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Abdulrehman T, Qadri S, Haik Y, Sultan A, Skariah S, Kumar S, Mendoza Z, Yadav KK, Titus A, Khader S. Advances in the targeted theragnostics of osteomyelitis caused by Staphylococcus aureus. Arch Microbiol 2024; 206:288. [PMID: 38834761 DOI: 10.1007/s00203-024-04015-2] [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: 03/31/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
Bone infections caused by Staphylococcus aureus may lead to an inflammatory condition called osteomyelitis, which results in progressive bone loss. Biofilm formation, intracellular survival, and the ability of S. aureus to evade the immune response result in recurrent and persistent infections that present significant challenges in treating osteomyelitis. Moreover, people with diabetes are prone to osteomyelitis due to their compromised immune system, and in life-threatening cases, this may lead to amputation of the affected limbs. In most cases, bone infections are localized; thus, early detection and targeted therapy may prove fruitful in treating S. aureus-related bone infections and preventing the spread of the infection. Specific S. aureus components or overexpressed tissue biomarkers in bone infections could be targeted to deliver active therapeutics, thereby reducing drug dosage and systemic toxicity. Compounds like peptides and antibodies can specifically bind to S. aureus or overexpressed disease markers and combining these with therapeutics or imaging agents can facilitate targeted delivery to the site of infection. The effectiveness of photodynamic therapy and hyperthermia therapy can be increased by the addition of targeting molecules to these therapies enabling site-specific therapy delivery. Strategies like host-directed therapy focus on modulating the host immune mechanisms or signaling pathways utilized by S. aureus for therapeutic efficacy. Targeted therapeutic strategies in conjunction with standard surgical care could be potential treatment strategies for S. aureus-associated osteomyelitis to overcome antibiotic resistance and disease recurrence. This review paper presents information about the targeting strategies and agents for the therapy and diagnostic imaging of S. aureus bone infections.
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Affiliation(s)
- Tahir Abdulrehman
- eHealth Program, DeGroote School of Business, McMaster University, Hamilton, ON, Canada
- Health Policy, Management and Informatics, Allied Health, Credit Valley Hospital, Mississauga, ON, Canada
| | - Shahnaz Qadri
- School of Pharmacy, Texas A&M University, Kingsville, USA.
| | - Yousef Haik
- Department of Mechanical & Nuclear Engineering, University of Sharjah, Sharjah, UAE.
| | - Ali Sultan
- Department of Immunology & Microbiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Sini Skariah
- Department of Immunology & Microbiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Shourya Kumar
- School of Engineering Medicine, Texas A&M University, Houston, TX, USA
| | - Zachary Mendoza
- School of Engineering Medicine, Texas A&M University, Houston, TX, USA
| | - Kamlesh K Yadav
- School of Engineering Medicine, Texas A&M University, Houston, TX, USA
| | - Anoop Titus
- Department of Preventive Cardiology, Houston Methodist, Houston, TX, USA
| | - Shameer Khader
- School of Public Health, Faculty of Medicine, Imperial College London, London, UK
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2
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Muslihati A, Septiani NLW, Gumilar G, Nugraha N, Wasisto HS, Yuliarto B. Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods. ACS Biomater Sci Eng 2024; 10:2041-2061. [PMID: 38526408 DOI: 10.1021/acsbiomaterials.3c01965] [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: 03/26/2024]
Abstract
In tropical and developing countries, mosquito-borne diseases by flaviviruses pose a serious threat to public health. Early detection is critical for preventing their spread, but conventional methods are time-consuming and require skilled technicians. Biosensors have been developed to address this issue, but cross-reactivity with other flaviviruses remains a challenge. Peptides are essentially biomaterials used in diagnostics that allow virological and serological techniques to identify flavivirus selectively. This biomaterial originated as a small protein consisting of two to 50 amino acid chains. They offer flexibility in chemical modification and can be easily synthesized and applied to living cells in the engineering process. Peptides could potentially be developed as robust, low-cost, sensitive, and selective receptors for detecting flaviviruses. However, modification and selection of the receptor agents are crucial to determine the effectiveness of binding between the targets and the receptors. This paper addresses two potential peptide nucleic acids (PNAs) and affinity peptides that can detect flavivirus from another target-based biosensor as well as the potential peptide behaviors of flaviviruses. The PNAs detect flaviviruses based on the nucleotide base sequence of the target's virological profile via Watson-Crick base pairing, while the affinity peptides sense the epitope or immunological profile of the targets. Recent developments in the functionalization of peptides for flavivirus biosensors are explored in this Review by division into electrochemical, optical, and other detection methods.
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Affiliation(s)
- Atqiya Muslihati
- Doctoral Program of Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- PT Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Ni Luh Wulan Septiani
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanotechnology Systems, National Research and Innovation Agency (BRIN), Kawasan Puspiptek, South Tangerang 15134, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency (BRIN), Bandung 40135, Indonesia
| | - Nugraha Nugraha
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
| | | | - Brian Yuliarto
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
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Singh G, Monga V. Peptide Nucleic Acids: Recent Developments in the Synthesis and Backbone Modifications. Bioorg Chem 2023; 141:106860. [PMID: 37748328 DOI: 10.1016/j.bioorg.2023.106860] [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: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
Nucleic acid represents the ideal drug candidate for protein targets that are hard to target or against which drug development is not easy. Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. PNAs and their analogues are endowed with exceptionally high affinity and specificity for receptor sites, essentially due to their polyamide backbone's uncharged and flexible nature. The present review compiled various strategies to modify the polypeptide backbone for improving the target selectivity and stability of the PNAs in the body. The investigated biological activities carried out on PNAs have also been summarized in the present review.
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Affiliation(s)
- Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, VPO-Ghudda, Bathinda 151401, Punjab, India.
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Mikame Y, Yamayoshi A. Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids. Pharmaceutics 2023; 15:2515. [PMID: 37896275 PMCID: PMC10609763 DOI: 10.3390/pharmaceutics15102515] [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: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Recent developments in artificial nucleic acid and drug delivery systems present possibilities for the symbiotic engineering of therapeutic oligonucleotides, such as antisense oligonucleotides (ASOs) and small interfering ribonucleic acids (siRNAs). Employing these technologies, triplex-forming oligonucleotides (TFOs) or peptide nucleic acids (PNAs) can be applied to the development of symbiotic genome-targeting tools as well as a new class of oligonucleotide drugs, which offer conceptual advantages over antisense as the antigene target generally comprises two gene copies per cell rather than multiple copies of mRNA that are being continually transcribed. Further, genome editing by TFOs or PNAs induces permanent changes in the pathological genes, thus facilitating the complete cure of diseases. Nuclease-based gene-editing tools, such as zinc fingers, CRISPR-Cas9, and TALENs, are being explored for therapeutic applications, although their potential off-target, cytotoxic, and/or immunogenic effects may hinder their in vivo applications. Therefore, this review is aimed at describing the ongoing progress in TFO and PNA technologies, which can be symbiotic genome-targeting tools that will cause a near-future paradigm shift in drug development.
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Affiliation(s)
- Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
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Jiang W, Aman R, Ali Z, Rao GS, Mahfouz M. PNA-Pdx: Versatile Peptide Nucleic Acid-Based Detection of Nucleic Acids and SNPs. Anal Chem 2023; 95:14209-14218. [PMID: 37696750 PMCID: PMC10535012 DOI: 10.1021/acs.analchem.3c01809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Monitoring diseases caused by pathogens or by mutations in DNA sequences requires accurate, rapid, and sensitive tools to detect specific nucleic acid sequences. Here, we describe a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, termed PNA-powered diagnostics (PNA-Pdx). PNA-Pdx employs PNA probes that bind specifically to a target and are then detected in lateral flow assays. This can precisely detect a specific pathogen or genotype genomic sequence. PNA probes can also be designed to invade double-stranded DNAs (dsDNAs) to produce single-stranded DNAs for precise CRISPR-Cas12b-based detection of genomic SNPs without requiring the protospacer-adjacent motif (PAM), as Cas12b requires PAM sequences only for dsDNA targets. PNA-Pdx identified target nucleic acid sequences at concentrations as low as 2 copies/μL and precisely detected the SARS-CoV-2 genome in clinical samples in 40 min. Furthermore, the specific dsDNA invasion by the PNA coupled with CRISPR-Cas12b precisely detected genomic SNPs without PAM restriction. Overall, PNA-Pdx provides a novel toolkit for nucleic acid and SNP detection as well as highlights the benefits of engineering PNA probes for detecting nucleic acids.
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Affiliation(s)
- Wenjun Jiang
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gundra S. Rao
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Dhuri K, Pradeep SP, Shi J, Anastasiadou E, Slack FJ, Gupta A, Zhong XB, Bahal R. Simultaneous Targeting of Multiple oncomiRs with Phosphorothioate or PNA-Based Anti-miRs in Lymphoma Cell Lines. Pharm Res 2022; 39:2709-2720. [PMID: 36071352 PMCID: PMC9879158 DOI: 10.1007/s11095-022-03383-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/27/2022] [Indexed: 01/29/2023]
Abstract
PURPOSE MicroRNAs (miRNAs) are short (~ 22 nts) RNAs that regulate gene expression via binding to mRNA. MiRNAs promoting cancer are known as oncomiRs. Targeting oncomiRs is an emerging area of cancer therapy. OncomiR-21 and oncomiR-155 are highly upregulated in lymphoma cells, which are dependent on these oncomiRs for survival. Targeting specific miRNAs and determining their effect on cancer cell progression and metastasis have been the focus of various studies. Inhibiting a single miRNA can have a limited effect, as there may be other overexpressed miRNAs present that may promote tumor proliferation. Herein, we target miR-21 and miR-155 simultaneously using nanoparticles delivered two different classes of antimiRs: phosphorothioates (PS) and peptide nucleic acids (PNAs) and compared their efficacy in lymphoma cell lines. METHODS Poly-Lactic-co-Glycolic acid (PLGA) nanoparticles (NPs) containing PS and PNA-based antimiR-21 and -155 were formulated, and comprehensive NP characterizations: morphology (scanning electron microscopy), size (differential light scattering), and surface charge (zeta potential) were performed. Cellular uptake analysis was performed using a confocal microscope and flow cytometry analysis. The oncomiR knockdown and the effect on downstream targets were confirmed by gene expression (real time-polymerase chain reaction) assay. RESULTS We demonstrated that simultaneous targeting with NP delivered PS and PNA-based antimiRs resulted in significant knockdown of miR-21 and miR-155, as well as their downstream target genes followed by reduced cell viability ex vivo. CONCLUSIONS This project demonstrated that targeting miRNA-155 and miR-21 simultaneously using nanotechnology and a diverse class of antisense oligomers can be used as an effective approach for lymphoma therapy.
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Affiliation(s)
- Karishma Dhuri
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Jason Shi
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Eleni Anastasiadou
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Anisha Gupta
- School of Pharmacy, University of Saint Joseph, West Hartford, CT, 06117, USA
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT, 06269, USA.
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7
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Panda M, Kalita E, Singh S, Kumar K, Rao A, Prajapati VK. MiRNA-SARS-CoV-2 dialogue and prospective anti-COVID-19 therapies. Life Sci 2022; 305:120761. [PMID: 35787998 PMCID: PMC9249409 DOI: 10.1016/j.lfs.2022.120761] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
Abstract
COVID-19 is a highly transmissible disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), affects 226 countries and continents, and has resulted in >6.2 million deaths worldwide. Despite the efforts of all scientific institutions worldwide to identify potential therapeutics, no specific drug has been approved by the FDA to treat the COVID-19 patient. SARS-CoV-2 variants of concerns make the potential of publicly known therapeutics to respond to and detect disease onset highly improbable. The quest for universal therapeutics pointed to the ability of RNA-based molecules to shield and detect the adverse effects of the COVID-19 illness. One such candidate, miRNA (microRNA), works on regulating the differential expression of the target gene post-transcriptionally. The prime focus of this review is to report the critical miRNA molecule and their regular expression in patients with COVID-19 infection and associated comorbidities. Viral and host miRNAs control the etiology of COVID-19 infection throughout the life cycle and host inflammatory response, where host miRNAs are identified as a double-edged showing as a proviral and antiviral response. The review also covered the role of viral miRNAs in mediating host cell signaling expression during disease pathology. Studying molecular interactions between the host and the SARS-CoV-2 virus during COVID-19 pathogenesis offers the chance to use miRNA-based therapeutics to reduce the severity of the illness. By utilizing an appropriate delivery vehicle, these small non-coding RNA could be envisioned as a promising biomarker in designing a practical RNAi-based treatment approach of clinical significance.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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8
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Apostolopoulos V, Bojarska J, Feehan J, Matsoukas J, Wolf W. Smart therapies against global pandemics: A potential of short peptides. Front Pharmacol 2022; 13:914467. [PMID: 36046832 PMCID: PMC9420997 DOI: 10.3389/fphar.2022.914467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/01/2022] [Indexed: 12/20/2022] Open
Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC, Australia
| | - Joanna Bojarska
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - John Matsoukas
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- NewDrug, Patras Science Park, Patras, Greece
| | - Wojciech Wolf
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
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9
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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10
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Todkari I, Gupta MK, Ganesh KN. Silver soldering of PNA:DNA duplexes: assembly of a triple duplex from bimodal PNAs with all-C on one face. Chem Commun (Camb) 2022; 58:4083-4086. [PMID: 35266467 DOI: 10.1039/d1cc07297h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA:bm-PNA duplexes endowed with all-C on either the t-amide or triazole face and mixed base sequence on the other face can be welded with silver ions through C:Ag+:C connects to give triple duplexes in one complex. The interplay of WC and Ag+-mediated duplexes leads to synergistic stability effects on both duplexes and the complex.
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Affiliation(s)
- Iranna Todkari
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India.
| | - Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
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11
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Delivering more for less: nanosized, minimal-carrier and pharmacoactive drug delivery systems. Adv Drug Deliv Rev 2021; 179:113994. [PMID: 34619287 DOI: 10.1016/j.addr.2021.113994] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022]
Abstract
Traditional nanoparticle carriers such as liposomes, micelles, and polymeric vehicles improve drug delivery by protecting, stabilizing, and increasing the circulatory half-life of the encapsulated drugs. However, traditional drug delivery systems frequently suffer from poor drug loading and require an excess of carrier materials. This carrier material excess poses an additional systemic burden through accumulation, if not degradable the need for metabolism, and potential toxicity. To address these shortcomings, minimal-carrier nanoparticle systems and pharmacoactive carrier materials have been developed. Both solutions provide drug delivery systems in which the majority of the nanoparticle is pharmacologically active. While minimal-carrier and pharmacoactive drug delivery systems can improve drug loading, they can also suffer from poor stability. Here, we review minimal-carrier and pharmacoactive delivery systems, discuss ongoing challenges and outline opportunities to translate minimal-carrier and pharmacoactive drug delivery systems into the clinic.
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12
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The Challenges and Opportunities in the Development of MicroRNA Therapeutics: A Multidisciplinary Viewpoint. Cells 2021; 10:cells10113097. [PMID: 34831320 PMCID: PMC8619171 DOI: 10.3390/cells10113097] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/22/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
microRNAs (miRs) are emerging as attractive therapeutic targets because of their small size, specific targetability, and critical role in disease pathogenesis. However, <20 miR targeting molecules have entered clinical trials, and none progressed to phase III. The difficulties in miR target identification, the moderate efficacy of miR inhibitors, cell type-specific delivery, and adverse outcomes have impeded the development of miR therapeutics. These hurdles are rooted in the functional complexity of miR's role in disease and sequence complementarity-dependent/-independent effects in nontarget tissues. The advances in understanding miR's role in disease, the development of efficient miR inhibitors, and innovative delivery approaches have helped resolve some of these hurdles. In this review, we provide a multidisciplinary viewpoint on the challenges and opportunities in the development of miR therapeutics.
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13
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Swenson CS, Lackey HH, Reece EJ, Harris JM, Heemstra JM, Peterson EM. Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics. RSC Chem Biol 2021; 2:1249-1256. [PMID: 34458838 PMCID: PMC8341200 DOI: 10.1039/d1cb00025j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Hershel H Lackey
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Eric J Reece
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Joel M Harris
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | | | - Eric M Peterson
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
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14
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Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers 2021; 112:e23460. [PMID: 34129732 DOI: 10.1002/bip.23460] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.
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Affiliation(s)
- J Dinithi R Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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15
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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16
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Dhuri K, Vyas RN, Blumenfeld L, Verma R, Bahal R. Nanoparticle Delivered Anti-miR-141-3p for Stroke Therapy. Cells 2021; 10:cells10051011. [PMID: 33922958 PMCID: PMC8145654 DOI: 10.3390/cells10051011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 01/14/2023] Open
Abstract
Ischemic stroke and factors modifying ischemic stroke responses, such as social isolation, contribute to long-term disability worldwide. Several studies demonstrated that the aberrant levels of microRNAs contribute to ischemic stroke injury. In prior studies, we established that miR-141-3p increases after ischemic stroke and post-stroke isolation. Herein, we explored two different anti-miR oligonucleotides; peptide nucleic acid (PNAs) and phosphorothioates (PS) for ischemic stroke therapy. We used US FDA approved biocompatible poly (lactic-co-glycolic acid) (PLGA)-based nanoparticle formulations for delivery. The PNA and PS anti-miRs were encapsulated in PLGA nanoparticles by double emulsion solvent evaporation technique. All the formulated nanoparticles showed uniform morphology, size, distribution, and surface charge density. Nanoparticles also exhibited a controlled nucleic acid release profile for 48 h. Further, we performed in vivo studies in the mouse model of ischemic stroke. Ischemic stroke was induced by transient (60 min) occlusion of middle cerebral artery occlusion followed by a reperfusion for 48 or 72 h. We assessed the blood-brain barrier permeability of PLGA NPs containing fluorophore (TAMRA) anti-miR probe after systemic delivery. Confocal imaging shows uptake of fluorophore tagged anti-miR in the brain parenchyma. Next, we evaluated the therapeutic efficacy after systemic delivery of nanoparticles containing PNA and PS anti-miR-141-3p in mice after stroke. Post-treatment differentially reduced both miR-141-3p levels in brain tissue and infarct injury. We noted PNA-based anti-miR showed superior efficacy compared to PS-based anti-miR. Herein, we successfully established that nanoparticles encapsulating PNA or PS-based anti-miRs-141-3p probes could be used as a potential treatment for ischemic stroke.
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Affiliation(s)
- Karishma Dhuri
- School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA;
| | - Rutesh N. Vyas
- Department of Neurosciences, UConn Health, Farmington, CT 06032, USA; (R.N.V.); (L.B.)
| | - Leslie Blumenfeld
- Department of Neurosciences, UConn Health, Farmington, CT 06032, USA; (R.N.V.); (L.B.)
| | - Rajkumar Verma
- Department of Neurosciences, UConn Health, Farmington, CT 06032, USA; (R.N.V.); (L.B.)
- Correspondence: (R.V.); (R.B.)
| | - Raman Bahal
- School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA;
- Correspondence: (R.V.); (R.B.)
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17
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Volpi S, Cancelli U, Neri M, Corradini R. Multifunctional Delivery Systems for Peptide Nucleic Acids. Pharmaceuticals (Basel) 2020; 14:14. [PMID: 33375595 PMCID: PMC7823687 DOI: 10.3390/ph14010014] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The number of applications of peptide nucleic acids (PNAs)-oligonucleotide analogs with a polyamide backbone-is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.
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Affiliation(s)
| | | | | | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (U.C.); (M.N.)
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18
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Dhuri K, Bechtold C, Quijano E, Pham H, Gupta A, Vikram A, Bahal R. Antisense Oligonucleotides: An Emerging Area in Drug Discovery and Development. J Clin Med 2020; 9:jcm9062004. [PMID: 32604776 PMCID: PMC7355792 DOI: 10.3390/jcm9062004] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/11/2022] Open
Abstract
Antisense oligonucleotides (ASOs) bind sequence specifically to the target RNA and modulate protein expression through several different mechanisms. The ASO field is an emerging area of drug development that targets the disease source at the RNA level and offers a promising alternative to therapies targeting downstream processes. To translate ASO-based therapies into a clinical success, it is crucial to overcome the challenges associated with off-target side effects and insufficient biological activity. In this regard, several chemical modifications and diverse delivery strategies have been explored. In this review, we systematically discuss the chemical modifications, mechanism of action, and optimized delivery strategies of several different classes of ASOs. Further, we highlight the recent advances made in development of ASO-based drugs with a focus on drugs that are approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) for clinical applications. We also discuss various promising ASO-based drug candidates in the clinical trials, and the outstanding opportunity of emerging microRNA as a viable therapeutic target for future ASO-based therapies.
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Affiliation(s)
- Karishma Dhuri
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT 06269, USA; (K.D.); (C.B.)
| | - Clara Bechtold
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT 06269, USA; (K.D.); (C.B.)
| | - Elias Quijano
- Department of Genetics, Yale University, New Haven, CT 06520, USA;
| | - Ha Pham
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232-5671, USA;
| | - Anisha Gupta
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA;
| | - Ajit Vikram
- Division of Cardiovascular Medicine, Department of Internal Medicine, The University of Iowa, Iowa City, IA 52242, USA;
| | - Raman Bahal
- Department of Pharmaceutical Science, University of Connecticut, Storrs, CT 06269, USA; (K.D.); (C.B.)
- Correspondence:
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