# Patent

## Title
Small molecule inhibitors of Dusp6 and uses therefor

## Abstract

Compounds that stimulate fibroblast growth factor production, and thus cell growth are provided. Also provided are compositions comprising the compounds and methods of using the compounds. The compounds can be used to treat wounds, to expand cell populations, such as hematopoietic cells, or to grow tissue in vitro, among other uses.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. patent application Ser. No. 14/795,056, filed Jul. 9, 2015, which is a continuation of U.S. patent application Ser. No. 13/256,584, filed Feb. 1, 2012, now U.S. Pat. No. 9,127,016, which is a National Stage of International Patent Application No. PCT/US2010/027900, filed Mar. 19, 2010, which claims the benefit of U.S. Provisional Patent Application No. 61/210,643, filed Mar. 20, 2009, each of which is herein incorporated by reference in its entirety.


STATEMENT REGARDING FEDERAL FUNDING
This invention was made with government support under Grant Nos. HD053287, HL088016, CA052995, MH074411, CA078039 awarded by the National Institutes of health. The government has certain rights in the invention.


The Sequence Listing associated with this application is filed in electronic format via EFS-Web and is hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is 1603951_ST25.txt. The size of the text file is 2,680 bytes, and the text file was created on Aug. 18, 2016.
Fibroblast Growth Factors (FGFs) are members of a large family of secreted glycoproteins that serve important functions in development, proliferation and cellular homeostasis. These ligands bind to single-pass transmembrane proteins of the receptor tyrosine kinase class to activate multiple signaling pathways including the rat sarcoma homologue (RAS)/mitogen-activated protein kinase (MAPK) cascade. The wide-ranging biological roles of FGFs and the multitude of signaling pathways activated by this family of ligands suggest that FGF signaling must be tightly regulated. Dual specificity phosphatase 6 (Dusp6) (also named MAP Kinase Phosphatase 3), Sproutys (Spry1-4) and Sef (similar expression to FGFs) proteins function as RAS/MAPK pathway feedback attenuators. Through their concerted activities FGF signaling is adjusted to optimal levels in embryogenesis (Thisse, B. et al. Dev Biol 287, 390-402 (2005) and Tsang, M. et al. Sci STKE 2004, pe17 (2004)). Sef and Spry proteins suppress RAS/MAPK signaling at multiple points within the pathway, while Dusp6 inhibits the pathway only by dephosphorylation of one class of the MAPK family, extracellular signal-regulated kinase (ERK). Sef, Dusp6 and Sprouty depletion in zebrafish or gene knock-out in mice have revealed the requirement for these proteins to limit FGF signaling during development and homeostasis (Thisse, B. et al. Dev Biol 287, 390-402 (2005); Abraira, V. E. et al. J Neurosci 27, 4273-82 (2007); Li, C., et al. Development 134, 167-76 (2007); and Maillet, M. et al. J Biol Chem 283, 31246-55 (2008)). The identification of small molecules that can reversibly modulate FGF signaling would provide useful tools to dissect the roles for this pathway in development that are not feasible with current genetic methods.
SUMMARY
The dual specificity phosphatase 6 (Dusp6) functions as a feedback regulator of fibroblast growth factor (FGF) signaling to limit the activity of extracellular signal regulated kinase (ERK) 1 and 2. A small molecule inhibitor of Dusp6, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), was identified using a transgenic zebrafish chemical screen. BCI treatment blocked Dusp6 activity and enhanced FGF target gene expression in zebrafish embryos. Docking simulations revealed an allosteric binding site for BCI within the phosphatase domain. Studies in vitro supported the model that BCI inhibits Dusp6 catalytic activation by ERK2. A temporal role for Dusp6 in restricting cardiac progenitors and controlling heart organ size was uncovered with BCI treatment at varying developmental stages. Using this in vivo zebrafish chemical screen, several novel compounds were found to target Dusp6, a component of the FGF signaling pathway that has eluded traditional high throughput in vitro screens.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a scheme for preparation of BCI and its analogs containing different amines.
FIGS. 2A-2C depict schemes for synthesis of compounds 14-16.
FIG. 3 depicts a scheme for synthesis of compound 17.
FIG. 4 depicts a scheme for synthesis of compound 18.
FIG. 5 depicts a scheme for synthesis of compound 19.
FIG. 6. Identification of a small molecule that activates FGF signaling in zebrafish. (a-c) Tg(Dusp6:d2EFP)pt6 embryos treated with BCI (b & b) exhibited increased d2EGFP fluorescence as compared to DMSO (a). (d-f) Embryos treated with BCI during gastrulation had expanded ntl expression at the 6-somite stage (e & f). (g & h) dusp6 mRNA was increased in BCI treated embryos. Note that the MHB, r4 and somites showed stronger dusp6 staining (h) than in DMSO treated (g). Red arrowheads demarcate the MHB. (i & j) BCI treatment during somitogenesis stages expanded the MHB and r3 and r5, as marked by eng3 and krox20 expression, respectively (j). (k) BCI treatment induced expression of the FGF target genes sef and spry4 as measured by RT-PCR. Histone H4 served as RNA loading control. (l) The chemical structure of BCI.
FIG. 7. BCI structure-activity relationship studies. (a-d) Lateral views of 30hpf embryos treated with the compounds shown. d2EGFP fluorescence was enhanced in BCI-treated embryos (b), while related analogs, shown in inner panels, had no effect, even at four-fold higher concentrations (c & d). Red arrowheads label the MHB.
FIG. 8A-8N. BCI does not hyperactivate FGF signaling in the absence of ligand and suppresses dusp6 over-expression. (8a-8d) Lateral views of 24hpf embryos. Tg(Dusp6:d2EGFP)pt6 embryos (8a and 8b) or Tg(Dusp6:d2EGFP)pt6;ace (8c and 8d) were treated with BCI (10 μM). The ace mutants do not show induction of d2EGFP within the MHB (red arrows) where FGF ligands are not present (3d). (3e-3m) Lateral views of shield stage embryos showing sef expression by in situ hybridization. Red brackets demarcate sef expression domain. Injection of dusp6, spry4 or dusp5 reduced sef expression (3f, 3i and 3l). BCI treatment restored sef expression in dusp6-injected embryos (i), but not in embryos injected with spry4 or dusp5 (8j and 8m). (8n) Graph depicting injection and BCI treatment results. Sef expression in mRNA-injected embryos is represented by color bars that denote normal (WT) expression in blue, weaker (-) expression in yellow and absent (--) expression in green.
FIG. 9. Ectopic expression of XFD blocks FGF signaling that is not reversed by BCI (a-c) Lateral view of Shield stage embryos stained showing sef expression as a marker for FGF activity. (a) uninjected control. (b) Embryo injected with XFD mRNA shows a marked reduction of sef expression. (c) Embryo injected with XFD, followed by incubation with 5 μM BCI did not restore sef expression.
FIG. 10A-10F. BCI directly inhibits Dusp6 in both chemical complementation and in pERK2 dephosphorylation assays. (a-d) Cell-based chemical complementation assay. TPA stimulation of HeLa cells induced ERK phosphorylation (red cells in a & b). In cells overexpressing Dusp6-Myc (green cells in c), p-ERK was abolished (green cells in c & d are outlined yellow cells in a & b). In the presence of BCI, pERK levels remained high (red cells in b), even in cells expressing high levels of Dusp6-Myc (outlined yellow cells in b). (e) Quantification of pERK levels in Dusp expressing cells. Cells expressing high levels of Dusp6 (upper panel) or Dusp1 (lower panel) were identified based on c-Myc immunostaining and analyzed for ERK phosphorylation using Kolmogorov-Smirnov (KS) statistics as described in Materials and Methods. pERK levels were normalized to Dusp transfected and vehicle treated cells. BCI inhibited Dusp6 and Dusp1 with IC50 values of 16.0 μM and 11.2 μM, respectively. Data are the averages±SD of quadruplicates from a single experiment that was repeated six times with similar results. (f) p-ERK2 in vitro dephosphorylation assay shows BCI (100 μM) specifically suppressed Dusp6 activity (lane 4) while a related analog, ICD (100 μM) did not (lane 5).
FIG. 11A-11C. BCI does not inhibit Cdc25B (11A), PTP1B (11B) or Dusp3/VHR (11C). Recombinant enzymes were incubated with OMFP in the presence of increasing concentration of BCI (15.2 nM-300 μM). BCI exhibited no activity in suppressing phophatase activity by these enzymes. Assays were performed in triplicates (individual graph represents a single experiment) for each phosphatase. Sodium orthovanadate (100 μM) completely inhibited all three phosphatases and represented 100% inhibition.
FIG. 12A-12B. BCI does not inhibit dephosphorylation of OMFP by Dusp6 (a) BCI did not suppress Dusp6 basal phosphatase activity toward OMFP. NSC95397 (2,3-bis(2-hydroxyethylthio)naphthalene-1,4-dione), a broad spectrum dual specificity phosphatase inhibitor, blocked basal Dusp6 activity toward OMFP. (b) A 10-fold excess of ERK2 (2.1 μg) stimulated (210 ng) Dusp6 dephosphorylation of OMFP by 6.5-fold and this induction was blocked by BCI. RFU, Relative Fluorescent Units were measured at excitation/emission wavelengths of 485/525 nm.
FIG. 13. Testing in vitro of the allosteric inhibition mechanism. ERK2 stimulated Dusp6 dephosphorylation of OMFP; and this induction was blocked by BCI. RFU, Relative Fluorescent Units were measured at excitation/emission wavelengths of 485/525 nm.
FIG. 14A-14O. Dusp6 and FGFs regulate heart size. (a-h & k-m) Hybridization in situ of treated embryos as indicated. (a, b, a′, b′) BCI treatment expanded gata4 expression in the caudal ALPM; blue box and brackets mark ALPM and caudal cardiac domain, respectively. (c & d) BCI increased nkx2.5 expression and expanded cardiac progenitor populations. (e & f) Fluorescent double in situ hybridization showing scl (green) and hand2 (red) expression in BCI-treated embryos. Reduction of scl expression with a concomitant expansion of hand2 in BCI-treated embryos (F). Red and green bracket show expression domains. (g & h) cmlc2 expression in 18-somite stage embryos showed an increase in cardiomyocytes in BCItreated embryos. (i & j) Larvae at 56hpf treated with BCI (from 40% epiboly for 8 hours) exhibited an enlarged heart. Red outline shows heart. These phenotypes correspond to expansion of vmhc (compare l to k and cmlc2 (compare n to m) staining (red arrowheads). (o) Graph showing temporal inhibition of Dusp6 from gastrula to somitogenesis stages resulted in cardiac expansion.
FIG. 15. BCI treatment from gastrula stage onwards resulted in enlarged hearts (a & b) Graph showing BCI treatment resulted in cardiac expansion as measured by cmlc2 and vmhc expression. Note that by the 8-somite stage, the ability of BCI to induce heart expansion was reduced.
FIG. 16 shows BCI expanded GFP expression in transgenic embryos. The EC50 was measured as 11.4 μM.
FIG. 17 shows toxicity and EC50 for selected BCI analogs in zebrafish.



DETAILED DESCRIPTION
The use of numerical values in the various ranges specified in this application, unless expressly indicated otherwise, are stated as approximations as though the minimum and maximum values within the stated ranges are both preceded by the word “about”. In this manner, slight variations above and below the stated ranges can be used to achieve substantially the same results as values within the ranges. Also, unless indicated otherwise, the disclosure of these ranges is intended as a continuous range including every value between the minimum and maximum values. For definitions provided herein, those definitions also refer to word forms, cognates and grammatical variants of those words or phrases.
As used herein, the terms “comprising,” “comprise” or “comprised,” and variations thereof, in reference to elements of an item, composition, apparatus, method, process, system, claim etc. are intended to be open-ended, meaning that the item, composition, apparatus, method, process, system, claim etc. includes those elements and other elements can be included and still fall within the scope/definition of the described item, composition, apparatus, method, process, system, claim etc. As used herein, “a” or “an” means one or more. As used herein “another” may mean at least a second or more.
As used herein, the terms “patient” or “subject” refer to members of the animal kingdom including but not limited to human beings.
The dual specificity phosphatase Dusp6 is a mitogen-activated protein kinase (MAPK) phosphatase, also known as MKP3, that functions as a feedback regulator of fibroblast growth factor (FGF) signaling to limit the activities of the extracellular regulated kinase ERK2. A small molecule inhibitor of Dusp6, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), was identified from a zebrafish chemical screen. Treatment with BCI blocked Dusp6 activity and expanded FGF target gene expression in the embryo as visualized with green fluorescent protein-labeled gene products. Herein, we report the design, synthesis, biological activity and structure-activity relationships (SAR) of BCI analogs. Syntheses of affinity versions of BCI will be disclosed.
The zebrafish embryo is a vertebrate animal model well-suited for high-content small molecule screening (Zon, L. I. et al. Nat Rev Drug Discov 4, 35-44 (2005) and Vogt, A. et al. Dev Dyn 238, 656-663 (2009)). Due to its small size, rapid development and ease of handling it is possible to identify compounds that affect developmental processes and chemical modulators of signaling pathways in vivo (Zon, L. I. et al. Nat Rev Drug Discov 4, 35-44 (2005) and Peterson, R. T., et al. Proc Natl Acad Sci USA 97, 12965-9 (2000)). Previous zebrafish chemical screens have relied on the observations of phenotypes generated by small molecules treatment. In one phenotypic screen, Dorsomorphin was identified as an inhibitor of Bone Morphogenetic Protein (BMP) as embryos exhibited patterning defects upon chemical treatment and subsequent studies utilizing Dorsomorphin in mice have revealed the importance of the BMP pathway in regulating iron metabolism (Yu, P. B. et al. Nat Chem Biol 4, 33-41 (2008)). Another example of the relevance of zebrafish screens was the discovery that Prostaglandin E2 is a key regulator of haematopoietic stem cells (HSC) homeostasis. These studies have shown that this pathway is conserved in vertebrates and provide the potential for using molecules to expand HSC to restore blood deficiencies in patients (North, T. E. et al. Nature 447, 1007-11 (2007)).
The generation of transgenic reporter lines in zebrafish offers alternative in vivo tools for chemical screening. Reporters for FGF signaling have been generated and allow for the live visualization of signaling activity during early development. Here, a chemical screen was performed with an FGF reporter transgenic line and identified a small molecule, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), that hyperactivated FGF signaling. Further analyses revealed that BCI blocked Dusp6 activity in zebrafish embryos and in cultured cells. Molecular modeling predicted an energetically favorable site for BCI binding on Dusp6 phosphatase domain and suggested a plausible allosteric mechanism of action, which was supported by in vitro assays. In one non-limiting example, described below, using BCI as a chemical probe, it was revealed that inhibition of Dusp6 activity during somitogenesis expanded cardiac progenitors at the expense of endothelial lineages. This example suggests that Dusp6 functions, at least in one instance, as an attenuator of FGF signaling in the cardiac field to regulate heart organ size. Further studies, also described below, indicate that a number of analogs of BCI have equal or better activity.
Thus, provided herein are compounds having the general formula:




where R1 and R3 represent one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; R2 is a primary or secondary amine (—NRH or —NRR′, forming, when incorporated into the compound, a secondary or tertiary amine); and R4 is ═O or —OH. In one embodiment, when R1 and R3 are H (that is, the aryl rings containing R1 and R3 contain only hydrogens) and R4 is ═O, R2 is not cyclohexylamine, cyclophenylamine, piperidine or morpholine. In one example, the compound has the formula:





with R1, R2, R3 and R4 defined as indicated above.

Examples of such compounds are depicted in Table 1, below. In one example, R3 is halo, that is, the ring to which R3 is attached may comprise one or more, independently, halo groups, e.g., F, Cl, Br and I. In one example, R3 is Br (a single Br). In another example, R2 is a C4-10 cycloalkylamine, including cyclobutylamine, cyclopentylamine, cyclohexylamine, cycloheptylamine, cyclooctylamine, cyclononylamine, and cyclodecylamine, for example, R2 may be cyclopentylamine or cycloheptylamine, or R1 is H, R2 is one of cyclopentylamine, cyclohexylamine, and cycloheptylamine, and R3 is Br. In one non-limiting embodiment, R1 is halo or dihalo, for example, 4-chloro or 3,4-dichloro.







TABLE 1





BCI analogs




















1


 






2


 






3


 









 









 






4


 






5


 






6


 






7


 






8


 






9


 






10


 






11


 






12


 






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14a


 






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15a


 






16


 






16a


 






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18


 






19


 






19b


 






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20a


 






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21a


 






22


 






22a


 






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23a


 






24


 






25a


 






25b


 






25


 






26


 






27


 






28a


 






28b


 






28


 






29


 






30


 






31a


 






31


 






32









The compound may be an enantiopure preparation consisting essentially of an (−) or (+) enantiomer of the compound, for example (−) BCI or (+) BCI, or may be a mixture of enantiomers in either equal (racemic) or unequal proportions.
In one non-limiting embodiment of the compounds, R4 is ═O. Additional examples of R2 include: t-Boc-cyclohexylamine, thiamorpholine, piperazine, methyl piperazine, acetyl piperazine, cyclopentylamine, cycloheptylamine and di-C1-4-alkylamine.
A compound consisting of a (−) enantiomer of a compound having the formula:




in which R1 represents one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; R2 is a primary or secondary amine; R3 is one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; and R4 is ═O or —OH.

As used herein, a ring structure showing a bond/group that is not attached to any single carbon atom, for example and without limitation, depicted as




can be substituted at any position with one or more groups designated “R”, and, unless indicated otherwise, each instance of R on the ring can be (independently) the same or different from other R moieties on the ring. Thus, if R is H, the group contains nothing but H groups. If R is “halo”, it is a single halo (e.g., F, Cl, Br and I) group. If R is one or more independently of halo and CN, the ring may comprise one, two, three, four, halo or CN groups, such as, for example and without limitation: 2, 3, 4, or 5 chloro; 2, 3, 4, or 5 bromo; 2, 3- or 3,4- or 4,5- or 2,4-dichloro; 3-bromo-4-chloro; 3-bromo-4-cyano, and any other possible permutation of the listed groups. Unless otherwise indicated, the described compounds include all stereoisomers or enantiomers and include preparations comprising one enantiomer (enantiopure compositions) and mixtures of enantiomers, such as racemic mixtures.

Also provided is a composition comprising one or more compounds of any one of claims 1-15 and a solvent or carrier, such as a pharmaceutically acceptable excipient. The compounds may be compounded or otherwise manufactured into a suitable composition for use, such as a pharmaceutical dosage form or drug product in which the compound or compounds are an active ingredient. Compositions may comprise a pharmaceutically acceptable carrier, or excipient. An excipient is an inactive substance used as a carrier for the active ingredients of a medication. Although “inactive,” excipients may facilitate and aid in increasing the delivery or bioavailability of an active ingredient in a drug product. Non-limiting examples of useful excipients include: antiadherents, binders, rheology modifiers, coatings, disintegrants, emulsifiers, oils, buffers, salts, acids, bases, fillers, diluents, solvents, flavors, colorants, glidants, lubricants, preservatives, antioxidants, sorbents, vitamins, sweeteners, etc., as are available in the pharmaceutical/compounding arts.
Useful dosage forms include: intravenous, intramuscular, or intraperitoneal solutions, oral tablets or liquids, topical ointments or creams and transdermal devices (e.g., patches). In one embodiment, the compound is a sterile solution comprising the active ingredient (drug, or compound), and a solvent, such as water, saline, lactated Ringer's solution, or phosphate-buffered saline (PBS). Additional excipients, such as polyethylene glycol, emulsifiers, salts and buffers may be included in the solution. In one embodiment, the composition is an injectable solution or gel, which is injected at a site in which cell growth is desired, such as at the site of a wound or defect. The composition may be a topical composition, such as a lotion, cream or ointment for use in wound healing, where the topical composition is applied to a wound, such as a cut or burn.
The compounds include pharmaceutically acceptable salts. Pharmaceutically acceptable salts are, because their solubility in water is greater than that of the initial or basic compounds, particularly suitable for medical applications. These salts have a pharmaceutically acceptable anion or cation. Suitable pharmaceutically acceptable acid addition salts of the compounds of the invention include, without limitation, salts of inorganic acids such as hydrochloric acid, hydrobromic, phosphoric, metaphosphoric, nitric and sulfuric acid, and of organic acids such as, for example, acetic acid, benzenesulfonic, benzoic, citric, ethanesulfonic, fumaric, gluconic, glycolic, isethionic, lactic, lactobionic, maleic, malic, methanesulfonic, succinic, p-toluenesulfonic and tartaric acid. Suitable pharmaceutically acceptable basic salts include without limitation, ammonium salts, alkali metal salts (such as sodium and potassium salts), alkaline earth metal salts (such as magnesium and calcium salts), and salts of trometamol (2-amino-2-hydroxymethyl-1,3-propanediol), diethanolamine, lysine or ethylenediamine Pharmaceutically acceptable salts may be prepared from the described compounds by any useful method, as are well known in the chemistry and pharmaceutical arts.
Also provided is a method of stimulating (e.g., inducing, increasing, up-regulating, etc.) cell growth in a population of cells—that is, in a culture of one or more cells, in a tissue, in an in vitro or ex vivo cell preparation obtained from a patient and optionally for replacement in the patient opr in another patient, in an organ, in an organism, etc. The method comprises contacting the cell population with a compound described herein in an amount effective to increase FGF secretion by the cell. In one embodiment, the method comprises applying the compound to a tissue in an organism, e.g., of a patient. In one embodiment, the tissue of the organism is damaged or deficient (e.g., is a wound or congenital defect). In another embodiment, the method can be used to expand a cell population or grow a tissue of a patient. For example, the method comprises obtaining cells from a patient and contacting the cells in vitro with the compound to expand the population of cells.
The compounds described herein can be readily synthesized by those of ordinary skill. The BCI molecule has four distinct sites of modification (R1, R2 and R3, and the carbonyl group, R4). BCI and its analogs containing different amines were synthesized following the general procedure depicted in FIG. 1. Briefly, condensation of 1-indanone with benzaldehyde is followed by bromination of benzylideneindanone (compound 1) provides 3-bromo-2-benzyliden-1-indanone (compound 2), a general precursor for the family of analogs. Treatment of compound 2 with 2 eq of primary or secondary amines provided analogs 3-13 in high yield.
Variations using substituted indanones or benzaldehydes provided easy access to other BCI analogs, such as compounds 14, 15 and 16 (See, FIGS. 2A-2C). Bromination of 1-indanone and treatment of bromoindanone with cyclohexylamine provided analog 17 (ICD), which lacks the benzylidene group (see FIG. 3). LAH reduction of BCI resulted in formation of amino alcohol 18 with a trans relationship between the amine and hydroxy groups (see FIG. 4). Compound 19, which contained biotin linked to ring A, was prepared from compound 2 and the easily available monobiotinylated diaminocyclohexane (see FIG. 5). Additional synthesis schemes are described in the Examples.
Example 1
(E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI) enhances FGF signaling
Zebrafish Chemical Screens.
Tg(dusp6:d2EGFP)pt6 embryos were obtained by natural crossings and incubated at 28.5° C. until they reached 24hpf. Five transgenic embryos were placed into each well from a 96-well plate in 200 μl of E3, and a 0.5% DMSO solution was added along with compound from each library at 10 μM. The NCI diversity set (NCI/NIH), the Natural Products library (MicroSource Discovery Systems Inc.) and Phosphatase targeted set (Chembridge) were screened in this study. (E)-2-Benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI; also known as NSC150117) was identified as a compound that enhanced fluorescence in treated transgenic embryos. Treated embryos were photographed under the same settings for exposure, gain and magnification for each picture using a MZFLIII (Leica) microscrope and fluorescent illumination for GFP using endow cube (Chroma Technology Corp., Rockingham, Vt.). Qimaging software and the Retiga Exi camera (Qimaging, Burnaby, BC Canada) were used to capture the images. Each experiment was repeated three times to show reproducibility of the assay and at least four of the five treated embryos exhibited the same phenotype.
Zebrafish RNA Microinjection
dusp6 and XFD mRNA for microinjection studies were generated as previously described (Tsang, M. et al. Development 131, 2769-79 (2004)). Both Dusp5 and Spry4 ORFs were amplified by RT-PCR from 24hpf zebrafish with the following primers:









Dusp5 Forward:



(SEQ ID NO: 1)



5′-AACTCGAGGCCATGAAGGTCTCCAGCATAGATTGCCG-3′



 



Dusp5 Reverse:



(SEQ ID NO: 2)



5′-AATCTAGATTAAGGCAGCGCAGTTATTGGACTC-3′



 



Spry4 Forward:



(SEQ ID NO: 3)



5′-ACTCGAGCCATGGAGTCAAGGGTTCCTCACCACATTC-3′



 



Spry4 Reverse:



(SEQ ID NO: 4)



5′-AATCTAGATCATGAGGCTTGTTTTTCTGGCTGAC-3′






Amplified PCR products were subcloned into pCS2+, sequenced verified and mRNAs were synthesized as described previously. Embryos were injected with 500 pg mRNA at the 1-2 cell stage, treated with 5 μM BCI at the 1000-cell stage and fixed at shield stage for in situ hybridization.

Chemical Complementation Assays in HeLa Cells.

These experiments were carried out essentially as described26. HeLa cells were obtained from ATCC (Manassas, Va.) and maintained in a humidified atmosphere of 5% CO2 at 37° C., Dulbecco's Minimum Essential Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, HyClone, Logan, Utah), and 1% penicillin-streptomycin (Life Technologies, Inc., Rockville, Md.). c-Myc-Dusp6 and c-Myc-Dusp1 (also known as CL100) (kindly provided by Dr. Stephen Keyse, University of Dundee) were subcloned into pcDNA3.1 for ectopic expression in mammalian cells50. HeLa cells (2,000) were plated in the wells of a collagen-coated 384-well plate (Falcon Biocoat) in the presence of FuGene 6 (Roche Biosciences) and c-Myc-Dusp6 or c-Myc-Dusp1 as described. After 20 h in culture, cells were treated in quadruplicate wells for 15 min with ten two-fold concentration gradients of BCI or phenylarsine oxide (PAO) and stimulated for 15 min with TPA (500 ng/ml). Cells were fixed and stained with Hoechst 33342 in 4% formaldehyde, permeabilized, and immunostained with a mixture of anti-pERK (1:200 dilution, Cell Signaling Technology) and anti-c-Myc (1:100 dilution, Santa Cruz Biotechnology) antibodies. Positive pERK and c-Myc-DUSP signals were visualized with AlexaFluor-594 (pERK) and Alexa-488 (c-Myc) conjugated secondary antibodies, respectively. Plates were analyzed by three-channel multiparametric analysis for p-ERK and c-Myc-DUSP intensities in an area defined by nuclear staining using the Compartmental Analysis Bioapplication on an ArrayScan II high-content reader (Cellomics, Pittsburgh, Pa.). Restoration of ERK phosphorylation by BCI in Dusp6 overexpressing cells was quantified by Kolmogorov-Smirnov (KS) statistics as described previously using DUSP-transfected and vehicle treated control wells26. One thousand individual cells were gated for Dusp-Myc expression based on c-Myc immunostaining and analyzed for ERK phosphorylation. A pERK cumulative distribution function (cdf) was established for each condition and compared to a reference cdf from Dusp-Myc expressing and vehicle-treated cells. High KS values denote large differences in ERK phosphorylation levels compared with vehicle control and indicate suppression of Dusp activity. To quantify restoration of Erk phosphorylation in the Dusp expressing cells after compound treatment, KS values for each condition were normalized to the average KS value from four wells transfected with Dusp1 or Dusp6 and treated with vehicle. Detail material and methods on in vitro phosphatase assays and chemical synthesis of BCI and related analogs are listed in Supplementary Methods online RT-PCR
Zebrafish embryos were treated at 24hpf for 6 hours with BCI at 10 μM and 20 μM followed by total RNA extraction with Trizol (Invitrogen). cDNA synthesis with SuperScript II Reverse Transcriptase (Invitrogen) was performed as described by manufacture's protocol and by Tsang et al. For PCR reaction, HotMaster Taq (Eppendorf) was used with the following primers:









(SEQ ID NO: 5)










Dusp6:
For 5′-CGTTCAGAGGGGTTGTCCG-3′



 









(SEQ ID NO: 6)










Dusp6:
Rev 5′-CTTCCCTGAACAGGAGACCC-3′



 









(SEQ ID NO: 7)










Spry4:
For 5′-GCGGAGCAGCCCAAGATACT-3′



 









(SEQ ID NO: 8)










Spry4:
Rev 5′-CAGGCAGGGCAAAACCAATGAG-3′



 









(SEQ ID NO: 9)










Sef:
For 5′-CCAGTCAGGACGCGGGTTCAT-3′



 









(SEQ ID NO: 10)










Sef:
Rev 5′-GTTAAAGTGGCGCTGCGAGTGGAG-3′



 









(SEQ ID NO: 11)










Histone H4:
For 5′-CACGAAACCCGCCATCCGTCG-3′



 









(SEQ ID NO: 12)










Histone H4:
Rev 5′-GTACAGAGTGCGTCCCTGCCG-3′






Cycle conditions were: 94° C. 30 sec, 55° C. 45 sec, 72° C. 40 sec, for 25 cycles. PCR products were resolved on 3% agarose gels.

Whole Mount In Situ Hybridization

In situ hybridization experiments were carried out as described previously (Kudoh, T. et al. Genome Res 11, 1979-87 (2001)). The probes eng3, krox20, sef, dusp6, gata4, nkx2.5, cmlc2, vmhc, scl, etsrp and hand2 were generated with a RNA labeling kit (Roche)(Tsang, M. et al. Development 131, 2769-79 (2004); Chen, J. N. et al. Development 122, 3809-16 (1996); Ekker, M., et al. Development 116, 1001-10 (1992); Liao, E. C. et al. Genes Dev 12, 621-6 (1998); Oxtoby, E. et al. Nucleic Acids Res 21, 1087-95 (1993); Pham, V. N. et al. Dev Biol 303, 772-83 (2007); Tsang, M., et al. Nat Cell Biol 4, 165-9 (2002); Yelon, D., et al. Dev Biol 214, 23-37 (1999); and Yelon, D. et al. Development 127, 2573-82 (2000)). The double fluorescent in situ hybridization protocol was described by Schoenbeck et al. (Dev Cell 13, 254-67 (2007)). Fluorescent in situ hybridizations were visualized by confocal microscopy. Single optical sections and z-series of flat-mounted stained embryos were collected with a confocal laser scan head (SP5, Leica Microsystems, Inc.) mounted on an inverted compound microscope (DMI6000, Leica Microsystems, Inc.). Images were scanned and compiled with NIH Image) software.
Phosphatase Assays In Vitro.
ERK dephosphorylation assays were performed as described previously with several modifications (Lazo, J. S. et al. J Pharmacol Exp Ther 322, 940-7 (2007)). Briefly, recombinant His-tagged Dusp6 (1.5 ng) was incubated for 20 minutes at 25° C. in the presence of 100 μM BCI, 100 μM ICD or 1 mM sodium orthovanadate. Tyrosine and threonine phosphorylated ERK2 (New England Biolabs; 10 ng) was added and reaction mixture (30 mM Tris-HCl, pH 7.0, 75 mM NaCl, 0.67 mM EDTA, 1 mM DTT and 0.033% bovine serum albumin) was incubated at 25° C. for a further 60 min ERK desphosphorylation was determined by Western blotting using 10% Tris-glycine gels and a monoclonal phospho-p44/42 MAPK antibody (Cell Signaling) at 1:1000 dilution. Total ERK was measured as a loading control using an anti-ERK antibody (Cell Signaling).
Cdc25B, PTP1B and VHR Assays In Vitro
Enzyme activities in the presence or absence of BCI were measured using the artificial substrate 3-O-methylfluorescein (OMFP) at concentrations equal to the Km of each enzyme (Cdc25B, PTP1B & Dusp3/VHR) and at optimal pH for individual enzyme activity in a 96-well microtiter plate assay based on previously described methods by Lazo et al. (J Med Chem 44, 4042-9 (2001) and Lazo, J. S. et al. Bioorg Med Chem 14, 5643-50 (2006)). Briefly, the standard assay conditions contained 0.02 mg/ml OMFP in assay buffer (30 mM Tris-HCl (pH8.0), 75 mM NaCl, 1 mM EDTA, 0.33% BSA and 1 mM DTT). Fluorescence emission was measured after a sixty-minute incubation period at ambient temperature using a multiwell plate reader (SpectraMax m5, Applied Biosystems; excitation 485 nm, emission 525 nm). Sodium orthovanadate (100 μM) was used as a positive control for full phosphatase inhibition. IC50 concentrations were determined from three experiments using 10 concentrations of BCI ranging from 300 μM to 15.2 nM and GraphPad Prism 5.0 software.
For OMFP based ERK2 induced activation of Dusp6, recombinant His-tagged Dusp6 was expressed from a bacterial expression vector and 250 ng were incubated with the indicated concentrations of NSC95397 or BCI. OMFP was added at its apparent Km (100 μM)(Vogt, A. et al. J Biol Chem 280, 19078-86 (2005)). The final reaction volume was 15 μl. After 1 h at RT, OMF fluorescence was measured on an M5 multimode reader (Molecular Devices) at excitation/emission wavelengths of 485/525 nm To assay activated Dusp6, 210 ng or 2.1 μg of recombinant ERK2 (Cell signaling) were added to Dusp6 (210 ng)/BCI (100 μM) mixtures to measure activation at 1:1 and 1:10 ratio of substrate to enzyme. OMFP was immediately added and fluorescence (ex485/em525 nm) was read every 10 min for 130 min Fold activation was calculated at 60 mins in each experiment.
Docking Simulations
A two-step process was adopted for predicting the optimal binding poses of BCI and assessing the potential mechanism of inhibition. First, unbiased docking simulations were performed where the target protein (Dusp6) was assumed to be rigid either in the low-activity state or the high-activity state. These simulations permitted us to build two hypotheses, one of which was supported by more detailed flexible docking simulations. The method and results from the two successive steps are described in more details.
Results
A Transgenic Zebrafish Screen Identifies a Small Molecule Activator of FGF Signaling
We previously described the generation of a transgenic zebrafish line, (Tg(Dusp6:d2EGFP)pt6) that expresses destabilized green fluorescent protein (d2EGFP) under the control of FGF signaling (Molina, G. A., et al. BMC Dev Biol 7, 62 (2007)). Using Tg(Dusp6:d2EGFP) embryos as a biosensor for FGF signaling, we screened over 5000 diverse compounds assembled from chemical libraries for small molecule modulators of this pathway. Five transgenic embryos at 24 hours post fertilization (hpf) were arrayed into each well of a 96-well plate containing test compounds at 10 μM. d2EGFP intensity in treated embryos was visually analyzed and compared to vehicle control (0.5% DMSO) after 6-8 hours. BCI enhanced d2EGFP fluorescence in a concentration-dependent manner and was detected as early as 2 hours post treatment (FIG. 6a-c). To confirm that BCI hyperactivated FGF signaling, we treated embryos prior to gastrulation (5hpf), and we analyzed by whole mount in situ hybridization, the expression of ntl (zebrafish brachyury), a known FGF target gene (Latinkic, B. V. et al. Genes Dev 11, 3265-76 (1997)). The expression of ntl was greatly expanded within the notochord and the tailbud at the 6-somite stage in BCI-treated embryos (FIG. 6d-f). Similarly, BCI treatment from the 1- to 10-somite stage resulted in a marked increase in expression of another FGF target gene, dusp6, as shown by the expansion of prospective mid-hindbrain boundary (MHB), rhombomere4 (r4) and the tailbud (FIG. 6g & h). The expanded brain structures were confirmed as BCI increased expression of engrailed3 (eng3), which labels MHB, and krox20, which demarcates r3 and r5 identity, consistent with previous observations from FGF bead implantation studies (FIG. 6i & j) (Maves, L., et al. Development 129, 3825-37 (2002)). To further demonstrate that BCI treatment hyperactivated FGF signaling, we measured an increase in the expression of sef and spry4 by semi-quantitative RT-PCR (FIG. 6k; n=3 for each gene) (Furthauer, M., et al. Development 128, 2175-86 (2001); Tsang, M., et al. Nat Cell Biol 4, 165-9 (2002); and Tsang, M. et al. Development 131, 2769-79 (2004)). These results confirmed that BCI enhanced FGF signaling in the zebrafish embryo, resulting in the increased transcription of several FGF target genes. We next determined the BCI structural features required to enhance FGF signaling. Two analogs, (E)-2-benzylidene-2,3-dihydro-1H-inden-1-one (BI) lacking the cyclohexylamino group, and 3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (ICD) lacking the benzylidene group were synthesized). The cyclohexylamino and benzylidene substituents were both required in enhancing d2EGFP fluorescence, as analogs lacking either group were inactive (FIG. 7).
BCI Inhibits Dusp6
To determine the mechanism for BCI's activity and to identify a potential target, we probed where this compound acts within the RAS/MAPK pathway. In BCI-treated transgenic embryos, increased d2EGFP expression was restricted to embryonic regions where FGFs are expressed (FIG. 1b & c). Furthermore, BCI treatment did not induce d2EGFP expression in the MHB of Tg(Dusp6:d2EGFP);ace mutant embryos, which are deficient in Fgf8 signaling (FIG. 8d) (Reifers, F. et al. Development 125, 2381-95 (1998)). Thus BCI did not enhance FGF signaling in the absence of ligand. We reasoned that BCI could block a feedback attenuator of the FGF pathway, thereby resulting in a net increase in transcription of target genes. To test this model, we determined if BCI could rescue phenotypes generated by ectopic expression of FGF inhibitors, Spry4, Dusp6 and a dominant negative receptor, XFD in zebrafish (Furthauer, M., et al. Development 128, 2175-86 (2001) and Tsang, M. et al. Development 131, 2769-79 (2004)). Injection of mRNA encoding dusp6, spry4, or XFD into 1-cell stage zebrafish embryos decreased sef expression (FIGS. 8f, 8k, and 8n and FIG. 9B). The addition of 5 μM BCI to dusp6-injected embryos rescued sef expression to control levels or higher (FIGS. 8g & 8n). In contrast, BCI treatment did not reverse the effects of spry4 or XFD mRNA, suggesting that BCI directly inactivated Dusp6 (FIGS. 8j and 8n and FIG. 9c). To determine if BCI could inhibit other Dusps, we first characterized zebrafish dusp5 and asked whether it could suppress FGF signaling similar to dusp6 (Qian, F. et al. Dev Dyn 233, 1163-72 (2005) and Sumanas, S., et al. Blood 106, 534-41 (2005)). Dusp5 has been shown to dephosphorylate activated ERK (p-ERK) and ectopic expression of zebrafish dusp5 inhibited sef transcription (FIGS. 8k and 8n) (Mandl, M., et al. Mol Cell Biol 25, 1830-45 (2005)). In contrast to observations with Dusp6 mRNA microinjections, BCI had little or no effect in reversing the phenotype caused by Dusp5 over-expression (FIGS. 8l & 8n). These observations indicated that BCI was specific for Dusp6. Although both Dusp6 and Dusp5 can dephosphorylate p-ERK and are highly conserved, their catalytic activities are quite different. Dusp6 phosphatase activity is subject to substrate binding and can be catalytically stimulated by ERK interaction (Mandl, M., et al. Mol Cell Biol 25, 1830-45 (2005) and Camps, M. et al. Science 280, 1262-5 (1998)). This substrate-induced catalytic activity has been described for several members of the Dusp family including Dusp1 (which is sensitive to BCI, as shown below), and Dusp422-24. In contrast, Dusp5 is constitutively activated and substrate binding has little consequence on catalytic rate. Thus the difference we noted with the ability of BCI to rescue Dusp6 but not Dusp5 over-expression in vivo suggested that BCI might suppress the activation of Dusp6 associated with substrate binding. Since Dusp6 directly dephosphorylates p-ERK, BCI should restore p-ERK levels in Dusp6 overexpressing cells. We tested this hypothesis in a cell-based chemical complementation assay25,26 in which HeLa cells were transiently transfected with Myc tagged human Dusp6 (Dusp6-Myc), stimulated with 12-O-tetradecanoylphorbol-13-acetate (TPA), and immunostained with anti-c-Myc (FIGS. 10c and d, green) and anti-p-ERK antibodies (FIGS. 10a and b, red), respectively. Upon TPA treatment, the RAS/MAPK pathway was activated leading to strong p-ERK staining in non-transfected cells, while in cells expressing Dusp6-Myc (FIG. 10c), p-ERK staining was abolished (FIG. 10a, Dusp6-Myc cells traced in yellow). BCI treatment of Dusp6-Myc transfected cells restored p-ERK levels after TPA addition, suggesting that BCI directly suppressed Dusp6-Myc function (FIG. 10b, Dusp6-Myc traced in yellow). In this assay, BCI also inhibited human Dusp1, whose catalytic activity, like Dusp6, is induced by substrate binding (FIG. 10e). IC50 values for DUSP6 and DUSP1 inhibition were consistent with hyperactivation of FGF signaling and d2EGFP expression at these concentrations in the zebrafish embryo (FIG. 10e). In contrast, treatment with ICD did not block Dusp6 or Dusp1 activity in the chemical complementation assays (FIG. 10e). Taken together, we have shown in biological systems BCI specifically inhibited Dusp1 and Dusp6, but not Dusp5.
We next addressed if BCI could directly inhibit Dusp6 activity in an in vitro pERK2 dephosphorylation assay. Recombinant Dusp6 completely dephosphorylated pERK2 in vitro as determined by immunoblotting with pERK specific antibodies (FIG. 10f, Lane 3). Addition of BCI prevented Dusp6-mediated pERK2 dephosphorylation as effectively as the generic tyrosine phosphatase inhibitor sodium orthovanadate (FIG. 10f, Lane 4 and 6, respectively). ICD did not block Dusp6 activity supporting the conclusion that BCI directly inhibited Dusp6 (FIG. 10f, Lane 5). Since many known small molecule phosphatase inhibitors exhibit low selectivity we determined whether BCI could suppress phosphatase activity from several related phosphatases. BCI did not block Cdc25B (Cell division cycle 25B), PTP1B (Protein Tyrosine Phosphatase 1B) or Dusp3/VHR activity implicating specificity of BCI is limited to a set of MAP Kinase Phosphatases (FIGS. 11A-11C). The mean in vitro values (μM n=3) for BCI against of recombinant human phosphatases Cdc25B, PTP1B and VHR were >300 for each phosphatase.
Computational Modeling Reveals a Putative BCI Binding Site within Dusp6
Crystal structures of several Dusp catalytic domains have been determined (Almo, S. C. et al. J Struct Funct Genomics 8, 121-40 (2007); Jeong, D. G. et al. Proteins 66, 253-8 (2007); Jeong, D. G. et al. J Mol Biol 360, 946-55 (2006); and Stewart, A. E., et al. Nat Struct Biol 6, 174-81 (1999)). In each case, the phosphatase domain encompasses a five/six-stranded β-sheet surrounded by five α-helices. These structures enabled us to perform unbiased docking simulations to identify potential BCI binding sites.
BCI was docked onto two different conformations of Dusp6 (MKP3): the low-activity form determined by X-ray crystallography (PDB ID: 1MKP) and the high-activity form obtained by homology modeling using ORCHESTRAR (Tripos, Inc., St. Louis, Mo.). From cluster analysis of the resulting BCI-bound conformations, we identified a number of potential binding sites on the low-activity form. The most favorable site among them was further assessed by flexible docking using multiple Dusp6 conformations generated by anisotropic network model (ANM) analysis and homology modeling. BCI was predicted to preferentially fit within a crevice between the general acid loop and helix α7, rather than interacting directly with the catalytic residues Asp262, Cys293, or Arg299. At this putative binding site, a close interaction of BCI with the backbone of the general acid loop and the sidechains of Trp264, Asn335 and Phe336 was predicted. Further docking simulations showed that BCI-Dusp1 interactions were comparable to those with Dusp6 rationalizing our observed activity data (FIG. 10e).
Unbiased Docking Simulations
BCI was docked onto two different conformations of Dusp6 (MKP3): the low-activity form determined by X-ray crystallography (PDB ID: 1MKP)(Stewart, A. E., et al. Nat Struct Biol 6, 174-81 (1999)) and the high-activity form obtained by homology modeling using ORCHESTRAR (Tripos, Inc., St. Louis, Mo.). We used as templates the structures of Dusp9 (MKP4; PDB ID: 2HXP; 80% sequence identity), Dusp10 (MKP5; PDB ID: 1ZZW; 47% sequence identity), and Dusp5 (VH3; PDB ID: 2G6Z; 44% sequence identity) in the high-activity state (Almo, S. C. et al. J Struct Funct Genomics 8, 121-40 (2007); Jeong, D. G. et al. Proteins 66, 253-8 (2007); and Jeong, D. G. et al. J Mol Biol 360, 946-55 (2006)). For BCI, 400 docking poses (200 per enantiomer) were generated using AutoDock4 for each conformation (see, Huey, R., et al. Journal of Computational Chemistry 28, 1145-1152 (2007) and Morris, G. M. et al. Journal of Computational Chemistry 19, 1639-1662 (1998)). Genetic algorithm population size was set to 250. Each docking pose was selected based on the energetic evaluation of up to 5×106 alternative conformations. The analysis of the resulting poses using an agglomerative clustering scheme revealed the clustering of a subset of binding poses in the vicinity of the active site in both conformations. In the low-activity state, the binding site was a crevice known to close upon catalytic activation of the enzyme. In the high-activity state this crevice is not accessible. Instead, a relatively more hydrophobic patch in the neighborhood of the active site was predicted to serve as an alternative binding site for the inhibitor (see, Lazo, J. S. et al. J Pharmacol Exp Ther 322, 940-7 (2007)). Based on these observations two potential inhibition mechanisms were hypothesized:
BCI binds the low-activity form of Dusp6 and restricts the mobility of the general acid loop so as to prevent ERK2 from inducing the conformational changes that lead to Dusp6 catalytic activation. This restricts ERK2 dephosphorylation to a basal catalytic rate.
BCI binds the ERK-activated Dusp6, and prevents ERK2 from optimally orienting itself, which leads to the inhibition of ERK2 dephosphorylation. In either case, BCI was not expected to prevent Dusp6-ERK2 complex formation due to the large surface area of interaction distributed over two domains of Dusp68.
Flexible Docking
Toward an assessment of the more likely inhibition mechanism among those hypothesized above, we further explored the binding properties of BCI by allowing the protein to undergo structural fluctuations in the neighborhood of the two above-defined states. Backbone flexibility was deduced from normal mode analysis and homology modeling calculations. Conformations accessible near the basal-activity state were sampled by using the anisotropic network model (ANM) in combination with all-atom energy minimization (Atilgan, A. R. et al. Biophys J 80, 505-15 (2001)). Third, fourth, and fifth ANM slow modes were found to set in motion the catalytic Asp262 close to the catalytic cavity (Eyal, E., et al. Bioinformatics 22, 2619-27 (2006)). The general acid loop was also observed to have a tendency to move towards the catalytic cavity in 10 ns long unbiased molecular dynamics simulations, in line with AMN calculations. NAMD software and the Charmm force field were used for energy minimization (MacKerell Jr., et al. J. Phys. Chem. 102, 3586-3616 (1998) and Phillips, J. C. et al. J Comput Chem 26, 1781-802 (2005)). For each α-carbon, harmonic restraints with a force constant of 40 kcal/mole/Å2 were defined to drive the motions along the selected ANM modes at steps of size<0.2 Å, similar to recently introduced ANM-steered simulations (Isin, B., et al. Biophys J 95, 789-803 (2008)). A total of twenty conformations were sampled along the selected modes by jointly optimizing backbone and side-chain conformations (Lovell, S. C., et al. Proteins 40, 389-408 (2000)). As for the high-activity state, multiple models generated with MODELLER were used as targets (Jones, G., Willett, et al. J Mol Biol 267, 727-48 (1997)). Asp262, Trp264, and Asn335 side chains were allowed to sample rotameric states from Penultimate library (Lovell, S. C., et al. Proteins 40, 389-408 (2000)).
At least 1000 docking poses for the basal and activated state were generated using GOLD and cluster analysis was performed (Jones, G., Willett, et al. J Mol Biol 267, 727-48 (1997)). Docking poses were scored using GoldScore, which is a weighted sum of van der Waals energy and hydrogen bond energy that implicitly accounts for charged interactions (Jones, G., et al. J Mol Biol 245, 45-53 (1995)). The most populated and energetically favorable clusters were examined to identify the most favorable docking solution. The most favorable cluster of BCI docking poses was located in the low-activity conformation. The corresponding GoldScore averaged over all binding poses for this cluster was found to be 47.2±2.1, in favor of the hypothesis (i). Finally, as a further verification, docking simulations were performed to compare the binding properties of BCI against Dusp5, Dusp1 and Dusp6. BCI was docked onto to the crystal structure of Dusp5 (PDB ID: 2G6Z) and a model of Dusp1 based on Dusp6 structure using the same procedure as described above for Dusp6. Docking to the Dusp5 crystal structure yielded much lower docking scores (27.9±1.4) due to lack of the crevice observed in Dusp6, explaining lack of activity against this constitutively active homolog. Docking of BCI to the Dusp1 model resulted in comparable interaction but lower Goldscores (37.4±2.9). The Dusp6 movies (not shown) were generated using energy minimization with harmonic constraints based on ANM modes, implemented following the procedure described in Isin, B., et al. (Biophys J 95, 789-803 (2008)). Movie 1, which shows intrinsic flexibility of the general acid loop was generated using 3rd, 4th, and 5th slow modes. Movie 2, which shows the catalytic activation of Dusp6 was generated using 5% of the entire spectrum of modes in the low frequency regime.
In the zebrafish microinjection assays, BCI inhibited ectopic expression of dusp6 but not dusp5, exhibiting specificity toward certain members of this phosphatase family (FIG. 8). To understand how BCI can block Dusp6 but not Dusp5, we compared the two phosphatase crystal structures. Structural superposition of Dusp5 and Dusp6 displayed that the particular crevice in Dusp6 that accommodates BCI binding that is not accessible in Dusp5. As a result, docking of BCI onto the same region of Dusp5 phosphatase domain resulted in energetically less favorable interactions. The relative positions of Asp262 and Asp232 in the respective phosphatases Dusp6 and Dusp5 differ by 5 Å after optimal superposition of the two structures, suggesting that their basal activities are determined by the relative location of these catalytic residues (Jeong, D. G. et al. Proteins 66, 253-8 (2007)). It was postulated that substrate binding to Dusp6 induces a conformational shift that reorients Asp262 towards the phosphatase loop, thereby creating a high activity enzyme (Owens, D. M. et al. Oncogene 26, 3203-13 (2007)). In support of this model, mutation of Asp262 to asparagine did not abolish basal phosphatase activity, but suppressed catalytic activation upon ERK binding (Stewart, A. E., et al. Nat Struct Biol 6, 174-81 (1999)). To further understand BCI action on Dusp6 mechanistically, we explored Dusp6 dynamics by particularly focusing on the ANM modes that induce conformational changes at the general acid loop. Our analysis showed that Dusp6 possesses an intrinsic, structure induced tendency to suitably reorient its general acid loop to position Asp262 closer to the phosphatase loop. Therefore, without any intent to be bound by this theory, we proposed that BCI binding to the accessible crevice in the low-activity form effectively blocks the flexibility of this loop, thereby preventing the interaction of Asp262 with the other catalytic residues. Such constraints on functional motions are likely to inhibit Dusp6 activation induced by ERK binding.
BCI is an Allosteric Inhibitor of Dusp6
We measured the dephosphorylation of a small molecule phosphatase substrate, 3-O-methylfluorescein phosphate (OMFP), by Dusp6 in the presence or absence of ERK2. Docking simulations predicted that BCI and OMFP could simultaneously bind within the phosphatase active site with OMFP interfacing with the core catalytic residues. This suggests that BCI would not block basal Dusp6 phosphatase activity toward OMFP. Indeed, at a concentration that inhibited ERK dephosphorylation in vitro (100 μM), BCI did not inhibit basal Dusp6 activity (FIG. 12a). Addition of ERK2 protein stimulated Dusp6 dephosphorylation of OMFP three-fold and this enhancement was significantly inhibited in the presence of BCI (57% inhibition) (FIG. 13). Increasing the ratio of ERK2 to Dusp6 (10:1) in the activation assay resulted in a 7-fold enhancement that was also suppressed by the addition of BCI (30% inhibition) (FIG. 12b). These data support the modeling predictions that BCI is a specific allosteric inhibitor of Dusp6 that prevents the catalytic stimulation of phosphatase activity induced by substrate binding.
The Role of Dusp6 and FGF in Regulating Heart Size
The identification of a small molecule that blocks the biologically relevant activity of Dusp6 and Dusp1 allowed us to probe the requirement for these enzymes in later developmental processes. Given that BCI could potentially block related members of the Dusp family, we examined the expression of other dusps in zebrafish. Detailed expression analyses of several dusps have been described and include dusp4, dusp1, dusp7, dusp5, and dusp22a (Qian, F. et al. Dev Dyn 233, 1163-72 (2005); Sumanas, S., et al. Blood 106, 534-41 (2005); Brown, J. L. et al. Proc Natl Acad Sci USA 105, 12337-42 (2008); Kudoh, T. et al. Genome Res 11, 1979-87 (2001); and Thisse, B. et al. Fast Release Clones: A High Throughput Expression Analysis. ZFIN Direct Data Submission (zfin.org) (2004)). Of these only Dusp6 functions as a feedback regulator of FGF/MAPK/ERK signaling and is expressed within the anterior lateral plate mesoderm, supporting the idea that this phosphatase plays a role in heart development. In early embryogenesis, Dusp6 is an important regulator of FGF signaling; knock-down with antisense morpholinos results in embryo polarity defects, which precludes the study of Dusp6's role in later development (Tsang, M. et al. Development 131, 2769-79 (2004)). In contrast, small molecules permit the analysis at later stages of development due to rapid and transient perturbation of their biological targets. Using BCI as a chemical probe, we asked how inhibiting Dusp6 activity would alter patterning and formation of the heart. The zebrafish heart develops from a small group of cardiac progenitor cells that can be identified by 5hpf within the mesodermal layer of the blastula stage embryo. During gastrulation, cardiac progenitor cells undergo cellular migration to form two bilateral populations known as the anterior lateral plate mesoderm (ALPM) located just behind the MHB, and begin to express the transcription factors nkx2.5 and gata4. Studies have described a role for Fgf8 in zebrafish heart development. In embryos harboring an fgf8 mutation, both atria and ventricular cells are reduced (Marques, S. R., et al. Dev Biol 321, 397-406 (2008) and Reifers, F., et al. Development 127, 225-35 (2000)). In agreement with the notion that FGF signaling plays a role in stipulating heart size, ectopic expression of a constitutively activated FGF receptor (Fgfr1) during somitogenesis stages expanded cardiac tissue (Marques, S. R., et al. Dev Biol 321, 397-406 (2008)). Therefore we used BCI to test if Dusp6 limits FGF signaling and restricts cardiac progenitors and heart organ size. In BCI-treated embryos a caudal expansion of gata4 in the ALPM was observed (compare FIGS. 14a & a′ to 14b & b′; 81%, n=16). The gata4 caudal expansion of the ALPM corresponds to where cardiac progenitors are situated at the 10-somite stage.
Examination of nkx2.5 expression in BCI-treated embryos showed expanded cardiac progenitor pools as compared to DMSO-treated embryos, confirming a specific effect on heart precursors (compare FIGS. 14d to 15d; 91%, n=11). While we noted an expansion of cardiac progenitors, it was not clear if this event was at the expense of other lineages. Recent studies have shown that there exists a repressive interaction between the vascular and hematopoietic precursors on cardiomyocyte progenitors that determine heart organ size (Schoenebeck, J. J., et al. Dev Cell 13, 254-67 (2007)). We analyzed expression of scl/tal1, a gene that is expressed in endothelial and blood lineages located within the rostral domain of the ALPM in BCItreated embryos from the 1-somite stage. Inhibition of Dusp6 resulted in a marked reduction in scl expression, suggesting that activation of FGF signaling expanded cardiac tissue at the expense of blood or endothelial progenitors (compare FIGS. 14f to 14e; 93%, n=15). Likewise, etsrp, a marker for vascular fate was also reduced in BCI-treated embryos (data not shown). The loss of endothelial and hematopoietic lineages was coupled with the concomitant expansion of cardiac hand2 expression at the 10-somite stage (FIG. 14f; 32%, n=19). This surplus of cardiac progenitors was also noted at the 18-somite stage by an increase in cells positive for cardiac myosin light chain 2 (cmlc2), which specifically labels differentiated cardiomyocytes (FIG. 14h; 81% n=16). To test whether the expansion of cardiac progenitors resulted in an increase in heart tissue, we analyzed treated embryos at larval stage. Embryos were treated at 40% epiboly, with BCI or DMSO, followed by compound washout the next day and further incubation until the embryos reached 56hpf. In BCI-treated larvae, we noted a marked expansion in cardiac tissue (FIG. 14j & o). To define the critical period as to when Dusp6 activity limits heart organ size, we treated embryos at the 1- and 8-somite stages. We observed larger hearts at both time points, however the frequency was reduced in embryos treated at the later stage (FIG. 14o). In situ analysis with probes for ventricular myosin heavy chain (vmhc) and cmlc2 confirmed that treated embryos exhibited enlarged hearts (FIG. 14l & n, and FIG. 15). Expansion was particularly notable for ventricular tissue, known to be sensitive to Fgf8 signaling (FIG. 14l) (Marques, S. R., et al. Dev Biol 321, 397-406 (2008) and Reifers, F., et al. Development 127, 225-35 (2000)). These results indicate that inhibition of Dusp6 by a small molecule inhibitor can induce an expansion of myocardial progenitors that ultimately increase heart size.
Discussion
The zebrafish embryo offers distinct advantages over traditional in vitro and cell-based chemical screens. With the generation of transgenic FGF reporter lines, it is possible to screen for novel compounds that modulate this pathway in vivo. In addition, live embryo screens allow for the elimination of toxic compounds and molecules that evoke non-specific effects on embryo differentiation. From a modest screen of approximately 5000 compounds, we identified BCI, a small molecule that enhanced FGF signaling. Subsequent in vitro phosphatase assays and docking simulations provided strong evidence that BCI suppressed the ERK-induced activation of Dusp6. The identification of BCI allowed us to directly probe the role of Dusp6 in heart formation during a critical period when cardiac specific transcription factors begin to be expressed and are consistent with studies when global activation of FGF signaling resulted in increased cardiac progenitors. Treatment with BCI resulted in the expansion of the cardiac field at the expense of endothelial lineages. The increase in cardiac progenitors resulted in enlarged hearts, suggesting that FGF signaling must be tightly regulated during this period to allow for proper cardiac morphogenesis to occur. The role for Dusp6 in controlling heart organ size is likely conserved with other vertebrates as disruption of Dusp6 was recently found to cause enlarged hearts (Maillet, M. et al. J Biol Chem 283, 31246-55 (2008)).
Previous high-throughput screens for Dusp6 and Dusp1 inhibitors involved in vitro assays with artificial substrates. Because these assays do not faithfully recapitulate phosphatase activity in a biological context, no specific Dusp6 inhibitors with in vivo activity have been identified (Ducruet, A. P., et al. Annu Rev Pharmacol Toxicol 45, 725-50 (2005)). The phosphatase catalytic site is highly conserved across all tyrosine phosphatases and crystal structures have revealed shallow catalytic pockets. These structural features have further hampered the identification of specific small molecule phosphatase inhibitors (Bakan, A., et al. Curr Med Chem 15, 2536-44 (2008)) Small molecules targeting Dusp1 identified from in vitro screens have exhibited promiscuous activity or lack potency (Lazo, J. S. et al. Bioorg Med Chem 14, 5643-50 (2006)). However, with the identification of a novel allosteric inhibitor and our understanding of its mechanism of action, it is possible to design new molecules based on BCI to block substrate induced Dusp function. This offers highly specific compounds to probe the role of Dusps in development, and potentially provide novel compounds for treatment of diseases that are dependent on FGF signaling such as wound repair and regeneration.
Example 2
Synthesis of BCI
BCI was synthesized by aldol condensation of 2,3-dihydro-1H-inden-1-one with benzaldehyde, bromination and SN2 addition of cyclohexylamine for subsequent studies. (E)-2-Benzylidene-2,3-dihydro-1H-inden-1-one (BI) and 3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (ICD) were prepared by bromination of 2,3-dihydro-1H inden-1-one and displacement of bromide with cyclohexylamine. All reactions were conducted in oven-dried glassware under a dry atmosphere. Starting materials, reagents and anhydrous solvents were purchased from commercial suppliers (Sigma-Aldrich and Fisher). Reactions were monitored by TLC on EM Science pre-coated silica gel 60 F254 plates, 250 μm layer thickness. Flash chromatography was performed over silica gel 60, 230-400 mesh. Low resolution mass spectra (MS) were obtained in electron ionization (EI) mode on a Hewlett Packard 5971 mass selective detector coupled to a Hewlett Packard 5890 Series II gas chromatograph equipped with a 30 m 5% phenyl methylsilicone capillary column from Supelco. High resolution mass spectra (HRMS) were obtained with an Applied Biosystems 4700 MALDI-TOF instrument using α-cyano-4-hydroxycinnamic acid as the matrix. Melting points were determined on a Fisher-Johns open stage apparatus and are uncorrected. 1H and 13C NMR spectra were recorded on a Varian Mercury spectrometer at 400 and 100 MHz, respectively, or a Bruker Avance spectrometer at 600 and 150 MHz, respectively. NMR chemical shifts were referenced to the residual CHCl3 signal (7.26 ppm downfield from Me4Si) and 13C NMR chemical shifts to the solvent CDCl3 signal (77.00 ppm downfield from Me4Si), respectively.
Example 3
(E)-2-Benzylidene-2,3-dihydro-1H-inden-1-one




(E)-2-Benzylidene-2,3-dihydro-1H-inden-1-one was synthesized as described by Hassner and Cromwell (J Am Soc Chem 80, 893-900 (1958). An ice bath-cooled mixture of 2,3-dihydro-1H-indan-1-one (2.0 g, 15.1 mmol) and benzaldehyde (1.6 g, 15.1 mmol) was treated dropwise with 4% ethanolic KOH (w/v) with stirring until precipitation ceased. After an additional 1 h of stirring at room temperature, the precipitate was collected by filtration, washed with cold H2O, then recrystallized from MeOH—H2O to give the title compound as straw-colored crystals (2.6 g, 78% yield): M.p. 109-110° C.; 1H NMR (400 MHz, CDCl3): δ 4.07 (s, 2H), 7.34-7.78 (m, 9H), 7.94 (d, 1H, J=7.6 Hz); 13C NMR (100 MHz, CDCl3): δ 33.3, 125.1, 128.0, 129.1, 130.5, 131.6, 132.6, 134.8, 136.4, 137.3, 139.6, 151.4, 194.3; MS (EI) m/z (relative intensity): 220 (M+•, 55), 219 (M−1, 100). HRMS (MALDI-TOF) calc'd for m/z 221.0966 [M+H]+, found 221.0970. CAS Registry No: [17434-21-8].
Example 4
(Z)-2-Benzylidene-3-bromo-2,3-dihydro-1H-inden-1-one




(Z)-2-Benzylidene-3-bromo-2,3-dihydro-1H-inden-1-one was generated as described by Pearson et al. (J Org Chem 27, 3038-3044 (1962)). Briefly, (E)-2-Benzylidene-2,3-dihydro-1H-inden-1-one (1.0 g, 4.5 mmol), N-bromosuccinimide (0.8 g, 4.5 mmol) and benzoyl peroxide (61 mg, 0.25 mmol) were dissolved in 15 mL of CCl4. The mixture stirred and heated to reflux for 1 h under a N2 atmosphere. The mixture was cooled to r.t. and stirred an additional 1 h. After filtration and concentration from solvent under vacuum, the resulting orange solid was recrystallized three times from CCl4 to give the title compound as a straw-colored solid (0.94 g, 70% yield): M.p. 118-119° C.; 1H NMR (400 MHz, CDCl3): δ 6.33 (s, 1H, C3-H), 7.19-7.85 (m, 10H, 9 aromatic, 1 vinyl); 13C NMR (100 MHz, CDCl3): δ □39.9, 127.4, 127.8, 128.4, 128.6, 128.7, 129.4, 134.1, 134.9, 135.6, 139.6, 141.9, 149.4, 192.8; MS (EI) m/z (relative intensity): 296 ([77Br]M+•, 14); HRMS (MALDI-TOF) calc'd for m/z 297.0102 [[77Br]M+H]+, found 297.0096. CAS Registry No: [5387-50-8].
Example 5
3-Bromo-2,3-dihydro-1H-inden-1-one




3-Bromo-2,3-dihydro-1H-inden-1-one was generated as described by Treibs and Schroth 34. 2,3-Dihydro-1H-indan-1-one (528 mg, 4 mmol), N-bromosuccinimide (684 mg, 4 mmol) and benzoyl peroxide (30 mg, 0.12 mmol) were dissolved in CCl4 (10 mL) and heated to reflux for 1 h under an N2 atmosphere. After cooling, succinimide was removed by filtration and the filtrate concentrated under high vacuum to yield the title compound as a straw-colored oil of >99% purity as seen by GC-MS and NMR that was used without further purification (428 mg, 51% yield). 1H NMR (600 MHz, CDCl3): δ 3.064 (dd, 1H, J=19.7, J=2.3 Hz, CH2), 3.370 (dd, 1H, J=19.7 Hz, J=7.2 Hz, CH2) 5.609 (dd, 1H, J=7.2 Hz, J=2.6 Hz, C3-H), 7.468-7.520 (m, 1H), 7.702-7.775 (m, 3H); 13C NMR (150 MHz, CDCl3): δ 40.28, 50.30, 127.29, 128.81, 128.86, 133.72, 138.00, 204.55; MS (EI) m/z (relative intensity): 208 ([77Br]M+•, 22). CAS Registry No: [40774-41-2].
Example 6
3-(Cyclohexylamino)-2,3-dihydro-1H-inden-1-one (ICD)




3-Bromo-2,3-dihydro-1H-inden-1-one (100 mg, 475 μmol) and cyclohexylamine (94 mg, 951 μmol) were dissolved in 2 mL of dry benzene and stirred under N2 until precipitation ceased ( ̃15 min) The cyclohexylamine.HBr was removed by filtration. The filtrate was applied to a flash SiO2 column that was developed with 8:1 hexanes-EtOAc to give the title compound as a clear oil (91 mg, 84% yield).
Example 7
General procedure for the synthesis of 2-benzylideneindan-1-ones
Corresponding indanone (20 mmol) and corresponding benzaldehyde (20 mmol) were dissolved in methanol (50 mL). Potassium hydroxide (280 mg, 5 mmol) was added in one portion and reaction mixture was stirred at rt for 24 h. Most of solvent was removed in vacuum, and reaction was quenched with water 100 mL. Product was extracted by dichloromethane (3×100 mL), combined organic fractions were dried over MgSO4, filtered and concentrated.
Example 8
(3-Bromo-2-(4-chlorobenzylidene)indan-1-one) 14a
2-(4-chlorobenzylidene)indan-1-one (2.44 g, 9.58 mmol) was dissolved in 35 mL of CCl4. N-bromosuccinimide (1.685 g, 9.58 mmol) and benzoyl peroxide (122 mg, 0.52 mmol) were added in one portion. The solution was then stirred under reflux for one hour and then filtered once cooled to room temperature. The precipitate was separated using flash column chromatography (15:1 Hexanes/EtOAc) provided 14a as white crystals.
Example 9
(4-(1-Bromo-3-oxoindan-2-ylidenemethyl)benzonitrile) 15a
4-(1-oxoindan-2-ylidenemethyl)benzonitrile (2.18 g, 8.9 mmol) was dissolved in carbon tetrachloride (40 mL). N-bromosuccinimide (1.58 g, 8.9 mmol) and benzoyl peroxide (100 mg) were added in one portion. Reaction mixture was reflux for 9 h, cooled down; precipitate was filtered off and washed with diethyl ether (10×30 mL) for removal of N-hydroxysuccinimide Precipitate was dried under vacuum, provided pure 15a.
Example 10
General Procedure for the Synthesis of Compounds 3-16 and 19-32
Corresponding 2-benzylidene-3-bromoindan-1-one 2 (299 mg, 1 mmol) or substituted analog was dissolved in benzene (10 mL). Corresponding amine (2 mmol) was added in one portion and reaction mixture was stirred for 24 h. Solvent was removed in vacuum and product was isolated by column chromatography (silica0.
Example 11
Synthesis of 2-Benzylidene-3-cycloheptylaminoindan-1-one (5)
2-Benzylidene-3-bromoindan-1-one 2 (299 mg, 1 mmol) was dissolved in benzene (10 mL). Cycloheptylamine (255 μL, 2 mmol) was added and reaction mixture was stirred for 24 h. Solvent was removed in vacuum and 5 (271 mg, 82%) was isolated as yellow crystals by column chromatography (Hexanes/EtOAc 9:1) followed by crystallization from dichloromethane with pentane.
Example 12
Synthesis of (2-Benzylidene-3-cyclohexylaminoindan-1-ol) 18
2-Benzylidene-3-cyclohexylamino-indan-1-one (3, BCI) (317 mg, 1 mmol) was dissolved in dry THF (15 mL) under nitrogen. Solution of LiAlH4 (76 mg, 2 mmol) in dry THF (10 mL) was added dropwise at 0° C. Solution was stirred overnight and quenched with 100 μL of water followed by 100 μL of 15% NaOH followed by 300 μL of water. Precipitate was filtered off and washed with ether (3×30 mL). Combined liquid was evaporated in vacuum, and residue was separated by column chromatography on silica (DCM-MeOH—NH4OH 100:1:0.5).
Example 13
Synthesis of (5-(2-Oxohexahydrothieno[3,4-d]imidazol-4-yl)-pentanoic acid (4-amino-cyclohexyl)amide) 19b
1,4-Diaminocyclohexane (37.6 mg, 0.33 mmol) was dissolved in dry DMF (3 mL) under nitrogen. Solution of NHS-Biotin (102.3 mg, 0.3 mmol) in dry DMF (3 mL) was added to stirred solution of diamine over a 15 min period. Reaction mixture was stirred for 16 h at ambient temperature. Dilution of reaction mixture with dry Et2O (50 mL) produced white precipitate. Precipitated 19b was filtered, washed with EtOAc (3×20 mL) for removing of NHS and dried in high vacuum.
Example 14
Characterization of Compounds
Table 2 contains characterization details for the indicated compounds.







TABLE 2







Characterization of BCI analogs














Compound
Yield
Rf
Mp (° C.)
1H NMR (CDCl3, 600 MHz): δ
13C NMR (CDCl3, 150 MHz): δ
HPLC/MS
HRMS





4
91%
0.20
Yellow
0.98-1.07 (m, 1H), 1.22-1.64 (m, 7H), 1.79
23.43, 23.69, 33.24, 34.40, 55.36,
VNK-164AAA >95%
Calcd. 304.1701


VNK-I-16

Hex/EA
oil
(br.s, 1H, NH), 2.94 (quintet, J = 6.6 Hz, 1H),
56.38, 124.04, 126.23, 128.61,
purity
Observed 304.1699




3:1

5.34 (s, 1H, CHN), 7.39-7.43 (m, 1H), 7.47 (t,
128.65, 129.69, 131.34, 134.47,






J = 7.2 Hz, 2H), 7.50 (d, J = 7.2 Hz, 1H), 7.66
134.72, 135.93, 137.57, 138.34,






(t, J = 7.8 Hz, 1H), 7.71 (d, J = 7.8 Hz, 1
152.55, 193.54


5
82%
0.25
Yellow
1.14-1.74 (m, 13H), 2.68-2.74 (m, 1H), 5.35
23.77, 23.90, 28.52, 28.68, 34.24,
VNK-165AAA >95%
Calcd. 332.2014


VNK-I-165

Hex/EA
crystals
(s, 1H), 7.40-7.44 (m, 1H), 7.48 (t, J = 7.2 Hz,
36.52, 54.25, 55.47, 124.21,
purity
Observed 332.2007




3:1
90-92
2H), 7.49-7.52 (m, 1H), 7.65-7.69 (m, 2H),
126.26, 128.64, 128.68, 129.75,






7.76 (s, 1H), 7.93 (d, J = 7.2 Hz, 1H), 7.96 (d,
131.50, 134.50, 134.84, 135.93,






J = 7.8 Hz, 2H).
137.44, 138.44, 152.70, 193.71.


6
69%
0.25
Orange
3.92 (br.s, 1H, NH), 6.01 (s, 1H), 6.78 (d, J =
53.50, 113.64, 118.53, 124.02,
VNK-149 >95%
Calcd. 312.1388


VNK-I-149

Hex/EA
crystals
8.4 Hz, 2H), 6.81 (t, J = 7.8 Hz, 1H), 7.24 (t, J =
125.41, 128.71, 129.15, 129.59,
purity
Observed 312.1390




3:1
153-155
7.8 Hz, 2H), 7.29-7.35 (m, 3H), 7.48 (t, J =
130.15, 132.07, 133.68, 135.33,






7.8 Hz, 1H), 7.54 (t, J = 7.8 Hz, 1H), 7.63 (d,
136.32, 136.78, 137.16, 146.93,






J = 7.8 Hz, 1H), 7.68 (d, J = 6.6 Hz, 2H), 7.80
152.68, 192.81






(d, J = 1.2 Hz, 1H), 7.90 (d, J = 7.2 Hz, 1H)


7
81%
0.55
Slightly
1.34-1.39 (m, 2H), 1.46-1.54 (m, 4H), 2.43
24.69 (CH2), 26.49 (CH2), 50.15
VNK-147 >95%
Calcd. 304.1704


VNK-I-147

Hex/EA
yellow
(br.s, 2H), 2.66-2.73 (m, 2H), 5.04 (d, J = 0.6
(CH2N), 65.04 (CHN), 124.17
purity
Observed 304.1700




1:1
crystals
Hz, 1H, CHN), 7.39-7.43 (m, 1H), 7.45-7.52
(CH), 126.81 (CH), 128.39 (CH),





140-142
(m, 3H), 7.61-7.67 (m, 2H), 7.74 (d, J = 1.2
128.66 (CH), 129.69 (CH), 132.63






Hz, 1H), 7.94 (d, J = 7.8 Hz, 1H), 8.08 (dd, J =
(CH), 133.96 (CH), 135.12 (C-q),






7.8 Hz, J = 1.2 Hz, 2H)
136.86 (CH), 137.83 (C-q), 138.37







(C-q), 149.68 (C-q), 193.65 (C═O)


8
89%
0.4
Yellow
VNK-I-053H:
VNK-I-053CC:
VNK-053 >95%
Calcd. 433.2491,


VNK-I-53

Hex/EA
crystals
0.89 (quin.d, J = 12.6 Hz, J = 3.0 Hz, 2H),
28.39, 31.80, 31.91, 32.48, 33.29,
purity
Observed 433.2491{grave over ( )}




1:1
179-181
1.05 (quin.a, J = 13.2 Hz, 2H), 1.24-1.31 (m,
49.15, 51.81, 55.45, 79.06, 124.10,






1H), 1.40 (br.s., 9H), 1.43 (s, 1H), 1.58 (d, J =
126.11, 128.72, 129.86, 131.31,






12.6 Hz, 1H), 1.76 (dt, J = 12.0 Hz, J = 2.4
134.68, 134.74, 136.11, 137.40,






Hz, 1H), 1.83 (d, J = 12.0 Hz, 1H), 2.30 (d, J =
138.09, 152.78, 155.16, 193.52






4.8 Hz, 1H), 3.26 (br.s., 1H), 4.34 (br.s.,






1H), 5.35 (d, J = 1.2 Hz, 1H), 7.38-7.50 (m,






4H), 7.62-7.67 (m, 2H), 7.75 (d, J = 1.2 Hz,






1H), 7.85 (d, J = 7.2 Hz, 1H), 7.89 (d, J = 7.2






Hz, 1H)


9
81%
0.45
Yellow
2.47 (br.s, 2H), 2.73 (br.s, 2H), 3.62 (t, J = 4.5
49.05 (CH2N), 64.41 (CHN), 67.29
VNK-148 >95%
Calcd. 304.1338


VNK-I-148

Hex/EA
crystals
Hz, 4H, CH2O), 5.08 (d, J = 0.6 Hz, 1H,
(CH2O), 124.31 (CH), 126.86
purity
Observed 304.1447




1:1
138-140
CHN), 7.42-7.50 (m, 3H), 7.51-7.55 (m, 1H),
(CH), 128.49 (CH), 129.08 (CH),






7.64 (d, J = 3.0 Hz, 2H), 7.76 (d, J = 1.2 Hz,
129.96 (CH), 132.36 (CH), 134.28






1H), 7.93 (d, J = 7.2 Hz, 1H), 7.99 (d, J = 7.2
(CH), 134.82 (C-q), 136.64 (C-q),






Hz, 2H)
137.28 (CH), 138.38 (C-q), 148.71







(C-q), 193.17 (C═O)


10
87%
0.30
Slightly
2.50-2.62 (m, 4H), 2.73-2.85 (m, 2H), 2.95-
28.41, 51.71, 65.80, 124.33,
VNK-177 >95%
Calcd. 322.1266


VNK-I-177

Hex/EA
yellow
3.05 (m, 2H), 5.09 (d, J = 1.2 Hz, 1H, CHN),
126.65, 128.42, 129.01, 129.96,
purity
Observed 322.1269




3:1
crystals
7.44 (d, J = 6.6 Hz, 1H), 7.47 (t, J = 7.2 Hz,
132.41, 134.40, 134.66, 136.69,





143-145
2H), 7.52 (ddd, J = 8.4 Hz, J = 6.0 Hz, J = 3.0
137.30, 138.24, 149.04, 193.16






Hz, 1H), 7.65-7.68 (m, 2H), 7.77 (d, J = 1.8






Hz, 1H), 7.96 (t, J = 8.4 Hz, 2H), 7.97 (s, 1H)


11
42%
0.20
Yellow
2.20-2.70, 4.97 (s, 1H, CHN), 7.28-7.33 (m,
64.18, 124.20, 126.83, 128.35,

Calcd. 305.1654


VNK-I-187

DCM
crystals
3H), 7.42 (d, J = 7.8 Hz, 1H), 7.50 (t, J = 7.2
128.84, 129.74, 132.41, 134.18,

Observed 305.1652





245-248
Hz, 1H), 7.55 (t, J = 7.2 Hz, 1H), 7.74 (d, J =
134.83, 137.09, 137.17, 138.24,






0.6 Hz, 1H), 7.91 (dd, J = 6.6 Hz, J = 1.8 Hz,
149.08, 193.39






2H), 7.94 (d, J = 7.2 Hz, 1H)


12
92%
0.55
Yellow
2.21 (s, 3H, CH3), 2.25-3.00 (m, 8H), 5.08 (s,
45.99, 55.42, 64.12, 124.22,
VNK-178 >95%
Calcd. 319.1810


VNK-I-178

DCM/MeOH/NH4OH
oil
1H, CHN), 7.42 (t, J = 7.2 Hz, 1H), 7.46 (t, J =
126.95, 128.45, 128.92, 129.80,
purity
Observed 319.1800




90:10:1

7.2 Hz, 2H), 7.48 (t, J = 7.2 Hz, 1H), 7.59
132.49, 134.14, 134.96, 137.09,






(td, J = 7.2 Hz, J = 1.2 Hz, 1H), 7.65 (d, J =
137.20, 138.29, 149.04, 193.39






7.8 Hz, 1H), 7.74 (d, J = 1.2 Hz, 1H), 7.92 (d,






J = 7.2 Hz, 1H), 8.01 (d, J = 1.2 Hz, 2H)


13
86%
0.20
Yellow
1.98 (s, 3H, CH3), 2.23 (t, J = 7.8 Hz, 1H),
21.28 (CH3), 41.82 (CH2), 46.60
VNK-179 >95%
Calcd. 347.1760


VNK-I-179

EtOAc
oil
2.57-2.62 (m, 1H), 2.65-2.69 (m, 1H), 2.77 (t,
(CH2), 48.02 (CH2), 49.36 (CH2),
purity
Observed 347.1766






J = 7.8 Hz, 1H), 3.20 (t, J = 9.0 Hz, 1H), 3.29
64.20 (CHN), 124.43 (CH), 126.69






(t, J = 9.0 Hz, 1H), 3.33-3.39 (m, 1H), 3.81 (d,
(CH), 128.50 (CH), 129.21 (CH),






J = 10.2 Hz, 1H), 5.16 (s, 1H, CHN), 7.41 (t,
130.06 (CH), 132.29 (CH), 134.41






J = 6.6 Hz, 1H), 7.45 (t, J = 7.2 Hz, 2H), 7.50
(CH), 134.64 (Cq), 136.43 (Cq),






(t, J = 7.2 Hz, 1H), 7.57 (d, J = 7.2 Hz, 1H),
137.43 (CH), 138.29 (Cq), 148.42






7.63 (t, J = 7.2 Hz, 1H), 7.76 (br.s, 1H), 7.91
(Cq), 168.88 (C═O(N)), 193.01






(d, J = 7.8 Hz, 1H), 7.95 (d, J = 7.8 Hz, 2H)
(C═O)


14
93%

118-122
0.99-1.14 (m, 5H), 1.37 (d, J = 12 Hz, 2H),
24.83, 24.89, 25.85, 33.60, 34.97,
VNK-183AAA >95%
Calcd. 352.1468


VNK-I-183



1.53-1.56 (m, 3 H), 1.65-1.68 (m, 1H), 1.77
124.26, 126.06, 128.73, 128.87,
purity
Observed 352.1466






(d, J = 12.6 Hz, 1H), 2.45-2.49 (m, 1H), 7.44
133.13, 133.28, 134.72, 135.81,






(dd, J = 6.6 Hz, J = 1.8 Hz 2H), 7.51 (td, J = 7.2
137.30, 138.79, 152.71, 193.50






Hz, J = 1.2 Hz, 1 H), 7.65-7.68 (m, 3 H) 7.93






(d, J = 7.8 Hz, 1 H), 7.97 (d, J = 8.4 Hz, 2 H).


15
88%
0.50
Yellow
0.97-1.83 (m, 11H), 2.49 (tt, J = 9.6 Hz, J =
24.80, 25.81, 33.45, 34.95, 52.58,
VNK-137 >95%
Calcd. [M + H]


VNK-I-137

Hex/EA
crystals
3.6 Hz, 1H), 5.30 (s, 1H), 7.53 (t, J = 7.2 Hz,
55.00, 112.62, 118.67, 124.46,
purity
343.1810




1:1
174-176
1H), 7.65 (d, J = 7.2 Hz, 1H), 7.69 (s, 1H),
126.06, 128.95, 131.29, 131.72,

Observed 343.1763






7.71 (t, J = 7.2 Hz, 1H), 7.75 (d, J = 8.4 Hz,
132.16, 132.18, 133.65, 135.12,






2H), 7.94 (d, J = 7.8 Hz, 1H), 8.17 (d, J = 8.4
137.02, 139.28, 141.44, 152.60,






Hz, 2H)
193.17


16
94%

162-164
0.94 (m, 2H), 1.04 (m, 3H), 1.24 (d, J = 12.6
24.79, 24.97, 25.83, 34.02, 34.82,
VNK-169 >95%
Calcd. [M + H]


VNK-I-169



Hz, 2H), 1.49 (d, J = 9.0 Hz, 2H), 1.57 (d, J =
52.85, 55.41, 117.46, 118.50,
purity
343.1810






12.0 Hz, 2H), 2.28 (m, 1H), 5.41 (s, 1H),
124.85, 129.98, 130.53, 130.55,

Observed 343.1808






7.47 (m, 3H), 7.76 (d, J = 8.4 Hz, 1H), 7.84 (s,
131.68, 132.35, 134.35, 137.13,






1H), 7.87 (d, J = 7.8 Hz, 2H), 7.98 (d, J = 6.6
138.26, 140.47, 153.34, 192.31






Hz, 2H)


17
84%

oil
1.06-1.21 (m, 4H), 1.21-1.34 (m, 2H), 1.59-
24.73, 24.92, 25.94, 33.12, 34.47,

Calcd. 230.1545


WD



1.65 (m, 1H), 1.70-1.83 (m, 3H), 1.95-2.05
46.01, 53.07, 55.23, 123.14,

Observed 230.1550


compound



(m, 1H), 2.45 (dd, J = 18.6 Hz, J = 3.0 Hz,
125.83, 128.41, 134.73, 136.52,


data



1H), 2.60-2.68 (m, 1H), 2.95 (dd, J = 6.7 Hz, J =
156.61, 204.77






18.6 Hz, 1H), 4.52 (dd, J = 6.6 Hz, J = 3.0






Hz, 1H), 7.38 (dd, J = 7.3 Hz, J = 0.9 Hz, 1H),






7.59 (dd, J = 7.2 Hz, J = 0.9 Hz, 1H), 7.63 (d,






J = 7.7 Hz, 1H), 7.69 (d, J = 7.7 Hz, 1H)


18
54%
0.30
oil
1.05-1.30 (m, 6H), 1.49 (d, J = 9.6 Hz, 1H),
25.00 (CH2), 25.11 (CH2), 26.10
VNK-146 >95%
Calcd. 320.2014


VNK-I-146

DCM/MeOH/NH4OH

1.57-1.64 (m, 2H), 1.71-1.77 (m, 1H), 2.01 (d,
(CH2), 32.74 (CH2), 34.64 (CH2),
purity
Observed 320.2004




90:10:1

J = 12 Hz, 1H), 2.50-2.56 (m, 1H, CHN), 5.15
53.25 (CH), 57.49 (CH), 76.25






(s, 1H, CH—NCy), 5.77 (s, 1H, CHOH), 6.93
(CHOH), 124.62 (CH), 125.25






(s, 1H), 7.30 (dd, J = 7.8 Hz, J = 7.2 Hz, 1H),
(CH), 126.20 (CH), 127.27 (CH),






7.31-7.34 (m, 2H), 7.35-7.38 (m, 1H), 7.39 (t,
128.33 (CH), 128.38 (CH), 128.






J = 7.8 Hz, 2 H), 7.55 (d, J = 7.2 Hz, 1H),
98 (CH), 136.90 (C-q), 143.39 (C-






7.67 (d, J = 7.2 Hz, 2H)
q), 134.61 (C-q), 148.79 (C-q)


19
47%

126-129
VNK-I-114H:
VNK-I-114CC:
VNK-108G >95%
Calcd. 559.2743,


VNK-108


(decomp.)
0.85-1.80 (m, 15 H), 2.08 (td, J = 7.2 Hz, J =
25.61, 28.00, 29.71, 31.51, 31.61,
purity
Observed 559.2750






2.4 Hz, 2H), 2.25-2.32 (m, 1H), 2.69 (d, J =
32.56, 33.29, 36.02, 40.54, 47.72,






12.6 Hz, 1H), 2.88 (dd, J = 13.2 Hz, J = 4.8
51.74, 55.41, 55.52, 60.12, 61.73,






Hz, 1H), 3.10 (td, J = 7.2 Hz, J = 4.8 Hz, 1H),
124.09, 126.13, 128.78, 129.94,






3.52-3.59 (m, 1H), 4.26 (dd, J = 6.0 Hz, J =
131.36, 134.65, 134.80, 136.25,






4.8 Hz, 1H), 4.47 (dd, J = 7.8 Hz, J = 5.4 Hz,
137.45, 137.98, 138.03, 152.80






1H), 5.15 (br.s, 1H), 5.37 (s, 1H), 5.55 (d, J =
163.48, 172.20, 193.62






6.0 Hz, 1H), 5.96 (d, J = 17.4 Hz, 1H), 7.39-






7.49 (m, 4H), 7.65-7.67 (m, 2H), 7.75 (br.s,






1H), 7.86 (d, J = 7.2 Hz, 2H), 7.89 (d, J = 7.8






Hz, 1H)


19b
91%

>300
VNK-MT-2_HH:
VNK-I-105DC:

Calcd. 341.2011,






(D2O, 600 MHz): δ 1.20-1.65 (m, 7H), 1.75-
(DMSO-d6, 150 MHz): δ 26.44,

Observed 341.2011






1.80 (m, 2H), 1.85-1.90 (m, 1H), 1.94-1.99
26.62, 29.30, 29.42, 32.41, 35.37,






(m, 1H), 2.02-2.06 (m, 2H), 2.07 (td, J = 7.2
35.65, 36.50, 41.29, 50.81, 50.94,






Hz, J = 3.0 Hz, 1 H), 2.09-2.13 (m, 1H), 2.54
56.70, 60.43, 62.29, 163.95,






(br.s, 4H), 2.66 (dd, J = 13.2 Hz, J = 4.2 Hz,
174.48






1H), 2.88 (dtd, J = 12.6 Hz, J = 4.8 Hz, J =






1.8 Hz, 1H), 3.08-3.14 (m, 1H), 3.19-3.26 (m,






1H), 3.61-3.65 (m, 3H), 4.32 (ddd, J = 13.8






Hz, J = 7.8 Hz, J = 4.2 Hz, 1H), 4.49 (ddd, J =






7.8 Hz, J = 5.4 Hz, J = 2.4 Hz, 1H)


20
32%
0.20
Orange
1.361 (d, 1H, J = 12.00), 1.643 (dd, 1H,
24.89 (CH2), 25.89 (CH2), 33.81
VNK-211 >95%
Calcd. [M + H]+ 348.1964,


VNK-I-211B

Hex/EA
crystals
J = 14.40), 1.747 (d, 1H, J = 12.60), 2.444 (m,
(CH2), 35.01 (CH2), 52.46 (CH),
purity
Observed 348.1907




3:1
112-113
1H), 3.901 (s, 3H), 5.342 (s, 1H), 6.993 (d,
55.41 (CH), 114.15 (CH), 124.06






2H, J = 9.00), 7.482 (td, 1H), 7.657 (d, 2H),
(CH), 126.02 (CH), 127.44 (CR3),






7.719 (ds, 1H), 7.918 (d, 1H, J = 7.80), 7.952
128.53 (CH), 133.82 (CH), 134.28






(d, 2H, J = 9.00)
(CH), 135.97 (CH), 137.69 (CR3),







152.73 (CR3), 160.98 (CR3),







193.72 (CO)


21
48%
0.20
Yellow
0.88-1.10 (m, 8 H), 1.27 (s, 1 H), 1.31-1.50
10.97, 14.07, 21.59, 23.00, 23.73,
VNK-212 >95%
Calcd. [M + H]+ 332.2014,


VNK-I-212

Hex/EA
oil
(m, 2 H), 1.51-1.54 (m, 2 H), 1.60-1.63 (m,
24.86, 24.99, 25.86, 28.93, 30.35,
purity
Observed 332.0384




9:1

3H), 1.69-1.71 (m, 2H), 2.43 (s, 4H), 5.38 (s,
33.85, 34.94, 38.72, 52.50, 55.33,






1H), 7.29 (s, 1H), 7.5 (dt, J = 1.2 Hz, 1 H),
68.15, 76.81, 77.02, 77.23, 124.09,






7.65-7.69 (m, 2H) 7.71-7.74 (m, 1H), 7.842
126.16, 128.57, 128.81, 128.84,






(d, J = 8.4 Hz, 2H), 7.92 (d, J = 7.8 Hz, 1 H)
129.47, 130.90, 131.42, 131.66,







131.96, 132.44, 134.45, 136.04,







137.50, 137.57, 140.25, 140.45,







152.86, 167.78, 193.77


22
66%
0.16
Yellow
0.94 (m, 2H), 1.04 (m, 3H), 1.24 (d, J = 9 Hz,
24.87, 25.01, 25.90, 34.04, 34.89,
VNK-215 >95%
Calcd. [M + H]+ 396.0963,


VNK-I-215

Hex/EA
crystals
1H), 1.49 (m, 2H), 1.54 (m, 2H), 1.60 (m,
52.73, 55.34, 125..54, 128.87,
purity
Observed 396.1009




9:1
131-133
1H), 2.32 (m, 1H), 5.35 (s, 1H), 7.42 (t, J =
129.59, 129.89, 130.09, 131.52,






7.2 Hz, 1H), 7.47 (t, J = 7.2 Hz, 2H), 7.62 (dd,
132.35, 134.72, 136.32, 136.85,






J = 8.2 Hz, J = 1.8 Hz, 1H), 7.77 (d, J = 7.8
137.83, 154.88, 192.66






Hz, 2H), 7.83 (d, J = 1.2 Hz, 1H), 7.87 (d, J =






7.2 Hz, 1H)


23
88%
0.07
yellow
0.88-1.63 (m, 11H), 2.33 (m, 1H), 3.93 (s,
11.11, 14.21, 23.14, 23.87, 24.97,
VNK-216 >95%
Calcd. [M + H]+ 348.1964


VNK-I-216

Hex/EA
oil
3H), 5.34 (s, 1H), 7.01 (dd, J = 8.4 Hz, J = 1.8
25.11, 25.93, 20.07, 30.49, 34.33,
purity
Observed 348.1874




5:1

Hz, 1H), 7.12 (d, J = 1.8 Hz), 7.39 (t, J = 7.2
34.95, 38.86, 52.62, 55.65, 55.93,






Hz, 1H), 7.45 (t, J = 7.8 Hz, 2H), 7.70 (s, 1H),
68.29, 109.86, 116.32, 126.05,






8.85 (t, J = 7.8 Hz, 3H)
128.16, 128.80, 128.95, 129.58,







131.04, 131.07, 131.17, 134.74,







135.17, 139.09, 156.08, 165.33,







192.19


24
88%

Yellow
Mixture of isomers
ND
Mixture of
Calcd. [M + H]+ 292.1701


VNK-I-217


oil
CSA-1-12B - pure,

isomers
Observed 292.1666






CSA-1-13B - isomerized

20:72 by








HPLC VNK-217


25
86%
0.27
yellow
0.92-1.12 (m, 5H), 1.30-1.37 (m, 1H), 1.46-
24.92 (CH2), 24.99 (CH2), 25.84
>95% purity
(M + H+):




Hex/EA
solid
1.565 (m, 2H), 1.57-1.68 (m, 3H), 2.3702.45
(CH2), 34.14 (CH2), 34.99 (CH2),

Calcd. [M + H]+ 378.2069,




1:1
161-163
(m, 1H), 3.88 (s, 3H), 3.94 (s, 3H), 5.28 (s,
52.39 (CH or CH3), 55.39 (CH or

Observed 378.2180






1H), 6.98 (d, J = 8.4 Hz, 2H), 7.01 (d, J = 8.4
CH3), 55.50 (CH or CH3), 55.75






Hz, 1H), 7.11 (s, 1H), 7.65 (s, 1H), 7.86 (d, J =
(CH or CH3), 109.76 (CH), 114.13






8.4 Hz, 1H), 7.88 (d, J = 8.4 Hz, 2H)
(CH), 115.83 (CH), 125.80 (CH),







127.59, 131.13, 133.38 (CH),







134.64 (CH), 136.51, 155.62,







160.72, 164.93, 192.17


26
79%
0.22
yellow
2.50 (br.s, 2H), 2.77 (br.s, 2H), 3.62 (br.s,
48.95 (CH2), 55.38 (CH3), 55.76
Purity >95%
Calcd. [M + H]+ 366.1705,




Hex/EA
solid
4H), 3.87 (s, 3H), 3.94 (s, 3H), 5.00 (s, 1H),
(CH3), 64.47 (CH), 67.37 (CH2),
by LC/MS
Observed 366.1795




1:1
156-158
6.98 (d, J = 8.4 Hz, 2H), 7.02 (dd, J = 8.4 Hz,
110.97 (CH), 113.92 (CH), 115.71






J = 2.4 Hz, 1H), 7.07 (d, J = 1.8 Hz, 1H), 7.65
(CH), 125.96 (CH), 127.66,






(d, J = 0.6 Hz, 1H), 7.88 (d, J = 8.4 Hz, 1H),
131.96, 134.31 (CH), 134.55,






7.95 (d, J = 8.4 Hz, 2H)
135.87 (CH), 151.15, 160.90,







164.53, 191.78


27
86%
0.40
yellow
2.49 (br.s, 2H), 2.75 (br.s, 2H), 3.62 (t, J = 4.2
49.03, 64.38, 67.26, 124.41,
Purity >95%
Calcd. [M + H]+ 340.1104,




Hex/EA
solid
Hz, 4H), 5.08 (d, J = 1.2 Hz, 1H), 7.45 (d, J =
126.88, 128.76, 129.20, 133.27,
by LC/MS
Observed 340.1132




1:1
175-177
8.4 Hz, 2H), 7.52-7.56 (m, 1H), 7.65-7.68 (m,
133.59, 134.42, 135.81, 136.01,






2H), 7.71 (d, J = 1.8 Hz, 1H), 7.95 (d, J = 8.4
137.03, 138.32, 148.50, 192.90






Hz, 1H), 7.97 (d, J = 8.4 Hz, 2H)


28
77%

yellow
0.95-1.17 (m, 5H), 1.35 (d, J = 12.6 Hz, 1H),
24.75 (CH2), 24.81 (CH2), 25.78
Purity >95%





solid
1.47 (s, 1H), 1.51-1.58 (m, 2H), 1.68 (t, J =
(CH2), 33.67 (CH2), 34.88 (CH2),
by LC/MS





176-178
13.8 Hz, 2H), 2.41 (tt, J = 10.2 Hz, J = 3.6
52.55 (CH), 54.99 (CH), 125.52






Hz, 1H), 5.27 (s, 1H), 7.45 (d, J = 8.4 Hz,
(CH), 128.95 (CH), 129.28 (CH),






2H), 7.64 (dd, J = 8.4 Hz, J = 1.2 Hz, 1H),
129.86 (C), 132.31 (CH), 133.02






7.69 (d, J = 1.8 Hz, 1H), 7.78 (d, J = 8.4 Hz,
(C), 133.10 (CH), 135.49 (CH),






1H), 7.80 (br.s, 1H), 7.93 (d, J = 8.4 Hz, 2H)
136.08 (C), 137.99 (C), 154.43







(C), 192.29 (C)


29
72%

yellow
2.49 (br.s, 2H), 2.73 (br.s, 2H), 3.62 (br.s,
48.99 (CH2), 64.16 (CH), 67.19
Purity >95%





solid
4H), 5.04 (s, 1H), 7.45 (d, J = 8,4 Hz, 2H),
(CH2), 125.67 (CH), 128.86 (CH),
by LC/MS





222-224
7.67 (d, J = 8.4 Hz, 1H), 7.71 (s, 1H), 7.80 (d,
129.68 (C), 129.96 (CH), 132.76






J = 8.4 Hz, 1H), 7.83 (s, 1H), 7.93 (d, J = 8.4
(CH), 132.98 (C), 133.61 (CH),






Hz, 2H)
136.26 (C), 136.34 (C), 136.58







(CH), 137.14 (C), 150.06 (C),







191.65 (C)


30
???
0.1
183-184
2.51 (br s, 2H), 2.74 (br.s, 2H), 3.62 (t, J = 4.2
30.96, 64.22, 67.23, 125.61,




Hex/EA

Hz, 4H), 5.09 (s, 1H), 7.44-7.50 (m, 3H), 7.66
128.57, 129.51, 129.92, 130.22,




9:1

(d, J = 1.8 Hz, 1H), 7.79 (d, J = .6 Hz, 1H), 7.81
132.38, 132.64, 134.57, 135.88,






(d, J = 8.4 Hz, 1H), 7.84 (d, J = 6 Hz, 1H), 7.98
137.22, 138.09, 150.28, ~192






(d, J = 6.6 Hz, 2H)


31
74%


32
72%
















TABLE 3







Characterization of bromobenzylidene indanones













Compound
Yield
Rf
Mp, ° C.
1H NMR (CDCl3, 600 MHz): δ
13C NMR (CDCl3, 150 MHz): δ
HRMS





14a
57%

168-170° C.
6.38 (s, 1H), 7.55 (d, J = 1.2 Hz, 2H),
42.52, 124.26, 127.07, 129.35,
Calcd.






7.57 (t, J = 0.6 Hz, 1H), 7.74 (s, 1 H),
130.11, 131.93, 133.73, 135.39,
(M − Br) 253.0420






7.74-7.77 (m, 4H), 7.93(d, J = 7.8
135.67, 135.76, 136.27, 136.94,
Observed 253.0339






Hz, 1 H)
150.44, 190.63


15a
83%
0.60
Colorless
1H NMR (DMSO-d6, 600 MHz): δ
13C NMR (DMSO-d6, 150 MHz): δ
Calcd.


VNK-I-132

DCM
crystals
7.16 (s, 1H), 7.65 (t, J = 7.2 Hz, 1H),
43.04, 112.44, 118.49, 123.72,
324.0024,





197-199
7.74 (s, 1H), 7.83-7.90 (m, 3H), 8.03
127.54, 130.44, 132.49, 132.70,
Observed 324.0060





(decomp.)
(d, J = 8.4 Hz, 2H), 8.11 (d, J = 8.4
133.83, 135.37, 136.47, 137.54,






Hz, 2H)
138.55, 150.89, 189.90


20a
28%

colorless
2.79 (s, 4.6H), 3.92 (s, 3H), 6.397 (s,
ND
Calcd.


VNK-I-211A


crystals
1H), 7.06 (d, J = 8.4 Hz, 2H), 7.78 (d,

[M − Br]+ 249.0916






J = 7.8 Hz, 1H), 7.84 (d, J = 9.0 Hz,

Observed 249.0723






2H), 7.91 (d, J = 7.8 Hz, 1H); 7.53 (t,






1H), 7.72 (t, 2H)


22a
10%
0.20
colorless
6.33 (s, 1H), 7.53 (m, 3H), 7.67 (dd,
41.72, 125.59, 129.22, 130.44,
Calcd.


VNK-I-215a

Hex/EA
crystals
J = 7.8 Hz, J = 1.2 Hz, 1H), 7.76 (t, J =
130.54, 131.09, 132.85, 133.39,
[M + H]+ 376.9171




15:1
188-190
5.4 Hz, 2H), 7.82 (d, J = 7.2 Hz,
133.73, 134.88, 135.26, 137.83,
Observed 376.9174






2H), 7.92 (s, 1H)
152.23, 189.87


23a
89%
0.40
Yellow
3.95 (s, 3H), 6.34 (s, 1H), 6.05 (dd, J =
43.08, 56.08, 110.25, 118.17, 126.14,
Calcd.


VNK-I-216a

Hex/EA
crystals
8.4 Hz, J = 1.8 Hz, 1H), 7.16 (d, J =
129.08, 129.88, 130.54, 132.54,
[M + H]+ 329.0177




3:1
146-148
2.4 Hz, 1H), 7.47 (t, J = 7.2 Hz,
133.78, 135.85, 136.01, 153.52,
Observed 329.0183






1H), 7.52 (t, J = 7.2 Hz, 2H), 7.68 (s,
165.89, 189.41






1H), 7.81 (d, J = 7.8 Hz, 2H), 2H,






7.84 (d, J = 8.4 Hz, 1H)


25a
91%

Yellow
3.91 (s, 3H), 3.96 (s, 3H), 6.32 (s,
43.89, 55.48, 55.91, 110.16, 114.52,





solid
1H), 7.03-7.08 (m, 3H), 7.18 (d, J =
117.81, 125.82, 126.32, 129.96,





171-173
1.8 Hz, 1H), 7.65 (s, 1H), 7.79 (d, J =
133.24, 134.69, 135.62, 153.19,






8.4 Hz, 2H), 7.84 (d, J = 8.4 Hz,
161.52, 165.52, 189.38






1H)


28a
78%

White solid
6.29 (s, 1H), 7.52 (d, J = 8.4 Hz,
41.23, 125.47, 129.42, 130.33,





199-201
2H), 7.68 (d, J = 8.4 Hz, 1H), 7.71
130.58, 131.67, 133.70, 133.77,






(s, 1H), 7.75 (d, J = 8.4 Hz, 2H),
135.04, 135.11, 136.13, 137.23,






7.78 (d, J = 8.4 hz, 1H), 7.93 (s, 1H)
151.90, 189.46


31a
74%

White solid
6.35 (s, 1H), 7.57 (t, J = 7.2 Hz, 1H),
41.90, 124.33, 127.12, 130.22,





216-219
7.61 (d, J = 8.4 Hz, 1H), 7.64 (d, J =
130.96, 131.27, 133.38, 133.41,






0.6 Hz, 1H), 7.66 (dd, J = 8.4 Hz, J =
133.79, 134.86, 135.88, 136.13,






2.4 Hz, 1H), 7.76 (td, J = 7.8 Hz, J =
136.91, 150.35, 190.34






0.6 Hz, 1H), 7.79 (d, J = 7.8 Hz,






1H), 7.91-7.95 (m, 2H)
















TABLE 4







Characterization of benzylidene indanones













Compound
Yield
Rf
Mp, ° C.
1H NMR (CDCl3, 600 MHz): δ
13C NMR (CDCl3, 150 MHz): δ
HRMS














25b
99%
slightly yellow
3.88 (s, 3H), 3.93 (s, 3H), 3.99 (s, 2H,
32.56, 55.40, 55.68, 109.75, 114.41, 115.08,




solid, mp =
CH2), 6.95-7.05 (m, 4H), 7.60 (t, J = 1.8
126.07, 128.33, 131.67, 132.35, 132.53,




146-148° C.
Hz, 1H), 7.64 (d, J = 9.0 Hz, 2H), 7.86 (d,
132.94, 152.35, 160.62, 165.03, 192.91





J = 8.4 Hz, 1H)


28b
97%
white solid
4.02 (s, 2H), 7.46 (d, J = 8.4 Hz, 2H),
32.04, 125.75, 129.33, 129.48, 129.90,




251-254
7.57-7.62 (m, 3H), 7.65 (t, J = 2.4 Hz, 1H),
131.46, 131.83, 133.25, 133.58, 134.39,





7.75 (br.s, 1H), 7.79 (d, J = 8.4 Hz, 1H)
135.98, 136.76, 150.95, 192.92









Example 15
Structure-Activity Relationship of BCI Analogs
We tested a series of structurally related analogs of BCI in an in vivo assay. As described in Molina et al. (Nature Chemical Biology, 2009), Tg(Dusp6:dsEGFP) embryos were treated at 24 hours post fertilization with increasing doses of compounds. After 6 hours treatment, embryos were imaged by the IXU ImageXpress (Molecular Devices), and images were processed by Definiens Software. The software identified bright head structures and measured fluorescence.
In a dose-dependent manner, BCI expanded GFP expression in transgenic embryos and the EC50 was measured as 11.4 μM (FIG. 16). Under similar conditions, BCI-related analogs were tested and EC50 values measured. In these studies, MT9 was at least 2.5 fold more potent than BCI, while other analogs were equipotent to BCI (FIG. 17).
We next addressed if BCI and related analogs are detrimental to zebrafish embryo survival after prolong exposure. Embryos soaked in BCI at high doses (>10 μM) for 24 hours resulted in embryo defects, such as tail necrosis and even death (FIG. 17). The percentage of embryos that died after 24 hours treatment was 100% at 20 μM. Treatment with the highly potent MT9 resulted in 100% lethality at lower doses (10 μM) than BCI. In contrast VNK215, which had similar activity to BCI was non-toxic, even as high as 40 μM (FIG. 17 and not shown).
Thus, the cyclohexoamino group of BCI appears important for that compound's potency in inhibiting Dusp6 and the addition of a bromine to the indanone group suppresses toxicity.
Example 16
BCI Structure-Activity Relationship Studies
Transgenic zebrafish embryos (24 hpf) were treated with 20 μM solution of BCI analogs in 0.5% aq DMSO and fluorescence photomicrographs were taken after 6 h. The effectiveness of BCI analogs was evaluated by densitometry (ImageJ) of d2EGFP intensity in the dorsal region.










TABLE 5








Activity



Compound
(BCI = 100)



















 1
0



 3 (BCI)
100



(−)-BCI
156



(+)-BCI
82



 4
123



 5
127



 6
7



 7
114



 8
Less than BCI



 9
114



10
27



11
22



12
0



13
47



14
52



15
20



16
Less than BCI



17 (ICD)
0



18
26



19
No activity,




trapped in yolk










Table 5 shows the in vivo activity of eighteen BCI analogs. First, the structural features required for the activity of BCI were determined Analog 1, lacking the cyclohexylamine group, and analog 17 (ICD), lacking the benzylidene group, were inactive. Reduction of the carbonyl group to an alcohol in analog 18 resulted in a significant loss of activity. Thus, for BCI, the amino group and benzylidene are important for the activity of BCI, and the carbonyl group is desirable.




Second, analogs 4-6, comprising different secondary amines were tested. In reference to the structure above, replacement of ring A of BCI with a cyclopentyl or cyloheptyl ring resulted in a significant increase of activity, whereas replacement of the flexible cyclohexylamine ring with a rigid phenyl group (analog 6) dramatically decreased activity. Molecular modeling suggested that the NH at C3 of the indanone forms a hydrogen bond with Trp264 in the binding site of Dusp6. To test this hypothesis, we synthesized compound 7, comprising a piperidine at C3. Unexpectedly, 7 was more active than BCI, despite the lack of a hydrogen bond donor.
Since we established that the group at the C3 of the indanone in the general scaffold can be a secondary or tertiary amine, we studied the effect of additional hydrogen bond donors/acceptors in the 4′ position of Ring B of BCI. Introduction of an additional amine in compound 8 resulted in significant loss of activity. Morpholine analog 9 had the same activity as piperidine analog 7. Thiomorpholine analog 10 and the three piperazine analogs 11-13, however, had much less activity.
A study of the structure-activity relationship on the periphery of other rings was then undertaken. Molecular modeling suggested that ring B is oriented out of the binding pocket, and substituents on this ring could affect activity only indirectly. We found that introduction of chloride in the p-position of ring B resulted in a loss of activity for 14 (52% as compared to BCI), whereas a more electron withdrawing cyano group at this position in 15 decreased activity even further (to 20%). Introduction of a cyano group to ring C in 16 also resulted in a decrease in activity. Finally, biotin-linked analog 19 was completely trapped in the yolk and showed no effect on FGF signaling.
We have separated the enantiomers of BCI by supercritical fluid chromatography over commercially available chiral columns (See, Cole, J., et al. Profiling the isomerization of biologically relevant (E)-(Z) isomers by supercritical fluid chromatography (SFC). LCGC The Application Notebook—Chromatography Online, 2009, June 1, 1-6 [erratum in September 2009, 51]) and determined that the activity of the levorotatory enantiomer is twice that of the dextrorotatory form. Establishment of the absolute configuration of each enantiomer is in progress.
Having described this invention above, it will be understood to those of ordinary skill in the art that the same can be performed within a wide and equivalent range of conditions, formulations and other parameters without affecting the scope of the invention or any embodiment thereof. Any document incorporated herein by reference is only done so to the extent of its technical disclosure and to the extent it is consistent with the present application and the disclosure provided herein. Deference is to be given to definitions, descriptions, wording, language, data, statements, etc. provided in the present document where any material disclosed in such incorporated references, to include definitions, descriptions, data and statements, conflicts with material provided in the present application.

## Claims

1. A compound having the formula:



in which R1 represents one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; R2 is a a secondary or tertiary amine group; R3 is one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; and R4 is ═O or —OH, wherein
when both R1 and R3 are H,
R4 is —OH, or
R3 is one or more independently of halo, C1-3 alkyl, C1-3 alkoxyl or —CN, and

when R1 is H and R4 is ═O, R3 is one or more independently of halo, C1-3 alkyl, C1-3 alkoxyl or —CN,
or a pharmaceutically-acceptable salt thereof.

2. The compound of claim 1 in which R2 is a C4-10 cycloalkylamine.

3. The compound of claim 1 in which R2 is one of cyclopentylamine and cycloheptylamine.

4. The compound of claim 1 consisting essentially of a (−) enantiomer of the compound.

5. The compound of claim 1 having the formula:

6. The compound of claim 1 in which R4 is ═O.

7. The compound of claim 6 in which R2 is one of 4-t-Boc-cyclohexylamine, thiamorpholine, piperazine, methyl piperazine, acetyl piperazine, cyclopentylamine, cycloheptylamine and di-C1-4-alkylamine.

8. The compound of claim 1 in which R4 is —OH.

9. The compound of claim 1, wherein R1 is 3,4-di-halo.

10. The compound of claim 1, wherein R1 is 3,4-dichloro.

11. The compound of claim 1, wherein R2 is one of C4-10 cycloalkylamine, 4-t-Boc-cyclohexylamine, thiamorpholine, piperazine, methyl piperazine, acetyl piperazine, phenylamine, piperidine, morpholine, biotin, and di-C1-4-alkylamine.

12. A composition comprising one or more compounds of claim 1 and a pharmaceutically acceptable excipient.

13. A method of inhibiting dual specificity phosphatase 6 (Dusp6)-induced dephosphorylation of extracellular signal-related kinase (ERK), comprising contacting a cell with a compound having the formula:



in which R1 represents one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; R2 is a secondary or tertiary amine group; R3 is one or more independently of H, halo, C1-3 alkyl, C1-3 alkoxyl or —CN; and R4 is ═O or —OH, wherein
when both R1 and R3 are H,
R4 is —OH, or
R3 is one or more independently of halo, C1-3 alkyl, C1-3 alkoxyl or —CN, and

when R1 is H and R4 is ═O, R3 is one or more independently of halo, C1-3 alkyl, C1-3 alkoxyl or —CN,
or a pharmaceutically-acceptable salt thereof, in an amount effective to inhibit dephosphorylation of ERK by Dusp6.

14. The method of claim 13, wherein R3 is halo.

15. The method of claim 14, where R3 is Br.

16. The method of claim 13, wherein R2 is a C4-10 cycloalkylamine.

17. The method of claim 13, wherein R2 is one of cyclopentylamine and cycloheptylamine.

18. The method of claim 13, wherein R1 is H, R2 is one of cyclopentylamine, cyclohexylamine, and cycloheptylamine, and R3 is Br.

19. The method of claim 18, wherein R2 is cyclohexylamine.

20. The method of claim 13, wherein the compound has the structure: