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Novel N-Acylethanolamide Derivatives Affect Body Weight and Energy Balance. Chem Biodivers 2023; 20:e202300212. [PMID: 37461813 DOI: 10.1002/cbdv.202300212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
Introduction - The obesity pandemic is multifactorial. Nutritional, pharmacologic and surgical interventions are limited in reach and efficacy, raising need for new therapeutics. Aims - Characterization of anorexigenic and cognitive effect and central mechanism of action of novel N-acylethanolamide derivatives. Methods - Sabra mice divided to similar experimental groups, injected IP with: oleyl-L-leucinolamide (1 A), linoleyl-L-leucinolamide (4 A), linoleyl-L-valinolamide (5 A), oleyl-oxycarbonyl-L-valinolamide (1 B), oleyl-oxycarbonyl-D-valinolamide (2 B), oleylamine-carbonyl-L-valinolamide (3 B), oleylamine-carbonyl-D-valinolamide (4 B), and oleyl-L-hydroxyvalineamide (5 B). Control group with vehicle. Body weight and food consumption followed for 39 days. Motor activity and cognitive function by open field test and eight-arm maze. Mice sacrificed and mechanism of action investigated by qPCR. The genes analyzed involved in energy balance and regulation of appetite. Catecholamines and serotonin evaluated. Results - Compounds 1 A, 5 A, 1 B-4 B, caused significant weight loss of 4.2-5.6 % and 5 A, 1 B-4 B, improved cognitive function following 8 i. p. injections of 1 mg/kg during 39 days, by different mechanisms. 5 A, 3 B and 4 B decreased food consumption, whereas 1 A, 5 A and 2 B increased motor activity. 1 A, 4 A, 1 B and 3 B elevated SIRT-1, associated with survival. POMC upregulated by 1 B and 2 B, CART by 1 B, 2 B and 1 A. NPY and CAMKK2 downregulated by 5 A. 4 B enhanced 5-HT levels. 4 A, 5 A, 1 B, 4 B, 5 B decreased FAAH, showing long lasting effect. Conclusions - These new compounds might be developed for the treatment of obesity and for improved cognitive function.
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Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon-Induced Excitation. Angew Chem Int Ed Engl 2023; 62:e202218770. [PMID: 36789791 DOI: 10.1002/anie.202218770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/16/2023]
Abstract
Possible routes for intra-cluster bond formation (ICBF) in protonated serine dimers have been studied. We found no evidence of ICBF following low energy collision-induced dissociation (in correspondence with previous works), however, we do observe clear evidence for ICBF following photon absorption in the 4.6-14 eV range. Moreover, the comparison of photon-induced dissociation measurements of the protonated serine dimer to those of a protonated serine dipeptide provides evidence that ICBF, in this case, involves peptide bond formation (PBF). The experimental results are supported by ab initio molecular dynamics and exploration of several excited state potential energy surfaces, unraveling a pathway for PBF following photon absorption. The combination of experiments and theory provides insight into the PBF mechanisms in clusters of amino acids, and reveals the importance of electronic excited states reached upon UV/VUV light excitation.
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Peptide Bond Formation in Protonated Serine Dimer Following VUV Photon‐Induced Excitation. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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4
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Publisher Correction: Sourcing Herod the Great's calcite-alabaster bathtubs by a multi-analytic approach. Sci Rep 2022; 12:9883. [PMID: 35701506 PMCID: PMC9198036 DOI: 10.1038/s41598-022-13308-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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5
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Optically Active Functionalized Building Blocks for Peptidyl Olefin Peptidomimetics. ChemistrySelect 2021. [DOI: 10.1002/slct.202102058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Development and characterisation of SMURF2-targeting modifiers. J Enzyme Inhib Med Chem 2021; 36:401-409. [PMID: 33430646 PMCID: PMC7808752 DOI: 10.1080/14756366.2020.1871337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The C2-WW-HECT-domain E3 ubiquitin ligase SMURF2 emerges as an important regulator of diverse cellular processes. To date, SMURF2-specific modulators were not developed. Here, we generated and investigated a set of SMURF2-targeting synthetic peptides and peptidomimetics designed to stimulate SMURF2’s autoubiquitination and turnover via a disruption of the inhibitory intramolecular interaction between its C2 and HECT domains. The results revealed the effects of these molecules both in vitro and in cellulo at the nanomolar concentration range. Moreover, the data showed that targeting of SMURF2 with either these modifiers or SMURF2-specific shRNAs could accelerate cell growth in a cell-context-dependent manner. Intriguingly, a concomitant cell treatment with a selected SMURF2-targeting compound and the DNA-damaging drug etoposide markedly increased the cytotoxicity produced by this drug in growing cells. Altogether, these findings demonstrate that SMURF2 can be druggable through its self-destructive autoubiquitination, and inactivation of SMURF2 might be used to affect cell sensitivity to certain anticancer drugs.
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Targeting Necrosis: Elastase-like Protease Inhibitors Curtail Necrotic Cell Death Both In Vitro and in Three In Vivo Disease Models. J Med Chem 2021; 64:1510-1523. [PMID: 33522230 DOI: 10.1021/acs.jmedchem.0c01683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Necrosis is the main mode of cell death, which leads to multiple clinical conditions affecting hundreds of millions of people worldwide. Its molecular mechanisms are poorly understood, hampering therapeutics development. Here, we identify key proteolytic activities essential for necrosis using various biochemical approaches, enzymatic assays, medicinal chemistry, and siRNA library screening. These findings provide strategies to treat and prevent necrosis, including known medicines used for other indications, siRNAs, and establish a platform for the design of new inhibitory molecules. Indeed, inhibitors of these pathways demonstrated protective activity in vitro and in vivo in animal models of traumatic brain injury, acute myocardial infarction, and drug-induced liver toxicity. Consequently, this study may pave the way for the development of novel therapies for the treatment, inhibition, or prevention of a large number of hitherto untreatable diseases.
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Abstract
Protein bonds between amino acids are one of the most important biological linkages that create life. The detection of amino acids in the interstellar environments and in meteorites may lead to the suggestion that amino acids came from outer space and that peptides bonds may have been created in the gas phase. Here we show experimentally the creation of covalent bonds, most likely peptide bonds, between serine dipeptides in the gas phase. More specifically, we show that spraying a solution of Ser-Ser dipeptides results, in addition to dipeptide clusters, in a peak with the same mass as the serine tetrapeptide, which also has the same fragmentation pattern. Moreover, we show that this mass is formed upon collision induced dissociation of clusters containing four serine dipeptides. Thence, if the dipeptide can be generated abiotically the polymerization process may occur spontaneously.
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How does the exosite of rhomboid protease affect substrate processing and inhibition? Protein Sci 2017; 26:2355-2366. [PMID: 28884847 DOI: 10.1002/pro.3294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 12/24/2022]
Abstract
Rhomboid proteases constitute a family of intramembrane serine proteases ubiquitous in all forms of life. They differ in many aspects from their soluble counterparts. We applied molecular dynamics (MD) computational approach to address several challenging issues regarding their catalytic mechanism: How does the exosite of GlpG rhomboid protease control the kinetics efficiency of substrate hydrolysis? What is the mechanism of inhibition by the non-competitive peptidyl aldehyde inhibitors bound to the GlpG rhomboid active site (AS)? What is the underlying mechanism that explains the hypothesis that GlpG rhomboid protease is not adopted for the hydrolysis of short peptides that do not contain a transmembrane domain (TMD)? Two fundamental features of rhomboid catalysis, the enzyme recognition and discrimination of substrates by TMD interactions in the exosite, and the concerted mechanism of non-covalent pre-catalytic complex to covalent tetrahedral complex (TC) conversion, provide answers to these mechanistic questions.
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Ligand-Substitution Reactions of the Tellurium Compound AS-101 in Physiological Aqueous and Alcoholic Solutions. Inorg Chem 2016; 55:10847-10850. [PMID: 27726342 DOI: 10.1021/acs.inorgchem.6b02138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since its first crystallization, the aqueous structure of the tellurium-containing experimental drug AS-101 has never been studied. We show that, under the aqueous conditions in which it is administered, AS-101 is subjected to an immediate ligand-substitution reaction with water, yielding a stable hydrolyzed oxide anion product that is identified, for the first time, to be TeOCl3-. Studying the structure of AS-101 in propylene glycol (PG), an alcoholic solvent often used for the topical and oral administration of AS-101, revealed the same phenomenon of ligand-substitution reaction between the alcoholic ligands. Upon exposure to water, the PG-substituted product is also hydrolyzed to the same tellurium(IV) oxide form, TeOCl3-.
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11
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A New Oxopiperazin-Based Peptidomimetic Molecule Inhibits Prostatic Acid Phosphatase Secretion and Induces Prostate Cancer Cell Apoptosis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Inside Cover: The Anticancer Activity of Organotelluranes: Potential Role in Integrin Inactivation (ChemBioChem 10/2016). Chembiochem 2016. [DOI: 10.1002/cbic.201600250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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The Anticancer Activity of Organotelluranes: Potential Role in Integrin Inactivation. Chembiochem 2016; 17:918-27. [PMID: 26991356 DOI: 10.1002/cbic.201500614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/08/2022]
Abstract
Organic Te(IV) compounds (organotelluranes) differing in their labile ligands exhibited anti-integrin activities in vitro and anti-metastatic properties in vivo. They underwent ligand substitution with l-cysteine, as a thiol model compound. Unlike inorganic Te(IV) compounds, the organotelluranes did not form a stable complex with cysteine, but rather immediately oxidized it. The organotelluranes inhibited integrin functions, such as adhesion, migration, and metalloproteinase secretion mediation in B16F10 murine melanoma cells. In comparison, a reduced derivative with no labile ligand inhibited adhesion of B16F10 cells to a significantly lower extent, thus pointing to the importance of the labile ligands of the Te(IV) atom. One of the organotelluranes inhibited circulating cancer cells in vivo, possibly by integrin inhibition. Our results extend the current knowledge on the reactivity and mechanism of organotelluranes with different labile ligands and highlight their clinical potential.
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14
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Lithium Aluminum Hydride Assay Suitable for the Organic Chemistry Laboratory. ChemistrySelect 2016. [DOI: 10.1002/slct.201600195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dual-drug RGD conjugates provide enhanced cytotoxicity to melanoma and non-small lung cancer cells. Biopolymers 2016; 106:160-171. [PMID: 26715008 DOI: 10.1002/bip.22800] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/02/2015] [Accepted: 12/18/2015] [Indexed: 01/22/2023]
Abstract
To enhance the efficacy of targeted drug delivery, four new peptide-ligand conjugates were synthesized, each consisting of a cyclic RGDfK penta-peptide loaded with two anticancer drugs. The drug release profiles in different media of these new compounds and their cytotoxic activity against melanoma and non-small lung cancer cell lines were evaluated and compared with those of their singly loaded analogs. The cyclic RGDfK penta-peptide was selected as a targeting moiety because of its high affinity and selectivity to the αv β3 integrin receptor, which is frequently over-expressed in various types of cancer cells. The peptide's core was modified at the side chain of its Lys residue by coupling it with a sixth amino acid (AA) - either Lys (5a) or Ser (5b) (Lys/Ser splitter), resulting in two functional sites which enabled the loading of two therapeutic equivalents onto a single targeting carrier. Using Lys as a splitter resulted in two primary amines. Consequently, conjugates 1a and 1b were synthesized by coupling of 2 Chlorambucils (CLBs) or 2 Camptothecins (CPTs), respectively, to the primary amines of 5a. Conjugate 1c was synthesized from 5b by loading two equivalents of CLB on the amine and the hydroxyl of the Ser splitter, resulting in a homodimeric system with two distinct conjugation sites - amide and ester. The heterodimeric conjugate 1d of CLB and CPT was synthesized by loading each one of the primary amines of 5a with two different drugs - CLB and CPT. The doubling of drug equivalents loaded onto the targeting peptide correlated with enhanced cytotoxic efficacy of the conjugates towards cancer cells. The versatility of chemical linkages of the drugs to the peptides resulted in conjugates with different drug release profiles. Molecular dynamics simulations performed on conjugate 1d demonstrated that this compound occupies a conformational space similar to the bio-active conformation of an integrin-bound cyclic RGD peptide reference peptide (c(RGDf(NMe)V). The modified position in 1d (relative to the reference peptide) points away from the integrin, leading us to hypothesize that this peptide binds the integrin in a manner similar to that of the reference peptide thereby fulfilling a crucial requirement for targeted delivery. The strategy of dual drug loading on a single peptide carrier, gives rise to drugs with different mechanisms of action and release profiles, thus substantially increasing the efficacy of selective killing of tumor cells and while reducing the risk of the development of drug resistance. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 160-171, 2016.
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Biolabile peptidyl delivery systems toward sequential drug release. Biopolymers 2016; 106:119-32. [DOI: 10.1002/bip.22794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/22/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
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17
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α¯ Aminoisobutyric Acid Leads a Fluorescent syn-bimane LASER Probe Across the Blood-brain Barrier. Med Chem 2016; 12:48-53. [DOI: 10.2174/1573406411666150518105010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/30/2015] [Accepted: 05/15/2015] [Indexed: 11/22/2022]
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18
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Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
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19
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Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Synthesis, biological studies and molecular dynamics of new anticancer RGD-based peptide conjugates for targeted drug delivery. Bioorg Med Chem 2015; 24:294-303. [PMID: 26719208 DOI: 10.1016/j.bmc.2015.12.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/07/2015] [Accepted: 12/11/2015] [Indexed: 01/22/2023]
Abstract
New cyclic RGD peptide-anticancer agent conjugates, with different chemical functionalities attached to the parent peptide were synthesized in order to evaluate their biological activities and to provide a comparative study of their drug release profiles. The Integrin binding c(RGDfK) penta-peptide was used for the synthesis of Camptothecin (CPT) carbamate and Chlorambucil (CLB) amide conjugates. Substitution of the amino acid Lys with Ser resulted in a modified c(RGDfS) with a new attachment site, which enabled the synthesis of an ester CLB conjugate. Functional versatility of the conjugates was reflected in the variability of their drug release profiles, while the conserved RGD sequence of a selective binding to the αv integrin family, likely preserved their recognition by the Integrin and consequently their favorable toxicity towards targeted cancer cells. This hypothesis was supported by a computational analysis suggesting that all conjugates occupy conformational spaces similar to that of the Integrin bound bio-active parent peptide.
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Antimicrobial benzodiazepine-based short cationic peptidomimetics. J Pept Sci 2015; 21:512-9. [PMID: 25807936 DOI: 10.1002/psc.2771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 02/11/2015] [Accepted: 02/18/2015] [Indexed: 11/11/2022]
Abstract
Antimicrobial peptides (AMPs) appear to be good candidates for the development of new antibiotic drugs. We describe here the synthesis of peptidomimetic compounds that are based on a benzodiazepine scaffold flanked with positively charged and hydrophobic amino acids. These compounds mimic the essential properties of cationic AMPs. The new design possesses the benzodiazepine scaffold that is comprised of two glycine amino acids and which confers flexibility and aromatic hydrophobic 'back', and two arms used for further synthesis on solid phase for incorporation of charged and hydrophobic amino acids. This approach allowed us a better understanding of the influence of these features on the antimicrobial activity and selectivity. A novel compound was discovered which has MICs of 12.5 µg/ml against Staphylococcus aureus and 25 µg/ml against Escherichia coli, similar to the well-known antimicrobial peptide MSI-78. In contrast to MSI-78, the above mentioned compound has lower lytic effect against mammalian red blood cells. These peptidomimetic compounds will pave the way for future design of potent synthetic mimics of AMPs for therapeutic and biomedical applications.
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"Switch off/switch on" regulation of drug cytotoxicity by conjugation to a cell targeting peptide. Eur J Med Chem 2014; 85:139-46. [PMID: 25084142 DOI: 10.1016/j.ejmech.2014.07.073] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022]
Abstract
Bi-nuclear amino acid platforms loaded with various drugs for conjugation to a peptide carrier were synthesized using simple and convenient orthogonally protective solid-phase organic synthesis (SPOS). Each arm of the platform carries a different anticancer agent linked through the same or different functional group, providing discrete chemo- and bio-release profiles for each drug, and also enabling "switch off/switch on" regulation of drug cytotoxicity by conjugation to the platform and to a cell targeting peptide. The versatility of this approach enables efficient production of drug-loaded platforms and determination of favorable drug combinations/modes of linkage for subsequent conjugation to a carrier moiety for targeted cancer cell therapy. The results presented here potentiate the application of amino acid platforms for targeted drug delivery (TDD).
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25
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From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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A new method for filtering of reactive "warheads" of transition-state analog protease inhibitors. Eur J Med Chem 2014; 77:134-8. [PMID: 24631732 DOI: 10.1016/j.ejmech.2014.02.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
In light of the major contribution of the reactive warhead to the binding energy trend in reversible covalent transition-state analog inhibitors of serine and cysteine hydrolases, would it be possible to rationally design and quickly filter such warheads, especially for large-scale screening? The previously defined W1 and W2 covalent descriptors quantitatively account for the energetic effect of the covalent bonds reorganization, accompanying enzyme-inhibitor covalent binding. The quantum mechanically calculated W1 and W2 reflect the warhead binding energy by modeling of the enzyme-inhibitor reaction core. Here, we demonstrate the use of these descriptors for warhead filtering, and examine its scope and limitations. The W1 and W2 descriptors provide a tool for rational design of various warheads as universal building blocks of real inhibitors without the requirement of 3D structural information about the target enzyme or QSAR studies. These warheads could then be used as hit structural templates in the subsequent optimization of inhibitors recognition sites.
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Application of EMBM to Structure-Based Design of Warheads for Protease Inhibitors. Mol Inform 2014; 33:36-42. [PMID: 27485197 DOI: 10.1002/minf.201300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
Most CADD tools handle non-covalent enzyme inhibitors, despite the growing interest of the pharma industry in covalent inhibitors. We have recently introduced an enzyme mechanism-based method, EMBM, as a computational tool for binding trend analysis and prediction of chemical sites (CS) of reversible covalent enzyme inhibitors. In the current study we demonstrate the utility of EMBM to structure-based applications. In this mode, the energy of the enzyme-inhibitor covalent bond is accounted for by the W1 and W2 covalent descriptors we have developed, whereas the non-covalent interactions between the inhibitor CS and the enzyme active site can be estimated directly on the 3D structure of the enzyme-inhibitor complex.
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Anti-neoplastic activity of 1,3-diaza-2-functionalized-adamantan-6-one compounds against melanoma cells. Med Chem 2013; 10:27-37. [PMID: 23627298 DOI: 10.2174/15734064113099900002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 04/22/2013] [Accepted: 04/22/2013] [Indexed: 11/22/2022]
Abstract
Four series of 1,3-diaza-2-functionalized-adamantan-6-one derivatives, bearing at the 2 position SO, SO₂, POCl and PO₂H functional groups, were synthesized via a key quadruple Mannich reaction, followed by transformation of an aminal functionality into the final 2-thia- and 2-phospha compounds. The compounds were tested for cytotoxic activity against the mouse B16-F10 melanoma cell line. Malignant melanoma is notorious for its high resistance to chemotherapy, and new anti-melanoma drugs are urgently needed. The 2-thia compounds exhibited poor proliferation inhibition activity, but the 2-phospha derivatives showed significant activity, with IC₅₀ values of 10-60 µM. The compounds induced cell death by G₂/M cell cycle arrest, which led to apoptosis, as determined by Annexin V-FITC/PI staining, mitochondrial membrane potential changes assessed by the JC-1 reagent, caspases 3 and 7 activation, and morphological changes.
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Peptidyl cyclopropenones: reversible inhibitors, irreversible inhibitors, or substrates of cysteine proteases? Protein Sci 2013; 22:788-99. [PMID: 23553793 DOI: 10.1002/pro.2260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 11/11/2022]
Abstract
Peptidyl cyclopropenones were previously introduced as selective cysteine protease reversible inhibitors. In the present study we synthesized one such peptidyl cyclopropenone and investigated its interaction with papain, a prototype cysteine protease. A set of kinetics, biochemical, HPLC, MS, and (13)C-NMR experiments revealed that the peptidyl cyclopropenone was an irreversible inhibitor of the enzyme, alkylating the catalytic cysteine. In parallel, this cyclopropenone also behaved as an alternative substrate of the enzyme, providing a product that was tentatively suggested to be either a spiroepoxy cyclopropanone or a gamma-lactone. Thus, a single family of compounds exhibits an unusual variety of activities, being reversible inhibitors, irreversible inhibitors and alternative substrates towards enzymes of the same family.
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The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations. J Chem Theory Comput 2012; 8:4663-71. [DOI: 10.1021/ct3003767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Differentiating serine and cysteine protease mechanisms by new covalent QSAR descriptors. Chembiochem 2011; 12:1023-6. [PMID: 21438106 PMCID: PMC3088911 DOI: 10.1002/cbic.201000459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Indexed: 11/11/2022]
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34
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The mechanism of papain inhibition by peptidyl aldehydes. Proteins 2010; 79:975-85. [DOI: 10.1002/prot.22939] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 10/31/2010] [Accepted: 11/02/2010] [Indexed: 01/27/2023]
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EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors. J Chem Inf Model 2010; 50:2256-65. [PMID: 21090595 DOI: 10.1021/ci100330y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We introduce an enzyme mechanism-based method (EMBM) aimed at rational design of chemical sites (CS) of reaction coordinate analog inhibitors. The energy of valence reorganization of CS, caused by the formation of the enzyme-inhibitor covalent complex, is accounted for by new covalent descriptors W1 and W2. We considered CS fragments with a carbonyl reactivity center, like in native protease substrates. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex, anionic TC(O-) or neutral TC(OH). The modeling on a reaction core allows generation of various CS and corresponding TC(O-) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine or cysteine hydrolases. Moreover, the approach avoids the need for 3D structure of the target enzyme, so EMBM may be used for ligand-based design. We have built a chemical site of inhibitors (CSI) databank with pairs of W1 and W2 descriptors precalculated for both CH₃O(-) and CH₃S(-) nucleophiles for every collected CS fragment. We demonstrated that contribution of a CS fragment to the binding affinity of an inhibitor depends on both its covalent reorganization during the chemical transformation and its noncovalent interactions in the enzyme active site. Consequently, prediction of inhibitors binding trend can be done only by accounting for all of these factors, using W1 and W2 in combination with noncovalent QSAR descriptors.
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A double heteroatom Mitsunobu coupling with amino hydroxybenzoic acids on solid phase: a novel application of the Mitsunobu reaction to form dendron building blocks. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.08.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Optically Active N- and C-Terminal Building Blocks for the Synthesis of Peptidyl Olefin Peptidomimetics. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000539] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Challenging a paradigm: theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain. Proteins 2010; 77:916-26. [PMID: 19688822 DOI: 10.1002/prot.22516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A central mechanistic paradigm of cysteine proteases is that the His-Cys catalytic diad forms an ion-pair NH(+)/S(-) already in the catalytically active free enzyme. Most molecular modeling studies of cysteine proteases refer to this paradigm as their starting point. Nevertheless, several recent kinetics and X-ray crystallography studies of viral and bacterial cysteine proteases depart from the ion-pair mechanism, suggesting general base catalysis. We challenge the postulate of the ion-pair formation in free papain. Applying our QM/SCRF(VS) molecular modeling approach, we analyzed all protonation states of the catalytic diad in free papain and its SMe derivative, comparing the predicted and experimental pK(a) data. We conclude that the His-Cys catalytic diad in free papain is fully protonated, NH(+)/SH. The experimental pK(a) = 8.62 of His159 imidazole in free papain, obtained by NMR-controlled titration and originally interpreted as the NH(+)/S(-) <==> N/S(-) NH(+)/S(-) <==> N/S(-) equilibrium, is now assigned to the NH(+)/SH <==> N/SH NH(+)/SH <==> N/SH equilibrium.
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Synthesis of orthogonally protected optically pure ketopiperazine, diketopiperazine, ketodiazepane, and 3-aminopyrrolidone building blocks for peptidomimetic combinatorial chemistry. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.12.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Structural and Spatial Considerations in the N,N′-Diacyl- and Bis(alkoxycarbonyl)bispidinone Series. J Org Chem 2008; 73:7793-6. [DOI: 10.1021/jo801423a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Optically Active γ-Hydroxy Sulfone Julia Reagents for the Synthesis of Peptidyl Olefin Peptidomimetics. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Efficient and Stereospecific Synthesis of (z)-Hex-3-Enedioic Acid, a Key Intermediate for Gly-Gly cis Olefin Isostere. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910008087071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Octa-O-bis-(R,R)-Tartarate Ditellurane (SAS)—a Novel Bioactive Organotellurium(IV) Compound: Synthesis, Characterization, and Protease Inhibitory Activity. ChemMedChem 2007; 2:1601-6. [PMID: 17680580 DOI: 10.1002/cmdc.200700155] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Octa-O-bis-(R,R)-Tartarate Ditellurane (SAS) is a new Te(IV) compound, comprised of two tellurium atoms, each liganded by four oxygen atoms from two carboxylates and two alkoxides of two tartaric acids. Unlike many other Te(IV) compounds, SAS was highly stable in aqueous solution. It interacted with thiols to form an unstable Te(SR)(4) product. The product of the interaction of SAS with cysteine was isolated and characterized by mass spectroscopy and elemental analysis. SAS selectively inactivated cysteine proteases, but it did not inactivate other families of proteolytic enzymes. It displayed selectivity towards the cysteine protease cathepsin B, a human enzyme of pharmaceutical interest, with a second order rate constant k(i)/K(i)=5900 M(-1) s(-1).
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Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases. Proteins 2007; 70:1578-87. [PMID: 17912756 DOI: 10.1002/prot.21727] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The pKa of the catalytic His57 N(epsilon)H in the tetrahedral complex (TC) of chymotrypsin with trifluoromethyl ketone inhibitors is 4-5 units higher relative to the free enzyme (FE). Such stable TC's, formed with transition state (TS) analog inhibitors, are topologically similar to the catalytic TS. Thus, analysis of this pKa shift may shed light on the role of water solvation in the general base catalysis by histidine. We applied our QM/SCRF(VS) approach to study this shift. The method enables explicit quantum mechanical DFT calculations of large molecular clusters that simulate chemical reactions at the active site (AS) of water solvated enzymes. We derived an analytical expression for the pKa dependence on the degree of water exposure of the ionizable group, and on the total charge in the enzyme AS, Q(A) and Q(B), when the target ionizable functional group (His57 in this study) is in the acidic (A) and basic (B) forms, respectively. Q2(B) > Q2(A) both in the FE and in the TC of chymotrypsin. Therefore, water solvation decreases the relative stability of the protonated histidine in both. Ligand binding reduces the degree of water solvation of the imidazole ring, and consequently elevates the histidine pKa. Thus, the binding of the ligand plays a triggering role that switches on the cascade of catalytic reactions in serine proteases.
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Asymmetric Induction by a Remote Chiral Substituent – Computationally Determined Stereodifferentiation in Michael Additions of α-Lithiated Allyl Sulfones. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700245] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Neutral and positively charged thiols synergize the effect of the immunomodulator AS101 as a growth inhibitor of Jurkat cells, by increasing its uptake. Biochem Pharmacol 2007; 74:712-22. [PMID: 17632085 DOI: 10.1016/j.bcp.2007.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/15/2007] [Accepted: 05/15/2007] [Indexed: 11/17/2022]
Abstract
The immunomodulator amonium trichloro[1,2-ethanediolato-O,O'] tellurate (AS101), a nontoxic tellurium(IV) compound, exhibited antitumoral activity in several preclinical and clinical studies. In this study, we investigated the synergism between thiols and AS101 in its antitumoral activity on Jurkat cells. AS101 induced a G2/M arrest in the cell cycle after 24h. Addition of the thiols 2-mercaptoethanol or cysteamine led to an induction of apoptosis. Other thiols, including glutathione (GSH) and cysteine, did not potentiate the effect of AS101. We propose that this is due to the alpha-carboxylate group present in the compounds formed between AS101 and these thiols. Programmed cell death was associated with the loss of mitochondrial transmembrane potential and activation of caspase-3 and -9. Elevation of intracellular reactive oxygen species (ROS) production was also demonstrated; the antioxidant catalase significantly reduced the apoptosis, suggesting that ROS play a key role in the apoptosis induced by AS101 and the thiols. Finally, we quantified the intracellular concentration of tellurium, using electron microscopy and energy-dispersive spectroscopy (EDS) analysis. The addition of cysteamine to AS101 significantly increased the concentration of tellurium within the cells. The results indicate that neutral or positively charged thiols but not negatively charged ones, increase the antitumoral effect of AS101 by increasing its uptake into the cells.
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The Cooperative Effect Between Active Site Ionized Groups and Water Desolvation Controls the Alteration of Acid/Base Catalysis in Serine Proteases. Chembiochem 2007; 8:1416-21. [PMID: 17600794 DOI: 10.1002/cbic.200700241] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
What is the driving force that alters the catalytic function of His57 in serine proteases between general base and general acid in each step along the enzymatic reaction? The stable tetrahedral complexes (TC) of chymotrypsin with trifluoromethyl ketone transition state analogue inhibitors are topologically similar to the catalytic transition state. Therefore, they can serve as a good model to study the enzyme catalytic reaction. We used DFT quantum mechanical calculations to analyze the effect of solvation and of polar factors in the active site of chymotrypsin on the pKa of the catalytic histidine in FE (the free enzyme), EI (the noncovalent enzyme inhibitor complex), and TC. We demonstrated that the acid/base alteration is controlled by the charged groups in the active site--the catalytic Asp102 carboxylate and the oxyanion. The effect of these groups on the catalytic His is modulated by water solvation of the active site.
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The Synthetic Tellurium Compound, AS101, Is a Novel Inhibitor of IL-1βConverting Enzyme. J Interferon Cytokine Res 2007; 27:453-62. [PMID: 17572009 DOI: 10.1089/jir.2007.0168] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The organotellurium compound, trichloro(dioxoethylene-O,O') tellurate (AS101) has been shown previously to exert diverse biologic activities both in vitro and in vivo. This compound was recently found to react with thiols and to catalyze their oxidation. This property of AS101 raises the possibility that it may serve as a cysteine protease inhibitor. In the present study, using a substrate-specific enzymatic assay, we show that treatment of caspase-1 (interleukin-1beta [IL-1beta] converting enzyme [ICE]) with AS101 inhibits its enzymatic activity in a dose-dependent manner. Moreover, the results show that AS101 treatment causes a significant reduction in the active form of IL-18 and IL-1beta in peripheral blood mononuclear cells (PBMC) and in human HaCat keratinocytes. We further demonstrate that the inhibitory effect of AS101 does not involve nitric oxide (NO) or interferon-gamma (IFN-gamma), two possible regulators of IL-18 production, and does not occur at the mRNA level, suggesting a posttranscriptional mechanism of action. More importantly, AS101 downregulates IL-18 and IL-1beta serum levels in a mouse model of lipopolysaccharide (LPS)-induced sepsis, resulting in increased survival. Recent studies emphasize the pathophysiologic role of IL-18 and IL-1beta in a variety of inflammatory diseases. Thus, their blockage by the nontoxic compound, AS101, currently used in clinical studies, may provide clinical advantage in the treatment of these diseases.
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Multifunctional tellurium molecule protects and restores dopaminergic neurons in Parkinson's disease models. FASEB J 2007; 21:1870-83. [PMID: 17314138 DOI: 10.1096/fj.06-7500com] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In Parkinson's disease (PD) dopaminergic neurons in the substantia nigra (SN) become dysfunctional and many ultimately die. We report that the tellurium immunomodulating compound ammonium trichloro(dioxoethylene-O,O'-)tellurate (AS101) protects dopaminergic neurons and improves motor function in animal models of PD. It is effective when administered systemically or by direct infusion into the brain. Multifunctional activities of AS101 were identified in this study. These were mainly due to the peculiar Tellur(IV)-thiol chemistry of the compound, which enabled the compound to interact with cysteine residues on both inflammatory and apoptotic caspases, resulting in their inactivation. Conversely, its interaction with a key cysteine residue on p21(ras), led to its activation, an obligatory activity for AS101-induced neuronal differentiation. Furthermore, AS101 inhibited IL-10, resulting in up-regulation of GDNF in the SN. This was associated with activation of the neuroprotective kinases Akt and mitogen-activated protein kinases, and up-regulation of the antiapoptotic protein Bcl-2. Inhibition of caspase-1 and caspase-3 activities were associated with decreased neuronal death and inhibition of IL-1beta. We suggest that, because multiple mechanisms are involved in the dysfunction and death of neurons in PD, use of a multifunctional compound, exerting antiapoptotic, anti-inflammatory, and neurotrophic-inducing capabilities may be potentially efficacious for the treatment of PD.
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