heritable diseases.

Studies that use δ-lactone 9, an activator of neurite growth in multiple classes of murine neurons, may lead to insights into neurological disorders. The pyrimidodiazepine 7, disrupts the leucyl-tRNA synthetase–RagD protein–protein interaction, which may improve our understanding of autophagy, aging, and immunosuppression via control of the mTORC1 signaling pathway.^, The benzannulated sultam 4 modulates lysosome acidification and thus serves as a probe for V-ATPase function, which has been associated with loss of bone density and decreased kidney function, among other conditions.^, Other compounds interact with targets implicated in Alzheimer’s disease (1), holoprosencephaly (2), schizophrenia (3), inflammatory diseases (5), lipid metabolism (6), and coronary artery disease (8). The remaining compounds shown are described in more detail in the vignettes in the main text. Properties relevant to their value as probes are discussed in Box 2.

Figure 2 |. Key transformations along the synthetic routes to selected compounds.

The general strategy of building (or purchasing) chiral building blocks, coupling them together, and cyclizing key linear intermediates via intramolecular transformations has generated a diverse array of chemical structures and biological activities in heritable disease and other areas of medicine. A | Chiral oxizolidinone 10 was functionalized strategically to afford intermediate 11, which subsequently underwent esterification and ring-closing metathesis to afford the Shh probe robotnikinin. B | Similarly, intermediate 13 was prepared from chiral ester 12. S_NAr-based cyclization afforded the benzannulated 8-membered ring (14) at the core of BRD0476, a probe for type-1 diabetes and JAK-STAT signaling. C | Intermediate 16, which was prepared from chiral acid 15 and closely resembles 13, was subjected to macrolactamization conditions to afford 12-membered macrocycle 17 en route to the autophagy probe BRD5631.

Figure 3 |. Chemical probes for cancer targets.

These probes include benzothiophene 18 and indoloquinolizine 20 as tools to study the cytoskeleton, a common cancer target;^, compounds like hydrazide 22 and benzannulated lactam 26 that are highly specific and can discriminate between proteins within the same sub-family; probes discovered via target-based screening that exhibit significant stereochemistry-based SAR, such as 19 and 25; dienone 24, which sensitizes p53-deficient cells to DNA-damaging agents; and probes of ostensibly “undruggable” cancer targets like transcription factors and protein–protein interactions, such as lactam 21 and dihydropyran 23. Other compounds shown are described in more detail in the vignettes in the main text. Properties relevant to their value as probes are discussed in Box 2.

Figure 4 |. Kinase affinity profiling reveals that BRD7880 is significantly more selective than tozasertib.

The KinomeScan assay reveals kinases for which a given small molecule shows significant affinity (compound decreases binding of control by >75%). Aurora kinases A, B, and C are shown in blue; other kinase binding partners are shown in red. Reproduced with permission from REF. .

Figure 5 |. Key transformations along the synthetic routes to selected compounds.

A | In a synthesis that resembles that of BRD0476, chiral oxazolidinone 27 was functionalized strategically to afford intermediate 28, which underwent S_NAr-based cyclization and further elaboration to provide BRD7880, a remarkably selective aurora kinase inhibitor. B | Fully synthetic analogs of rocaglate natural products originated from hydroxyflavone 30. Rohinitib, a probe for HSF1 activity, and other rocaglate derivatives were synthesized via a biomimetic approach, proceeding through key intermediate 31. C | Starting from imine 32, linear intermediate 33 was generated via a diastereo- and enantioselective nitro-Mannich reaction. After cyclization to afford lactam 34, appendage decoration furnished the BRD7/9 inhibitor LP99 as a single stereoisomer. D | The asymmetric synthesis of ABL127, a potent and selective probe of PME-1, was achieved via generation of ketene 36 from carboxylic acid 35, followed by a [2+2] cycloaddition that was rendered enantioselective via a chiral nucleophilic catalyst.

Figure 6 |. Chemical probes and clinical candidates for infectious disease targets.

A library of chiral azetidines originally designed to mimic CNS-active compounds has afforded promising compounds against parasites like Leishmania donovani (the causative agent of visceral leishmaniasis; 45) and Plasmodium falciparum (the causative agent of malaria; 38–39, BRD7929).^,,, Macrocycle 37 (malaria) and benzannulated lactam 42 (Chagas disease) also exhibit antiparasitic activity.^, Target-based and phenotypic screening strategies were used to identify oxazocane 41 and bridged bicyclic 43, which have bactericidal properties.^, The Pictet-Spengler-derived spirocycles 40 and 44 show antimalarial and antiviral activity, respectively.^, Other compounds shown are described in more detail in the vignettes in the main text. Properties relevant to their value as probes are discussed in Box 2.

Figure 7 |. Key transformations along the synthetic routes to selected compounds.

A | One synthetic route to NITD609, a potent nMoA antimalarial, involved an enantioselective aza-Diels–Alder reaction between indole 46 and ketimine 47 to afford spirocycle 48, which is one step from NITD609. B | The synthesis of antimalarial BRD7929 contained two key cyclizations. First, treatment of chloride 50 with strong base supplied azetidine 51. Subsequent functionalization furnished RCM substrate 52, which was cyclized to diazocine 53 en route to BRD7929. C | From aniline 54, imine 55 was an ideal substrate for a diastereo- and enantioselective Povarov reaction. The resulting tetrahydroquinoline 56 was readily converted to BRD0761, which shows nMoA activity against C. difficile. D | Similar to BRD7929, the tuberculosis probe BRD4592 was accessed via a chiral azetidine (59), which in turn was generated from chloride 58 and amino alcohol 57.

Figure 8 |. Stereo view of BRD4592 (cyan) bound at the interface of the α and β subunits of tryptophan synthase.

X-ray crystallography was used to solve the co-crystal structure of BRD4592 and tryptophan synthase. Hydrogen bonds and water molecules shown as dashed lines and red spheres, respectively. Reproduced with permission from REF. .