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1.  Identification of Influenza Endonuclease Inhibitors Using a Novel Fluorescence Polarization Assay 
ACS chemical biology  2012;7(3):526-534.
Influenza viruses have been responsible for the largest pandemics in the previous century. Although vaccination and prophylactic antiviral therapeutics are the primary defense against influenza virus, there is a pressing need to develop new antiviral agents to circumvent the limitations of current therapies. The endonuclease activity of the influenza virus PAN protein is essential for virus replication and is a promising target for novel anti-influenza drugs. To facilitate the discovery of endonuclease inhibitors, we have developed a high-throughput fluorescence polarization (FP) assay, utilizing a novel fluorescein-labeled compound (Kd = 0.378 μM) and a PAN construct, to identify small molecules that bind to the PAN endonuclease active site. Several known 4-substituted 2,4-dioxobutanoic acid inhibitors with high and low affinities have been evaluated in this FP-based competitive binding assay, and there was a general correlation between binding and the reported inhibition of endonuclease activity. Additionally, we have demonstrated the utility of this assay for identifying endonuclease inhibitors in a small diverse targeted fragment library. These fragment hits were used to build a follow up library that that led to new active compounds which demonstrate FP binding and anti-influenza activities in plaque inhibition assays. The assay offers significant advantages over previously reported assays, and is suitable for high-throughput and fragment-based screening studies. Additionally the demonstration of the applicability of a mechanism-based ‘targeted fragment’ library supports the general potential of this novel approach for other enzyme targets. These results serve as a sound foundation for the development of new therapeutic leads targeting influenza endonuclease.
PMCID: PMC3960075  PMID: 22211528
2.  The development and application of small molecule modulators of SF3b as therapeutic agents for cancer 
Drug discovery today  2012;18(1-2):43-49.
The identification of potent spliceosome modulators that demonstrate antitumor activity indicates that this complex may be a target for drug development. Several natural products have been demonstrated to bind to the SF3b1 subunit of this macromolecule and these agents modulate alternative RNA splicing. In this article we describe their biological properties, discuss the validity of the spliceosome as a therapeutic target, and propose that alteration of alternative splicing represents a viable approach for inducing tumor-selective cytotoxicity.
PMCID: PMC3596818  PMID: 22885522
Spliceosome; alternative splicing; sudemycin; SF3b
3.  Quinazolines as Adenosine Receptor Antagonists: SAR and Selectivity for A2B Receptors 
We have recently reported the discovery of numerous new compounds that are selective inhibitors of all of the subtypes of the adenosine receptor family via a pharmacophore database searching and screening strategy. During the course of this work we made the unexpected discovery of a potent A2B receptor antagonist, 4-methyl-7-methoxyquinazolyl-2-(2′-amino-4′-imidazolinone) (38, CMB 6446), which showed selectivity for this receptor and functioned as an antagonist, with a binding Ki value of 112 nM. We explored the effects of both substituent- and ring-structural variations on the receptor affinity in this series of derivatives, which were found to be mostly non-selective adenosine receptor ligands with Ki values in the micromolar range. Since no enhancement of A2B receptor affinity of 38 was achieved, the previously reported pharmacophore-based searching strategy yielded the most potent and selective structurally-related hit in the database originally searched.
PMCID: PMC3460516  PMID: 12467710
4.  Radiosynthesis of Antitumor Spliceosome Modulators 
A set of novel antitumor agents (the sudemycins) has recently been described that are analogs of the natural product FR901464. We report the radiosynthesis of two of these antitumor drug lead compounds, using a three step procedure: 1) ester hydrolysis, 2) Lindlar’s catalyst/tritium gas to give a (S,Z)-4-acetoxypent-2-enoic acid derivative, and finally 3) amide bond formation. These labelled analogs are useful in developing a better understanding of the pharmacological properties of this new class of therapeutic lead compounds.
PMCID: PMC3105125  PMID: 21531567
sudemycin; alkyne reduction; tritiation; spliceosome; antitumor; Lindlar catalyst
5.  Sudemycins, novel small molecule analogues of FR901464, induce alternative gene splicing 
ACS chemical biology  2011;6(6):582-589.
Two unrelated bacterial natural products, FR901464 and pladienolide B, have previously been shown to have significant anti-tumor activity in vivo. These compounds target the SF3b subunit of the spliceosome, with a derivative of pladienolide (E7107) entering clinical trials for cancer. However, due to the structural complexity of these molecules, their research and development has been significantly constrained. We have generated a set of novel analogues (Sudemycins) that possess the pharmacophore that is common to FR901464 and pladienolide, via a flexible enantioselective route, and allows for the production of gram quantities of drug. These compounds demonstrate cytotoxicity towards human tumor cell lines in culture and exhibit antitumor activity in a xenograft model. Here, we present evidence that Sudemycins are potent modulators of alternative splicing in human cells, both of endogenous genes and from minigene constructs. Furthermore, levels of alternative splicing are increased in tumor cells relative to normal cells and these modifications can be observed in human tumor xenografts in vivo following exposure of animals to the drug. In addition, the change in the splicing pattern observed with the Sudemycins are similar to that observed with Spliceostatin A, a molecule known to interact with the SF3b subunit of the spliceosome. Hence, we conclude that Sudemycins can regulate the production of alternatively spliced RNA transcripts and these alterations are more prevalent in tumor, as compared to normal cells, following drug exposure. These studies suggest that modulation of alternative splicing may play a role in the antitumor activity of this class of agents.
PMCID: PMC3113647  PMID: 21344922
6.  Design, synthesis and initial biological evaluation of a novel pladienolide analog scaffold† 
MedChemComm  2011;2(9):904-908.
A novel and simplified synthetic scaffold based on pladienolide was designed using a consensus pharmacophore hypothesis. An initial target was synthesized and evaluated to examine the role of the 3-hydroxy group and the methyl groups present at positions 10, 16, 20, 22 in 1, on biological activity. We report the first totally synthetic analog of this macrolide that shows biological activity. Our novel synthetic strategy enables the rapid synthesis of other new analogs of pladienolide in order to develop selective anticancer lead compounds.
PMCID: PMC3171832  PMID: 21927710
7.  Structure-Activity Relationships of Substituted 1-Pyridyl-2-Phenyl-1,2-Ethanediones: Potent, Selective Carboxylesterase Inhibitors 
Journal of medicinal chemistry  2010;53(24):8709-8715.
Inhibition of intestinal carboxylesterases may allow modification of the pharmacokinetics/pharmacodynamic profile of existing drugs by altering half-life or toxicity. Since previously identified diaryl ethane-1,2-dione inhibitors are decidedly hydrophobic, a modified dione scaffold was designed and elaborated into a >300 member library, which was subsequently screened to establish the SAR for esterase inhibition. This allowed the identification of single digit nanomolar hiCE inhibitors that showed improvement in both selectivity and measured solubility.
PMCID: PMC3022373  PMID: 21105730
8.  Evaluation of Diarylureas for Activity Against Plasmodium falciparum 
ACS medicinal chemistry letters  2010;1(9):460-465.
A library of diarylurea IGFR inhibitors was screened for activity against chloroquine-sensitive (3D7) and chloroquine-resistant (K1) strains of Plasmodium falciparum. The 4-aminoquinaldine-derived diarylureas displayed promising antimalarial potency. Further exploration of the B ring of 4-aminoquinaldinyl ureas allowed identification of several quinaldin-4-yl ureas 4{13, 39} and 4{13, 58} sufficiently potent against both 3D7 and K1 strains to qualify as bone fide leads.
PMCID: PMC3019604  PMID: 21243104
Malaria; diarylurea
9.  Synthetic mRNA Splicing Modulator Compounds with In Vivo Anti-tumor Activity 
Journal of medicinal chemistry  2009;52(22):6979-6990.
We report our progress on the development of new synthetic anti-cancer lead compounds that modulate the splicing of mRNA. We also report the synthesis evaluation of new biologically active ester and carbamate analogs. Further, we describe initial animal studies demonstrating the antitumor efficacy of compound 5 in vivo. Additionally, we report the enantioselective and diastereospecific synthesis of a new 1,3-dioxane series of active analogs. We confirm that compound 5 inhibits the splicing of mRNA in both cell-free nuclear extracts and in a cell-based dual-reporter mRNA splicing assay. In summary, we have developed totally synthetic novel spliceosome modulators as therapeutic lead compounds for a number of highly aggressive cancers. Future efforts will be directed toward the more complete optimization of these compounds as potential human therapeutics.
PMCID: PMC2801547  PMID: 19877647
10.  Design and Synthesis of a Novel Tyrosine Kinase Inhibitor Template 
Bioorganic & medicinal chemistry  2009;17(9):3308-3316.
We report the design and synthesis of an insulin receptor kinase family-targeted inhibitor template using the inhibitor conformation observed in an IGF1R/inhibitor co-crystal complex by application of a novel molecular design approach that we have recently published. The synthesis of the template involves a one pot Opatz cyclization reaction that provides a versatile indole ester in good yields. We also developed the required chemistry to elaborate this template with additional substituents and have used this chemistry to prepare some initial compounds that show selective inhibition of anaplastic lymphoma kinase (ALK).
PMCID: PMC2696309  PMID: 19362847
Anaplastic lymphoma kinase; ALK; de novo ligand design; kinase template synthesis; insulin receptor kinase family; inhibitor design
11.  Anaplastic lymphoma kinase: role in cancer pathogenesis and small-molecule inhibitor development for therapy 
Anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase in the insulin receptor superfamily, was initially identified in constitutively activated oncogenic fusion forms – the most common being nucleophosmin-ALK – in anaplastic large-cell lymphomas, and subsequent studies have identified ALK fusions in diffuse large B-cell lymphomas, systemic histiocytosis, inflammatory myofibroblastic tumors, esophageal squamous cell carcinomas and non-small-cell lung carcinomas. More recently, genomic DNA amplification and protein overexpression, as well as activating point mutations, of ALK have been described in neuroblastomas. In addition to those cancers for which a causative role for aberrant ALK activity is well validated, more circumstantial links implicate the full-length, normal ALK receptor in the genesis of other malignancies – including glioblastoma and breast cancer – via a mechanism of receptor activation involving autocrine and/or paracrine growth loops with the reported ALK ligands, pleiotrophin and midkine. This review summarizes normal ALK biology, the confirmed and putative roles of ALK in the development of human cancers and efforts to target ALK using small-molecule kinase inhibitors.
PMCID: PMC2780428  PMID: 19275511
anaplastic large-cell lymphoma; anaplastic lymphoma kinase; esophageal squamous cell carcinoma; glioblastoma; inflammatory myofibroblastic tumor; midkine; neuroblastoma; non-small-cell lung carcinoma; pleiotrophin; targeted cancer therapy; tyrosine kinase inhibitor
12.  Anti-tumor Compounds Based on a Natural Product Consensus Pharmacophore 
Journal of medicinal chemistry  2008;51(19):6220-6224.
We report the design and highly enantioselective synthesis of a potent analog of the spliceosome inhibitor FR901464, based on a non-natural product scaffold. The design of this compound was facilitated by a pharmacophore hypothesis that assumed key interaction types that are common to FR901464 and an otherwise unrelated natural product (pladienolide). The synthesis allows for the preparation of numerous novel analogs. We present results on the in vitro activity for this compound against several tumor cell lines.
PMCID: PMC2701350  PMID: 18788726
13.  Activating mutations in ALK provide a therapeutic target in neuroblastoma 
Nature  2008;455(7215):975-978.
Neuroblastoma, an embryonal tumor of the peripheral sympathetic nervous system, accounts for approximately 15% of all deaths due to childhood cancer1. High-risk neuroblastomas, prevalent in the majority of patients, are rapidly progressive; even with intensive myeloablative chemotherapy, relapse is common and almost uniformly fatal2,3. Here we report the detection of previously unknown mutations in the ALK gene, which encodes a receptor tyrosine kinase, in 8% of primary neuroblastomas. Five non-synonymous sequence variations were identified in the kinase domain of ALK, of which three were somatic and two were germline. The most frequent mutation, F1174L, was also identified in three different neuroblastoma cell lines. ALK cDNAs encoding the F1174L and R1275Q variants, but not the wild-type ALK cDNA, transformed IL-3-dependent murine hematopoietic Ba/F3 cells to cytokine-independent growth. Ba/F3 cells expressing these mutations were sensitive to a small-molecule inhibitor of ALK, TAE6844. Furthermore, two human neuroblastoma cell lines harboring the F1174L mutation were sensitive to the inhibitor. Cytotoxicity was associated with increased levels of apoptosis as measured by TUNEL-labeling. shRNA-mediated knockdown of ALK expression in neuroblastoma cell lines with the F1174L mutation also resulted in apoptosis and impaired cell proliferation. Thus, activating alleles of the ALK receptor tyrosine kinase are present in primary neuroblastoma tumors and in established neuroblastoma cell lines, and confer sensitivity to ALK inhibition with small molecules, providing a molecular rationale for targeted therapy of this disease.
PMCID: PMC2587486  PMID: 18923525
14.  Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease 
PLoS Pathogens  2012;8(8):e1002830.
Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral replication. Translation of viral mRNAs by the host ribosome requires mRNA capping for recognition and binding, and the necessary mRNA caps are cleaved or “snatched” from host pre-mRNAs by the PA endonuclease. The structure-based development of inhibitors that target PA endonuclease is now possible with the recent crystal structure of the PA catalytic domain. In this study, we sought to understand the molecular mechanism of inhibition by several compounds that are known or predicted to block endonuclease-dependent polymerase activity. Using an in vitro endonuclease activity assay, we show that these compounds block the enzymatic activity of the isolated PA endonuclease domain. Using X-ray crystallography, we show how these inhibitors coordinate the two-metal endonuclease active site and engage the active site residues. Two structures also reveal an induced-fit mode of inhibitor binding. The structures allow a molecular understanding of the structure-activity relationship of several known influenza inhibitors and the mechanism of drug resistance by a PA mutation. Taken together, our data reveal new strategies for structure-based design and optimization of PA endonuclease inhibitors.
Author Summary
Seasonal and pandemic influenza have enormous impacts on global public health. The rapid emergence of influenza virus strains that are resistant to current antiviral therapies highlights the urgent need to develop new therapeutic options. A promising target for drug discovery is the influenza virus PA protein, whose endonuclease enzymatic activity is essential for the “cap-snatching” step of viral mRNA transcription that allows transcripts to be processed by the host ribosome. Here, we describe a structure-based analysis of the mechanism of inhibition of the influenza virus PA endonuclease by small molecules. Our X-ray crystallographic studies have resolved the modes of binding of known and predicted inhibitors, and revealed that they directly block the PA endonuclease active site. We also report a number of molecular interactions that contribute to binding affinity and specificity. Our structural results are supported by biochemical analyses of the inhibition of enzymatic activity and computational docking experiments. Overall, our data reveal exciting strategies for the design and optimization of novel influenza virus inhibitors that target the PA protein.
PMCID: PMC3410894  PMID: 22876176

Results 1-14 (14)