Carlo Ballatore

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Organization: University of Pennsylvania
Department: Department of Chemistry, School of Arts and Sciences
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Co-reporter:Pierrik Lassalas; Bryant Gay; Caroline Lasfargeas; Michael J. James; Van Tran; Krishna G. Vijayendran; Kurt R. Brunden; Marisa C. Kozlowski; Craig J. Thomas; Amos B. SmithIII; Donna M. Huryn
Journal of Medicinal Chemistry 2016 Volume 59(Issue 7) pp:3183-3203
Publication Date(Web):March 11, 2016
DOI:10.1021/acs.jmedchem.5b01963
The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure–property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group.
Co-reporter:Anne-Sophie Cornec, Michael J. James, Jane Kovalevich, John Q. Trojanowski, Virginia M.-Y. Lee, Amos B. Smith III, Carlo Ballatore, Kurt R. Brunden
Bioorganic & Medicinal Chemistry Letters 2015 Volume 25(Issue 21) pp:4980-4982
Publication Date(Web):1 November 2015
DOI:10.1016/j.bmcl.2015.03.002
Previous studies revealed that examples of the non-naturally occurring microtubule (MT)-stabilizing triazolopyrimidines are both brain penetrant and orally bioavailable, indicating that this class of compounds may be potentially attractive in the development of MT-stabilizing therapies for the central nervous system (CNS). We now report on the pharmacokinetics (PK), pharmacodynamics (PD), and metabolism of a selected triazolopyrimidine congener, (S)-3-(4-(5-chloro-7-((1,1,1-trifluoropropan-2-yl)amino)-[1,2,4]triazolo[1,5-a]pyrimidin-6-yl)-3,5-difluorophenoxy)-propan-1-ol (4). These studies revealed that 4 exhibits longer brain than plasma half-life that may be exploited to achieve a selective accumulation of the compound within the CNS. Furthermore, compound metabolism studies suggest that in plasma 4 is rapidly oxidized at the terminal hydroxyl group to form a comparatively inactive carboxylic acid metabolite. Peripheral administration of relatively low doses of 4 to normal mice was found to produce a significant elevation in acetylated α-tubulin, a marker of stable MTs, in the brain. Collectively, these results indicate that 4 may effectively target brain MTs at doses that produce minimal peripheral exposure.
Co-reporter:Kevin Lou ; Yuemang Yao ; Adam T. Hoye ; Michael J. James ; Anne-Sophie Cornec ; Edward Hyde ; Bryant Gay ; Virginia M.-Y. Lee ; John Q. Trojanowski ; Amos B. Smith ; III; Kurt R. Brunden
Journal of Medicinal Chemistry 2014 Volume 57(Issue 14) pp:6116-6127
Publication Date(Web):July 3, 2014
DOI:10.1021/jm5005623
Microtubule (MT) stabilizing drugs hold promise as potential treatments for Alzheimer’s disease (AD) and related tauopathies. However, thus far epothilone D has been the only brain-penetrant MT-stabilizer to be evaluated in tau transgenic mice and in AD patients. Furthermore, this natural product exhibits potential deficiencies as a drug candidate, including an intravenous route of administration and the inhibition of the P-glycoprotein (Pgp) transporter. Thus, the identification of alternative CNS-active MT-stabilizing agents that lack these potential limitations is of interest. Toward this objective, we have evaluated representative compounds from known classes of non-naturally occurring MT-stabilizing small molecules. This led to the identification of selected triazolopyrimidines and phenylpyrimidines that are orally bioavailable and brain-penetrant without disruption of Pgp function. Pharmacodynamic studies confirmed that representative compounds from these series enhance MT-stabilization in the brains of wild-type mice. Thus, these classes of MT-stabilizers hold promise for the development of orally active, CNS-directed MT-stabilizing therapies.
Co-reporter:Xiaozhao Wang, Li Liu, Longchuan Huang, Katie Herbst-Robinson, Anne-Sophie Cornec, Michael J. James, Shimpei Sugiyama, Marcella Bassetto, Andrea Brancale, John Q. Trojanowski, Virginia M.-Y. Lee, Amos B. Smith III, Kurt R. Brunden, and Carlo Ballatore
ACS Medicinal Chemistry Letters 2014 Volume 5(Issue 9) pp:1015
Publication Date(Web):July 24, 2014
DOI:10.1021/ml5002085
A series of derivatives of the known thromboxane A2 prostanoid (TP) receptor antagonists, 3-(6-((4-chlorophenyl)sulfonamido)-5,6,7,8-tetrahydronaphthalen-1-yl)propanoic acid and 3-(3-(2-((4-chlorophenyl)sulfonamido)ethyl)phenyl) propanoic acid, were synthesized in which the carboxylic acid functional group was replaced with substituted cyclopentane-1,3-dione (CPD) bioisosteres. Characterization of these molecules led to the discovery of remarkably potent new analogues, some of which were considerably more active than the corresponding parent carboxylic acid compounds. Depending on the choice of the C2 substituent of the CPD unit, these new derivatives can produce either a reversible or an apparent irreversible inhibition of the human TP receptor. Given the potency and the long-lasting inhibition of TP receptor signaling, these novel antagonists may comprise promising leads for the development of antithromboxane therapies.Keywords: carboxylic acid bioisostere; Cyclopentane-1,3-dione; thromboxane A2; thromboxane receptor antagonists
Co-reporter:Dr. Carlo Ballatore; Donna M. Huryn ; Amos B. Smith III
ChemMedChem 2013 Volume 8( Issue 3) pp:385-395
Publication Date(Web):
DOI:10.1002/cmdc.201200585

Abstract

The carboxylic acid functional group can be an important constituent of a pharmacophore, however, the presence of this moiety can also be responsible for significant drawbacks, including metabolic instability, toxicity, as well as limited passive diffusion across biological membranes. To avoid some of these shortcomings while retaining the desired attributes of the carboxylic acid moiety, medicinal chemists often investigate the use of carboxylic acid (bio)isosteres. The same type of strategy can also be effective for a variety other purposes, for example, to increase the selectivity of a biologically active compound or to create new intellectual property. Several carboxylic acid isosteres have been reported, however, the outcome of any isosteric replacement cannot be readily predicted as this strategy is generally found to be dependent upon the particular context (i.e., the characteristic properties of the drug and the drug–target). As a result, screening of a panel of isosteres is typically required. In this context, the discovery and development of novel carboxylic acid surrogates that could complement the existing palette of isosteres remains an important area of research. The goal of this Minireview is to provide an overview of the most commonly employed carboxylic acid (bio)isosteres and to present representative examples demonstrating the use and utility of each isostere in drug design.

Co-reporter:Carlo Ballatore ; Kurt R. Brunden ; Donna M. Huryn ; John Q. Trojanowski ; Virginia M.-Y. Lee ;Amos B. Smith ; III
Journal of Medicinal Chemistry 2012 Volume 55(Issue 21) pp:8979-8996
Publication Date(Web):September 28, 2012
DOI:10.1021/jm301079z
The microtubule (MT) associated protein tau, which is highly expressed in the axons of neurons, is an endogenous MT-stabilizing agent that plays an important role in axonal transport. Loss of MT-stabilizing tau function, caused by misfolding, hyperphosphorylation, and sequestration of tau into insoluble aggregates, leads to axonal transport deficits with neuropathological consequences. Several in vitro and preclinical in vivo studies have shown that MT-stabilizing drugs can be utilized to compensate for the loss of tau function and to maintain/restore effective axonal transport. These findings indicate that MT-stabilizing compounds hold considerable promise for the treatment of Alzheimer disease and related tauopathies. The present article provides a synopsis of the key findings demonstrating the therapeutic potential of MT-stabilizing drugs in the context of neurodegenerative tauopathies, as well as an overview of the different classes of MT-stabilizing compounds.
Co-reporter:Carlo Ballatore, Alex Crowe, Francesco Piscitelli, Michael James, Kevin Lou, Gabrielle Rossidivito, Yuemang Yao, John Q. Trojanowski, Virginia M.-Y. Lee, Kurt R. Brunden, Amos B. Smith III
Bioorganic & Medicinal Chemistry 2012 20(14) pp: 4451-4461
Publication Date(Web):
DOI:10.1016/j.bmc.2012.05.027
Co-reporter:Carlo Ballatore ; James H. Soper ; Francesco Piscitelli ; Michael James ; Longchuan Huang ; Onur Atasoylu ; Donna M. Huryn ; John Q. Trojanowski ; Virginia M.-Y. Lee ; Kurt R. Brunden ;Amos B. Smith ; III
Journal of Medicinal Chemistry 2011 Volume 54(Issue 19) pp:6969-6983
Publication Date(Web):August 24, 2011
DOI:10.1021/jm200980u
Cyclopentane-1,3-diones are known to exhibit pKa values typically in the range of carboxylic acids. To explore the potential of the cyclopentane-1,3-dione unit as a carboxylic acid isostere, the physical–chemical properties of representative congeners were examined and compared with similar derivatives bearing carboxylic acid or tetrazole residues. These studies suggest that cyclopentane-1,3-diones may effectively substitute for the carboxylic acid functional group. To demonstrate the use of the cyclopentane-1,3-dione isostere in drug design, derivatives of a known thromboxane A2 prostanoid (TP) receptor antagonist, 3-(3-(2-(4-chlorophenylsulfonamido)ethyl)phenyl)propanoic acid (12), were synthesized and evaluated in both functional and radioligand-binding assays. A series of mono- and disubstituted cyclopentane-1,3-dione derivatives (41–45) were identified that exhibit nanomolar IC50 and Kd values similar to 12. Collectively, these studies demonstrate that the cyclopentane-1,3-dione moiety comprises a novel isostere of the carboxylic acid functional group. Given the combination of the relatively strong acidity, tunable lipophilicity, and versatility of the structure, the cyclopentane-1,3-dione moiety may constitute a valuable addition to the palette of carboxylic acid isosteres.
Co-reporter:Carlo Ballatore ; Kurt R. Brunden ; Francesco Piscitelli ; Michael J. James ; Alex Crowe ; Yuemang Yao ; Edward Hyde ; John Q. Trojanowski ; Virginia M.-Y. Lee ;Amos B. Smith ; III
Journal of Medicinal Chemistry 2010 Volume 53(Issue 9) pp:3739-3747
Publication Date(Web):April 14, 2010
DOI:10.1021/jm100138f
Agents capable of preventing the misfolding and sequestration of the microtubule-stabilizing protein tau into insoluble fibrillar aggregates hold considerable promise for the prevention and/or treatment of neurodegenerative tauopathies such as Alzheimer’s disease. Because tauopathies are characterized by amyloidosis that is restricted to the central nervous system (CNS), plausible candidate compounds for in vivo evaluation must both prevent tau fibrillization and achieve significant brain levels. Recently, we reported the discovery of the aminothienopyridazine (ATPZ) class of tau aggregation inhibitors and now describe a series of new analogues that are both effective inhibitors of tau fibrillization and display significant brain-to-plasma exposure ratios after administration to mice. Further, two of the most promising examples, 15 and 16, were found to reach significant brain exposure levels following oral administration. Taken together, these results suggest that examples from the ATPZ class hold promise as candidates for in vivo efficacy studies in animal models of neurodegenerative tauopathies.
Co-reporter:Francesco Piscitelli, Carlo Ballatore, Amos B. Smith III
Bioorganic & Medicinal Chemistry Letters 2010 Volume 20(Issue 2) pp:644-648
Publication Date(Web):15 January 2010
DOI:10.1016/j.bmcl.2009.11.055
A traceless solid supported protocol for the synthesis of 2-aminobenzothiazoles is described, employing resin-bound acyl-isothiocyanate and a series of anilines. Cyclization of the resulting N-acyl, N′-phenyl-thioureas generates the 2-aminobenzothiazole scaffold, which can be further elaborated prior to hydrazine-mediated cleavage of the final products from the carboxy-polystyrene resin. A small, focused library of 2-aminobenzothiazoles was prepared.
Co-reporter:Carlo Ballatore, Bin Zhang, John Q. Trojanowski, Virginia M.-Y. Lee, Amos B. Smith III
Bioorganic & Medicinal Chemistry Letters 2008 Volume 18(Issue 23) pp:6119-6121
Publication Date(Web):1 December 2008
DOI:10.1016/j.bmcl.2008.10.024
We report the synthesis and blood–brain barrier (BBB)-permeability of 14C-CNDR-29, a paclitaxel C-10 carbamate derivative shown to be devoid of P-glycoprotein (Pgp)-interactions, in an in situ mouse brain perfusion model, in comparison with 14C-paclitaxel. The results presented reveal a 3- to 4-fold higher BBB-permeability for the C-10 modified taxane compared to paclitaxel. These results support the notion that circumvention of Pgp-mediated efflux can lead to higher BBB-permeability. Further studies however are needed to evaluate the therapeutic potential of the C-10 carbamates paclitaxel derivatives for the treatment of CNS diseases.
Co-reporter:Carlo Ballatore, Edward Hyde, Robert F. Deiches, Virginia M.-Y. Lee, John Q. Trojanowski, Donna Huryn, Amos B. Smith III
Bioorganic & Medicinal Chemistry Letters 2007 Volume 17(Issue 13) pp:3642-3646
Publication Date(Web):1 July 2007
DOI:10.1016/j.bmcl.2007.04.058
A series of paclitaxel C-10 carbamates was synthesized and evaluated in a bi-directional permeability assay in comparison with paclitaxel and the blood–brain barrier-permeable C-10 ester derivative, TX-67. A number of the carbamates were found not to be substrates for Pgp. Moreover, when tested for Pgp-inhibitory potential, representative compounds proved to be devoid of Pgp interactions. Side-by-side comparison between TX-67 and the corresponding C-10 carbamate, CNDR-3, revealed a significantly longer half-life for CNDR-3 in both mouse and human plasma, suggesting that this class of derivatives is appropriate for further in vivo evaluation.A series of paclitaxel C-10 carbamates was synthesized and evaluated in a bi-directional permeability assay in comparison with paclitaxel and the blood–brain barrier-permeable C-10 ester derivative, TX-67.
2-(benzyloxy)-1,3-difluorobenzene
2-Cyclopenten-1-one,2-cyclohexyl-3-hydroxy-
4(1H)-PYRIMIDINONE, 6-HYDROXY-2-PYRAZINYL-5-(2,4,6-TRIFLUOROPHENYL)-
Pyrimidine, 4,6-dichloro-2-pyrazinyl-5-(2,4,6-trifluorophenyl)-
8-HYDROXY-7-(2,4,6-TRIFLUOROPHENYL)-5H-PYRIDO[2,3-B]PYRAZIN-6-ONE
3-CYCLOBUTENE-1,2-DIONE, 3-HYDROXY-4-[(PHENYLMETHYL)AMINO]-
Pyrimidine, 4,6-dichloro-2-(2-pyridinyl)-5-(2,4,6-trifluorophenyl)-
4(1H)-PYRIMIDINONE, 6-HYDROXY-2-(2-PYRIDINYL)-5-(2,4,6-TRIFLUOROPHENYL)-