1
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Krochtová K, Janovec L, Bogárová V, Halečková A, Kožurková M. Interaction of 3,9-disubstituted acridine with single stranded poly(rA), double stranded poly(rAU) and triple stranded poly(rUAU): molecular docking - A spectroscopic tandem study. Chem Biol Interact 2024; 394:110965. [PMID: 38552767 DOI: 10.1016/j.cbi.2024.110965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
RNA plays an important role in many biological processes which are crucial for cell survival, and it has been suggested that it may be possible to inhibit individual processes involved in many diseases by targeting specific sequences of RNA. The aim of this work is to determine the affinity of novel 3,9-disubstited acridine derivative 1 with three different RNA molecules, namely single stranded poly(rA), double stranded homopolymer poly(rAU) and triple stranded poly(rUAU). The results of the absorption titration assays show that the binding constant of the novel derivative to the RNA molecules was in the range of 1.7-6.2 × 104 mol dm-3. The fluorescence and circular dichroism titration assays revealed considerable changes. The most significant results in terms of interpreting the nature of the interactions were the melting temperatures of the RNA samples in complexes with the 1. In the case of poly(rA), denaturation resulted in a self-structure formation; increased stabilization was observed for poly(rAU), while the melting points of the ligand-poly(rUAU) complex showed significant destabilization as a result of the interaction. The principles of molecular mechanics were applied to propose the non-bonded interactions within the binding complex, pentariboadenylic acid and acridine ligand as the study model. Initial molecular docking provided the input structure for advanced simulation techniques. Molecular dynamics simulation and cluster analysis reveal π - π stacking and the hydrogen bonds formation as the main forces that can stabilize the binding complex. Subsequent MM-GBSA calculations showed negative binding enthalpy accompanied the complex formation and proposed the most preferred conformation of the interaction complex.
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Affiliation(s)
- Kristína Krochtová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Ladislav Janovec
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Viktória Bogárová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Annamária Halečková
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Mária Kožurková
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic.
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2
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Novel insights on nucleopeptide binding: A spectroscopic and in silico investigation on the interaction of a thymine-bearing tetrapeptide with a homoadenine DNA. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117975] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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3
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Chowdhury S, Kanrar K, Bhuiya S, Das S. The alkaloid cryptolepine as a source of polyadenylate targeting therapeutic agent: Induction of self-assembly in the polyadenylate moiety. Arch Biochem Biophys 2021; 712:109042. [PMID: 34562470 DOI: 10.1016/j.abb.2021.109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 09/04/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
RNAs have become a well-known target for chemotherapeutic agents in the recent years. The tails of most eukaryotic m-RNA are characterized by the presence of a long polyadenylate sequence which plays an important role in its growth and maturation. This lays emphasis on development of molecular probes that target the polyadenylate sequence. Cryptolepine (hereafter, CRP) is an indoloquinoline alkaloid well known for its anti-malarial activities. A series of spectroscopic experiments namely absorption studies, fluorimetric studies and circular dichroism studies show that cryptolepine binds with single-stranded polyriboadenylic acid (hereafter, ss-poly (rA)) with a binding constant of ∼5 × 103 M-1 at 25 °C. Moreover thermal denaturation experiments show that the bound form of polyriboadenylic acid shows a characteristic transition profile. Such a profile is indicative of the ability of cryptolepine to induce self-assembly in the polyriboadenylic acid sequence on binding to it. Such ability of CRP to modulate the structural conformation of poly (rA), which in turn may cause functional aspects of the RNA to change, may give us a chance to develop effective alkaloid based chemotherapeutic agents.
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Affiliation(s)
- Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Kasturi Kanrar
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Sutanwi Bhuiya
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India.
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4
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Chowdhury S, Bhuiya S, Haque L, Das S. Influence of position of hydroxyl group of flavonoids on their binding with single stranded polyriboadenylic acid: A spectroscopic evaluation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119008. [PMID: 33038855 DOI: 10.1016/j.saa.2020.119008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Single stranded polyriboadenylic acid [poly (rA)] has been accepted widely as a suitable drug target owing to its vital role in the development of cancer since it controls gene expression during cell growth and differentiation. The biological properties of poly (rA) depend on its structural morphology. Pharmacologically active flavonoids can act as suitable binders to poly (rA) and significantly change its biophysical properties. Different factors favour flavonoid-poly (rA) binding. In our present work we have explored the role played by the position of hydroxyl groups in the flavonoids namely 3, 5, 6 and 7 hydroxyflavones in their course of interaction with poly (rA). A range of spectroscopic experiments reveal that 3HF binds best to poly (rA) among the four chosen flavonoids. This is probably due to the presence of a hydroxyl group in '3' position that enables it to exhibit ESIPT phenomenon which is missing for the other used flavonoids.
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Affiliation(s)
- Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Sutanwi Bhuiya
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Lucy Haque
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188 Raja S. C. Mallick Road, Kolkata 700032, India.
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5
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Safakish M, Hajimahdi Z, Vahabpour R, Zabihollahi R, Zarghi A. Novel Benzoxazin-3-one Derivatives: Design, Synthesis, Molecular Modeling, Anti-HIV-1 and Integrase Inhibitory Assay. Med Chem 2020; 16:938-946. [DOI: 10.2174/1573406415666190826161123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 01/17/2023]
Abstract
Introduction:
Integrase is a validated drug target for anti-HIV-1 therapy. The second
generation integrase inhibitors display π-stacking interaction ability with 3’-end nucleotide as a
streamlined metal chelating pharmacophore.
Method:
In this study, we introduced benzoxazin-3-one scaffold for integrase inhibitory potential
as bioisostere replacement strategy of 2-benzoxazolinone.
Results:
Molecular modeling studies revealed that amide functionality alongside oxadiazole heteroatoms
and sulfur in the second position of oxadiazole ring could mimic the metal chelating
pharmacophore. The halobenzyl ring occupies hydrophobic site created by the cytidylate nucleotide
(DC-16).
Conclusion:
The most potent and selective compound displayed 110 μM IC50 with a selectivity
index of more than 2.
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Affiliation(s)
- Mahdieh Safakish
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Hajimahdi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rouhollah Vahabpour
- Medical Lab Technology Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Zabihollahi
- Medical Lab Technology Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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6
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Fik-Jaskółka MA, Mkrtchyan AF, Saghyan AS, Palumbo R, Belter A, Hayriyan LA, Simonyan H, Roviello V, Roviello GN. Biological macromolecule binding and anticancer activity of synthetic alkyne-containing L-phenylalanine derivatives. Amino Acids 2020; 52:755-769. [PMID: 32430874 DOI: 10.1007/s00726-020-02849-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 01/17/2023]
Abstract
Herein, we described the synthesis of two L-phenylalanines α-derivatized with a terminal alkyne moiety whose structures differed by phenyl ring halogen substitution (two o-Cl in 1 vs. one p-Br in 2) and investigated their effect on biological macromolecules and living cells. We explored their interaction with quadruplex DNA (G4 DNA), using tel26 and c-myc as models, and bovine serum albumin (BSA). By CD spectroscopy, we found that 1 caused minor tel26 secondary structure changes, leading also to a slight thermal stabilization of this hybrid antiparallel/parallel G4 structure, while the c-myc parallel topology remained essentially unchanged upon 1 binding. Other CD evidences showed the ability of 1 to bind BSA, while molecular docking studies suggested that the same molecule could be housed into the hydrophobic cavity between sub-domains IIA, IIB, and IIIA of the protein. Furthermore, preliminary aggregation studies, based on concentration-dependent spectroscopic experiments, suggested the ability of 1 to aggregate forming noncovalent polymeric systems in aqueous solution. Differently from 1, the bromine-modified compound was able to bind Cu(II) ion, likely with the formation of a CuL2 complex, as found by UV spectroscopy. Finally, cell tests excluded any cytotoxic effect of both compounds toward normal cells, but showed slight antiproliferative effects of 2 on PC3 cancerous cells at 24 h, and of 1 on both T98G and MDA-MB-231 cancer cells at 48 h.
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Affiliation(s)
- Marta A Fik-Jaskółka
- Department of Bioinorganic Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 8, 61-614, Poznan, Poland.,Centre for Advanced Technology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 10, 61-614, Poznan, Poland.,Istituto di Biostrutture e Bioimmagini, IBB-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Anna F Mkrtchyan
- Scientific and Production Center, Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056, Yerevan, Armenia.,Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025, Yerevan, Armenia
| | - Ashot S Saghyan
- Scientific and Production Center, Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056, Yerevan, Armenia.,Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025, Yerevan, Armenia
| | - Rosanna Palumbo
- Istituto di Biostrutture e Bioimmagini, IBB-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Liana A Hayriyan
- Scientific and Production Center, Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056, Yerevan, Armenia.,Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025, Yerevan, Armenia
| | - Hayarpi Simonyan
- Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025, Yerevan, Armenia
| | - Valentina Roviello
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, IBB-CNR, Via Mezzocannone 16, 80134, Naples, Italy.
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7
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Synthesis and characterization of pyrrolo[1,2-a]quinoline derivatives for their larvicidal activity against Anopheles arabiensis. Struct Chem 2020. [DOI: 10.1007/s11224-020-01516-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Zhao D, Lu K, Liu G, Hou J, Yuan L, Ma L, Liu J, He J. PEP-FOLD design, synthesis, and characteristics of finger-like polypeptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117401. [PMID: 31394393 DOI: 10.1016/j.saa.2019.117401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Polypeptides with finger-like structures can often intercalate into the grooves of DNA, thereby affecting DNA repair or activating gene transcription, both of which are crucial for the regulation of physiological processes. Their conserved amino acid sequence and simple structure have provided useful elements for the design and assembly of functional molecules. In this paper, using the C2H2 zinc finger domain and the PEP-FOLD3 online simulation platform 11 polypeptides containing 22 amino acid residues were designed. In addition, the CD spectroscopy was combined with the fluorescence spectroscopy to study the polypeptide structures and their interaction with DNA. Results showed that although addition of zinc ions affected the polypeptide structure, particularly of the polypeptides A4, B1, and B3, zinc ion was not an essential factor for increasing polypeptide-DNA interactions. Our study revealed an increase in the interaction strength between mutated polypeptides and DNA, suggesting that mutations disrupt polypeptide structure, and polypeptides interact with DNA by groove and electrostatic binding. Mutations at the 12th and 15th amino acid residues had the greatest effect. The stronger binding between A2 or B2 and DNA indicates that the polypeptide has a spatial structure that can stably interact with DNA. The structure and characteristics of these polypeptide domains can provide information for the design and development of new polypeptide functional molecules, which could have potential significance and applications. However, this information also suggests that there are many challenges facing polypeptide design due to the synergistic effects between the side chains of amino acid residues.
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Affiliation(s)
- Dongxin Zhao
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China.
| | - Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China; School of Chemical Engineering and Food Science, Zhengzhou Institute of Technology, Zhengzhou 450044, China
| | - Guangbin Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450007, China
| | - Juhong Hou
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Libo Yuan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Li Ma
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Juan He
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
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9
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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10
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Roviello GN. Novel insights into nucleoamino acids: biomolecular recognition and aggregation studies of a thymine-conjugated L-phenyl alanine. Amino Acids 2018; 50:933-941. [PMID: 29766280 DOI: 10.1007/s00726-018-2562-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 03/28/2018] [Indexed: 01/30/2023]
Abstract
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase-amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model. The biomolecular recognition seems to rely on the ability of the novel compound to bind aromatic and heteroaromatic moieties in protein and nucleic acids, not hindered by its propensity to self-assemble in aqueous solution, behavior suggested by dynamic light scattering (DLS) and CD spectroscopy in concentration- and temperature-dependent experiments. Finally, the high stability in human serum concurs to define the picture of the nucleoamino amide: this enzymatically stable drug candidate could interfere with protein and single-stranded nucleic acid-driven biological processes, particularly those associated with mRNA poly(A) tail, and its self-assembling nature, in analogy to other L-Phe-based systems, discloses new scenarios in drug delivery technology.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini-CNR (UOS Napoli centro), 80134, Naples, Italy.
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11
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Musumeci D, Roviello V, Roviello GN. DNA- and RNA-binding ability of oligoDapT, a nucleobase-decorated peptide, for biomedical applications. Int J Nanomedicine 2018; 13:2613-2629. [PMID: 29750033 PMCID: PMC5936014 DOI: 10.2147/ijn.s156381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Nucleobase-bearing peptides and their interaction with DNA and RNA are an important topic in the development of therapeutic approaches. On one hand, they are highly effective for modulating the nucleic-acid-based biological processes. On the other hand, they permit to overcome some of the main factors limiting the therapeutic efficacy of natural oligonucleotides, such as their rapid degradation by nucleases. Methods and results This article describes the synthesis and characterization of a novel thymine-bearing nucleoamino acid based on the l-diaminopropionic acid (l-Dap) and its solid phase oligomerization to α-peptides (oligoDapT), characterized using mass spectrometry, spectroscopic techniques, and scanning electron microscopy (SEM) analysis. The interaction of the obtained nucleopeptide with DNA and RNA model systems as both single strands (dA12, rA12, and poly(rA)) and duplex structures (dA12/dT12 and poly(rA)/poly(rU)) was investigated by means of circular dichroism (CD) and ultraviolet (UV) experiments. From the analysis of our data, a clear ability of the nucleopeptide to bind nucleic acids emerged, with oligoDapT being able to form stable complexes with both unpaired and double-stranded DNA and RNA. In particular, dramatic changes in the dA12/dT12 and poly(rA)/poly(rU) structures were observed as a consequence of the nucleopeptide binding. CD titrations revealed that multiple peptide units bound all the examined nucleic acid targets, with TLdap/A or TLdap/A:T(U) ratios >4 in case of oligoDapT/DNA and ~2 in oligoDapT/RNA complexes. Conclusion Our findings seem to indicate that Dap-based nucleopeptides are interesting nucleic acid binding-tools to be further explored with the aim to efficiently modulate DNA- and RNA-based biological processes.
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Affiliation(s)
- Domenica Musumeci
- CNR-Institute of Biostructure and Bioimaging, Naples, Italy.,Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and Centro Servizi Metereologici Avanzati, University of Naples Federico II, Naples, Italy
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12
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Haque L, Bhuiya S, Das S. Self-structure assembly in single stranded polyriboadenylic acid by benzophenanthridine alkaloid: Spectroscopic and calorimetric exploration. Int J Biol Macromol 2018; 106:1130-1138. [DOI: 10.1016/j.ijbiomac.2017.08.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
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13
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Musumeci D, Roviello GN, Rigione G, Capasso D, Di Gaetano S, Riccardi C, Roviello V, Montesarchio D. Benzodifuran Derivatives as Potential Antiproliferative Agents: Possible Correlation between Their Bioactivity and Aggregation Properties. Chempluschem 2016; 82:251-260. [PMID: 31961558 DOI: 10.1002/cplu.201600547] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 01/24/2023]
Abstract
To further explore the properties and bioactivity of benzodifurans, three compounds in this class were synthesised and characterised using spectroscopic and spectrometric techniques, as well as SEM and thermogravimetric analysis. The synthesised compounds showed interesting antiproliferative activity on different human cancer cells (HeLa, Hep-G2, WM266), whereas no relevant cytotoxic effect was observed on healthy control cells. To study the possible mechanism of action of the benzodifurans, their ability to bind various model DNA systems, their aggregation properties, and their ability to bind biologically relevant metal ions was evaluated. The molecules were found to form monodisperse nanoaggregates stable at physiological temperature, which are likely related to the observed bioactivity.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giuseppina Rigione
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
| | - Domenica Capasso
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
| | - Valentina Roviello
- Centro Regionale di Competenza (CRdC) Tecnologie, Via Nuova Agnano 11, 80125, Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
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14
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Roviello GN, Musumeci D. Synthetic approaches to nucleopeptides containing all four nucleobases, and nucleic acid-binding studies on a mixed-sequence nucleo-oligolysine. RSC Adv 2016; 6:63578-63585. [PMID: 28496969 PMCID: PMC5361140 DOI: 10.1039/c6ra08765e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/27/2016] [Indexed: 11/21/2022] Open
Abstract
In this article we describe two solid-phase synthetic routes to obtain a nucleo-oligolysine α-peptide containing all four natural nucleobases.
In this article we describe two solid-phase synthetic routes to obtain a nucleo-oligolysine α-peptide containing all four natural nucleobases. The first one is based on the oligomerization of the nucleobase-containing monomers, easily synthesized as herein described. The second strategy has the advantage of avoiding the solution synthesis of the monomeric building blocks, leading to the final nucleopeptide by direct solid-phase couplings of the suitably protected nucleobases with the free amino groups on the growing peptide chain still anchored to the resin. Both strategies are general and can be applied to the synthesis of nucleopeptides having backbones formed by any other diamino acid moiety decorated with the four nucleobases. We also report the CD and UV studies on the hybridization properties of the obtained nucleopeptide, containing all four nucleobases on alternate lysines in the sequence, towards complementary DNA and RNA strands. The nucleo-oligolysine with a mixed-base sequence did not prove to bind complementary DNA, but was able to recognize the complementary RNA forming a complex with a higher melting temperature than that of the corresponding RNA/RNA natural duplex and comparable with that of the analogous PNA/RNA system.
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Affiliation(s)
- Giovanni N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone 16 , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
| | - Domenica Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone 16 , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585.,Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy . ; Tel: +39-81-674143
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15
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Roviello GN, Roviello V, Autiero I, Saviano M. Solid phase synthesis of TyrT, a thymine-tyrosine conjugate with poly(A) RNA-binding ability. RSC Adv 2016; 6:27607-27613. [PMID: 29057072 PMCID: PMC5647564 DOI: 10.1039/c6ra00294c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/01/2016] [Indexed: 01/15/2023] Open
Abstract
TyrT nucleoamino amide interacts with poly(A) RNA.
The present work deals with the synthesis and characterization of a novel nucleoamino acid derivative based on a l-tyrosine moiety to which a thymine nucleobase was anchored by means of an amide bond to the N-alpha group. This derivative, denominated by us TyrT, belongs to the family of the nucleobase–amino acid conjugates that show a wide range of biological activities, frequently associated with their ability to interact with nucleic acids. In this respect, the interaction of TyrT with poly(A), a proposed RNA target for anticancer strategies, was studied by circular dichroism (CD) which suggested its ability to bind this RNA. Moreover, the modification of the morphology of a sample of TyrT in the presence of poly(A) was visualised by scanning electron microscopy (SEM) which was in agreement with the evidence that the thyminyl l-tyrosine interacts with poly(A). Finally, computational analyses have been performed to hypothesize the binding mode from a structural point of view, suggesting that the binding is mainly kept via hydrophobic contacts, reproducing a stacking-like interaction between the thymine ring of TyrT and the two successive adenine rings of a poly(A) model.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR (UOS Napoli Centro) , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , Università di Napoli "Federico II" , 80125 Napoli , Italy
| | - Ida Autiero
- Istituto di Biostrutture e Bioimmagini - CNR (UOS Napoli Centro) , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
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16
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Roviello GN, Vicidomini C, Di Gaetano S, Capasso D, Musumeci D, Roviello V. Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide. RSC Adv 2016; 6:14140-14148. [PMID: 29057071 PMCID: PMC5635565 DOI: 10.1039/c5ra25809j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA12) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.
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Affiliation(s)
- G N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - C Vicidomini
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - S Di Gaetano
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - D Capasso
- Università di Napoli "Federico II" , Dipartimento di Farmacia , 80134 Napoli , Italy
| | - D Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
- Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy
| | - V Roviello
- Università di Napoli "Federico II" , Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , 80125 Napoli , Italy
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Kumar GS, Basu A. The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures. Biochim Biophys Acta Gen Subj 2015; 1860:930-944. [PMID: 26522497 DOI: 10.1016/j.bbagen.2015.10.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/06/2015] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND RNA has now emerged as a potential target for therapeutic intervention. RNA targeted drug design requires detailed thermodynamic characterization that provides new insights into the interactions and this together with structural data, may be used in rational drug design. The use of calorimetry to characterize small molecule-RNA interactions has emerged as a reliable and sensitive tool after the recent advancements in biocalorimetry. SCOPE OF THE REVIEW This review summarizes the recent advancements in thermodynamic characterization of small molecules, particularly some natural alkaloids binding to various RNA structures. Thermodynamic characterization provides information that can supplement structural data leading to more effective drug development protocols. MAJOR CONCLUSIONS This review provides a concise report on the use of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques in characterizing small molecules, mostly alkaloids-RNA interactions with particular reference to binding of tRNA, single stranded RNA, double stranded RNA, poly(A), triplex RNA. GENERAL SIGNIFICANCE It is now apparent that a combination of structural and thermodynamic data is essential for rational design of specific RNA targeted drugs. Recent advancements in biocalorimetry instrumentation have led to detailed understanding of the thermodynamics of small molecules binding to various RNA structures paving the path for the development of many new natural and synthetic molecules as specific binders to various RNA structures. RNA targeted drug design, that remained unexplored, will immensely benefit from the calorimetric studies leading to the development of effective drugs for many diseases.
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Affiliation(s)
- Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| | - Anirban Basu
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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