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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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2
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Salim H, Pero-Gascon R, Pont L, Giménez E, Benavente F. A review of sample preparation for purification of microRNAs and analysis by mass spectrometry methods. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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3
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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4
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Kaysheva AL, Isaeva AI, Pleshakova TO, Shumov ID, Valueva AA, Ershova MO, Ivanova IA, Ziborov VS, Iourov IY, Vorsanova SG, Ryabtsev SV, Archakov AI, Ivanov YD. Detection of Circulating Serum microRNA/Protein Complexes in ASD Using Functionalized Chips for an Atomic Force Microscope. Molecules 2021; 26:5979. [PMID: 34641523 PMCID: PMC8512613 DOI: 10.3390/molecules26195979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs, which circulate in blood, are characterized by high diagnostic value; in biomedical research, they can be considered as candidate markers of various diseases. Mature microRNAs of glial cells and neurons can cross the blood-brain barrier and can be detected in the serum of patients with autism spectrum disorders (ASD) as components of macrovesicles, macromolecular protein and low-density lipoprotein particles. In our present study, we have proposed an approach, in which microRNAs in protein complexes can be concentrated on the surface of AFM chips with oligonucleotide molecular probes, specific against the target microRNAs. MicroRNAs, associated with the development of ASD in children, were selected as targets. The chips with immobilized molecular probes were incubated in serum samples of ASD patients and healthy volunteers. By atomic force microscopy (AFM), objects on the AFM chip surface have been revealed after incubation in the serum samples. The height of these objects amounted to 10 nm and 6 nm in the case of samples of ASD patients and healthy volunteers, respectively. MALDI-TOF-MS analysis of protein components on the chip surface allowed us to identify several cell proteins. These proteins are involved in the binding of nucleic acids (GBG10, RT24, RALYL), in the organization of proteasomes and nucleosomes (PSA4, NP1L4), and participate in the functioning of the channel of active potassium transport (KCNE5, KCNV2).
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Affiliation(s)
- Anna L. Kaysheva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Arina I. Isaeva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Anastasia A. Valueva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Maria O. Ershova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Irina A. Ivanova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya St. 13 Bd.2, 125412 Moscow, Russia
| | | | - Svetlana G. Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Taldomskaya St. 2, 125412 Moscow, Russia;
| | | | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
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5
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Tanaka M, Chock PB. Oxidative Modifications of RNA and Its Potential Roles in Biosystem. Front Mol Biosci 2021; 8:685331. [PMID: 34055897 PMCID: PMC8149912 DOI: 10.3389/fmolb.2021.685331] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Elevated level of oxidized RNA was detected in vulnerable neurons in Alzheimer patients. Subsequently, several diseases and pathological conditions were reported to be associated with RNA oxidation. In addition to several oxidized derivatives, cross-linking and unique strand breaks are generated by RNA oxidation. With a premise that dysfunctional RNA mediated by oxidation is the pathogenetic molecular mechanism, intensive investigations have revealed the mechanism for translation errors, including premature termination, which gives rise to aberrant polypeptides. To this end, we and others revealed that mRNA oxidation could compromise its translational activity and fidelity. Under certain conditions, oxidized RNA can also induce several signaling pathways, to mediate inflammatory response and induce apoptosis. In this review, we focus on the oxidative modification of RNA and its resulting effect on protein synthesis as well as cell signaling. In addition, we will also discuss the potential roles of enzymatic oxidative modification of RNA in mediating cellular effects.
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Affiliation(s)
- Mikiei Tanaka
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - P Boon Chock
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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Tran HV, Piro B. Recent trends in application of nanomaterials for the development of electrochemical microRNA biosensors. Mikrochim Acta 2021; 188:128. [PMID: 33740140 DOI: 10.1007/s00604-021-04784-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023]
Abstract
The biology of the late twentieth century was marked by the discovery in 1993 of a new class of small non-coding ribonucleic acids (RNAs) which play major roles in regulating the translation and degradation of messenger RNAs. These small RNAs (18-25 nucleotides), called microRNAs (miRNAs), are implied in several biological processes such as differentiation, metabolic homeostasis, or cellular apoptosis and proliferation. The discovery in 2008 that the presence of miRNAs in body fluids could be correlated with cancer (prostate, breast, colon, lung, etc.) or other diseases (diabetes, heart diseases, etc.) has made them new key players as biomarkers. Therefore, miRNA detection is of considerable significance in both disease diagnosis and in the study of miRNA function. Until these days, more than 1200 miRNAs have been identified. However, traditional methods developed for conventional DNA does not apply satisfactorily for miRNA, in particular due to the low expression level of these miRNA in biofluids, and because they are very short strands. Electrochemical biosensors can provide this sensitivity and also offer the advantages of mass fabrication, low-cost, and potential decentralized analysis, which has wide application for microRNAs sensing, with many promising results already reported. The present review summarizes some newly developed electrochemical miRNA detection methods.
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Affiliation(s)
- Hoang Vinh Tran
- School of Chemical Engineering, Hanoi University of Science and Technology (HUST), 1st Dai Co Viet Road, Hanoi, Vietnam.
| | - Benoit Piro
- ITODYS, CNRS, Université de Paris, F-75006, Paris, France
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7
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Xu D, Wang Y. Protein-free ribosomal RNA scaffolds can assemble poly-lysine oligos from charged tRNA fragments. Biochem Biophys Res Commun 2021; 544:81-85. [PMID: 33545497 PMCID: PMC7936610 DOI: 10.1016/j.bbrc.2021.01.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 01/28/2023]
Abstract
Ribosomal protein synthesis is a central process of the modern biological world. Because the ribosome contains proteins itself, it is very important to understand its precursor and evolution. Small ribozymes have demonstrated the principle of "RNA world" hypothesis, but protein free peptide ligase remains elusive. In this report, we have identified two fragments in the peptidyl transfer center that can synthesize a 9-mer poly-lysine in a solution contains Mg2+. This result is deduced from isotope-shifting in high resolution MS. To our best knowledge, this is the longest peptide oligo that can be synthesized by a pure ribozyme. Via single molecule FRET experiments, we have demonstrated the ligase mechanism was probably by substrate proximity via dimerization. We prospect that these RNA fragments can be useful to synthesize template free natural and non-natural peptides, to be model system for peptidyl transfer reaction mechanism and can shed light to the evolution of ribosome.
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Affiliation(s)
- Doris Xu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.
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8
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Katsura S, Furuishi T, Ueda H, Yonemochi E. Cholesteryl-Conjugated Ribonuclease A Exhibits Enzyme Activity in Aqueous Solution and Resistance to Dimethyl Sulfoxide. ACS OMEGA 2021; 6:533-543. [PMID: 33458505 PMCID: PMC7807799 DOI: 10.1021/acsomega.0c05016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Using bovine pancreatic ribonuclease A (RNase A) and cholesterol, we synthesized cholesteryl-conjugated ribonuclease A (CHRNase A) to evaluate the influence of a conjugated hydrophobic moiety on protein function. Nuclear magnetic resonance and matrix-assisted laser desorption/ionization time-of-flight spectrometry suggested that one cholesteryl group was conjugated to RNase A. Differential scanning calorimetry indicated that CHRNase A was denatured in the solid state but was folded in phosphate buffer (0.05 mol/L, pH 6.5). CHRNase A resembled RNase A in its secondary structure, but circular dichroism (CD) spectra revealed that the helical content of CHRNase A was decreased and the tertiary structure of CHRNase A differed from that of RNase A. Furthermore, fluorescence measurements, CD spectra, an 8-anilino-1-naphthalenesulfonic acid ammonium salt-based assay, and surface tension measurements suggested that cholesterol was conjugated to a tyrosine residue on the protein surface. The relative activity of CHRNase A to RNase A was 79 ± 7%, and the enzyme activity of CHRNase A by adding β-cyclodextrin (β-CyD) increased to 129 ± 7%. Therefore, we considered that the cholesteryl group interacted with substrate (cytidine 2'3'-cyclic monophosphate monosodium salt) to inhibit the enzyme reaction. Finally, the environment around tyrosine residues in CHRNase A in dimethyl sulfoxide was similar to that of native RNase A in phosphate buffer (0.05 mol/L, pH 6.5). These results suggest that cholesterol conjugation to RNase A altered RNase A functionality, including improvement of RNase A resistance to dimethyl sulfoxide and modulation of the ability of β-CyD to control RNase A enzymatic activity.
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Affiliation(s)
- Shinji Katsura
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
- Formulation
Research Laboratory, Taiho Pharmaceutical
Co., Ltd., 224-2, Ebisuno, Hiraishi, Kawauchi-cho, Tokushima 771-0194, Japan
| | - Takayuki Furuishi
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Haruhisa Ueda
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Etsuo Yonemochi
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
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9
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Ionic matrices for matrix-assisted laser desorption/ionization mass spectrometry analysis of microRNA biomarkers. Anal Chim Acta 2020; 1139:169-177. [PMID: 33190701 DOI: 10.1016/j.aca.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 11/20/2022]
Abstract
The use of ionic matrices (IMs) was evaluated as an alternative to conventional matrices to analyze microRNAs (miRNAs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). 2, 4, 6-Trihydroxyacetophenone (THAP), 6-aza-2-thiothymine (ATT) and 3-hydroxypicolinic acid (3-HPA) and their IMs with pyridine (PYR) and butylamine (BA) were studied to analyze a standard mixture of miRNAs: miR-21, let-7g and iso-miR-16. Among all the studied matrices, ATT-PYR at 75 mg/mL in acetonitrile (MeCN):H2O (50:50, v/v) was selected as the optimal. Furthermore, addition of ammonium citrate dibasic (AC) as signal enhancer was mandatory to obtain an appropriate miRNA detection. ATT-PYR provided the best sensitivity, with limit of detection (LOD) up to 5 nM (equivalent to 1 fmol in the spot) and excellent spot-to-spot repeatability due to the improved homogeneity of the spots compared to the conventional matrices. The applicability of the established method to direct, multiplex and untargeted analysis of miRNAs in serum samples was also investigated.
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Farooq QUA, Haq NU, Aziz A, Aimen S, Inam ul Haq M. Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190204154653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background:
Mass spectrometry is a tool used in analytical chemistry to identify components
in a chemical compound and it is of tremendous importance in the field of biology for high
throughput analysis of biomolecules, among which protein is of great interest.
Objective:
Advancement in proteomics based on mass spectrometry has led the way to quantify multiple
protein complexes, and proteins interactions with DNA/RNA or other chemical compounds which
is a breakthrough in the field of bioinformatics.
Methods:
Many new technologies have been introduced in electrospray ionization (ESI) and Matrixassisted
Laser Desorption/Ionization (MALDI) techniques which have enhanced sensitivity, resolution
and many other key features for the characterization of proteins.
Results:
The advent of ambient mass spectrometry and its different versions like Desorption Electrospray
Ionization (DESI), DART and ELDI has brought a huge revolution in proteomics research.
Different imaging techniques are also introduced in MS to map proteins and other significant biomolecules.
These drastic developments have paved the way to analyze large proteins of >200kDa easily.
Conclusion:
Here, we discuss the recent advancement in mass spectrometry, which is of great importance
and it could lead us to further deep analysis of the molecules from different perspectives and
further advancement in these techniques will enable us to find better ways for prediction of molecules
and their behavioral properties.
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Affiliation(s)
- Qurat ul Ain Farooq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Noor ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Abdul Aziz
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Sara Aimen
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Muhammad Inam ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
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Yu Z, Cowan JA. Metal complexes promoting catalytic cleavage of nucleic acids-biochemical tools and therapeutics. Curr Opin Chem Biol 2018; 43:37-42. [PMID: 29153936 PMCID: PMC5847438 DOI: 10.1016/j.cbpa.2017.10.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/26/2017] [Accepted: 10/29/2017] [Indexed: 01/21/2023]
Abstract
The development of metal complexes that promote degradation of nucleic acids has garnered significant interest as a result of their broad range of potential application. This review focuses on recent progress in the design and synthesis of metal complexes as artificial nucleases that promote either hydrolytic or oxidative cleavage of nucleic acids. Illustrative examples demonstrate the versatility of artificial nucleases for in vitro applications as molecular tools to address biochemical problems, as well as their potential use as therapeutic agents. We also address future challenges for improvement and avenues for further investigation.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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12
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Pinkham AM, Yu Z, Cowan JA. Attenuation of West Nile Virus NS2B/NS3 Protease by Amino Terminal Copper and Nickel Binding (ATCUN) Peptides. J Med Chem 2018; 61:980-988. [PMID: 29301071 DOI: 10.1021/acs.jmedchem.7b01409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Andrew M. Pinkham
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Zhen Yu
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - J. A. Cowan
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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13
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Wu HT, Li K, Wang G, Yang XX, Zhu A, Xu XP, Li M, Wu YS, Liu TC. Development of a high-throughput and sensitive assay of fusion genes in lung cancer by array-based MALDI-TOFMS. RSC Adv 2018; 8:27935-27945. [PMID: 35548167 PMCID: PMC9087866 DOI: 10.1039/c8ra05165h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 07/07/2018] [Indexed: 11/21/2022] Open
Abstract
ALK (anaplastic lymphoma kinase gene), ROS1 (ros proto-oncogene 1) and RET (ret proto-oncogene) fusions are oncogenic drivers in non-small cell lung cancer (NSCLC). Methods like fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are highly sensitive but subjectively analyzed, labor intensive, expensive and unsuitable for multiple fusion gene screening. This study aimed to establish a high-throughput, sensitive and cost-effective screening method (array-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, array-based MALDI-TOFMS) for ALK, ROS1 and RET fusion detection. This method was established with three fusion gene positive cell lines (H2228, ALK positive; HCC78, ROS1 positive; LC-2/AD, RET positive) and negative samples. Then, 34 clinical samples were selected and detected by Sanger sequencing, next generation sequencing (NGS) and array-based MALDI-TOFMS. The results were compared and analyzed and Sanger sequencing was considered the standard. 7 cases showed ALK fusions, 1 case showed ROS1 fusions, no case showed RET fusions and 4 cases were both ALK and ROS1 fusions. Results showed that array-based MALDI-TOFMS was 100% concordant with Sanger sequencing and NGS 82.3%. In this study, we reported the utility of array-based MALDI-TOFMS in the assessment of ALK, ROS1 and RET fusions in routine lung biopsies of FFPE and fresh tissue specimens. Besides, this method may also be applied to the diagnosis, monitoring and prognosis of illness. This study established a high-throughput, sensitive and cost-effective method to detect three lung fusion genes of 96 samples at one time.![]()
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Affiliation(s)
- Han-Tao Wu
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Kun Li
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Gang Wang
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Xue-Xi Yang
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Anna Zhu
- Guangzhou Darui Biotechnology Co. Ltd
- Guangzhou 510665
- China
| | - Xu-Ping Xu
- Guangzhou Darui Biotechnology Co. Ltd
- Guangzhou 510665
- China
| | - Ming Li
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ying-Song Wu
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Tian-Cai Liu
- Institute of Antibody Engineering
- School of Laboratory Medicine and Biotechnology
- Southern Medical University
- Guangzhou 510515
- P. R. China
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14
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Ross MJ, Fidai I, Cowan JA. Analysis of Structure-Activity Relationships Based on the Hepatitis C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK⋅Cu Complex. Chembiochem 2017; 18:1743-1754. [PMID: 28628737 PMCID: PMC5970367 DOI: 10.1002/cbic.201700228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 01/06/2023]
Abstract
New therapeutics for targeting the hepatitis C virus (HCV) have been released in recent years. Although they are less prone to resistance, they are still administered in cocktails as a combination of drugs targeting various aspects of the viral life cycle. Herein, we aim to contribute to an arsenal of new HCV therapeutics by targeting the HCV internal ribosomal entry sequence (IRES) RNA through the development of catalytic metallodrugs that function to degrade rather than inhibit the target molecule. Based on a previously characterized HCV IRES stem-loop IIb RNA-targeting metallopeptide Cu-GGHYrFK (1⋅Cu), an all-l analogue (3⋅Cu) and a series of additional complexes with single alanine substitutions in the targeting domain were prepared and screened to determine the influence each amino acid side chain on RNA localization and recognition, and catalytic reactivity toward the RNA. Additional substitutions of the tyrosine position in complex 3⋅Cu were also investigated. Good agreement between calculated and measured binding affinities provided support for in silico modeling of the SLIIb RNA binding site and correlations with RNA cleavage sites. Examination of the cleavage products from reaction of the Cu complexes with SLIIb provided mechanistic insights, with the first observation of the 5'-geminal diol and 5'-phosphopropenal as products through the use of a Cu⋅ATCUN catalytic motif. Together, the data yielded insights into structure-function relationships that will guide future optimization efforts.
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Affiliation(s)
- Martin James Ross
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210
| | - Insiya Fidai
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210
- The Biophysics Graduate Program, The Ohio State University, 1790 Riverstone Dr., Delaware, OH 43015
| | - J. A. Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210
- The Biophysics Graduate Program, The Ohio State University, 1790 Riverstone Dr., Delaware, OH 43015
- Center for RNA Biology, 1790 Riverstone Dr., Delaware, OH 43015
- MetalloPharm, 1790 Riverstone Dr., Delaware, OH 43015
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Yu Z, Cowan JA. Catalytic Metallodrugs: Substrate-Selective Metal Catalysts as Therapeutics. Chemistry 2017; 23:14113-14127. [PMID: 28688119 DOI: 10.1002/chem.201701714] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
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16
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Ross MJ, Bradford SS, Cowan JA. Catalytic metallodrugs based on the LaR2C peptide target HCV SLIV IRES RNA. Dalton Trans 2015; 44:20972-82. [PMID: 26583601 PMCID: PMC4691540 DOI: 10.1039/c5dt02837j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Prior work has demonstrated the potential effectiveness of a new class of metallopeptides as catalytic metallodrugs that target HCV IRES SLIIb RNA (Cu-GGHYrFK, 1). Herein new catalytic metallodrugs (GGHKYKETDLLILFKDDYFAKKNEERK, 2; and GGHKYKETDL, 3) are described based on the LaR2C peptide that has been shown to bind to the SLIV HCV IRES domain. In vitro fluorescence assays yielded KD values ∼10 μM for both peptides and reaction of the copper derivatives with SLIV RNA demonstrated initial rates comparable across different assays as well as displaying pseudo-Michaelis-Menten behavior. The sites of reaction and cleavage mechanisms were determined by MALDI-TOF mass spectrometry. The primary site of copper-promoted SLIV cleavage is shown to occur in the vicinity of the 5'-G17C18A19C20-3' sequence that corresponds to a known binding site of the RM2 motif of the human La protein and has previously been reported to be important for viral translation. This domain also flanks the internal start codon (AUG). Both copper complexes also showed efficacy in an HCV replicon assay (IC50 = 0.75 μM for 2-Cu, and 2.17 μM for 3-Cu) and show potential for treatment of hepatitis C, complementing other marketed drugs by acting on a distinct therapeutic target by a novel mechanism of action.
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Affiliation(s)
- Martin James Ross
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Seth S. Bradford
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - J. A. Cowan
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
- MetalloPharm, 1790 Riverstone Dr., Delaware, OH 43015
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17
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Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res 2014; 42:12758-67. [PMID: 25313156 PMCID: PMC4227780 DOI: 10.1093/nar/gku934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
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Affiliation(s)
- Shakti Ingle
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Robert N Azad
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Swapan S Jain
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Thomas D Tullius
- Department of Chemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA
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18
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Inactivation of sortase A mediated by metal ATCUN complexes. J Biol Inorg Chem 2014; 19:1327-39. [PMID: 25217034 DOI: 10.1007/s00775-014-1190-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/24/2014] [Indexed: 02/07/2023]
Abstract
Catalytic metallopeptides that target the membrane-associated sortase A transpeptidase have been developed and evaluated as irreversible inactivators of SrtA∆N59 (sortase A, lacking the initial membrane-binding domain). The copper-binding GGH tripeptide ATCUN motif was linked to amidated forms of the cell wall sorting signal, LPET and LPETG, as sortase-targeting moieties. The resulting metallopeptides were used to determine half maximal inhibitory concentrations (IC₅₀) and rate constants for time-dependent sortase A inactivation. Michaelis-Menten behavior was observed for the catalytic metallopeptides, and k(cat), K(M) and k(cat)/K(M) parameters were obtained as 0.080 ± 0.002 min⁻¹, 23 ± 2 μM and 0.0035 ± 0.0003 μM⁻¹ min⁻¹, respectively. Concentration-dependent inhibition of SrtA∆N59 by the metallopeptides revealed IC₅₀ values ranging from 570 to 700 µM, while Cu-GGH, which lacked a targeting motif, had no measurable IC₅₀ value (>2,000 µM). Time-dependent inactivation of SrtA revealed a range of catalytic activities, with Cu-GGHGLPETG-NH2 demonstrating the fastest rate of inactivation in the presence of ascorbate and hydrogen peroxide coreactants. The active site of the enzyme comprises residues Cys-184, Arg-197 and His-120. LC-MS/MS analysis of the reaction products demonstrated modification of Cys-184 to cysteine sulfonic acid (+48 amu). Results obtained from a DTNB assay support oxidation of the Cys-184 residue. LC-MS/MS also suggested oxidation of the Arg-197 containing peptide. 2D NMR analysis was performed to assess the possible oxidation of His-120, however, none was observed. These compounds possess the potential for irreversible inactivation of SrtA through oxidative modification of essential residues required for substrate binding.
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Bradford SS, Ross MJ, Fidai I, Cowan JA. Insight into the recognition, binding, and reactivity of catalytic metallodrugs targeting stem loop IIb of hepatitis C IRES RNA. ChemMedChem 2014; 9:1275-85. [PMID: 24756921 PMCID: PMC4163017 DOI: 10.1002/cmdc.201400070] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Indexed: 01/20/2023]
Abstract
The complex Cu-GGHYrFK-amide (1-Cu) was previously reported as a novel metallotherapeutic that catalytically inactivates stem loop IIb (SLIIb) of the hepatitis C virus (HCV) internal ribosomal entry site (IRES) RNA and demonstrates significant antiviral activity in a cellular HCV replicon assay. Herein we describe additional studies focused on understanding the cleavage mechanism as well as the relationship of catalyst configuration to structural recognition and site-selective cleavage of the structured RNA motif. These are advanced by use of a combination of MALDI-TOF mass spectrometry, melting temperature determinations, and computational analysis to develop a structural model for binding and reactivity toward SLIIb of the IRES RNA. In addition, the binding, reactivity, and structural chemistry of the all-D-amino acid form of this metallopeptide, complex 2-Cu, are reported and compared with those of complex 1-Cu. In vitro RNA binding and cleavage assays for complex 2-Cu show a KD value of 76 ± 3 nM, and Michaelis-Menten parameters of kcat =0.14 ± 0.01 min(-1) and KM =7.9 ± 1.2 μM, with a turnover number exceeding 40. In a luciferase-based cellular replicon assay Cu-GGhyrfk-amide shows activity similar to that of the 1-Cu parent peptide, with an IC50 value of 1.9 ± 0.4 μM and cytotoxicity exceeding 100 μM. RT-PCR experiments confirm a significant decrease in HCV RNA levels in replicon assays for up to nine days when treated with complex 1-Cu in three-day dosing increments. This study shows the influence that the α-carbon stereocenter has for this new class of compounds, while detailed mass spectrometry and computational analyses provide new insight into the mechanisms of recognition, binding, and reactivity.
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Affiliation(s)
- Seth S. Bradford
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Martin James Ross
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Insiya Fidai
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - J. A. Cowan
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
- MetalloPharm LLC, 1790 Riverstone Drive, Delaware, OH 43015
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20
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Santiago-Morales J, Rosal R, Hernando MD, Ulaszewska MM, García-Calvo E, Fernández-Alba AR. Fate and transformation products of amine-terminated PAMAM dendrimers under ozonation and irradiation. JOURNAL OF HAZARDOUS MATERIALS 2014; 266:102-13. [PMID: 24384376 DOI: 10.1016/j.jhazmat.2013.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/30/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
This article deals with the degradation of a third-generation (G3) poly(amidoamine) (PAMAM) dendrimer under ozonation and irradiation. The identification and quantification of G3 PAMAM dendrimer and its transformation products has been performed by liquid chromatography-electrospray ionization-hybrid quadrupole time-of-flight-mass spectrometry. The dendrimer was completely depleted by ozone in less than 1 min. The effect of ultraviolet irradiation was attributed to hydroxyl-mediated oxidation. The transformation products were attributed to the oxidation of amines, which resulted in highly oxidized structures with abundance of carboxylic acids, which started from the formation of amine oxide and the scission of the CN bond of the amide group. We studied the toxicity of treated mixtures for six different organisms: the acute toxicity for the bacterium Vibrio fischeri and the microcrustacean Daphnia magna, the multigenerational growth inhibition of the alga Pseudokirchneriella subcapitata, and the seed germination phytotoxicity of Licopersicon esculentum, Lactuca sativa and Lolium perenne. Ozonation and irradiation originated transformation products are more toxic than the parent dendrimer. The toxicity of the dendrimer for the green alga was linked to a strong increase of intracellular reactive oxygen species with intense lipid peroxidation.
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Affiliation(s)
- Javier Santiago-Morales
- Department of Chemical Engineering, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Roberto Rosal
- Department of Chemical Engineering, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain; Advanced Study Institute of Madrid, IMDEA Agua, Parque Científico Tecnológico, 28805 Alcalá de Henares, Madrid, Spain.
| | - María D Hernando
- Spanish National Institute for Agricultural and Food Research and Technology - INIA, Crta. de la Coruña, km 7.5, 28040 Madrid, Spain
| | - Maria M Ulaszewska
- Advanced Study Institute of Madrid, IMDEA Agua, Parque Científico Tecnológico, 28805 Alcalá de Henares, Madrid, Spain
| | - Eloy García-Calvo
- Department of Chemical Engineering, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain; Advanced Study Institute of Madrid, IMDEA Agua, Parque Científico Tecnológico, 28805 Alcalá de Henares, Madrid, Spain
| | - Amadeo R Fernández-Alba
- Advanced Study Institute of Madrid, IMDEA Agua, Parque Científico Tecnológico, 28805 Alcalá de Henares, Madrid, Spain; Pesticide Residue Research Group, Department of Hydrogeology and Analytical Chemistry, University of Almería, 04120 Almería, Spain
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21
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Joyner JC, Cowan JA. Target-directed catalytic metallodrugs. Braz J Med Biol Res 2013; 46:465-85. [PMID: 23828584 PMCID: PMC3854446 DOI: 10.1590/1414-431x20133086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/11/2013] [Indexed: 01/08/2023] Open
Abstract
Most drugs function by binding reversibly to specific biological targets, and therapeutic effects generally require saturation of these targets. One means of decreasing required drug concentrations is incorporation of reactive metal centers that elicit irreversible modification of targets. A common approach has been the design of artificial proteases/nucleases containing metal centers capable of hydrolyzing targeted proteins or nucleic acids. However, these hydrolytic catalysts typically provide relatively low rate constants for target inactivation. Recently, various catalysts were synthesized that use oxidative mechanisms to selectively cleave/inactivate therapeutic targets, including HIV RRE RNA or angiotensin converting enzyme (ACE). These oxidative mechanisms, which typically involve reactive oxygen species (ROS), provide access to comparatively high rate constants for target inactivation. Target-binding affinity, co-reactant selectivity, reduction potential, coordination unsaturation, ROS products (metal-associated vs metal-dissociated; hydroxyl vs superoxide), and multiple-turnover redox chemistry were studied for each catalyst, and these parameters were related to the efficiency, selectivity, and mechanism(s) of inactivation/cleavage of the corresponding target for each catalyst. Important factors for future oxidative catalyst development are 1) positioning of catalyst reduction potential and redox reactivity to match the physiological environment of use, 2) maintenance of catalyst stability by use of chelates with either high denticity or other means of stabilization, such as the square planar geometric stabilization of Ni- and Cu-ATCUN complexes, 3) optimal rate of inactivation of targets relative to the rate of generation of diffusible ROS, 4) targeting and linker domains that afford better control of catalyst orientation, and 5) general bio-availability and drug delivery requirements.
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Affiliation(s)
- J C Joyner
- Evans Laboratory of Chemistry, Ohio State University, Columbus, OH 43210, USA.
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22
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Uchiyama Y, Hayasaka T, Masaki N, Watanabe Y, Masumoto K, Nagata T, Katou F, Setou M. Imaging mass spectrometry distinguished the cancer and stromal regions of oral squamous cell carcinoma by visualizing phosphatidylcholine (16:0/16:1) and phosphatidylcholine (18:1/20:4). Anal Bioanal Chem 2013; 406:1307-16. [PMID: 23728729 DOI: 10.1007/s00216-013-7062-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/22/2013] [Accepted: 05/10/2013] [Indexed: 12/28/2022]
Abstract
Most oral cancers are oral squamous cell carcinoma (OSCC). The anatomical features of OSCC have been histochemically evaluated with hematoxylin and eosin. However, the border between the cancer and stromal regions is unclear and large portions of the cancer and stromal regions are resected in surgery. To reduce the resected area and maintain oral function, a new method of diagnosis is needed. In this study, we tried to clearly distinguish the border on the basis of biomolecule distributions visualized by imaging mass spectrometry (IMS). In the IMS dataset, eleven signals were significantly different in intensity (p < 0.01) between the cancer and stromal regions. Two signals at m/z 770.5 and m/z 846.6 were distributed in each region, and a clear border was revealed. Tandem mass spectrometric (MS/MS) analysis identified these signals as phosphatidylcholine (PC) (16:0/16:1) at m/z 770.5 in the cancer region and PC (18:1/20:4) at m/z 846.6 in the stromal region. Moreover, the distribution of PC species containing arachidonic acid in the stromal region suggests that lymphocytes accumulated in response to the inflammation caused by cancer invasion. In conclusion, the cancer and stromal regions of OSCCs were clearly distinguished by use of these PC species and IMS analysis, and this molecular identification can provide important information to elucidate the mechanism of cancer invasion.
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Affiliation(s)
- Yoshiyuki Uchiyama
- Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
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23
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Joyner JC, Keuper KD, Cowan JA. Kinetics and Mechanisms of Oxidative Cleavage of HIV RRE RNA by Rev-Coupled Transition Metal Chelates. Chem Sci 2013; 4:1707-1718. [PMID: 23626900 PMCID: PMC3634708 DOI: 10.1039/c3sc22135k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Catalytic metallodrugs were used to oxidatively cleave HIV-1 Rev Response Element RNA (RRE RNA), and the mechanisms of RNA cleavage were studied using a combination of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), fluorescence spectroscopy, and gel electrophoresis. The metallodrugs, which contained combinations of the transition metals Fe2+, Co2+, Ni2+, and Cu2+ and the Rev-coupled chelators DOTA, DTPA, EDTA, NTA, tripeptide GGH, and tetrapeptide KGHK, bind to and cleave HIV RRE RNA through heretofore unknown oxidative mechanisms. The broad spectrum of metal catalysts and co-reagents provided a means for systematic variation of oxidative reactivity without significant perturbation of binding between catalyst and RNA. Detailed MS analyses were used to monitor formation of RNA fragments containing terminal 2',3'-cyclic phosphate (2',3'-cPO4), 3'-phosphate (3'-PO4), 3'-phosphoglycolate (3'-PG), 5'- hydroxyl (5'-OH), 5'- phosphate (5'-PO4) and other nascent overhangs at sites of cleavage. The distinct overhangs corresponded to distinct mechanisms of oxidative hydrogen-abstraction (H abstraction), hydrolysis, and/or endonucleolysis, allowing a dissection of the contributions of various mechanisms of oxidative cleavage. Rapid co-reactant- and catalyst-dependent formation of fragments containing terminal 3'-PG, 3'-PO4 and 5'-PO4 overhangs appeared to be initiated primarily by H abstraction events. The standard thiobarbituric acid (TBA) assay was employed herein in a novel usage to monitor the formation of base 2-hydroxypropenal products produced by 4'-H abstraction in RNA. Formation of an adduct with TBA was monitored by fluorescence, and its quantification correlated with the formation of 3'-PG monitored by MALDI-TOF MS, confirming oxidative 4'-H abstraction as a major mechanism of rapid catalyst-mediated cleavage of RRE RNA. Rapid formation of 3'-PO4 overhangs was most likely a result of 5'-H abstraction. Apparent rates of formation of 3'-PG (a unique product of 4'-H abstraction) at differing nucleotide positions within the RNA were used to triangulate probable 3D positions of metal centers and establish the distance-dependence of 4'-H abstraction for certain catalytic metallodrugs.
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Affiliation(s)
- Jeff C. Joyner
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
- The Ohio State Biochemistry Program, 784 Biological Sciences 484 W. 12th Avenue, Columbus, Ohio 43210
| | - Kevin D. Keuper
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - J. A. Cowan
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
- The Ohio State Biochemistry Program, 784 Biological Sciences 484 W. 12th Avenue, Columbus, Ohio 43210
- MetalloPharm LLC, 1790 Riverstone Drive, Delaware, OH 43015
- The Ohio State University Center for RNA Biology
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24
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Joyner JC, Hodnick WF, Cowan AS, Tamuly D, Boyd R, Cowan JA. Antimicrobial metallopeptides with broad nuclease and ribonuclease activity. Chem Commun (Camb) 2013; 49:2118-20. [PMID: 23380915 DOI: 10.1039/c3cc38977d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metallopeptides containing both the complex Cu(2+)-glycyl-glycyl-histidine (Cu-GGH) and the sequence WRWYCR were shown to possess antimicrobial activity against a variety of pathogenic bacteria, as well as bind to and cleave a variety of nucleic acids, suggesting potential mechanisms for antimicrobial activity that involve binding and/or irreversible cleavage of bacterial nucleic acids.
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Affiliation(s)
- Jeff C Joyner
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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