A Fluorogenic Disaccharide Substrate for α-Mannosidases Enables High-Throughput Screening and Identification of an Inhibitor of the GH92 Virulence Factor from Streptococcus pneumoniae.

Trimming of host glycans is a mechanism that is broadly employed by both commensal and pathogenic microflora to enable colonization. Host glycan trimming by the opportunistic Gram-positive bacterium Streptococcus pneumoniae has been demonstrated to be an important mechanism of virulence. While S. pneumoniae employs a multitude of glycan processing enzymes, the exo-mannosidase SpGH92 has been shown to be an important virulence factor. Accordingly, SpGH92 is hypothesized to be a target for much-needed new treatments of S. pneumoniae infection. Here we report the synthesis of 4-methylumbelliferyl α-d-mannopyranosyl-(1→2)-ß-d-mannopyranoside (Manα1,2Manß-4MU) as a fluorogenic disaccharide substrate and development of an assay for SpGH92 that overcomes its requirement for +1 binding site occupancy. We miniaturize our in vitro assay and apply it to a high-throughput screen of >65 000 compounds, identifying a single inhibitory chemotype, LIPS-343. We further show that Manα1,2Manß-4MU is also a substrate of the human Golgi-localized α-mannosidase MAN1A1, suggesting that this substrate should be useful for assessing the activity of this and other mammalian α-mannosidases.

Discovery of SY-5609: A Selective, Noncovalent Inhibitor of CDK7.

CDK7 has emerged as an exciting target in oncology due to its roles in two important processes that are misregulated in cancer cells: cell cycle and transcription. This report describes the discovery of SY-5609, a highly potent (sub-nM CDK7 Kd) and selective, orally available inhibitor of CDK7 that entered the clinic in 2020 (ClinicalTrials.gov Identifier: NCT04247126). Structure-based design was leveraged to obtain high selectivity (>4000-times the closest off target) and slow off-rate binding kinetics desirable for potent cellular activity. Finally, incorporation of a phosphine oxide as an atypical hydrogen bond acceptor helped provide the required potency and metabolic stability. The development candidate SY-5609 displays potent inhibition of CDK7 in cells and demonstrates strong efficacy in mouse xenograft models when dosed as low as 2 mg/kg.

Discovery and Characterization of SY-1365, a Selective, Covalent Inhibitor of CDK7.

Recent studies suggest that targeting transcriptional machinery can lead to potent and selective anticancer effects in cancers dependent on high and constant expression of certain transcription factors for growth and survival. Cyclin-dependent kinase 7 (CDK7) is the catalytic subunit of the CDK-activating kinase complex. Its function is required for both cell-cycle regulation and transcriptional control of gene expression. CDK7 has recently emerged as an attractive cancer target because its inhibition leads to decreased transcript levels of oncogenic transcription factors, especially those associated with super-enhancers. Here, we describe a selective CDK7 inhibitor SY-1365, which is currently in clinical trials in populations of patients with ovarian and breast cancer (NCT03134638). In vitro, SY-1365 inhibited cell growth of many different cancer types at nanomolar concentrations. SY-1365 treatment decreased MCL1 protein levels, and cancer cells with low BCL2L1 (BCL-XL) expression were found to be more sensitive to SY-1365. Transcriptional changes in acute myeloid leukemia (AML) cell lines were distinct from those following treatment with other transcriptional inhibitors. SY-1365 demonstrated substantial antitumor effects in multiple AML xenograft models as a single agent; SY-1365-induced growth inhibition was enhanced in combination with the BCL2 inhibitor venetoclax. Antitumor activity was also observed in xenograft models of ovarian cancer, suggesting the potential for exploring SY-1365 in the clinic in both hematologic and solid tumors. Our findings support targeting CDK7 as a new approach for treating transcriptionally addicted cancers. SIGNIFICANCE: These findings demonstrate the molecular mechanism of action and potent antitumor activity of SY-1365, the first selective CDK7 inhibitor to enter clinical investigation.

Converting cycloalkanones into N-heterocycles: formal synthesis of (-)-gephyrotoxin 287C.

The photochemical rearrangement of N-activated lactams enables their ring contraction concomitant with the migration of a carbon onto a nitrogen atom. When coupled with the Beckmann rearrangement, this photochemical ring contraction converts cycloalkanones into N-heterocycles in a few steps and in a stereospecific manner. To showcase the method, we performed an efficient formal synthesis of (-)-gephyrotoxin 287C.

Enantioselective total synthesis and biological evaluation of (+)-kibdelone A and a tetrahydroxanthone analogue.

The total synthesis of kibdelone A has been accomplished via In(III)-catalyzed arylation of a heterocyclic quinone monoketal and iodine-mediated oxidative photochemical electrocyclization for construction of the ABCD ring moiety. Enzymatic dihydroxylation of methyl 2-halobenzoate substrates was employed for synthesis of activated 2-halo-cyclohexene F-ring fragments. A one pot oxa-Michael/Friedel-Crafts process allowed access to the first simplified DEF ring analogues of the kibdelones.

Polycyclic xanthone natural products: structure, biological activity and chemical synthesis.

Polycyclic xanthone natural products are a family of polyketides which are characterized by highly oxygenated, angular hexacyclic frameworks. In the last decade, this novel class of molecules has attracted noticeable attention from the synthetic and biological communities due to emerging reports of their potential use as antitumour agents. The aim of this article is to highlight the most recent developments of this subset of the xanthone family by detailing the innate challenges of the construction of this class of natural products, new synthetic approaches, and pharmacological data.

Photochemical rearrangement of N-mesyloxylactams: stereospecific formation of N-heterocycles.

N-Mesyloxylactams undergo an efficient ring-contraction to N-heterocycles of various ring sizes. Yields increase with the degree of substitution α to the carbonyl. The stereochemical information of a chiral migrating carbon is conserved making this reaction a synthetically useful complement to the well-known Hofmann, Curtius, Lossen, and Schmidt rearrangements.

Photochemical rearrangement of N-chlorolactams: a route to N-heterocycles through concerted ring contraction.

We report a novel ring contraction allowing the direct conversion of N-chlorolactams to their corresponding ring-contraction N-heterocycles upon photolysis. Results show that the rearrangement occurs with a variety of N-chlorolactams and that the greater the substitution at the migrating carbon, the greater the yield of product. Importantly, stereochemistry at the migrating carbon is conserved in the product. Rearranged products were isolated as their methyl carbamates in yields varying from 17% to 58%, with the major side product being the recyclable parent lactam.

Biaryl guanidine inhibitors of in vitro HCV-IRES activity.

A structure-activity relationship analysis was carried out on a high-throughput small molecule screening lead for HCV-IRES translation inhibition. The study led to the identification of a guanidine-based structure with low microM inhibitory activity.

Optimizing the antibacterial activity of a lead structure discovered by "SAR by MS" technology.

We report on lead optimization of a compound that was originally discovered to bind bacterial 23S rRNA near the L11 binding site and inhibit translation in vitro, but lacked detectable antibacterial activity. In this study, we were able to generate compounds with antibacterial activity against Gram-negative and Gram-positive pathogens, including a methicillin-resistant S. aureus strain.