Timothy M Dore

New York University Abu Dhabi, Abū Z̧aby, Abu Dhabi, United Arab Emirates

Are you Timothy M Dore?

Claim your profile

Publications (31)115.59 Total impact

  • Source

    Full-text · Dataset · Jan 2016
  • [Show abstract] [Hide abstract]
    ABSTRACT: Spatio-temporal release of biologically relevant small molecules provides exquisite control over the activation of receptors and signaling pathways. This can be accomplished via a photochemical reaction that releases the desired small molecule in response to irradiation with light. A series of biologically-relevant signaling molecules (serotonin, octopamine, capsaicin, N-vanillyl-nonanoylamide, estradiol, and tyrosine) that contain a phenol moiety were conjugated to the 8-bromo-7-hydroxyquinolinyl (BHQ) or 8-cyano-7-hydroxyquinolinyl (CyHQ) photoremovable protecting groups (PPGs). The CyHQ caged compounds proved sensitive toward 1PE and 2PE processes with quantum efficiencies of 0.2-0.4 upon irradiation at 365 nm and two-photon action cross sections of 0.15-0.31 GM when irradiated at 740 nm. All but one BHQ caged compound, BHQ-estradiol, were found to be sensitive to photolysis through 1PE and 2PE with quantum efficiencies of 0.30-0.40 and two photon cross sections of 0.40-0.60 GM. Instead of releasing estradiol, BHQ-estradiol underwent debromination.
    No preview · Article · Nov 2015 · Photochemical and Photobiological Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Ras converting enzyme 1 (Rce1) is an endoprotease that catalyzes processing of the C-terminus of Ras protein by removing -aaX from the CaaX motif. The activity of Rce1 is crucial for proper localization of Ras to the plasma membrane where it functions. Ras is responsible for transmitting signals related to cell proliferation, cell cycle progression, and apoptosis. The disregulation of these pathways due to constitutively active oncogenic Ras can ultimately lead to cancer. Ras, its effectors and regulators, and the enzymes that are involved in its maturation process are all targets for anti-cancer therapeutics. Key enzymes required for Ras maturation and localization are the farnesyltransferase (FTase), Rce1, and isoprenylcysteine carboxyl methyltransferase (ICMT). Among these proteins, the physiological role of Rce1 in regulating Ras and other CaaX proteins has not been fully explored. Small-molecule inhibitors of Rce1 could be useful as chemical biology tools to understand further the downstream impact of Rce1 on Ras function and serve as potential leads for cancer therapeutics. Structure-activity relationship (SAR) analysis of a previously reported Rce1 inhibitor, NSC1011, has been performed to generate a new library of Rce1 inhibitors. The new inhibitors caused a reduction in Rce1 in vitro activity, exhibited low cell toxicity, and induced mislocalization of EGFP-Ras from the plasma membrane in human colon carcinoma cells giving rise to a phenotype similar to that observed with siRNA knockdowns of Rce1 expression. Several of the new inhibitors were more effective at mislocalizing K-Ras compared to a potent farnesyltransferase inhibitor (FTI), which is significant because of the preponderance of K-Ras mutations in cancer.
    Full-text · Article · Nov 2015 · Bioorganic & medicinal chemistry
  • [Show abstract] [Hide abstract]
    ABSTRACT: A number of processes operating during the first cell cleavages enable the left-right (LR) axis to be consistently oriented during Xenopus laevis development. Prior work showed that secondary organizers induced in frog embryos after cleavage stages (i.e. conjoined twins arising from ectopic induced primary axes) correctly pattern their own LR axis only when a primary (early) organizer is also present. This instructive effect confirms the unique LR patterning functions that occur during early embryogenesis, but leaves open the question: which mechanisms that operate during early stages are also involved in the orientation of later-induced organizers? We sought to distinguish the two phases of LR patterning in secondary organizers (LR patterning of the primary twin and the later transfer of this information to the secondary twin) by perturbing only the latter process. Here, we used reagents that do not affect primary LR patterning at the time secondary organizers form to inhibit each of 4 mechanisms in the induced twin. Using pharmacological, molecular-genetic, and photo-chemical tools, we show that serotonergic and gap-junctional signaling, but not proton or potassium flows, are required for the secondary organizer to appropriately pattern its LR axis in a multicellular context. We also show that consistently-asymmetric gene expression begins prior to ciliary flow. Together, our data highlight the importance of physiological signaling in the propagation of cleavage-derived LR orientation to multicellular cell fields.
    No preview · Article · Oct 2014 · The International journal of developmental biology
  • [Show abstract] [Hide abstract]
    ABSTRACT: Serotonin (5-HT) is a neuromodulator involved in regulating mood, appetite, memory, learning, pain, and establishment of left-right (LR) asymmetry in embryonic development. To explore the role of 5-HT in physiology, we have created two forms of "caged" 5-HT, BHQ-O-5HT and BHQ-N-5HT. When exposed to 365 or 740 nm light, BHQ-O-5HT releases 5-HT through one- or two-photon excitation, respectively. BHQ-O-5HT mediated changes in neural activity in cultured mouse primary sensory neurons and the trigeminal ganglion and optic tectum of intact zebrafish larvae in the form of high-amplitude spiking in response to light. In Xenopus laevis embryos, light-activated 5-HT increased the occurrence of LR patterning defects. Maximal rates of LR defects were observed when 5-HT was released at stage 5 compared with stage 8. These experiments show the potential for BHQ-caged serotonins in studying 5-HT-regulated physiological processes.
    No preview · Article · Dec 2013 · Chemistry & biology
  • Timothy M. Dore · Walter K. Schmidt

    No preview · Article · Jan 2013
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Photoremovable protecting groups (PPGs) when conjugated to biological effectors forming "caged compounds" are a powerful means to regulate the action of physiologically active messengers in vivo through 1-photon excitation (1PE) and 2-photon excitation (2PE). Understanding the photodeprotection mechanism is important for their physiological use. We compared the quantum efficiencies and product outcomes in different solvent and pH conditions for the photolysis reactions of (8-chloro-7-hydroxyquinolin-2-yl)methyl acetate (CHQ-OAc) and (8-bromo-7-hydroxyquinolin-2-yl)methyl acetate (BHQ-OAc), representatives of the quinoline class of phototriggers for biological use, and conducted nanosecond time-resolved spectroscopic studies using transient emission (ns-EM), transient absorption (ns-TA), transient resonance Raman (ns-TR(2)), and time-resolved resonance Raman (ns-TR(3)) spectroscopies. The results indicate differences in the photochemical mechanisms and product outcomes, and reveal that the triplet excited state is most likely on the pathway to the product and that dehalogenation competes with release of acetate from BHQ-OAc, but not CHQ-OAc. A high fluorescence quantum yield and a more efficient excited-state proton transfer (ESPT) in CHQ-OAc compared to BHQ-OAc explain the lower quantum efficiency of CHQ-OAc relative to BHQ-OAc.
    Full-text · Article · May 2012 · Chemistry - A European Journal
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The creation of caged molecules involves the attachment of protecting groups to biologically active compounds such as ligands, substrates and drugs that can be removed under specific conditions. Photoremovable caging groups are the most common due to their ability to be removed with high spatial and temporal resolution. Here, the synthesis and photochemistry of a caged inhibitor of protein farnesyltransferase is described. The inhibitor, FTI, was caged by alkylation of a critical thiol group with a bromohydroxycoumarin (Bhc) moiety. While Bhc is well established as a protecting group for carboxylates and phosphates, it has not been extensively used to cage sulfhydryl groups. The resulting caged molecule, Bhc-FTI, can be photolyzed with UV light to release the inhibitor that prevents Ras farnesylation, Ras membrane localization and downstream signaling. Finally, it is shown that Bhc-FTI can be uncaged by two-photon excitation to produce FTI at levels sufficient to inhibit Ras localization and alter cell morphology. Given the widespread involvement of Ras proteins in signal transduction pathways, this caged inhibitor should be useful in a plethora of studies.
    Full-text · Article · May 2012 · ChemBioChem
  • [Show abstract] [Hide abstract]
    ABSTRACT: The cover picture shows confocal microscope images of cells from a murine fibroblast line (ciras) that expresses an oncogenic variant of H‐ras; the cells are stained with 4′,6‐diamidino‐2‐phenylindole (blue) and Alexa‐Fluor488‐phalloidin conjugate (green) to highlight the nuclei and actin fibers, respectively. On p. 1009 ff., M. D. Distefano et al. describe how photolysis of the cells in the presence Bhc‐FTI (left‐hand structure), a caged protein farnesyltransferase inhibitor (FTI), either by irradiation at 400 or 800 nm (two‐photon excitation) results in the release of FTI (right‐hand structure) and inhibition of H‐ras prenylation, thus causing a dramatic change in cell morphology (compare cells at left to those at right). Caged FTIs such as the one described here could be particularly useful for studying developmental and differentiation processes that involve temporal regulation of Ras‐like proteins. The ability to uncage FTIs through a two‐photon process also opens up the possibility of performing such experiments in tissue samples and even whole organisms where light penetration and phototoxicity are relevant concerns.
    No preview · Article · May 2012 · ChemBioChem
  • Source

    Preview · Dataset · Apr 2012
  • [Show abstract] [Hide abstract]
    ABSTRACT: Photoremovable protecting groups (PPGs) when conjugated to biological effectors forming “caged compounds” are a powerful means to regulate the action of physiologically active messengers in vivo through 1-photon excitation (1PE) and 2-photon excitation (2PE). Understanding the photodeprotection mechanism is important for their physiological use. We compared the quantum efficiencies and product outcomes in different solvent and pH conditions for the photolysis reactions of (8-chloro-7-hydroxyquinolin-2-yl)methyl acetate (CHQ-OAc) and (8-bromo-7-hydroxyquinolin-2-yl)methyl acetate (BHQ-OAc), representatives of the quinoline class of phototriggers for biological use, and conducted nanosecond time-resolved spectroscopic studies using transient emission (ns-EM), transient absorption (ns-TA), transient resonance Raman (ns-TR2), and time-resolved resonance Raman (ns-TR3) spectroscopies. The results indicate differences in the photochemical mechanisms and product outcomes, and reveal that the triplet excited state is most likely on the pathway to the product and that dehalogenation competes with release of acetate from BHQ-OAc, but not CHQ-OAc. A high fluorescence quantum yield and a more efficient excited-state proton transfer (ESPT) in CHQ-OAc compared to BHQ-OAc explain the lower quantum efficiency of CHQ-OAc relative to BHQ-OAc.
    No preview · Article · Apr 2012 · Central European Journal of Chemistry
  • [Show abstract] [Hide abstract]
    ABSTRACT: To better understand the deprotection reaction of the new promising phototrigger compound BHQ-OAc (8-bromo-7-hydroxyquinoline acetate), we present a detailed comparison of the UV-vis absorption, resonance Raman, and fluorescence spectra of BHQ-OAc with its parent compound 7-hydroxyquinoline in different solvents. The steady-state absorption and resonance Raman spectra provide fundamental information about the structure, properties, and population distribution of the different prototropic forms present under the different solvent conditions examined. The species present in the excited states that emit strongly were detected by fluorescence spectra. It is shown that the ground-state tautomerization process of BHQ-OAc is disfavored compared with that of 7-HQ in aqueous solutions. The observation of the tautomeric form of BHQ-OAc in neutral aqueous solutions demonstrates the occurrence of the excited-state proton-transfer process, which would be a competing process for the deprotection reaction of BHQ-OAc in aqueous solutions.
    No preview · Article · Sep 2011 · The Journal of Physical Chemistry A
  • Timothy M. Dore · Hunter C. Wilson
    [Show abstract] [Hide abstract]
    ABSTRACT: The localized release of bioactive molecules from “caged compounds” through two-photon excitation (2PE) is an emerging technology for the study of biological processes in cell and tissue culture and whole animals. Several advantages are realized when 2PE drives the activation of the biological effector: (1) excitation is tightly localized to femtoliter-sized volumes; (2) there is less photodamage to biological tissues; and (3) deeper penetration into the sample is achieved. A barrier to widespread use and an expansion of applications for the pinpoint three-dimensional delivery of biological effectors are the small number of available caging groups and phototriggers with sufficient sensitivity to 2PE, appropriate photolysis kinetics, and necessary physiological compatibility. Chromophores based on nitrobenzyl, nitroindoline, coumarin, ortho-hydroxycinnamic acid, quinoline, and other structural motifs have been designed to regulate the action of biologically active compounds with 2PE. Design principles from structure–property relationships elucidated for two-photon absorbing materials can be applied to the design of caging groups and phototriggers for high efficiency 2PE-mediated release of bioeffectors. The conjugation size, symmetry, and the strength of donor and acceptor groups impact the overall sensitivity to 2PE, but these factors must be balanced with the need for biocompatibility and the ability to drive photochemical reactions with rapid kinetics.
    No preview · Chapter · Jan 2011
  • W.K. Schmidt · T.M. Dore
    [Show abstract] [Hide abstract]
    ABSTRACT: Rce1p (FACE-2, Type II CAAX prenyl endopeptidase) mediates proteolytic trimming of the C-terminal aaX tripeptide from CaaX proteins that have undergone isoprenylation. Medically relevant targets of Rce1p include the Ras and Ras-related GTPases (e.g., N-Ras, H-Ras, K-Ras, Rho, etc.), which are often mutated in cancer. Rce1p orthologs are present in all branches of life, but only eukaryotic orthologs are known to interact with isoprenylated substrates. A common feature of Rce1p proteins is that they are integral membrane proteins having multiple membrane spans. Eukaryotic Rce1p has been localized to the endoplasmic reticulum (ER), whereas prokaryotic orthologs are presumably located on the plasma membrane. The mechanism and structure of Rce1p, however, remain unresolved. Investigations into the biological role of eukaryotic Rce1p have revealed that Rce1p is not essential for life at the unicellular level, but its absence leads to embryonic lethality in mice and abnormal physiology upon tissue-specific disruption. Multiple assays have been developed for monitoring both the in vitro and in vivo activity of Rce1p. These have been advantageous for investigating the enzymatic properties and physiological role of Rce1p, including its impact on the subcellular localization of substrates. Rce1p is an important proteolytic enzyme to the biomedical community, yet some issues, such as its structure, catalytic mechanism, substrate selectivity, and potential for pharmacological inhibition, remain unresolved.
    No preview · Article · Jan 2011 · Enzymes
  • Michael C. Pirrung · Timothy M. Dore · Yue Zhu · Vipul S. Rana
    [Show abstract] [Hide abstract]
    ABSTRACT: The photochemical deprotection of compound (I) in the presence of isopropyl thioxanthone as a two-photon sensitizer is reported.
    No preview · Article · Dec 2010 · ChemInform
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Dipeptidyl (acyloxy)methyl ketones (AOMKs) have been identified as mechanism-based inhibitors of certain cysteine proteases. These compounds are also inhibitors of the integral membrane proteins Rce1p and Ste24p, which are proteases that independently mediate a cleavage step associated with the maturation of certain isoprenylated proteins. The enzymatic mechanism of Rce1p is ill-defined, whereas Ste24p is a zinc metalloprotease. Rce1p is required for the proper processing of the oncoprotein Ras and is viewed as a potential target for cancer therapy. In this study, we synthesized a small library of dipeptidyl AOMKs to investigate the structural elements that contribute to the inhibitor properties of this class of molecules toward Rce1p and Ste24p. The compounds were evaluated using a fluorescence-based in vitro proteolysis assay. The most potent dipeptidyl AOMKs contained an arginine residue and the identity of the benzoate group strongly influenced potency. A 'warhead' free AOMK inhibited Rce1p and Ste24p. The data suggest that the dipeptidyl AOMKs are not mechanism-based inhibitors of Rce1p and Ste24p and corroborate the hypothesis that Rce1p is not a cysteine protease.
    Full-text · Article · Sep 2010 · Bioorganic & medicinal chemistry
  • Michael C Pirrung · Timothy M Dore · Yue Zhu · Vipul S Rana
    [Show abstract] [Hide abstract]
    ABSTRACT: The photoremovable protecting group NPPoc has little sensitivity to two-photon excitation, limiting its use in applications requiring high spatial control of its photochemistry. In the presence of a triplet sensitizer with a large two-photon absorption cross-section, however, the two-photon uncaging action cross-section is improved to levels useful in a variety of applications.
    No preview · Article · Aug 2010 · Chemical Communications

  • No preview · Article · Aug 2010
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: To investigate the substituent effect on the distribution of the forms of the ground-state species of 8-substituted 7-hydroxyquinolines, ultraviolet-absorption and resonance Raman experiments were performed for 8-chloro-7-hydroxyquinoline (CHQ-OAc) and 8-cyano-7-hydroxyquinoline (CyHQ-OAc) in acetonitrile (MeCN), in NaOH-H(2)O/MeCN (60:40, v/v, pH 11-12), and in H(2)O/MeCN (60:40, v/v, pH 6-7) solutions, and these results were compared to those previously reported for the 8-bromo-7-hydroxyquinoline (BHQ-OAc) compound. Swapping a bromine atom in BHQ-OAc for a chlorine atom in CHQ-OAc causes the amount of the tautomeric species to become larger, although the neutral species is still the predominant species for both systems in water-rich solutions. The absorption spectra and the resonance Raman spectra of CyHQ-OAc suggest that, because of the strong electron-withdrawing nature of the cyano substituent, a measurable amount of the anionic species is present and the tautomeric species cannot be easily detected in water-rich solutions. The results reported here reveal large substituent effects on the distribution of the different forms of the XHQ-OAc compounds in largely aqueous solutions. The steric effect of the 8-substituted group and competitive hydrogen bonding between the 8-substituted group and water molecules hinders the formation of a cyclic BHQ-OAc-water complex, and the electron-withdrawing property of the 8-substituted group enhances the deprotonation of the phenol group while disfavoring the formation of the positively charged quinoline nitrogen. We briefly discuss the implications of the substituent effects for using these compounds as phototriggers.
    Full-text · Article · Feb 2010 · The Journal of Physical Chemistry A
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The 8-bromo-7-hydroxyquinolinyl group (BHQ) is a derivative of 7-hydroxyquinoline (7-HQ) and BHQ molecules coexisting as different forms in aqueous solution. Absorption and resonance Raman spectroscopic methods were used to examine 8-bromo-7-hydroxyquinoline protected acetate (BHQ-OAc) in acetonitrile (MeCN), H(2)O/MeCN (60:40, v/v, pH 6 approximately 7), and NaOH-H(2)O/MeCN (60:40, v/v, pH 11 approximately 12) to obtain a better characterization of the forms of the ground-state species of BHQ-OAc in aqueous solutions and to examine their properties. The absorption spectra of BHQ-OAc in water show no absorption bands of the tautomeric species unlike the strong band at about 400 nm observed for the tautomeric form in 7-HQ aqueous solution. The resonance Raman spectra in conjunction with Raman spectra predicted from density functional theory (DFT) calculations reveal the observation of a double Raman band system characteristic of the neutral form (the nominal C=C ring stretching, C-N stretching, and O-H bending modes at 1564 and 1607 cm(-1)) and a single Raman band diagnostic of the enol-deprotonated anionic form (the nominal C=C ring, C-N, and C-O(-) stretching modes in the 1593 cm(-1) region). These results suggest that the neutral form of BHQ-OAc is the major species in neutral aqueous solution. There is a modest increase in the amount of the anionic form and a big decrease in the amount of the tautomeric form of the molecules for BHQ-OAc compared to 7-HQ in neutral aqueous solution. The presence of the 8-bromo group and/or competitive hydrogen bonding that hinder the formation and transfer process of a BHQ-OAc-water cyclic complex may be responsible for this large substituent effect.
    Full-text · Article · Apr 2009 · The Journal of Physical Chemistry A

Publication Stats

1k Citations
115.59 Total Impact Points

Institutions

  • 2013-2015
    • New York University Abu Dhabi
      Abū Z̧aby, Abu Dhabi, United Arab Emirates
  • 2002-2012
    • University of Georgia
      • • Department of Chemistry
      • • Center for Advanced Ultrastructural Research
      Атина, Georgia, United States
  • 2010
    • University of California, Riverside
      • Department of Chemistry
      Riverside, California, United States
  • 2006
    • Johns Hopkins University
      • Department of Chemistry
      Baltimore, Maryland, United States
  • 2004
    • University of Oregon
      • Institute of Molecular Biology
      Eugene, Oregon, United States
  • 2003
    • Athens State University
      • Department of Chemistry
      Athens, Alabama, United States