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Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3. Int J Mol Sci 2019; 21:ijms21010214. [PMID: 31892271 PMCID: PMC6982223 DOI: 10.3390/ijms21010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines. Biophys Chem 2018; 234:24-33. [PMID: 29407768 DOI: 10.1016/j.bpc.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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Sherstyuk YV, Zakharenko AL, Kutuzov MM, Sukhanova MV, Lavrik OI, Silnikov VN, Abramova TV. Synthesis of a series of NAD+ analogues, potential inhibitors of PARP 1, using ADP conjugates functionalized at the terminal phosphate group. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017010095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A versatile strategy for the design and synthesis of novel ADP conjugates and their evaluation as potential poly(ADP-ribose) polymerase 1 inhibitors. Mol Divers 2016; 21:101-113. [PMID: 27677737 DOI: 10.1007/s11030-016-9703-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/12/2016] [Indexed: 12/24/2022]
Abstract
A versatile strategy for the synthesis of [Formula: see text] mimetics was developed, involving an efficient pyrophosphate linkage formation in key conjugates containing a functional amino group which acts as useful reactive anchor for further derivatization. These [Formula: see text] mimetics consist of ADP conjugated through a diphosphate chain to an extended aliphatic linker bearing an aromatic acid residue. A number of conjugates containing aromatic carboxylic acids were found to inhibit poly(ADP-ribose) synthesis catalyzed by poly(ADP-ribose) polymerase-1 (PARP-1). A new class of potential PARP-1 inhibitors mimicking [Formula: see text], a substrate in the PARP-1 catalyzed reaction, was proposed.
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Tarasenko YV, Abramova TV, Mamatuk VI, Silnikov VN. Effective Synthesis of Fluorescently Labeled Morpholino Nucleoside Triphosphate Derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:32-42. [PMID: 26810366 DOI: 10.1080/15257770.2015.1114125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Morpholino nucleoside triphosphates (A, U, G, C, T) bearing the active functional amino group tethered to morpholine residue and their fluorescently labeled derivatives were synthesized. All compounds were characterized by (1)H, (13)C, and (31)P NMR, and mass spectrometry. A possibility of using fluorescently labeled morpholino nucleoside triphosphates as chain terminators in DNA sequencing is discussed.
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Affiliation(s)
- Yuliya V Tarasenko
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Lavrent'ev Ave 8, Novosibirsk 630090 , Russian Federation
| | - Tatyana V Abramova
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Lavrent'ev Ave 8, Novosibirsk 630090 , Russian Federation
| | - Viktor I Mamatuk
- b Institute of Organic Chemistry SB RAS , Lavrent'ev Ave 9, Novosibirsk 630090 , Russian Federation
| | - Vladimir N Silnikov
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Lavrent'ev Ave 8, Novosibirsk 630090 , Russian Federation.,c NanoTech-S LLS , Lavrent'ev Ave 8, Novosibirsk 630090 , Russian Federation
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Bockman MR, Kalinda AS, Petrelli R, De la Mora-Rey T, Tiwari D, Liu F, Dawadi S, Nandakumar M, Rhee KY, Schnappinger D, Finzel BC, Aldrich CC. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem 2015; 58:7349-7369. [PMID: 26299766 PMCID: PMC4667793 DOI: 10.1021/acs.jmedchem.5b00719] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alvin S. Kalinda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Riccardo Petrelli
- Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surrendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madhumitha Nandakumar
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA,Corresponding Author Footnote: To whom correspondence should be addressed. Phone 612-625-7956. Fax 612-626-3114.
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Abramova TV, Belov SS, Tarasenko YV, Silnikov VN. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics. Beilstein J Org Chem 2014; 10:1151-8. [PMID: 24991266 PMCID: PMC4077379 DOI: 10.3762/bjoc.10.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 12/14/2022] Open
Abstract
An efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.
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Affiliation(s)
- Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Sergey S Belov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia ; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Yulia V Tarasenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
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Abramova TV, Kasakin MF, Tarasenko IV, Lomzov AA, Koval' VV, Pyshnyĭ DV, Sil'nikov VN. [Synthesis and properties of methylene carboxamide mimetics of nucleic acids based on morpholine nucleosides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [PMID: 23189560 DOI: 10.1134/s1068162012040024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Uracyl and adenine containing oligocarboxamide mimetics of nucleic acids based on morpholine nucleosides (MorGly) are synthesized using peptide chemistry methods. Conditions for an analysis of homogeneity of protonated at physiological pH oligomers using a capillary electrophoresis are proposed. Studies of thermostability of complementary complexes formed by MorGly oligomers revealed that melting temperature dramatically depends on heterocyclic base composition (uracyl or adenine). Cooperative interactions realized at junctions in tandem complexes give more contribution to the thermostability in the case of complexes formed by modified oligomers than native oligodeoxyriboadenilates. Adenine containing MorGly oligomers form more stable complexes with poly(U) than native oligodeoxyriboadenilate of the same length. Complexes formed by modified oligomers with polyribonucleotides are more stable in compare with polydeoxyribonucleotide.
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Kasakin MF, Abramova TV, Sil'nikov VN. [Synthesis of 2'-aminometylmorpholino nucleoside analogues containing 4'-carboxymethyl lynker group]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 37:830-5. [PMID: 22497082 DOI: 10.1134/s1068162011060070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple and effective method for the synthesis of 2'-aminomethylmorpholino-4'-carboxymethyl nucleoside analogues and Boc-modified derivatives as synthons for peptide synthesis was developed.
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Bell NM, Micklefield J. Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications. Chembiochem 2010; 10:2691-703. [PMID: 19739190 DOI: 10.1002/cbic.200900341] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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