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Penchovsky R, Georgieva AV, Dyakova V, Traykovska M, Pavlova N. Antisense and Functional Nucleic Acids in Rational Drug Development. Antibiotics (Basel) 2024; 13:221. [PMID: 38534656 DOI: 10.3390/antibiotics13030221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
This review is focused on antisense and functional nucleic acid used for completely rational drug design and drug target assessment, aiming to reduce the time and money spent and increase the successful rate of drug development. Nucleic acids have unique properties that play two essential roles in drug development as drug targets and as drugs. Drug targets can be messenger, ribosomal, non-coding RNAs, ribozymes, riboswitches, and other RNAs. Furthermore, various antisense and functional nucleic acids can be valuable tools in drug discovery. Many mechanisms for RNA-based control of gene expression in both pro-and-eukaryotes and engineering approaches open new avenues for drug discovery with a critical role. This review discusses the design principles, applications, and prospects of antisense and functional nucleic acids in drug delivery and design. Such nucleic acids include antisense oligonucleotides, synthetic ribozymes, and siRNAs, which can be employed for rational antibacterial drug development that can be very efficient. An important feature of antisense and functional nucleic acids is the possibility of using rational design methods for drug development. This review aims to popularize these novel approaches to benefit the drug industry and patients.
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Affiliation(s)
- Robert Penchovsky
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Antoniya V Georgieva
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Vanya Dyakova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Martina Traykovska
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Nikolet Pavlova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
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2
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Ormazábal A, Palma J, Pierdominici-Sottile G. Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods. Methods Mol Biol 2024; 2741:207-238. [PMID: 38217656 DOI: 10.1007/978-1-0716-3565-0_12] [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] [Indexed: 01/15/2024]
Abstract
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.
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Affiliation(s)
- Agustín Ormazábal
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Juliana Palma
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Gustavo Pierdominici-Sottile
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina.
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3
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Dhuri K, Duran T, Chaudhuri B, Slack FJ, Vikram A, Glazer PM, Bahal R. Head-to-head comparison of in vitro and in vivo efficacy of pHLIP-conjugated anti-seed gamma peptide nucleic acids. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101584. [PMID: 38144419 PMCID: PMC10745205 DOI: 10.1016/j.xcrp.2023.101584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
Gamma peptide nucleic acids (γPNAs) have recently garnered attention in diverse therapeutic and diagnostic applications. Serine and diethylene-glycol-containing γPNAs have been tested for numerous RNA-targeting purposes. Here, we comprehensively evaluated the in vitro and in vivo efficacy of pH-low insertion peptide (pHLIP)-conjugated serine and diethylene-based γPNAs. pHLIP targets only the acidic tumor microenvironment and not the normal cells. We synthesized and parallelly tested pHLIP-serine γPNAs and pHLIP-diethylene glycol γPNAs that target the seed region of microRNA-155, a microRNA that is upregulated in various cancers. We performed an all-atom molecular dynamics simulation-based computational study to elucidate the interaction of pHLIP-γPNA constructs with the lipid bilayer. We also determined the biodistribution and efficacy of the pHLIP constructs in the U2932-derived xenograft model. Overall, we established that the pHLIP-serine γPNAs show superior results in vivo compared with the pHLIP-diethylene glycol-based γPNA.
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Affiliation(s)
- Karishma Dhuri
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Tibo Duran
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
- Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Frank J. Slack
- HMS Initiative for RNA Medicine, Department of Pathology, BIDMC Cancer Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Ajit Vikram
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
- Lead contact
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4
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Tamez A, Nilsson L, Mihailescu MR, Evanseck JD. Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation. J Chem Theory Comput 2023. [PMID: 37195939 DOI: 10.1021/acs.jctc.2c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
γ-Modified peptide nucleic acids (γPNAs) serve as potential therapeutic agents against genetic diseases. Miniature poly(ethylene glycol) (miniPEG) has been reported to increase solubility and binding affinity toward genetic targets, yet details of γPNA structure and dynamics are not understood. Within our work, we parameterized missing torsional and electrostatic terms for the miniPEG substituent on the γ-carbon atom of the γPNA backbone in the CHARMM force field. Microsecond timescale molecular dynamics simulations were carried out on six miniPEG-modified γPNA duplexes from NMR structures (PDB ID: 2KVJ). Three NMR models for the γPNA duplex (PDB ID: 2KVJ) were simulated as a reference for structural and dynamic changes captured for the miniPEG-modified γPNA duplex. Principal component analysis performed on the γPNA backbone atoms identified a single isotropic conformational substate (CS) for the NMR simulations, whereas four anisotropic CSs were identified for the ensemble of miniPEG-modified γPNA simulations. The NMR structures were found to have a 23° helical bend toward the major groove, consistent with our simulated CS structure of 19.0°. However, a significant difference between simulated methyl- and miniPEG-modified γPNAs involved the opportunistic invasion of miniPEG through the minor and major groves. Specifically, hydrogen bond fractional analysis showed that the invasion was particularly prone to affect the second G-C base pair, reducing the Watson-Crick base pair hydrogen bond by 60% over the six simulations, whereas the A-T base pairs decreased by only 20%. Ultimately, the invasion led to base stack reshuffling, where the well-ordered base stacking was reduced to segmented nucleobase stacking interactions. Our 6 μs timescale simulations indicate that duplex dissociation suggests the onset toward γPNA single strands, consistent with the experimental observation of decreased aggregation. To complement the insight of miniPEG-modified γPNA structure and dynamics, the new miniPEG force field parameters allow for further exploration of such modified γPNA single strands as potential therapeutic agents against genetic diseases.
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Affiliation(s)
- Angel Tamez
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institute, Solnavägen 1, 171 77 Solna, Sweden
| | - Mihaela-Rita Mihailescu
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffrey D Evanseck
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Ghasemi F, Salimi A. Advances in 2d Based Field Effect Transistors as Biosensing Platforms: From Principle to Biomedical Applications. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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6
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Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
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Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
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7
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Economos NG, Quijano E, Carufe KEW, Perera J, Glazer P. Antispacer peptide nucleic acids for sequence-specific CRISPR-Cas9 modulation. Nucleic Acids Res 2022; 50:e59. [PMID: 35235944 PMCID: PMC9177974 DOI: 10.1093/nar/gkac095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022] Open
Abstract
Despite the rapid and broad implementation of CRISPR-Cas9-based technologies, convenient tools to modulate dose, timing, and precision remain limited. Building on methods using synthetic peptide nucleic acids (PNAs) to bind RNA with unusually high affinity, we describe guide RNA (gRNA) spacer-targeted, or 'antispacer', PNAs as a tool to modulate Cas9 binding and activity in cells in a sequence-specific manner. We demonstrate that PNAs rapidly and efficiently target complexed gRNA spacer sequences at low doses and without design restriction for sequence-selective Cas9 inhibition. We further show that short PAM-proximal antispacer PNAs achieve potent cleavage inhibition (over 2000-fold reduction) and that PAM-distal PNAs modify gRNA affinity to promote on-target specificity. Finally, we apply antispacer PNAs for temporal regulation of two dCas9-fusion systems. These results present a novel rational approach to nucleoprotein engineering and describe a rapidly implementable antisense platform for CRISPR-Cas9 modulation to improve spatiotemporal versatility and safety across applications.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Elias Quijano
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - J Dinithi R Perera
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
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8
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Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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9
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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10
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Kalayan J, Curtis RA, Warwicker J, Henchman RH. Thermodynamic Origin of Differential Excipient-Lysozyme Interactions. Front Mol Biosci 2021; 8:689400. [PMID: 34179093 PMCID: PMC8226134 DOI: 10.3389/fmolb.2021.689400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 01/15/2023] Open
Abstract
Understanding the intricate interplay of interactions between proteins, excipients, ions and water is important to achieve the effective purification and stable formulation of protein therapeutics. The free energy of lysozyme interacting with two kinds of polyanionic excipients, citrate and tripolyphosphate, together with sodium chloride and TRIS-buffer, are analysed in multiple-walker metadynamics simulations to understand why tripolyphosphate causes lysozyme to precipitate but citrate does not. The resulting multiscale decomposition of energy and entropy components for water, sodium chloride, excipients and lysozyme reveals that lysozyme is more stabilised by the interaction of tripolyphosphate with basic residues. This is accompanied by more sodium ions being released into solution from tripolyphosphate than for citrate, whilst the latter instead has more water molecules released into solution. Even though lysozyme aggregation is not directly probed in this study, these different mechanisms are suspected to drive the cross-linking between lysozyme molecules with vacant basic residues, ultimately leading to precipitation.
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Affiliation(s)
- Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Robin A Curtis
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Departments of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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11
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Roy S, Ali A, Bhattacharya S. Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies. J Phys Chem B 2021; 125:5489-5501. [PMID: 34029082 DOI: 10.1021/acs.jpcb.0c10991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interactions of intermolecular G-quadruplex RNA and small molecules have been investigated by computational studies. Various anthraquinone, bisbenzimidazole, and carbazole-benzimidazole based ligands have shown a distinct preference to G-quadruplex structures as opposed to the corresponding duplex forms of DNA that were docked with telomeric G-quadruplex RNA. The comparative binding study of such ligands with G-quadruplex (G4) RNA showed higher binding affinities toward carbazole-benzimidazole ligands than those of the anthraquinone and bisbenzimidazole based ligands. A molecular dynamics simulation study was used to examine quadruplex-ligand interactions. Analysis of the binding free energy indicated the formation of the thermodynamically favorable RNA-ligand complex. The formation of several H-bonding interactions and the change of the solvent accessible surface area (SASA) also support the effective binding of the carbazole-benzimidazole ligands with G4 RNA structures. Thus, the library screening approach has assisted in getting a structure-activity relationship for the selected small molecules toward the G-quadruplex RNA binding, which can be applied in the targeting of G-quadruplex RNA medicated anticancer therapeutics.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India
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12
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Finotti A, Gasparello J, Casnati A, Corradini R, Gambari R, Sansone F. Delivery of Peptide Nucleic Acids Using an Argininocalix[4]arene as Vector. Methods Mol Biol 2021; 2211:123-143. [PMID: 33336275 DOI: 10.1007/978-1-0716-0943-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The importance of peptide nucleic acids (PNAs) for alteration of gene expression is nowadays firmly established. PNAs are characterized by a pseudo-peptide backbone composed of N-(2-aminoethyl)glycine units and have been found to be excellent candidates for antisense and antigene therapies. Recently, PNAs have been demonstrated to alter the action of microRNAs and thus can be considered very important tools for miRNA therapeutics. In fact, the pharmacological modulation of microRNA activity appears to be a very interesting approach in the development of new types of drugs. Among the limits of PNAs in applied molecular biology, the delivery to target cells and tissues is of key importance. The aim of this chapter is to describe methods for the efficient delivery of unmodified PNAs designed to target microRNAs involved in cancer, using as model system miR-221-3p and human glioma cells as in vitro experimental cellular system. The methods employed to deliver PNAs targeting miR-221-3p here presented are based on a macrocyclic multivalent tetraargininocalix[4]arene used as non-covalent vector for anti-miR-221-3p PNAs. High delivery efficiency, low cytotoxicity, maintenance of the PNA biological activity, and easy preparation makes this vector a candidate for a universal delivery system for this class of nucleic acid analogs.
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Affiliation(s)
- Alessia Finotti
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.
| | - Jessica Gasparello
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Gambari
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.,Interuniversity Consortium for Biotechnology, Trieste University, Trieste, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy.
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13
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Topham CM, Smith JC. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J Comput Aided Mol Des 2021; 35:355-369. [PMID: 33624202 DOI: 10.1007/s10822-021-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 24 Avenue Jacques Besse, 81500, Lavaur, France.
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
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14
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Alenaizan A, Barnett JL, Hud NV, Sherrill CD, Petrov AS. The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs. Nucleic Acids Res 2021; 49:79-89. [PMID: 33300028 PMCID: PMC7797056 DOI: 10.1093/nar/gkaa1159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
The helical structures of DNA and RNA were originally revealed by experimental data. Likewise, the development of programs for modeling these natural polymers was guided by known structures. These nucleic acid polymers represent only two members of a potentially vast class of polymers with similar structural features, but that differ from DNA and RNA in the backbone or nucleobases. Xeno nucleic acids (XNAs) incorporate alternative backbones that affect the conformational, chemical, and thermodynamic properties of XNAs. Given the vast chemical space of possible XNAs, computational modeling of alternative nucleic acids can accelerate the search for plausible nucleic acid analogs and guide their rational design. Additionally, a tool for the modeling of nucleic acids could help reveal what nucleic acid polymers may have existed before RNA in the early evolution of life. To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA.
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Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Joshua L Barnett
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0765, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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15
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Moccia M, Mercurio FA, Langella E, Piacenti V, Leone M, Adamo MFA, Saviano M. Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach. Front Chem 2020; 8:568575. [PMID: 33330358 PMCID: PMC7719796 DOI: 10.3389/fchem.2020.568575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
In the present work, structural features of the interaction between peptide nucleic acid (PNA)-based analogs of the tumor-suppressor microRNA-34a with both its binding sites on MYCN mRNA were investigated. In particular, the region from base 1 to 8 ("seed" region) of miR-34a was reproduced in the form of an 8-mer PNA fragment (tiny PNA), and binding to target 3'UTR MYCN mRNA, was studied by a seldom reported and detailed NMR characterization, providing evidence for the formation of anti-parallel duplexes with a well-organized structural core. The formation of PNA-3'UTR duplexes was also confirmed by Circular Dichroism, and their melting curves were measured by UV spectroscopy. Nevertheless, this study offered a valuable comparison between molecular dynamics predictions and experimental evidence, which showed great correlation. Preliminary uptake assays were carried out in Neuroblastoma Kelly cells, using short peptide conjugates as carriers and FITC fluorescent tag for subcellular localization. Moderate internalization was observed without the use of transfecting agents. The reported results corroborate the interest toward the design and development of chimeric PNA/RNA sequences as effective RNA-targeting agents.
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Affiliation(s)
- Maria Moccia
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Emma Langella
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Valerio Piacenti
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Mauro F. A. Adamo
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
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16
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Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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17
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Sharpe DJ, Röder K, Wales DJ. Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers. J Phys Chem B 2020; 124:4062-4068. [PMID: 32336100 PMCID: PMC7304908 DOI: 10.1021/acs.jpcb.0c01420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Artificial
analogues of the natural nucleic acids have attracted
interest as a diverse class of information storage molecules capable
of self-replication. In this study, we use the computational potential
energy landscape framework to investigate the structural and dynamical
properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA),
which are derived from their respective RNA and DNA analogues by inversion
of a single chiral center in the sugar moiety of the nucleotides.
For an octameric XyNA sequence and the analogue dXyNA, we observe
facile conformational transitions between a left-handed helix, which
is the free energy global minimum, and a ladder-type structure with
approximately zero helicity. The competing ensembles are better separated
in the dXyNA, making it a more suitable candidate for a molecular
switch, whereas the XyNA exhibits additional flexibility. Both energy
landscapes exhibit greater frustration than we observe in RNA or DNA,
in agreement with the higher degree of optimization expected from
the principle of minimal frustration in evolved biomolecules.
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Affiliation(s)
- Daniel J Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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19
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Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
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20
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Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. J Chem Theory Comput 2019; 15:6422-6432. [PMID: 31553600 PMCID: PMC6889957 DOI: 10.1021/acs.jctc.9b00519] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
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21
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Fortunati S, Rozzi A, Curti F, Giannetto M, Corradini R, Careri M. Novel amperometric genosensor based on peptide nucleic acid (PNA) probes immobilized on carbon nanotubes-screen printed electrodes for the determination of trace levels of non-amplified DNA in genetically modified (GM) soy. Biosens Bioelectron 2019; 129:7-14. [PMID: 30682690 DOI: 10.1016/j.bios.2019.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 02/09/2023]
Abstract
A novel amperometric genosensor based on PNA probes covalently bound on the surface of Single Walled Carbon Nanotubes - Screen Printed Electrodes (SWCNT-SPEs) was developed and validated in samples of non-amplified genomic DNA extracted from genetically modified (GM)-Soy. The sandwich assay is based on a first recognition of a 20-mer portion of the target DNA by a complementary PNA Capture Probe (CP) and a second hybridization with a PNA Signalling Probe (SP), with a complementary sequence to a different portion of the target DNA. The SP was labelled with biotin to measure current signal by means of a final incubation of an Alkaline Phosphatase-streptavidin conjugate (ALP-Strp). The electrochemical detection was carried out using hydroquinone diphosphate (HQDP) as enzymatic substrate. The genoassay provided a linear range from 250 pM to 2.5 nM, LOD of 64 pM and LOQ of 215 pM Excellent selectivity towards one base mismatch (1-MM) or scrambled (SCR) sequences was obtained. A simple protocol for extraction and analysis of non-amplified soybean genomic DNA without sample treatment was developed and validated. Our study provides insight into how the outstanding recognition efficiency of PNAs can be combined with the unique properties of CNTs in terms of signal response enhancement for direct detection of genomic DNA samples at the level of interest without previous amplification.
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Affiliation(s)
- Simone Fortunati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Federica Curti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Marco Giannetto
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Maria Careri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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22
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Padhi S, Pradhan M, Bung N, Roy A, Bulusu G. TPP riboswitch aptamer: Role of Mg 2+ ions, ligand unbinding, and allostery. J Mol Graph Model 2019; 88:282-291. [PMID: 30818079 DOI: 10.1016/j.jmgm.2019.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023]
Abstract
Riboswitches are non-coding RNAs that regulate gene expression in response to the binding of metabolites. Their abundance in bacteria makes them ideal drug targets. The prokaryotic thiamine pyrophosphate (TPP) riboswitch regulates gene expression in a wide range of bacteria by undergoing conformational changes in response to the binding of TPP. Although an experimental structure for the aptamer domain of the riboswitch is now available, details of the conformational changes that occur during the binding of the ligand, and the factors that govern these conformational changes, are still not clear. This study employs microsecond-scale molecular dynamics simulations to provide insights into the functioning of the riboswitch aptamer in atomistic detail. A mechanism for the transmission of conformational changes from the ligand-binding site to the P1 switch helix is proposed. Mg2+ ions in the binding site play a critical role in anchoring the ligand to the riboswitch. Finally, modeling the egress of TPP from the binding site reveals a two-step mechanism for TPP unbinding. Findings from this study can motivate the design of future studies aimed at modulating the activity of this drug target.
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Affiliation(s)
- Siladitya Padhi
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Meenakshi Pradhan
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Navneet Bung
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Arijit Roy
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India.
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23
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Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S. Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. Genes (Basel) 2018; 9:E329. [PMID: 29958477 PMCID: PMC6070936 DOI: 10.3390/genes9070329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Sequence databases and transcriptome-wide mapping have revealed different reversible and dynamic chemical modifications of the nitrogen bases of RNA molecules. Modifications occur in coding RNAs and noncoding-RNAs post-transcriptionally and they can influence the RNA structure, metabolism, and function. The result is the expansion of the variety of the transcriptome. In fact, depending on the type of modification, RNA molecules enter into a specific program exerting the role of the player or/and the target in biological and pathological processes. Many research groups are exploring the role of RNA modifications (alias epitranscriptome) in cell proliferation, survival, and in more specialized activities. More recently, the role of RNA modifications has been also explored in stem cell biology. Our understanding in this context is still in its infancy. Available evidence addresses the role of RNA modifications in self-renewal, commitment, and differentiation processes of stem cells. In this review, we will focus on five epitranscriptomic marks: N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, Pseudouridine (Ψ) and Adenosine-to-Inosine editing. We will provide insights into the function and the distribution of these chemical modifications in coding RNAs and noncoding-RNAs. Mainly, we will emphasize the role of epitranscriptomic mechanisms in the biology of naïve, primed, embryonic, adult, and cancer stem cells.
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Affiliation(s)
- Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Chiara Argentati
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Martina Bazzucchi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
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24
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Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
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25
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Bahal R, Manna A, Hsieh WC, Thadke SA, Sureshkumar G, Ly DH. RNA-Templated Concatenation of Triplet Nucleic-Acid Probe. Chembiochem 2018; 19:674-678. [PMID: 29323790 DOI: 10.1002/cbic.201700574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Indexed: 01/21/2023]
Abstract
Template-directed synthesis offers several distinct benefits over conventional laboratory creation, including unsurpassed reaction rate and selectivity. Although it is central to many biological processes, such an approach has rarely been applied to the in situ synthesis and recognition of biomedically relevant target. Towards this goal, we report the development of a three-codon nucleic-acid probe containing a C-terminal thioester group and an N-terminal cysteine that is capable of undergoing template-directed oligomerization in the presence of an RNA target and self-deactivation in its absence. The work has implications for the development of millamolecular nucleic-acid probes for targeting RNA-repeated expansions associated with myotonic dystrophy type 1 and other related neuromuscular and neurodegenerative disorders.
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Affiliation(s)
- Raman Bahal
- School of Pharmacy, University of Connecticut, 69 N. Eagleville Road, Storrs, CT, 06269, USA
| | - Arunava Manna
- Department of Chemistry, Institute for Biomolecular Design and Discovery (IBD), and CNAST, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Wei-Che Hsieh
- Department of Chemistry, Institute for Biomolecular Design and Discovery (IBD), and CNAST, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Shivaji A Thadke
- Department of Chemistry, Institute for Biomolecular Design and Discovery (IBD), and CNAST, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Gopalsamy Sureshkumar
- Department of Chemistry, Institute for Biomolecular Design and Discovery (IBD), and CNAST, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Danith H Ly
- Department of Chemistry, Institute for Biomolecular Design and Discovery (IBD), and CNAST, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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26
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Mlýnský V, Bussi G. Exploring RNA structure and dynamics through enhanced sampling simulations. Curr Opin Struct Biol 2018; 49:63-71. [PMID: 29414513 DOI: 10.1016/j.sbi.2018.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 01/23/2023]
Abstract
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided.
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Affiliation(s)
- Vojtěch Mlýnský
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy.
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27
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Chawla M, Autiero I, Oliva R, Cavallo L. Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair. Phys Chem Chem Phys 2018; 20:3699-3709. [DOI: 10.1039/c7cp07400j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quantum mechanics and molecular dynamics methods are used to compare the non-natural 4AP–DAP base pair to natural base pairs.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Ida Autiero
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies
- University Parthenope of Naples
- Centro Direzionale Isola C4
- Naples
- Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
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28
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Elskens J, Manicardi A, Costi V, Madder A, Corradini R. Synthesis and Improved Cross-Linking Properties of C5-Modified Furan Bearing PNAs. Molecules 2017; 22:molecules22112010. [PMID: 29156637 PMCID: PMC6150320 DOI: 10.3390/molecules22112010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 12/21/2022] Open
Abstract
Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the α- or γ-position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, γ-l-lysine and γ-l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis. It was shown that the l-lysine γ-modification had a beneficial effect on crosslink efficiency due to pre-organization of the PNA helix and a favorable electrostatic interaction between the positively-charged lysine and the negatively-charged DNA backbone. Moreover, the crosslink yield could be optimized by carefully choosing the type of furan PNA monomer. This work is the first to describe a selective and biocompatible furan crosslinking strategy for crosslinking of γ-modified PNA sequences towards single-stranded DNA.
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Affiliation(s)
- Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Valentina Costi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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29
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Han S. Evaluation of the Amber Force Fields for Molecular Dynamics Simulation of a PNA-DNA Duplex. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sanghwa Han
- Department of Biochemistry; Kangwon National University; Chuncheon 24341 Korea
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30
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Jana K, Bandyopadhyay T, Ganguly B. Designed inhibitors with hetero linkers for gastric proton pump H +,K +-ATPase: Steered molecular dynamics and metadynamics studies. J Mol Graph Model 2017; 78:129-138. [PMID: 29055186 DOI: 10.1016/j.jmgm.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 02/07/2023]
Abstract
Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H+,K+-ATPase in a K+ competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH2 linker units may not help it to function as a better acid suppressant. We have exploited the role of linker unit to enhance the efficacy of such reversible acid suppressant drug molecules using hetero linker, i.e., disulfide and peroxy linkers. The logarithm of partition coefficient defined for a drug molecule relates to the partition coefficient, which allows the optimum solubility characteristics to reach the active site. The logarithm of partition coefficient calculated for the designed inhibitors suggests that inhibitors would possibly reach the active site in sufficient concentration like in the case of SCH28080. The steered molecular dynamics studies have revealed that the Inhibitor-1 with disulfide linker unit is more stable at the active site due to greater noncovalent interactions compared to the SCH28080. Centre of mass distance analysis suggests that the Cysteine-813 amino acid residue selectively plays an important role in the inhibition of H+,K+-ATPase for Inhibitor-1. Furthermore, the quantum chemical calculations with M11L/6-31+G(d,p) level of theory have been performed to account the noncovalent interactions responsible for the stabilization of inhibitor molecules in the active site gorge of the gastric proton pump at different time scale. The hydrogen bonding and hydrophobic interaction studies corroborate the center of mass distance analysis as well. Well-tempered metadynamics free energy surface and center of mass separation analysis for the Inhibitor-1 is in good agreement with the steered molecular dynamics results. The torsional angle of the linker units seems to be crucial for better efficacy of drug molecules. The torsional angle of linker units of SCH28080 (COCH2C) and of Inhibitor 1 (CSSC) prefers to lie within ∼60°-90° for a longer time during the simulations, whereas, the peroxy linker (COOC) of Inhibitor 2 prefers to adopt ∼120-160°. Therefore, it appears that the smaller torsion angle of linker units can achieve better interactions with the active site residues of H+,K+-ATPase to inhibit the acid secretion activity. The reversible drug molecules with disulfide linker unit would be a promising candidate as proton pump antagonist to H+,K+-ATPase.
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Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research, CSIR, CSMCRI, Bhavnagar 364002, Gujarat, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research, CSIR, CSMCRI, Bhavnagar 364002, Gujarat, India.
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31
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Manicardi A, Rozzi A, Korom S, Corradini R. Building on the peptide nucleic acid (PNA) scaffold: a biomolecular engineering approach. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1371720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alex Manicardi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
- Organic and Biomimetic Chemistry Research Group (OBCR), Department of Organic and Macromolecular Chemistry, Faculty of Sciences – Ghent University Campus Sterre, Belgium
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
| | - Saša Korom
- National Institute for Biostructures and Biosystems (INBB), Roma, Italy
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
- National Institute for Biostructures and Biosystems (INBB), Roma, Italy
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32
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Saarbach J, Masi D, Zambaldo C, Winssinger N. Facile access to modified and functionalized PNAs through Ugi-based solid phase oligomerization. Bioorg Med Chem 2017. [PMID: 28624242 DOI: 10.1016/j.bmc.2017.05.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide nucleic acids (PNAs) derivatized with functional molecules are increasingly used in diverse biosupramolecular applications. PNAs have proven to be highly tolerant to modifications and different applications benefit from the use of modified PNAs, in particular modifications at the γ position. Herein we report simple protocols to access modified PNAs from iterative Ugi couplings which allow modular modifications at the α, β or γ position of the PNA backbone from simple starting materials. We demonstrate the utility of the method with the synthesis of several bioactive small molecules (a peptide ligand, a kinase inhibitor and a glycan)-PNA conjugates.
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Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Daniela Masi
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Claudio Zambaldo
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland.
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