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Zhang C, Chen S, Fu X, Dedkova LM, Hecht SM. Enhancement of N-Methyl Amino Acid Incorporation into Proteins and Peptides Using Modified Bacterial Ribosomes and Elongation Factor P. ACS Chem Biol 2024. [PMID: 38769080 DOI: 10.1021/acschembio.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
N-Methylated amino acids are constituents of natural bioactive peptides and proteins. Nα-methylated amino acids appear abundantly in natural cyclic peptides, likely due to their constraint of peptide conformation and contribution to peptide stability. Peptides containing Nα-methylated amino acids have long been prepared by chemical synthesis. While such natural peptides are not produced ribosomally, recent ribosomal strategies have afforded Nα-methylated peptides. Presently, we define new strategies for the ribosomal incorporation of Nα-methylated amino acids into peptides and proteins. First, we identify modified ribosomes capable of facilitating the incorporation of six N-methylated amino acids into antibacterial scorpion peptide IsCT. Also synthesized analogously was a protein domain (RRM1) from hnRNP LL; improved yields were observed for nearly all tested N-methylated amino acids. Computational modeling of the ribosomal assembly illustrated how the distortion imposed by N-methylation could be compensated by altering the nucleotides in key 23S rRNA positions. Finally, it is known that incorporation of multiple prolines (an N-alkylated amino acid) ribosomally can be facilitated by bacterial elongation factor P. We report that supplementing endogenous EF-P during IsCT peptide and RRM1 protein synthesis gave improved yields for most of the N-methylated amino acids studied.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xuan Fu
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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2
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Ecker DJ, Aiello CD, Arron JR, Bennett CF, Bernard A, Breakefield XO, Broderick TJ, Callier SL, Canton B, Chen JS, Fishburn CS, Garrett B, Hecht SM, Janowitz T, Kliegman M, Krainer A, Louis CU, Lowe C, Sehgal A, Tozan Y, Tracey KJ, Urnov F, Wattendorf D, Williams TW, Zhao X, Hayden MR. Opportunities and challenges for innovative and equitable healthcare. Nat Rev Drug Discov 2024; 23:321-322. [PMID: 38409339 DOI: 10.1038/d41573-024-00032-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
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3
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Daskalova SM, Dedkova LM, Maini R, Talukder P, Bai X, Chowdhury SR, Zhang C, Nangreave RC, Hecht SM. Elongation Factor P Modulates the Incorporation of Structurally Diverse Noncanonical Amino Acids into Escherichia coli Dihydrofolate Reductase. J Am Chem Soc 2023; 145:23600-23608. [PMID: 37871253 PMCID: PMC10762953 DOI: 10.1021/jacs.3c07524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The introduction of noncanonical amino acids into proteins and peptides has been of great interest for many years and has facilitated the detailed study of peptide/protein structure and mechanism. In addition to numerous nonproteinogenic α-l-amino acids, bacterial ribosome modification has provided the wherewithal to enable the synthesis of peptides and proteins with a much greater range of structural diversity, as has the use of endogenous bacterial proteins in reconstituted protein synthesizing systems. In a recent report, elongation factor P (EF-P), putatively essential for enabling the incorporation of contiguous proline residues into proteins, was shown to facilitate the introduction of an N-methylated amino acid in addition to proline. This finding prompted us to investigate the properties of this protein factor with a broad variety of structurally diverse amino acid analogues using an optimized suppressor tRNAPro that we designed. While these analogues can generally be incorporated into proteins only in systems containing modified ribosomes specifically selected for their incorporation, we found that EF-P could significantly enhance their incorporation into model protein dihydrofolate reductase using wild-type ribosomes. Plausibly, the increased yields observed in the presence of structurally diverse amino acid analogues may result from the formation of a stabilized ribosomal complex in the presence of EF-P that provides more favorable conditions for peptide bond formation. This finding should enable the facile incorporation of a much broader structural variety of amino acid analogues into proteins and peptides using native ribosomes.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chao Zhang
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C Nangreave
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Fu X, Shang Y, Chen S, Dedkova LM, Hecht SM. Activation of d-Asparagine and d-Glutamine Derivatives Using the Mitsunobu Reaction. Org Lett 2023. [PMID: 36800493 DOI: 10.1021/acs.orglett.3c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Seven d-amino acid derivatives having reactive side chains have been activated to afford their respective 3,5-dinitrobenzyl esters using the Mitsunobu reaction. This esterification was found to be difficult using traditional methods involving 3,5-dinitrobenzyl chloride under alkaline conditions. The conversion of a tRNA to the respective d-glutaminyl-tRNA using d-glutamine 3,5-dinitrobenzyl ester was catalyzed by a flexizyme, followed by purification to remove all the unacylated tRNAs and other byproducts. Both d- and l-glutamine were incorporated from their aminoacyl-tRNAs into a model peptide structurally related to IFN-β.
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Affiliation(s)
- Xuan Fu
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuqin Shang
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Chen S, Ji X, Dedkova LM, Potuganti GR, Hecht SM. Site-Selective Tyrosine Phosphorylation in the Activation of the p50 Subunit of NF-κB for DNA Binding and Transcription. ACS Chem Biol 2023; 18:59-69. [PMID: 36534507 PMCID: PMC10026595 DOI: 10.1021/acschembio.2c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The family of NF-κB transcriptional activators controls the expression of many genes, including those involved in cell survival and development. The family consists of homo- and heterodimers constituted by combinations of five subunits. Subunit p50 includes 13 tyrosine residues, but the relationship between specific tyrosine phosphorylations and p50 function is not well understood. Subunits of p50 and p65 prepared in vitro formed a heterodimer, but this NF-κB would not bind to the interleukin-2 (IL-2) promoter DNA. Treatment of p50 with guanosine triphosphate (GTP) and a lysate from activated Jurkat cells, effected rapid p50 phosphorylation, and, in the presence of wild-type subunit p65, was accompanied on the same time scale by IL-2 promoter DNA binding. Modified p50s containing one of seven stoichiometrically phosphorylated tyrosines in NF-κB p50/p65 heterodimers, included three that facilitated binding to the IL-2 DNA promoter region to a greater extent than the wild type. One of these three stoichiometrically phosphorylated p50/p65 heterodimers of NF-κB, containing pTyr60 in the p50 subunit, was treated with a lysate from activated Jurkat cells + GTP and shown to be phosphorylated on the same time scale as wild-type p50. This modified NF-κB also developed IL-2 promoter DNA binding activity on the same time scale as the wild type but exhibited greater binding to the IL-2 DNA promoters than the wild type. The nature of this enhanced binding was studied in greater detail using a metabolically stable pTyr derivative at position 60 of p50 and cellular phosphatases. We suggest that enhanced DNA binding of modified NF-κB containing pTyr60 in the p50 subunit may reflect stoichiometric NF-κB phosphorylation at a site that is not normally fully phosphorylated, or not phosphorylated at all, and is relatively resistant to the effects of Jurkat cell tyrosine phosphatase activity. This conclusion was reinforced by demonstrating that modification of Tyr60 of p50 with a metabolically stable methylenephosphonate moiety further increased the stability of the formed NF-κB p50/p65 heterodimer against the action of activated Jurkat cell phosphatases.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Gal Reddy Potuganti
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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6
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Zhang C, Bai X, Chen S, Dedkova LM, Hecht SM. Local Conformational Constraint of Firefly Luciferase Can Affect the Energy of Bioluminescence and Enzyme Stability. CCS Chem 2022; 4:1695-1707. [PMID: 36939446 PMCID: PMC10022883 DOI: 10.31635/ccschem.022.202101733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Conformational dynamics contribute importantly to enzyme catalysis, such that targeted conformational constraint may affect catalysis. Firefly luciferases undergo extensive structural change during catalysis; key residues form a hydrophobic pocket, excluding water and enabling maximally energetic light production. Point mutants almost always luminesce at longer wavelengths (lower energy) than the wild type. Conformational constraint, using dipeptide analogue 3 at a position critical for optimized excited state structure, produced luciferase emission at a shorter wavelength by ~10 nm. In comparison, introduction of conformationally constrained analogues 4, 5, or 7 afforded luciferases emitting at longer wavelengths, while a related unconstrained luciferase (analogue 6) exhibited wild-type emission. The constrained luciferases tested were more stable than the wild type. Protein modeling demonstrated that the "inside" or "outside" orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength, respectively. More broadly, these results suggest that local conformational constraint can control specific elements of enzyme behavior, both in vitro and in vivo. This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position. The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Xiaoguang Bai
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Shengxi Chen
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
| | - Larisa M. Dedkova
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
- Corresponding authors: ;
| | - Sidney M. Hecht
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287
- Corresponding authors: ;
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7
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Hecht SM. Expansion of the Genetic Code Through the Use of Modified Bacterial Ribosomes. J Mol Biol 2022; 434:167211. [PMID: 34419431 PMCID: PMC9990327 DOI: 10.1016/j.jmb.2021.167211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Biological protein synthesis is mediated by the ribosome, and employs ~20 proteinogenic amino acids as building blocks. Through the use of misacylated tRNAs, presently accessible by any of several strategies, it is now possible to employ in vitro and in vivo protein biosynthesis to elaborate proteins containing a much larger variety of amino acid building blocks. However, the incorporation of this broader variety of amino acids is limited to those species utilized by the ribosome. As a consequence, virtually all of the substrates utilized over time have been L-α-amino acids. In recent years, a variety of structural and biochemical studies have provided important insights into those regions of the 23S ribosomal RNA that are involved in peptide bond formation. Subsequent experiments, involving the randomization of key regions of 23S rRNA required for peptide bond formation, have afforded libraries of E. coli harboring plasmids with the rrnB gene modified in the key regions. Selections based on the use of modified puromycin derivatives with altered amino acids then identified clones uniquely sensitive to individual puromycin derivatives. These clones often recognized misacylated tRNAs containing altered amino acids similar to those in the modified puromycins, and incorporated the amino acid analogues into proteins. In this fashion, it has been possible to realize the synthesis of proteins containing D-amino acids, β-amino acids, phosphorylated amino acids, as well as long chain and cyclic amino acids in which the nucleophilic amino group is not in the α-position. Of special interest have been dipeptides and dipeptidomimetics of diverse utility.
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Affiliation(s)
- Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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8
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Chen S, Ji X, Dedkova LM, Hecht SM. Site-selective incorporation of phosphorylated tyrosine into the p50 subunit of NF-κB and activation of its downstream gene CD40. Chem Commun (Camb) 2021; 57:12651-12654. [PMID: 34766616 DOI: 10.1039/d1cc04726d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NF-κB family of transcriptional activators is responsible for the expression of numerous genes that control key functions such as cell development and survival. Subunit p50 has been studied extensively and is known to include 13 tyrosines, but the extent and pattern of tyrosine phosphorylation that accompanies p50 function has not been defined in the literature, especially at the level of selectivity of gene expression. In this study, phosphorylated tyrosine (pTyr) was site-selectively incorporated into the p50 subunit using an E. coli in vitro expression system containing a modified ribosome. In human T cells, the NF-κBs containing a pTyr at position 60 or 82 of p50 strongly increased the expression of CD40, which is a potential target for cancer or viral immunotherapy. Promoter DNA binding was studied for CD40 promoters, and verified two pTyr residues in NF-κB p50/p65 heterodimers that facilitated this process, and that support the possible importance of phosphorylation stoichiometry. This study defines a new approach for studying tyrosine residues whose phosphorylation alters protein binding to DNA promoters, and contributes to the facility of DNA expression.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe 85287, USA.
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe 85287, USA.
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe 85287, USA.
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe 85287, USA.
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Zhang C, Talukder P, Dedkova LM, Hecht SM. Facilitated synthesis of proteins containing modified dipeptides. Bioorg Med Chem 2021; 41:116210. [PMID: 34022527 DOI: 10.1016/j.bmc.2021.116210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
The elaboration of peptides and proteins containing non-proteinogenic amino acids has been realized using several complementary strategies, including chemical synthesis, ribosome- or non-ribosome-mediated elaboration, intein-mediated polypeptide rearrangements, or some combination of these strategies. All of these have strengths and limitations, and significant efforts have been focused on minimizing the effects of limitations, to improve the overall utility of individual strategies. Our laboratory has studied ribosomally mediated peptide and protein synthesis involving a wide variety of non-proteinogenic amino acids, and in recent years we have described a novel strategy for the selection of modified bacterial ribosomes. These modified ribosomes have enabled the incorporation into peptides and proteins of numerous modified amino acids not accessible using wild-type ribosomes. This has included d-amino acids, β-amino acids, dipeptides and dipeptidomimetic species, as well as phosphorylated amino acids. Presently, we have considered novel strategies for incorporating non-proteinogenic amino acids in improved yields. This has included the incorporation of non-proteinogenic amino acids into contiguous positions, a transformation known to be challenging. We demonstrate the preparation of this type of protein modification by utilizing a suppressor tRNACUA activated with a dipeptide consisting of two identical non-proteinogenic amino acids, in the presence of modified ribosomes selected to recognize such dipeptides. Also, we demonstrate that the use of bis-aminoacylated suppressor tRNAs, shown previously to increase protein yields significantly in vitro, can be extended to the use of non-proteinogenic amino acids.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
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Zhang C, Bai X, Dedkova LM, Hecht SM. Protein synthesis with conformationally constrained cyclic dipeptides. Bioorg Med Chem 2020; 28:115780. [PMID: 33007560 DOI: 10.1016/j.bmc.2020.115780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 01/27/2023]
Abstract
We have synthesized several conformationally constrained dipeptide analogues as possible substrates for incorporation into proteins. These have included three cyclic dipeptides formed from Boc derivatives of 2,4-diaminobutyric acid, ornithine and lysine, having 5-, 6-, and 7-membered lactam rings, respectively. These dipeptides were used to activate a suppressor tRNA transcript, the latter of which had been prepared by in vitro transcription. Using modified E. coli ribosomes described previously, these activated suppressor tRNAs enabled the incorporation of the three cyclic dipeptides into dihydrofolate reductase (DHFR) at positions 18 and 49. The suppression yields increased with increasing lactam ring size and were found to proceed in suppression yields ranging from 3.4 to 8.9% at two different protein sites for the 5-, 6- and 7-membered lactam dipeptides. The greater facility of incorporation of the 7-membered lactam prompted us to prepare two 7-membered cyclic acylhydrazides (4 and 5) by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDCI)-mediated cyclization of amino acids having selectively protected hydrazine functional groups in their side chains. In common with the lactam dipeptides, acylhydrazide dipeptides 4 and 5 could be used to activate the same suppressor tRNA transcript and to incorporate the cyclic dipeptides into DHFR. They were incorporated into the same two DHFR sites in suppression yields ranging from 8.3 to 11.2%.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
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11
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Liu J, Bandyopadhyay I, Zheng L, Khdour OM, Hecht SM. Antiferroptotic Activity of Phenothiazine Analogues: A Novel Therapeutic Strategy for Oxidative Stress Related Disease. ACS Med Chem Lett 2020; 11:2165-2173. [PMID: 33214825 DOI: 10.1021/acsmedchemlett.0c00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Ferroptosis is an iron-catalyzed, nonapoptotic form of regulated necrosis that has been implicated in the pathological cell death associated with various disorders including neurodegenerative diseases (e.g., Friedreich's ataxia (FRDA), Alzheimer's disease, and Parkinson's disease), stroke, and traumatic brain injury. Recently, we showed that lipophilic methylene blue (MB) and methylene violet (MV) analogues both promoted increased frataxin levels and mitochondrial biogenesis, in addition to their antioxidant activity in cultured FRDA cells. Presently, we report the synthesis of series of lipophilic phenothiazine analogues that potently inhibit ferroptosis. The most promising compounds (1b-5b) exhibited an improved protection compared to the parent phenothiazine against erastin- and RSL3-induced ferroptotic cell death. These analogues have equivalent or better potency than ferrostatin-1 (Fer-1) and liproxstatin-1 (Lip-1), that are among the most potent inhibitors of this regulated cell death described so far. They represent novel lead compounds with therapeutic potential in relevant ferroptosis-driven disease models such as FRDA.
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12
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Daskalova SM, Eisenhauer BM, Gao M, Feng X, Ji X, Cheng Q, Fahmi N, Khdour OM, Chen S, Hecht SM. An assay for DNA polymerase β lyase inhibitors that engage the catalytic nucleophile for binding. Bioorg Med Chem 2020; 28:115642. [PMID: 32773093 DOI: 10.1016/j.bmc.2020.115642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 11/16/2022]
Abstract
DNA polymerase β (Pol β) repairs cellular DNA damage. When such damage is inflicted upon the DNA in tumor cells treated with DNA targeted antitumor agents, Pol β thus diminishes their efficacy. Accordingly, this enzyme has long been a target for antitumor therapy. Although numerous inhibitors of the lyase activity of the enzyme have been reported, none has yet proven adequate for development as a therapeutic agent. In the present study, we developed a new strategy to identify lyase inhibitors that critically engage the lyase active site primary nucleophile Lys72 as part of the binding interface. This involves a parallel evaluation of the effect of the inhibitors on the wild-type DNA polymerase β (Pol β) and Pol β modified with a lysine analogue at position 72. A model panel of five structurally diverse lyase inhibitors identified in our previous studies (only one of which has been published) with unknown modes of binding were used for testing, and one compound, cis-9,10-epoxyoctadecanoic acid, was found to have the desired characteristics. This finding was further corroborated by in silico docking, demonstrating that the predominant mode of binding of the inhibitor involves an important electrostatic interaction between the oxygen atom of the epoxy group and Nε of the main catalytic nucleophile, Lys72. The strategy, which is designed to identify compounds that engage certain structural elements of the target enzyme, could find broader application for identification of ligands with predetermined sites of binding.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Brian M Eisenhauer
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xizhi Feng
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Qi Cheng
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - NourEddine Fahmi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States; Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
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13
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Zhang C, Chen S, Dedkova LM, Hecht SM. Effects of Nucleobase Amino Acids on the Binding of Rob to Its Promoter DNA: Differential Alteration of DNA Affinity and Phenotype. Biochemistry 2020; 59:2111-2119. [PMID: 32412234 DOI: 10.1021/acs.biochem.0c00290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleic acid binding proteins have been studied extensively, but the nature of the interactions that control their affinity, selectivity, and DNA and RNA functions is still not well understood. To understand the nature and functional consequences of such interactions, we introduced nucleobase amino acids at specific positions of the transcriptional regulator Rob protein in vivo and succeeded in demonstrating that an alteration of the protein-DNA affinity can affect specific phenotypes associated with Rob protein-DNA interactions. Previously, we inserted different nucleobase amino acids in lieu of Arg40; this residue is known (via X-ray crystallography) to interact with the micF DNA promoter A-box residue Gua6. The interactions predominantly involved Watson-Crick-like H bonding. The present study focused primarily on the micF DNA promoter B-box; the crystallographically determined interaction involves H bonding between the agmatine moiety of Arg90 within an HTH motif of Rob and a phosphate oxygen anion to the 5'-side of Thy14. We had two main goals, the first of which was to demonstrate enhanced Rob-binding to the micF promoter DNA and the functional consequences resulting from the interaction of micF DNA with Rob analogues containing Arg90 nucleobase mimics. The second was to explore the possible functional consequences of enhancing the protein-DNA affinity with nucleobase replacements, which mechanistically mediate interactions differently than those reported to be operative for specific protein-DNA interactions. Nucleobase replacement at position 90 with Arg isosteres enhanced the Rob protein-micF DNA affinity in parallel with increasing antibiotic and Hg2+ resistance, while aromatic amino acid replacements increased the affinity but not the antibiotic or Hg2+ resistance. The demonstration of an increased affinity through strong base stacking interactions was notable.
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Zhang C, Chen S, Bai X, Dedkova LM, Hecht SM. Alteration of Transcriptional Regulator Rob In Vivo: Enhancement of Promoter DNA Binding and Antibiotic Resistance in the Presence of Nucleobase Amino Acids. Biochemistry 2020; 59:1217-1220. [PMID: 32157864 DOI: 10.1021/acs.biochem.0c00103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of proteins that bind selectively to nucleic acid sequences is an ongoing challenge. We previously synthesized nucleobase amino acids designed to replace proteinogenic amino acids; these were incorporated into proteins to bind specific nucleic acids predictably. An early example involved selective cell free binding of the hnRNP LL RRM1 domain to its i-motif DNA target via Watson-Crick-like H-bonding interactions. In this study, we employ the X-ray crystal structure of transcriptional regulator Rob bound to its micF promoter, which occurred without DNA distortion. Rob proteins modified in vivo with nucleobase amino acids at position 40 exhibited altered DNA promoter binding, as predicted on the basis of their Watson-Crick-like H-bonding interactions with promoter DNA A-box residue Gua-6. Rob protein expression ultimately controls phenotypic changes, including resistance to antibiotics. Although Rob proteins with nucleobase amino acids were expressed in Escherichia coli at levels estimated to be only a fraction of that of the wild-type Rob protein, those modified proteins that bound to the micF promoter more avidly than the wild type in vitro also produced greater resistance to macrolide antibiotics roxithromycin and clarithromycin in vivo, as well as the β-lactam antibiotic ampicillin. Also demonstrated is the statistical significance of altered DNA binding and antibiotic resistance for key Rob analogues. These preliminary findings suggest the ultimate utility of nucleobase amino acids in altering and controlling preferred nucleic acid target sequences by proteins, for probing molecular interactions critical to protein function, and for enhancing phenotypic changes in vivo by regulatory protein analogues.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Abstract
Dengue virus (DENV) is the most common human arboviral infection worldwide and can present with severe clinical manifestations. Timely DENV detection improves clinical outcomes, and identification of the DENV serotype (DENV-1-4) may provide beneficial epidemiologic data to inform the initiation of control measures. Here, DENV RNA-triggered, enzyme-free tandem toehold-mediated displacement reactions were developed to identify and serotype DENV in RNA controls and contrived samples through the amplification of a fluorescent signal detected by the use of a fluorescent scanner and a confocal microscope. Each DENV serotype was detected selectively using both imaging methods. In addition, a 384-well plate was used to prepare an array for diagnosis of the four DENV RNA serotypes from contrived clinical samples. The four serotypes of dengue virus were detected using novel enzyme-free amplification reactions, which are more facile than amplification using reverse transcriptase PCR.
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Affiliation(s)
- Mingxuan Gao
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Jesse J. Waggoner
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia 30322, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
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Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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17
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Abstract
Genetic code expansion has enabled many noncanonical amino acids to be incorporated into proteins in vitro and in cellulo. These have largely involved α-l-amino acids, reflecting the substrate specificity of natural aminoacyl-tRNA synthetases and ribosomes. Recently, modified E. coli ribosomes, selected using a dipeptidylpuromycin analogue, were employed to incorporate dipeptides and dipeptidomimetics. Presently, we report the in cellulo incorporation of a strongly fluorescent oxazole amino acid (lacking an asymmetric center or α-amino group) by using modified ribosomes and pyrrolysyl-tRNA synthetase (PylRS). Initially, a plasmid encoding the RRM1 domain of putative transcription factor hnRNP LL was cotransformed with plasmid pTECH-Pyl-OP in E. coli cells, having modified ribosomes able to incorporate dipeptides. Cell incubation in a medium containing oxazole 2 resulted in the elaboration of RRM1 containing the oxazole. Green fluorescent protein, previously expressed in vitro with several different oxazole amino acids at position 66, was also expressed in cellulo containing oxazole 2; the incorporation was verified by mass spectrometry. Finally, oxazole 2 was incorporated into position 13 of MreB, a bacterial homologue of eukaryotic cytoskeletal protein actin F. Modified MreB expressed in vitro and in cellulo comigrated with wild type. E. coli cells expressing the modified MreB were strongly fluorescent and retained the E. coli cell rod-like phenotype. For each protein studied, the incorporation of oxazole 2 strongly increased oxazole fluorescence, suggesting its potential utility as a protein tag. These findings also suggest the feasibility of dramatically increasing the repertoire of amino acids that can be genetically encoded for protein incorporation in cellulo.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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Bandyopadhyay I, Chowdhury SR, Visavadiya NP, Hecht SM, Khdour OM. Chemical synthesis of lipophilic methylene blue analogues which increase mitochondrial biogenesis and frataxin levels. Data Brief 2018; 20:1105-1114. [PMID: 30225325 PMCID: PMC6139889 DOI: 10.1016/j.dib.2018.08.156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/24/2018] [Indexed: 02/04/2023] Open
Abstract
As part of an ongoing program to develop potential therapeutic agents for the treatment of the neurodegenerative disease Friedreich׳s ataxia (FRDA), we have prepared a number of lipophilic methylene blue analogues. Some of these compounds significantly increase mitochondrial biogenesis and frataxin levels in cultured Friedreich’s ataxia cells [1]. This data article describes the chemical synthesis and full physicochemical characterization of the new analogues.
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Affiliation(s)
- Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Nishant P Visavadiya
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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Khdour OM, Bandyopadhyay I, Visavadiya NP, Roy Chowdhury S, Hecht SM. Phenothiazine antioxidants increase mitochondrial biogenesis and frataxin levels in Friedreich's ataxia cells. Medchemcomm 2018; 9:1491-1501. [PMID: 30288223 DOI: 10.1039/c8md00274f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022]
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease that is linked to transcriptional repression of the nuclear FXN gene encoding the essential mitochondrial protein frataxin (FXN). Compounds that increase frataxin levels may enable effective therapeutic intervention for blunting disease progression. Recently, we showed that lipophilic methylene violet (MV) and methylene blue (MB) analogues both conferred benefit to cultured FRDA cells in several regards, including ROS suppression, maintenance of mitochondrial membrane potential and increased ATP production. Some of the MB analogues were also shown to promote increased frataxin levels and mitochondrial biogenesis. Presently, we report that two of the MV analogues studied previously (1 and 2) also increased frataxin levels and mitochondrial biogenesis significantly. Because the substitution pattern in the two series of compounds was not the same, we also prepared new MV derivatives having the same substitution pattern as the original MB derivatives studied to enable a more direct comparison. Two of the new MV compounds, 4b and 6b, exhibited enhanced antioxidant capability, increased frataxin levels and mitochondrial biogenesis, and improved aconitase activity. These encouraging findings demonstrated that the MV analogues had better overall activity with less cytotoxicity.
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Affiliation(s)
- Omar M Khdour
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA .
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
| | - Nishant P Visavadiya
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA .
| | - Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
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20
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Khdour OM, Bandyopadhyay I, Chowdhury SR, Visavadiya NP, Hecht SM. Lipophilic methylene blue analogues enhance mitochondrial function and increase frataxin levels in a cellular model of Friedreich's ataxia. Bioorg Med Chem 2018; 26:3359-3369. [PMID: 29773347 DOI: 10.1016/j.bmc.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/25/2018] [Accepted: 05/03/2018] [Indexed: 01/31/2023]
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder resulting from reduced expression of the protein frataxin (FXN). Although its function is not fully understood, frataxin appears to help assemble iron sulfur clusters; these are critical for the function of many proteins, including those needed for mitochondrial energy production. Finding ways to increase FXN levels has been a major therapeutic strategy for this disease. Previously, we described a novel series of methylene violet analogues and their structural optimization as potential therapeutic agents for neurodegenerative and mitochondrial disorders. Presently, a series of methylene blue analogues has been synthesized and characterized for their in vitro biochemical and biological properties in cultured Friedreich's ataxia lymphocytes. Favorable methylene blue analogues were shown to increase frataxin levels and mitochondrial biogenesis, and to improve aconitase activity. The analogues were found to be good ROS scavengers, and able to protect cultured FRDA lymphocytes from oxidative stress resulting from inhibition of complex I and from glutathione depletion. The analogues also preserved mitochondrial membrane potential and augmented ATP production. Our results suggest that analogue 5, emerging from the initial structure of the parent compound methylene blue (MB), represents a promising lead structure and lacks the cytotoxicity associated with the parent compound MB.
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Affiliation(s)
- Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Nishant P Visavadiya
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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Daskalova SM, Bai X, Hecht SM. Study of the Lyase Activity of Human DNA Polymerase β Using Analogues of the Intermediate Schiff Base Complex. Biochemistry 2018; 57:2711-2722. [PMID: 29625008 DOI: 10.1021/acs.biochem.8b00308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerase β (Pol β) participates in mammalian base excision repair. The enzyme has a two-domain architecture, reflecting its dual functionality. The polymerase activity, which replaces damaged nucleosides removed during an initial excision process, is within the C-terminal 31 kDa domain, while the N-terminal 8 kDa domain participates in a lyase function, working to remove a 5'-deoxyribose phosphate (5'-dRP) moiety from the damaged DNA substrate. The currently accepted mechanism of the lyase reaction involves a transient covalent enzyme-DNA intermediate in the form of a Schiff base connecting Lys72 of the enzyme with the 5'-dRP moiety. The Schiff base intermediate is resolved via a β-elimination reaction, initiated by abstraction of a C2'-H atom from the 5'-dRP moiety. Presently, we describe the preparation of three Pol β enzymes modified at position 72 with aminooxy or hydrazinyl analogues of lysine. These enzymes form transient covalent bonds with the 5'-dRP moiety of the damaged DNA, in the form of an oxime or hydrazone, respectively. Both types of enzyme DNA intermediates are ultimately resolved by the lyase activities of each of the modified enzymes. Unsurprisingly, the formation and resolution of these E-S complexes proceed with diminished kinetics, and with an altered pH profile. The performed experiments provide additional support for Schiff base formation as an obligatory intermediate on the pathway to DNA repair, as well as for the proposed participation of Lys72 in effecting opening of the 5'-dRP ring via protonation of the ring oxygen atom, and for complex resolution via a β-elimination reaction.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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22
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Mastroeni D, Nolz J, Khdour OM, Sekar S, Delvaux E, Cuyugan L, Liang WS, Hecht SM, Coleman PD. Oligomeric amyloid β preferentially targets neuronal and not glial mitochondrial-encoded mRNAs. Alzheimers Dement 2018; 14:775-786. [PMID: 29396107 DOI: 10.1016/j.jalz.2017.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/28/2017] [Accepted: 12/07/2017] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Our laboratories have demonstrated that accumulation of oligomeric amyloid β (OAβ) in neurons is an essential step leading to OAβ-mediated mitochondrial dysfunction. METHODS Alzheimer's disease (AD) and matching control hippocampal neurons, astrocytes, and microglia were isolated by laser-captured microdissection from the same subjects, followed by whole-transcriptome sequencing. Complementary in vitro work was performed in OAβ-treated differentiated SH-SY5Y, followed by the use of a novel CoQ10 analogue for protection. This compound is believed to be effective both in suppressing reactive oxygen species and also functioning in mitochondrial electron transport. RESULTS We report decreases in the same mitochondrial-encoded mRNAs in Alzheimer's disease laser-captured CA1 neurons and in OAβ-treated SH-SY5Y cells, but not in laser-captured microglia and astrocytes. Pretreatment with a novel CoQ10 analogue, protects neuronal mitochondria from OAβ-induced mitochondrial changes. DISCUSSION Similarity of expression changes in neurons from Alzheimer's disease brain and neuronal cells treated with OAβ, and the effect of a CoQ10 analogue on the latter, suggests a pretreatment option to prevent OAβ toxicity, long before the damage is apparent.
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Affiliation(s)
- Diego Mastroeni
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ.
| | - Jennifer Nolz
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ
| | | | - Elaine Delvaux
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
| | | | | | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ
| | - Paul D Coleman
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
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Gao M, Daniel D, Zou H, Jiang S, Lin S, Huang C, Hecht SM, Chen S. Rapid detection of a dengue virus RNA sequence with single molecule sensitivity using tandem toehold-mediated displacement reactions. Chem Commun (Camb) 2018; 54:968-971. [DOI: 10.1039/c7cc09131a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Novel tandem toehold-mediated displacement reactions were developed to detect dengue virus RNA. As few as 6 copies of RNA per sample were detected.
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Affiliation(s)
- Mingxuan Gao
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
| | - Douglas Daniel
- Biodesign Center for Innovations in Medicine, Arizona State University
- Tempe 85287
- USA
| | - Hongyan Zou
- College of Pharmaceutical Sciences, Southwest University
- Chongqing
- P. R. China
- Ministry of Education Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Southwest University
- Chongqing
| | - Shuoxing Jiang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University
- Tempe 85287
- USA
| | - Su Lin
- Biodesign Center for Innovations in Medicine, Arizona State University
- Tempe 85287
- USA
| | - Chengzhi Huang
- College of Pharmaceutical Sciences, Southwest University
- Chongqing
- P. R. China
- Ministry of Education Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Southwest University
- Chongqing
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
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Abstract
In a recent study, several new derivatives of antimycin A (AMA) were produced by means of a novel transacylation reaction, and these were shown to mediate selective toxicity toward cultured A549 human lung epithelial adenocarcinoma cells, as compared with WI-38 normal human lung fibroblasts. The purpose of our study was to investigate whether the analogues all expressed their cytotoxicity by the same mechanism. This was done by studying the effects of the compounds in several types of cell lines. In comparison with 2-O-methylantimycin, which acts at the locus of Bcl-2, none of the new derivatives exhibited a difference in cytotoxicity toward cells expressing different levels of Bcl-2. In cell lines that over- or underexpress estrogen or Her2 receptors, AMA analogue 2 exhibited Her2 receptor dependency at low concentration. Three compounds (1, 4, and 6) exhibited concentration-dependent increases in reactive oxygen species, with 6 being especially potent. Compounds 5 and 6 diminished mitochondrial membrane potential more potently than AMA, and 1 also displayed enhanced activity relative to 2-4. Interestingly, only 1 and AMA displayed strong inhibition of the respiratory chain, as measured by monitoring NADH (reduced nicotinamide adenine dinucleotide) oxidase. Because four of the analogues have positively charged substituents, two of these (4 and 6) were studied to see whether the observed effects were due to much higher level of accumulation within the mitochondria. Their presence in the mitochondria was not dramatically enhanced. Neither of the two presently characterized mechanisms of cell killing by AMA can fully account for the observed results.
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Affiliation(s)
- Yanmin Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Arnaud Chevalier
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Omar M Khdour
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Larisa Morales Soto
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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Chen S, Maini R, Bai X, Nangreave RC, Dedkova LM, Hecht SM. Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated IκB-α and Its Interaction with NF-κB. J Am Chem Soc 2017; 139:14098-14108. [PMID: 28898075 PMCID: PMC5901656 DOI: 10.1021/jacs.7b05168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges that have been shown to have a negative effect on protein translation. Bis-o-nitrobenzyl protection of tyrosine phosphate enabled its incorporation into DHFR and IκB-α using wild-type ribosomes, and the elaborated proteins could subsequently be deprotected by photolysis. Also investigated in parallel was the re-engineering of the 23S rRNA of Escherichia coli, guided by the use of a phosphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphotyrosine into proteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation. Selection of a library of modified ribosomal clones with phosphorylated puromycin identified six modified ribosome variants having mutations in nucleotides 2600-2605 of 23S rRNA; these had enhanced sensitivity to the phosphorylated puromycin. The six clones demonstrated some sequence homology in the region 2600-2605 and incorporated unprotected phosphotyrosine into IκB-α using a modified gene having a TAG codon in the position corresponding to amino acid 42 of the protein. The purified phosphorylated protein bound to a phosphotyrosine specific antibody and permitted NF-κB binding to a DNA duplex sequence corresponding to its binding site in the IL-2 gene promoter. Unexpectedly, phosphorylated IκB-α also mediated the exchange of exogenous DNA into an NF-κB-cellular DNA complex isolated from the nucleus of activated Jurkat cells.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C. Nangreave
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Roy Chowdhury S, Khdour OM, Bandyopadhyay I, Hecht SM. Lipophilic methylene violet analogues as modulators of mitochondrial function and dysfunction. Bioorg Med Chem 2017; 25:5537-5547. [PMID: 28927904 DOI: 10.1016/j.bmc.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022]
Abstract
In an effort to identify methylene blue analogues having improved antioxidant activity, a series of new methylene violet analogues have been designed and synthesized. The analogues were prepared following a synthetic route that is more efficient than the previously reported methods, both in terms of yield and purity of the final products. The route involves the Smiles rearrangement as one of the crucial steps. Smiles rearrangement of suitably substituted diphenyl sulfide intermediates afforded the corresponding phenothiazine analogues in high yields, which were subsequently converted to the final products. The methylene violet analogues were evaluated for their ability to preserve mitochondrial function in Friedreich's ataxia (FRDA) lymphocytes. The analogues were shown to be efficient ROS scavengers, and able to protect cultured FRDA lymphocytes from oxidative stress resulting from inhibition of complex I. The analogues also preserved mitochondrial membrane potential and augmented ATP production. The analogues were found to be better antioxidants than the parent compounds methylene blue and methylene violet.
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Affiliation(s)
- Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
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27
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Arutla V, Leal J, Liu X, Sokalingam S, Raleigh M, Adaralegbe A, Liu L, Pentel PR, Hecht SM, Chang Y. Prescreening of Nicotine Hapten Linkers in Vitro To Select Hapten-Conjugate Vaccine Candidates for Pharmacokinetic Evaluation in Vivo. ACS Comb Sci 2017; 19:286-298. [PMID: 28383252 PMCID: PMC5916772 DOI: 10.1021/acscombsci.6b00179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since the demonstration of nicotine vaccines as a possible therapeutic intervention for the effects of tobacco smoke, extensive effort has been made to enhance nicotine specific immunity. Linker modifications of nicotine haptens have been a focal point for improving the immunogenicity of nicotine, in which the evaluation of these modifications usually relies on in vivo animal models, such as mice, rats or nonhuman primates. Here, we present two in vitro screening strategies to estimate and predict the immunogenic potential of our newly designed nicotine haptens. One utilizes a competition enzyme-linked immunoabsorbent assay (ELISA) to profile the interactions of nicotine haptens or hapten-protein conjugates with nicotine specific antibodies, both polyclonal and monoclonal. Another relies on computational modeling of the interactions between haptens and amino acid residues near the conjugation site of the carrier protein to infer linker-carrier protein conjugation effect on antinicotine antibody response. Using these two in vitro methods, we ranked the haptens with different linkers for their potential as viable vaccine candidates. The ELISA-based hapten ranking was in an agreement with the results obtained by in vivo nicotine pharmacokinetic analysis. A correlation was found between the average binding affinity (IC50) of the haptens to an anti-Nic monoclonal antibody and the average brain nicotine concentration in the immunized mice. The computational modeling of hapten and carrier protein interactions helps exclude conjugates with strong linker-carrier conjugation effects and low in vivo efficacy. The simplicity of these in vitro screening strategies should facilitate the selection and development of more effective nicotine conjugate vaccines. In addition, these data highlight a previously under-appreciated contribution of linkers and hapten-protein conjugations to conjugate vaccine immunogenicity by virtue of their inclusion in the epitope that binds and activates B cells.
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Affiliation(s)
- Viswanath Arutla
- Biodesign Center for BioEnergetics, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Joseph Leal
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Xiaowei Liu
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Sriram Sokalingam
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Michael Raleigh
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota 55404, United States
| | - Adejimi Adaralegbe
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
| | - Li Liu
- Biodesign Center for Personalized Diagnostics, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
- Department of Biomedical Informatics, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Paul R. Pentel
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota 55404, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yung Chang
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287, United States
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, United States
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28
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Bai X, Talukder P, Daskalova SM, Roy B, Chen S, Li Z, Dedkova LM, Hecht SM. Enhanced Binding Affinity for an i-Motif DNA Substrate Exhibited by a Protein Containing Nucleobase Amino Acids. J Am Chem Soc 2017; 139:4611-4614. [PMID: 28263595 DOI: 10.1021/jacs.6b11825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Several variants of a nucleic acid binding motif (RRM1) of putative transcription factor hnRNP LL containing nucleobase amino acids at specific positions have been prepared and used to study binding affinity for the BCL2 i-motif DNA. Molecular modeling suggested a number of amino acids in RRM1 likely to be involved in interaction with the i-motif DNA, and His24 and Arg26 were chosen for modification based on their potential ability to interact with G14 of the i-motif DNA. Four nucleobase amino acids were introduced into RRM1 at one or both of positions 24 and 26. The introduction of cytosine nucleobase 2 into position 24 of RRM1 increased the affinity of the modified protein for the i-motif DNA, consistent with the possible Watson-Crick interaction of 2 and G14. In comparison, the introduction of uracil nucleobase 3 had a minimal effect on DNA affinity. Two structurally simplified nucleobase analogues (1 and 4) lacking both the N-1 and the 2-oxo substituents were also introduced in lieu of His24. Again, the RRM1 analogue containing 1 exhibited enhanced affinity for the i-motif DNA, while the protein analogue containing 4 bound less tightly to the DNA substrate. Finally, the modified protein containing 1 in lieu of Arg26 also bound to the i-motif DNA more strongly than the wild-type protein, but a protein containing 1 both at positions 24 and 26 bound to the DNA less strongly than wild type. The results support the idea of using nucleobase amino acids as protein constituents for controlling and enhancing DNA-protein interaction. Finally, modification of the i-motif DNA at G14 diminished RRM1-DNA interaction, as well as the ability of nucleobase amino acid 1 to stabilize RRM1-DNA interaction.
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Affiliation(s)
- Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sasha M Daskalova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Basab Roy
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Zhongxian Li
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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Daskalova SM, Bhattacharya C, Dedkova LM, Hecht SM. Probing the Flexibility of the Catalytic Nucleophile in the Lyase Catalytic Pocket of Human DNA Polymerase β with Unnatural Lysine Analogues. Biochemistry 2017; 56:500-513. [PMID: 28005340 DOI: 10.1021/acs.biochem.6b00807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA polymerase β (Pol β) is a key enzyme in mammalian base excision repair (BER), contributing stepwise 5'-deoxyribose phosphate (dRP) lyase and "gap-filling" DNA polymerase activities. The lyase reaction is believed to occur via a β-elimination reaction following the formation of a Schiff base between the dRP group at the pre-incised apurinic/apyrimidinic site and the ε-amino group of Lys72. To probe the steric constraints on the formation and subsequent resolution of the putative Schiff base intermediate within the lyase catalytic pocket, Lys72 was replaced with each of several nonproteinogenic lysine analogues. The modified Pol β enzymes were produced by coupled in vitro transcription and translation from a modified DNA template containing a TAG codon at the position corresponding to Lys72. In the presence of a misacylated tRNACUA transcript, suppression of the UAG codon in the transcribed mRNA led to elaboration of full length Pol β having a lysine analogue at position 72. Replacement of the primary nucleophilic amine with a secondary amine in the form of N-methyllysine (4) affected mainly the stability of the Schiff base intermediate and resulted in relatively moderate inhibition of lyase activity and BER. Elongation of the side chain of the catalytic residue by one methylene group, achieved by introduction of homolysine (6) at position 72, apparently shifted the amino group to a position less favorable for Schiff base formation. Interestingly, this effect was attenuated when the side chain was elongated by replacing one side-chain methylene group with a bridging S atom (thialysine, 2). In comparison, replacement of lysine 72 with an analogue having a guanidine moiety in lieu of an ε-amino group (homoarginine, 5) or a sterically constrained secondary amine (piperidinylalanine, 3) led to almost complete suppression of dRP excision activity and the ability of Pol β to support BER. These results help to define the tolerance of Pol β to subtle local structural and functional alterations.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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30
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Chevalier A, Khdour OM, Schmierer M, Bandyopadhyay I, Hecht SM. Influence of substituent heteroatoms on the cytoprotective properties of pyrimidinol antioxidants. Bioorg Med Chem 2017; 25:1703-1716. [PMID: 28189395 DOI: 10.1016/j.bmc.2017.01.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/18/2017] [Accepted: 01/21/2017] [Indexed: 01/04/2023]
Abstract
Recently, we described the optimization of novel pyrimidinol-based antioxidants as potential therapeutic molecules for targeting mitochondrial diseases. That study focused on improving the potency and metabolic stability of pyrimidinol antioxidants. This led us to consider the possibility of altering the positions of the exocyclic alkoxy and alkylamino substituents on the pyrimidinol scaffold. Twelve new analogues were prepared and their biological activities were investigated. The metabolic stability of the prepared regioisomers was also assessed in vitro using bovine liver microsomes. Unexpectedly, the 2-alkoxy-4-alkylamino substituted pyrimidinol antioxidants were found to have properties in protecting mitochondrial function superior to the isomeric 4-alkoxy-2-alkylamino substituted pyrimidinols evaluated in all earlier studies. This observation suggests a possible mode of action involving the intermediacy of an ortho-iminoquinone, a species not previously associated with mitochondrial respiratory chain function.
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Affiliation(s)
- Arnaud Chevalier
- Biodesign Center for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Margaret Schmierer
- Biodesign Center for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
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31
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Zhang Y, Jiang S, Zhang D, Bai X, Hecht SM, Chen S. DNA–affibody nanoparticles for inhibiting breast cancer cells overexpressing HER2. Chem Commun (Camb) 2017; 53:573-576. [DOI: 10.1039/c6cc08495h] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A DNA tetrahedron–affibody–drug nanoparticle is a highly efficient tool to deliver doxorubicin (DOX) to HER2 overexpressing cancer cells specifically. It represents a highly efficacious agent for selectively inhibiting cancer cells which overexpress HER2 receptor.
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Affiliation(s)
- Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University
- Xi'an 710061
- China
- Biodesign Center for BioEnergetics
- Arizona State University
| | - Shuoxing Jiang
- Biodesign Center for BioEnergetics
- Arizona State University
- Tempe 85287
- USA
| | - Dongdong Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University
- Xi'an 710061
- China
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics
- Arizona State University
- Tempe 85287
- USA
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics
- Arizona State University
- Tempe 85287
- USA
| | - Shengxi Chen
- Biodesign Center for BioEnergetics
- Arizona State University
- Tempe 85287
- USA
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32
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Chevalier A, Zhang Y, Khdour OM, Kaye JB, Hecht SM. Mitochondrial Nitroreductase Activity Enables Selective Imaging and Therapeutic Targeting. J Am Chem Soc 2016; 138:12009-12. [PMID: 27571326 DOI: 10.1021/jacs.6b06229] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitroreductase (NTR) activities have been known for decades, studied extensively in bacteria and also in systems as diverse as yeast, trypanosomes, and hypoxic tumors. The putative bacterial origin of mitochondria prompted us to explore the possible existence of NTR activity within this organelle and to probe its behavior in a cellular context. Presently, by using a profluorescent near-infrared (NIR) dye, we characterize the nature of NTR activity localized in mammalian cell mitochondria. Further, we demonstrate that this mitochondrially localized enzymatic activity can be exploited both for selective NIR imaging of mitochondria and for mitochondrial targeting by activating a mitochondrial poison specifically within that organelle. This constitutes a new mechanism for mitochondrial imaging and targeting. These findings represent the first use of mitochondrial enzyme activity to unmask agents for mitochondrial fluorescent imaging and therapy, which may prove to be more broadly applicable.
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Affiliation(s)
- Arnaud Chevalier
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Yanmin Zhang
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Justin B Kaye
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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33
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Kendrick S, Kang HJ, Alam MP, Madathil MM, Agrawal P, Gokhale V, Yang D, Hecht SM, Hurley LH. Correction to "The Dynamic Character of the BCL2 Promoter i-Motif Provides a Mechanism for Modulation of Gene Expression by Compounds That Bind Selectively to the Alternative DNA Hairpin Structure". J Am Chem Soc 2016; 138:11408. [PMID: 27571358 PMCID: PMC8154439 DOI: 10.1021/jacs.6b07292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Chevalier A, Alam MP, Khdour OM, Schmierer M, Arce PM, Cripe CD, Hecht SM. Optimization of pyrimidinol antioxidants as mitochondrial protective agents: ATP production and metabolic stability. Bioorg Med Chem 2016; 24:5206-5220. [PMID: 27624526 DOI: 10.1016/j.bmc.2016.08.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 12/19/2022]
Abstract
Previously we described a novel series of pyrimidinol antioxidants and their structural optimization as potential therapeutic agents for neurodegenerative and mitochondrial disorders. Our initial lead compound was a potent antioxidant in vitro, but was subsequently found to exhibit poor stability to oxidative metabolism. The current study focused on balancing potency with metabolic stability through structural modification, and involved modifications at positions 2 and 4 of the pyrimidinol redox core, likely sites of oxidative metabolism. Eight new analogues have been prepared and their ability to suppress lipid peroxidation and reactive oxygen species (ROS), and to preserve mitochondrial membrane potential (Δψm) and support ATP production, has been investigated. The metabolic stability of the prepared compounds was also assessed in vitro using bovine liver microsomes to obtain preliminary insight on this class of compounds. This study revealed the complexity of balancing reasonable metabolic stability with efficient antioxidant properties. While a few analogues appear promising, especially in terms of metabolic stability, a 4-isopropoxy derivative conserved the favorable biological activity and exhibited good metabolic stability. The favorable metabolic stability conferred by the combination of the azetidine and isopropoxy moieties in analogue 6 makes this compound an excellent candidate for further evaluation.
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Affiliation(s)
- Arnaud Chevalier
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Mohammad Parvez Alam
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Margaret Schmierer
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Pablo M Arce
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Cameron D Cripe
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States.
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35
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Roy B, Talukder P, Kang HJ, Tsuen SS, Alam MP, Hurley LH, Hecht SM. Interaction of Individual Structural Domains of hnRNP LL with the BCL2 Promoter i-Motif DNA. J Am Chem Soc 2016; 138:10950-62. [DOI: 10.1021/jacs.6b05036] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Basab Roy
- Biodesign
Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign
Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hyun-Jin Kang
- College
of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Shujian S. Tsuen
- Biodesign
Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Mohammad P. Alam
- Biodesign
Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Laurence H. Hurley
- College
of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- Arizona
Cancer Center and BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Sidney M. Hecht
- Biodesign
Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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36
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Talukder P, Dedkova LM, Ellington AD, Yakovchuk P, Lim J, Anslyn EV, Hecht SM. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins. Bioorg Med Chem 2016; 24:4177-4187. [PMID: 27452282 DOI: 10.1016/j.bmc.2016.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 01/13/2023]
Abstract
Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail.
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Affiliation(s)
- Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew D Ellington
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Petro Yakovchuk
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jaebum Lim
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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37
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Affiliation(s)
- Arnaud Chevalier
- Biodesign Center for BioEnergetics
and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yanmin Zhang
- Biodesign Center for BioEnergetics
and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Omar M. Khdour
- Biodesign Center for BioEnergetics
and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics
and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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38
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Chowdhury SR, Chauhan PS, Dedkova LM, Bai X, Chen S, Talukder P, Hecht SM. Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes. Biochemistry 2016; 55:2427-40. [PMID: 27050631 DOI: 10.1021/acs.biochem.6b00102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Described herein are the synthesis and photophysical characterization of a library of aryl-substituted oxazole- and thiazole-based dipeptidomimetic analogues, and their incorporation into position 66 of green fluorescent protein (GFP) in lieu of the natural fluorophore. These fluorescent analogues resemble the fluorophore formed naturally by GFP. As anticipated, the photophysical properties of the analogues varied as a function of the substituents at the para position of the phenyl ring. The fluorescence emission wavelength maxima of compounds in the library varied from ∼365 nm (near-UV region) to ∼490 nm (visible region). The compounds also exhibited a large range of quantum yields (0.01-0.92). The analogues were used to activate a suppressor tRNACUA and were incorporated into position 66 of GFP using an in vitro protein biosynthesizing system that employed engineered ribosomes selected for their ability to incorporate dipeptides. Four analogues with interesting photophysical properties and reasonable suppression yields were chosen, and the fluorescent proteins (FPs) containing these fluorophores were prepared on a larger scale for more detailed study. When the FPs were compared with the respective aminoacyl-tRNAs and the actual dipeptide analogues, the FPs exhibited significantly enhanced fluorescence intensities at the same concentrations. Part of this was shown to be due to the presence of the fluorophores as an intrinsic element of the protein backbone. There were also characteristic shifts in the emission maxima, indicating the environmental sensitivity of these probes. Acridon-2-ylalanine and oxazole 1a were incorporated into positions 39 and 66 of GFP, respectively, and were shown to form an efficient Förster resonance energy transfer (FRET) pair, demonstrating that the analogues can be used as FRET probes.
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Affiliation(s)
- Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Pradeep S Chauhan
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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39
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Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA–Protein Interaction. Biochemistry 2015; 54:7457-69. [DOI: 10.1021/acs.biochem.5b01085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Poulami Talukder
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Petro Yakovchuk
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michelle M. Spiering
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad P. Alam
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Manikandadas M. Madathil
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Stephen J. Benkovic
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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40
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Gerasimova YV, Yakovchuk P, Dedkova LM, Hecht SM, Kolpashchikov DM. Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors. RNA 2015; 21:1834-43. [PMID: 26289345 PMCID: PMC4574759 DOI: 10.1261/rna.052613.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/13/2015] [Indexed: 05/06/2023]
Abstract
Mutations in ribosomal RNA (rRNA) have traditionally been detected by the primer extension assay, which is a tedious and multistage procedure. Here, we describe a simple and straightforward fluorescence assay based on binary deoxyribozyme (BiDz) sensors. The assay uses two short DNA oligonucleotides that hybridize specifically to adjacent fragments of rRNA, one of which contains a mutation site. This hybridization results in the formation of a deoxyribozyme catalytic core that produces the fluorescent signal and amplifies it due to multiple rounds of catalytic action. This assay enables us to expedite semi-quantification of mutant rRNA content in cell cultures starting from whole cells, which provides information useful for optimization of culture preparation prior to ribosome isolation. The method requires less than a microliter of a standard Escherichia coli cell culture and decreases analysis time from several days (for primer extension assay) to 1.5 h with hands-on time of ∼10 min. It is sensitive to single-nucleotide mutations. The new assay simplifies the preliminary analysis of RNA samples and cells in molecular biology and cloning experiments and is promising in other applications where fast detection/quantification of specific RNA is required.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, USA
| | - Petro Yakovchuk
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Larisa M Dedkova
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, USA National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, USA Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, USA
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41
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Maini R, Dedkova LM, Paul R, Madathil MM, Chowdhury SR, Chen S, Hecht SM. Ribosome-Mediated Incorporation of Dipeptides and Dipeptide Analogues into Proteins in Vitro. J Am Chem Soc 2015; 137:11206-9. [PMID: 26301427 DOI: 10.1021/jacs.5b03135] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Plasmids containing 23S rRNA randomized at positions 2057-2063 and 2502-2507 were introduced into Escherichia coli, affording a library of clones which produced modified ribosomes in addition to the pre-existing wild-type ribosomes. These clones were screened with a derivative of puromycin, a natural product which acts as an analogue of the 3'-end of aminoacyl-tRNA and terminates protein synthesis by accepting the growing polypeptide chain, thereby killing bacterial cells. The puromycin derivative in this study contained the dipeptide p-methoxyphenylalanylglycine, implying the ability of the modified ribosomes in clones sensitive to this puromycin analogue to recognize dipeptides. Several clones inhibited by the puromycin derivative were used to make S-30 preparations, and some of these were shown to support the incorporation of dipeptides into proteins. The four incorporated species included two dipeptides (Gly-Phe (2) and Phe-Gly (3)), as well as a thiolated dipeptide analogue (4) and a fluorescent oxazole (5) having amine and carboxyl groups approximately the same distance apart as in a normal dipeptide. A protein containing both thiolated dipeptide 4 and a 7-methoxycoumarin fluorophore was found to undergo fluorescence quenching. Introduction of the oxazole fluorophore 5 into dihydrofolate reductase or green fluorescent protein resulted in quite strong enhancement of its fluorescence emission, and the basis for this enhancement was studied. The aggregate results demonstrate the feasibility of incorporating dipeptides as a single ribosomal event, and illustrate the lack of recognition of the central peptide bond in the dipeptide, potentially enabling the incorporation of a broad variety of structural analogues.
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Manikandadas M Madathil
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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42
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Maini R, Chowdhury SR, Dedkova LM, Roy B, Daskalova SM, Paul R, Chen S, Hecht SM. Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids. Biochemistry 2015; 54:3694-706. [PMID: 25982410 PMCID: PMC4472090 DOI: 10.1021/acs.biochem.5b00389] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/16/2015] [Indexed: 02/04/2023]
Abstract
In an earlier study, β³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different β-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate β-amino acids into DHFR, in spite of the use of a single puromycin for the selection of the individual clones. In this study, we examine the extent to which the structure of the β³-puromycin employed for ribosome selection influences the regio- and stereochemical preferences of the modified ribosomes during protein synthesis; the mechanistic probe was a single suppressor tRNA(CUA) activated with each of four methyl-β-alanine isomers (1-4). The modified ribosomes were found to incorporate each of the four isomeric methyl-β-alanines into DHFR but exhibited a preference for incorporation of 3(S)-methyl-β-alanine (β-mAla; 4), i.e., the isomer having the same regio- and stereochemistry as the O-methylated β-tyrosine moiety of β³-puromycin. Also conducted were a selection of clones that are responsive to β²-puromycin and a demonstration of reversal of the regio- and stereochemical preferences of these clones during protein synthesis. These results were incorporated into a structural model of the modified regions of 23S rRNA, which included in silico prediction of a H-bonding network. Finally, it was demonstrated that incorporation of 3(S)-methyl-β-alanine (β-mAla; 4) into a short α-helical region of the nucleic acid binding domain of hnRNP LL significantly stabilized the helix without affecting its DNA binding properties.
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MESH Headings
- Alanine/analogs & derivatives
- Alanine/chemistry
- Alanine/metabolism
- Escherichia coli/enzymology
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/biosynthesis
- Heterogeneous-Nuclear Ribonucleoprotein L/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/genetics
- Humans
- Hydrogen Bonding
- Models, Molecular
- Molecular Dynamics Simulation
- Mutant Proteins/biosynthesis
- Mutant Proteins/chemistry
- Mutant Proteins/genetics
- Nucleotide Motifs
- Peptidyl Transferases/genetics
- Peptidyl Transferases/metabolism
- Protein Conformation
- Protein Stability
- Puromycin/analogs & derivatives
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Ribosomes/metabolism
- Stereoisomerism
- Substrate Specificity
- Tetrahydrofolate Dehydrogenase/biosynthesis
- Tetrahydrofolate Dehydrogenase/chemistry
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sasha M. Daskalova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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43
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Yu Z, Paul R, Bhattacharya C, Bozeman TC, Rishel MJ, Hecht SM. Structural features facilitating tumor cell targeting and internalization by bleomycin and its disaccharide. Biochemistry 2015; 54:3100-9. [PMID: 25905565 PMCID: PMC4440614 DOI: 10.1021/acs.biochem.5b00277] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have shown previously that the bleomycin (BLM) carbohydrate moiety can recapitulate the tumor cell targeting effects of the entire BLM molecule, that BLM itself is modular in nature consisting of a DNA-cleaving aglycone which is delivered selectively to the interior of tumor cells by its carbohydrate moiety, and that there are disaccharides structurally related to the BLM disaccharide which are more efficient than the natural disaccharide at tumor cell targeting/uptake. Because BLM sugars can deliver molecular cargoes selectively to tumor cells, and thus potentially form the basis for a novel antitumor strategy, it seemed important to consider additional structural features capable of affecting the efficiency of tumor cell recognition and delivery. These included the effects of sugar polyvalency and net charge (at physiological pH) on tumor cell recognition, internalization, and trafficking. Since these parameters have been shown to affect cell surface recognition, internalization, and distribution in other contexts, this study has sought to define the effects of these structural features on tumor cell recognition by bleomycin and its disaccharide. We demonstrate that both can have a significant effect on tumor cell binding/internalization, and present data which suggests that the metal ions normally bound by bleomycin following clinical administration may significantly contribute to the efficiency of tumor cell uptake, in addition to their characterized function in DNA cleavage. A BLM disaccharide-Cy5** conjugate incorporating the positively charged dipeptide d-Lys-d-Lys was found to associate with both the mitochondria and the nuclear envelope of DU145 cells, suggesting possible cellular targets for BLM disaccharide-cytotoxin conjugates.
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Affiliation(s)
- Zhiqiang Yu
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Trevor C Bozeman
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael J Rishel
- ‡GE Global Research, 1 Research Circle, Niskayuna, New York 12309, United States
| | - Sidney M Hecht
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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44
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Mastroeni D, Khdour OM, Arce PM, Hecht SM, Coleman PD. Novel antioxidants protect mitochondria from the effects of oligomeric amyloid beta and contribute to the maintenance of epigenome function. ACS Chem Neurosci 2015; 6:588-98. [PMID: 25668062 DOI: 10.1021/cn500323q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Alzheimer's disease is associated with metabolic deficits and reduced mitochondrial function, with the latter due to the effects of oligomeric amyloid beta peptide (AβO) on the respiratory chain. Recent evidence has demonstrated reduction of epigenetic markers, such as DNA methylation, in Alzheimer's disease. Here we demonstrate a link between metabolic and epigenetic deficits via reduction of mitochondrial function which alters the expression of mediators of epigenetic modifications. AβO-induced loss of mitochondrial function in differentiated neuronal cells was reversed using two novel antioxidants (1 and 2); both have been shown to mitigate the effects of reactive oxygen species (ROS), and compound 1 also restores adenosine triphosphate (ATP) levels. While both compounds were effective in reducing ROS, restoration of ATP levels was associated with a more robust response to AβO treatment. Our in vitro system recapitulates key aspects of data from Alzheimer's brain samples, the expression of epigenetic genes in which are also shown to be normalized by the novel analogues.
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Affiliation(s)
- Diego Mastroeni
- L.J.
Roberts Alzheimer’s Disease Center, Banner Sun Health Research Institute, 10515 West Santa Fe Drive, Sun City, Arizona 85351, United States
- School
for Mental Health and Neuroscience (MHeNS), Department of Psychiatry
and Neuropsychology, Faculty of Health, Medicine and Life Sciences,
European Graduate School of Neuroscience (EURON), Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Omar M. Khdour
- Center
for BioEnergetics, Biodesign Institute, and Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Pablo M. Arce
- Center
for BioEnergetics, Biodesign Institute, and Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul D. Coleman
- L.J.
Roberts Alzheimer’s Disease Center, Banner Sun Health Research Institute, 10515 West Santa Fe Drive, Sun City, Arizona 85351, United States
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45
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Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM. Tryptophan-based fluorophores for studying protein conformational changes. Bioorg Med Chem 2014; 22:5924-34. [PMID: 25284250 PMCID: PMC4254292 DOI: 10.1016/j.bmc.2014.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022]
Abstract
With the continuing interest in deciphering the interplay between protein function and conformational changes, small fluorescence probes will be especially useful for tracking changes in the crowded protein interior space. Presently, we describe the potential utility of six unnatural amino acid fluorescence donors structurally related to tryptophan and show how they can be efficiently incorporated into a protein as fluorescence probes. We also examine the various photophysical properties of the new Trp analogues, which are significantly redshifted in their fluorescence spectra relative to tryptophan. In general, the Trp analogues were well tolerated when inserted into Escherichia coli DHFR, and did not perturb enzyme activity, although substitution for Trp22 did result in a diminution in DHFR activity. Further, it was demonstrated that D and E at position 37 formed efficient FRET pairs with acridon-2-ylalanine (Acd) at position 17. The same was also true for a DHFR construct containing E at position 79 and Acd at position 17. Together, these findings demonstrate that these tryptophan analogues can be introduced into DHFR with minimal disruption of function, and that they can be employed for the selective study of targeted conformational changes in proteins, even in the presence of unmodified tryptophans.
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Affiliation(s)
- Poulami Talukder
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - C Tony Liu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Edwin A Baldwin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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46
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Bernatchez JA, Paul R, Tchesnokov EP, Ngure M, Beilhartz GL, Berghuis AM, Lavoie R, Li L, Auger A, Melnyk RA, Grobler JA, Miller MD, Hazuda DJ, Hecht SM, Götte M. Derivatives of mesoxalic acid block translocation of HIV-1 reverse transcriptase. J Biol Chem 2014; 290:1474-84. [PMID: 25355312 DOI: 10.1074/jbc.m114.614305] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pyrophosphate mimic and broad spectrum antiviral phosphonoformic acid (PFA, foscarnet) was shown to freeze the pre-translocational state of the reverse transcriptase (RT) complex of the human immunodeficiency virus type 1 (HIV-1). However, PFA lacks a specificity domain, which is seen as a major reason for toxic side effects associated with the clinical use of this drug. Here, we studied the mechanism of inhibition of HIV-1 RT by the 4-chlorophenylhydrazone of mesoxalic acid (CPHM) and demonstrate that this compound also blocks RT translocation. Hot spots for inhibition with PFA or CPHM occur at template positions with a bias toward pre-translocation. Mutations at active site residue Asp-185 compromise binding of both compounds. Moreover, divalent metal ions are required for the formation of ternary complexes with either of the two compounds. However, CPHM contains both an anchor domain that likely interacts with the catalytic metal ions and a specificity domain. Thus, although the inhibitor binding sites may partly overlap, they are not identical. The K65R mutation in HIV-1 RT, which reduces affinity to PFA, increases affinity to CPHM. Details with respect to the binding sites of the two inhibitors are provided on the basis of mutagenesis studies, structure-activity relationship analyses with newly designed CPHM derivatives, and in silico docking experiments. Together, these findings validate the pre-translocated complex of HIV-1 RT as a specific target for the development of novel classes of RT inhibitors.
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Affiliation(s)
- Jean A Bernatchez
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Rakesh Paul
- the Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
| | - Egor P Tchesnokov
- the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Marianne Ngure
- the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Greg L Beilhartz
- the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Albert M Berghuis
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada, the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Rico Lavoie
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Lianhai Li
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Anick Auger
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Roman A Melnyk
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Jay A Grobler
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Michael D Miller
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Daria J Hazuda
- Merck Research Laboratories, West Point, Pennsylvania 19486-8000, and
| | - Sidney M Hecht
- the Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287
| | - Matthias Götte
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada, the Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada, the Department of Medicine, Division of Experimental Medicine, McGill University, Quebec H3A 1A3, Canada
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47
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Yu X, Talukder P, Bhattacharya C, Fahmi NE, Lines JA, Dedkova LM, LaBaer J, Hecht SM, Chen S. Probing of CD4 binding pocket of HIV-1 gp120 glycoprotein using unnatural phenylalanine analogues. Bioorg Med Chem Lett 2014; 24:5699-5703. [PMID: 25453804 DOI: 10.1016/j.bmcl.2014.10.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 01/18/2023]
Abstract
CD4-gp120 interaction is the first step for HIV-1 entry into host cells. A highly conserved pocket in gp120 protein is an attractive target for developing gp120 inhibitors or novel HIV detection tools. Here we incorporate seven phenylalanine derivatives having different sizes and steric conformations into position 43 of domain 1 of CD4 (mD1.2) to explore the architecture of the 'Phe43 cavity' of HIV-1 gp120. The results show that the conserved hydrophobic pocket in gp120 tolerates a hydrophobic side chain of residue 43 of CD protein, which is 12.2 Å in length and 8.0 Å in width. This result provides useful information for developing novel gp120 inhibitors or new HIV detection tools.
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Affiliation(s)
- Xiaobo Yu
- Center for Personalized Diagnostics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Poulami Talukder
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Chandrabali Bhattacharya
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Jamie A Lines
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Larisa M Dedkova
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA.
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Abstract
The bleomycins (BLMs) are a family of antitumor antibiotics used clinically for anticancer chemotherapy. Their antitumor selectivity derives at least in part from their ability to target tumor cells, a property that resides in the carbohydrate moiety of the antitumor agent. In earlier studies, we have demonstrated that the tumor cell selectivity resides in the mannose carbamoyl moiety of the BLM saccharide and that both the BLM disaccharide and monosaccharide containing the carbamoyl moiety were capable of the delivery/uptake of a conjugated cyanine dye into cultured cancer cell lines. Presently, the nature of the participation of the carbamoyl moiety has been explored further to provide compounds of utility for defining the nature of the mechanism of tumor cell recognition and uptake by BLM saccharides and in the hope that more efficient compounds could be identified. A library of seven disaccharide-Cy5** dye conjugates was prepared that are structural analogues of the BLM disaccharide. These differed from the natural BLM disaccharide in the position, orientation, and substitution of the carbamoyl group. Studies of these compounds in four matched sets of tumor and normal cell lines revealed a few that were both tumor cell selective and internalized 2-4-fold more efficiently than the natural BLM disaccharide.
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Affiliation(s)
- Manikandadas M Madathil
- Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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Schroeder BR, Ghare MI, Bhattacharya C, Paul R, Yu Z, Zaleski PA, Bozeman TC, Rishel MJ, Hecht SM. The disaccharide moiety of bleomycin facilitates uptake by cancer cells. J Am Chem Soc 2014; 136:13641-56. [PMID: 25184545 PMCID: PMC4183664 DOI: 10.1021/ja507255g] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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The disaccharide moiety is responsible
for the tumor cell targeting
properties of bleomycin (BLM). While the aglycon (deglycobleomycin)
mediates DNA cleavage in much the same fashion as bleomycin, it exhibits
diminished cytotoxicity in comparison to BLM. These findings suggested
that BLM might be modular in nature, composed of tumor-seeking and
tumoricidal domains. To explore this possibility, BLM analogues were
prepared in which the disaccharide moiety was attached to deglycobleomycin
at novel positions, namely, via the threonine moiety or C-terminal
substituent. The analogues were compared with BLM and deglycoBLM for
DNA cleavage, cancer cell uptake, and cytotoxic activity. BLM is more
potent than deglycoBLM in supercoiled plasmid DNA relaxation, while
the analogue having the disaccharide on threonine was less active
than deglycoBLM and the analogue containing the C-terminal disaccharide
was slightly more potent. While having unexceptional DNA cleavage
potencies, both glycosylated analogues were more cytotoxic to cultured
DU145 prostate cancer cells than deglycoBLM. Dye-labeled conjugates
of the cytotoxic BLM aglycons were used in imaging experiments to
determine the extent of cell uptake. The rank order of internalization
efficiencies was the same as their order of cytotoxicities toward
DU145 cells. These findings establish a role for the BLM disaccharide
in tumor targeting/uptake and suggest that the disaccharide moiety
may be capable of delivering other cytotoxins to cancer cells. While
the mechanism responsible for uptake of the BLM disaccharide selectively
by tumor cells has not yet been established, data are presented which
suggest that the metabolic shift to glycolysis in cancer cells may
provide the vehicle for selective internalization.
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Affiliation(s)
- Benjamin R Schroeder
- Department of Chemistry, University of Virginia , Charlottesville, Virginia 22904, United States
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Abstract
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Bleomycins A5 and B2 were used to study the
structural features in hairpin DNAs conducive to strong BLM–DNA
interaction. Two members of a 10-hairpin DNA library previously found
to bind most tightly to these BLMs were subsequently noted to share
the sequence 5′-ACGC (complementary strand sequence 5′-GCGT).
Each underwent double-strand cleavage at five sites within, or near,
an eight base pair region of the DNA duplex which had been randomized
to create the original library. A new hairpin DNA library was selected
based on affinity for immobilized Fe(III)·BLM A5.
Two of the 30 newly identified DNAs also contained the sequence 5′-ACGC/5′-GCGT.
These DNAs bound to the Fe(II)·BLMs more tightly than any DNA
characterized previously. Surface plasmon resonance confirmed tight
Fe(III)·BLM B2 binding and gave an excellent fit for
a 1:1 binding model, implying the absence of significant secondary
binding sites. Fe(II)·BLM A5 was used to assess sites
of double-strand DNA cleavage. Both hairpin DNAs underwent double-strand
cleavage at five sites within or near the original randomized eight
base region. For DNA 12, four of the five double-strand
cleavages involved independent single-strand cleavage reactions; DNA 13 underwent double-strand DNA cleavage by independent single-strand
cleavages at all five sites. DNA 14, which bound Fe·BLM
poorly, was converted to a strong binder (DNA 15) by
insertion of the sequence 5′-ACGC/5′-GCGT. These findings
reinforce the idea that tighter DNA binding by Fe·BLM leads to
increased double-strand cleavage by a novel mechanism and identify
a specific DNA motif conducive to strong BLM binding and cleavage.
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Affiliation(s)
- Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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