1
|
Upton C, Healey J, Rothnie AJ, Goddard AD. Insights into membrane interactions and their therapeutic potential. Arch Biochem Biophys 2024; 755:109939. [PMID: 38387829 DOI: 10.1016/j.abb.2024.109939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Recent research into membrane interactions has uncovered a diverse range of therapeutic opportunities through the bioengineering of human and non-human macromolecules. Although the majority of this research is focussed on fundamental developments, emerging studies are showcasing promising new technologies to combat conditions such as cancer, Alzheimer's and inflammatory and immune-based disease, utilising the alteration of bacteriophage, adenovirus, bacterial toxins, type 6 secretion systems, annexins, mitochondrial antiviral signalling proteins and bacterial nano-syringes. To advance the field further, each of these opportunities need to be better understood, and the therapeutic models need to be further optimised. Here, we summarise the knowledge and insights into several membrane interactions and detail their current and potential uses therapeutically.
Collapse
Affiliation(s)
- Calum Upton
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Joseph Healey
- Nanosyrinx, The Venture Centre, University of Warwick Science Park, Coventry, CV4 7EZ, UK
| | - Alice J Rothnie
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Alan D Goddard
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK.
| |
Collapse
|
2
|
Yang HW, Ju SP, Hsieh YT, Yang YC. Design single-stranded DNA aptamer of cluster of differentiation 47 protein by stochastic tunnelling-basin hopping-discrete molecular dynamics method. J Biomol Struct Dyn 2024; 42:3969-3982. [PMID: 37261868 DOI: 10.1080/07391102.2023.2217511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
The formation of the Cluster of Differentiation 47 (CD47, PDB code: 2JJT)/signal regulatory protein α (SIRPα) complex is very important as it protects healthy cells from immune clearance while promoting macrophage phagocytosis for tumour elimination. Although several antibodies have been developed for cancer therapy, new function-blocking aptamers are still under development. This study aims to design the aptamer AptCD47, which can block the formation of the CD47/SIRPα complex. This study employs the MARTINI coarse-grained (CG) force field and the stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method to identify the most stable AptCD47/CD47 complexes. Coarse-grained molecular dynamics (CGMD) simulations were used to obtain root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses. The results demonstrate that the formation of AptCD47/CD47 complexes renders the CD47 structure more stable than the single CD47 molecule in a water environment. The minimum energy pathway (MEP) obtained by the nudged elastic band (NEB) method indicates that the binding processes of 5'-ATTCAATTCC-3' and 5'-AGTGCAATCT-3' to CD47 are barrierless, which is much lower than the binding barrier of SIRPα to CD47 of about 14.23 kcal/mol. Therefore, these two AptCD47/CD47 complexes can create a high spatial binding barrier for SIRPα, preventing the formation of a stable CD47/SIRPα complex. The proposed numerical process with the MARTINI CG force field can be used to design CD47 aptamers that efficiently block SIRPα from binding to CD47.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hung-Wei Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan City, Taiwan
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yun-Te Hsieh
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yung-Cheng Yang
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| |
Collapse
|
3
|
Zahiri M, Kamali H, Abnous K, Mohammad Taghdisi S, Nekooei S, Nekooei N, Ramezani M, Alibolandi M. Synthesis of folate targeted theranostic cubosomal platform for co-delivery of bismuth oxide and doxorubicin to melanoma in vitro and in vivo. Eur J Pharm Biopharm 2024; 198:114259. [PMID: 38479563 DOI: 10.1016/j.ejpb.2024.114259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Liquid crystalline nanoparticles (LCNPs) have gained much attention in cancer nanomedicines due to their unique features such as high surface area, storage stability, and sustained-release profile. In the current study, a novel LCNP for co-encapsulation of Bi2O3 and hydrophilic doxorubicin (DOX) was fabricated and functionalized with folic acid (FA) to achieve efficient tumor targeting toward CT-scan imaging and chemotherapy of melanoma in vitro and in vivo. LCNPs Bi2O3 NPs were prepared using glycerol monooleate-pluronic F-127 (GMO/PF127/water). Firstly, GMO/water were homogenized to prepare LC gel. Then, the stabilizer aqueous solution (PF127/Bi2O3/DOX) was added to the prepared LC gel and homogenized using homogenization and ultrasonication. The formulated NPs exhibited superior stability with encapsulation efficiency. High cytotoxicity and cellular internalization of the FA-Bi2O3-DOX-NPs were observed in comparison with Bi2O3-DOX-NPs and the free DOX in folate-receptor (FR) overexpressing cells (B16F10) in vitro. Moreover, ideal tumor suppression with increased survival rate were observed in tumorized mice treated with FA-Bi2O3-DOX-NPs compared to those treated with non-targeted one. On the other hand, the CT-imaging ability of the Bi2O3-DOX-NPs was tested inB16F10 tumor-bearing mice. The obtained data indicated a high potential of the developed targeted theranostic FA-Bi2O3-DOX-NPs for diagnostics and treatment of melanoma.
Collapse
Affiliation(s)
- Mahsa Zahiri
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosein Kamali
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sirous Nekooei
- Department of Radiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negar Nekooei
- Department of Radiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
4
|
Bisht A, Bhowmik S, Patel P, Gupta GD, Kurmi BD. Aptamer as a targeted approach towards treatment of breast cancer. J Drug Target 2024:1-19. [PMID: 38512151 DOI: 10.1080/1061186x.2024.2333866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Aptamers, a novel type of targeted ligand used in drug delivery, have quickly gained popularity due to their high target specificity and affinity. Different aptamer-mediated drug delivery systems, such as aptamer-drug conjugate (ApDC), aptamer-siRNA, and aptamer-functionalised nanoparticle systems, are currently being developed for the successful treatment of cancer based on the excellent properties of aptamers. These systems can decrease potential toxicity and enhance therapeutic efficacy by targeting the drug moiety. In this review, we provide an overview of recent developments in aptamer-mediated delivery systems for cancer therapy, specifically for breast cancer, and talk about the potential applications and current issues of novel aptamer-based techniques. This study in aptamer technology for breast cancer therapy highlights key aptamers targeting well-established biomarkers such as HER2, oestrogen receptor, and progesterone receptor. Additionally, we explore the potential of aptamers in overcoming various challenges such as drug resistance and improving the delivery of therapeutic agents. This review aims to provide a deeper understanding of the present aptamer-based targeted delivery applications through in-depth analysis to increase efficacy and create new therapeutic approaches that may ultimately lead to better treatment outcomes for cancer patients.
Collapse
Affiliation(s)
- Anjali Bisht
- Department of Pharmaceutical Quality Assurance, ISF College Pharmacy, Moga, India
| | | | - Preeti Patel
- Department of Pharmaceutical Chemistry, ISF College Pharmacy, Moga, India
| | | | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College Pharmacy, Moga, India
| |
Collapse
|
5
|
Seo HS, Han JH, Lim J, Bae GH, Byun MJ, Wang CPJ, Han J, Park J, Park HH, Shin M, Park TE, Kim TH, Kim SN, Park W, Park CG. Enhanced Postsurgical Cancer Treatment Using Methacrylated Glycol Chitosan Hydrogel for Sustained DNA/Doxorubicin Delivery and Immunotherapy. Biomater Res 2024; 28:0008. [PMID: 38532906 PMCID: PMC10964224 DOI: 10.34133/bmr.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 03/28/2024] Open
Abstract
Background: Cancer recurrence and metastasis are major contributors to treatment failure following tumor resection surgery. We developed a novel implantable drug delivery system utilizing glycol chitosan to address these issues. Glycol chitosan is a natural adjuvant, inducing dendritic cell activation to promote T helper 1 cell immune responses, macrophage activation, and cytokine production. Effective antigen production by dendritic cells initiates T-cell-mediated immune responses, aiding tumor growth control. Methods: In this study, we fabricated multifunctional methacrylated glycol chitosan (MGC) hydrogels with extended release of DNA/doxorubicin (DOX) complex for cancer immunotherapy. We constructed the resection model of breast cancer to verify the anticancer effects of MGC hydrogel with DNA/DOX complex. Results: This study demonstrated the potential of MGC hydrogel with extended release of DNA/DOX complex for local and efficient cancer therapy. The MGC hydrogel was implanted directly into the surgical site after tumor resection, activating tumor-related immune cells both locally and over a prolonged period of time through immune-reactive molecules. Conclusions: The MGC hydrogel effectively suppressed tumor recurrence and metastasis while enhancing immunotherapeutic efficacy and minimizing side effects. This biomaterial-based drug delivery system, combined with cancer immunotherapy, can substantial improve treatment outcomes and patient prognosis.
Collapse
Affiliation(s)
- Hee Seung Seo
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jun-Hyeok Han
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jaesung Lim
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Ga-Hyun Bae
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of MetaBioHealth,
SKKU Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Min Ji Byun
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Chi-Pin James Wang
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jieun Han
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Institute of Biotechnology and Bioengineering, College of Biotechnology and Bioengineering, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Juwon Park
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School Medicine,
University of Hawai'i at Manoa, Honolulu, HI 96813, USA
| | - Hee Ho Park
- Department of Bioengineering,
Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Mikyung Shin
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Tae-Eun Park
- Department of Biomedical Engineering,
Ulsan National Institute of Science and Technology, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Tae-Hyung Kim
- School of Integrative Engineering,
Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Se-Na Kim
- Research and Development Center,
MediArk Inc., 1, Chungdae-ro, Seowon-gu, Cheongju, Chungcheongbuk 28644, Republic of Korea
| | - Wooram Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of MetaBioHealth,
SKKU Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Institute of Biotechnology and Bioengineering, College of Biotechnology and Bioengineering, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Biomaterials Research Center,
Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Chun Gwon Park
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Biomedical Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| |
Collapse
|
6
|
Mohammadinejad A, Gaman LE, Aleyaghoob G, Gaceu L, Mohajeri SA, Moga MA, Badea M. Aptamer-Based Targeting of Cancer: A Powerful Tool for Diagnostic and Therapeutic Aims. Biosensors (Basel) 2024; 14:78. [PMID: 38391997 PMCID: PMC10887380 DOI: 10.3390/bios14020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Cancer is known as one of the most significant causes of death worldwide, and, in spite of novel therapeutic methods, continues to cause a considerable number of deaths. Targeted molecular diagnosis and therapy using aptamers with high affinity have become popular techniques for pathological angiogenesis and cancer therapy scientists. In this paper, several aptamer-based diagnostic and therapeutic techniques such as aptamer-nanomaterial conjugation, aptamer-drug conjugation (physically or covalently), and biosensors, which have been successfully designed for biomarkers, were critically reviewed. The results demonstrated that aptamers can potentially be incorporated with targeted delivery systems and biosensors for the detection of biomarkers expressed by cancer cells. Aptamer-based therapeutic and diagnostic methods, representing the main field of medical sciences, possess high potential for use in cancer therapy, pathological angiogenesis, and improvement of community health. The clinical use of aptamers is limited due to target impurities, inaccuracy in the systematic evolution of ligands via exponential enrichment (SELEX)stage process, and in vitro synthesis, making them unreliable and leading to lower selectivity for in vivo targets. Moreover, size, behavior, probable toxicity, low distribution, and the unpredictable behavior of nanomaterials in in vivo media make their usage in clinical assays critical. This review is helpful for the implementation of aptamer-based therapies which are effective and applicable for clinical use and the design of future studies.
Collapse
Affiliation(s)
- Arash Mohammadinejad
- Department of Fundamental, Prophylactic and Clinical Disciplines, Faculty of Medicine, Transilvania University of Brasov, 500019 Brașov, Romania;
- Research Center for Fundamental Research and Prevention Strategies in Medicine, Research and Development Institute of Transilvania University of Brasov, 500484 Brașov, Romania
| | - Laura Elena Gaman
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 020021 Bucharest, Romania;
| | - Ghazaleh Aleyaghoob
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran;
- Department of Chemistry, Payame Noor University, Tehran 19395-4697, Iran
| | - Liviu Gaceu
- Faculty of Food and Tourism, Transilvania University of Brasov, 500014 Brașov, Romania;
| | - Seyed Ahmad Mohajeri
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad 9177948954, Iran;
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 9177948954, Iran
| | - Marius Alexandru Moga
- Department of Medical and Surgical Specialties, Faculty of Medicine, Transilvania University of Brasov, 500019 Brașov, Romania;
- Centre for Applied Medicine and Intervention Strategies in Medical Practice, Research and Development Institute of Transilvania University of Brasov, 500484 Brașov, Romania
| | - Mihaela Badea
- Department of Fundamental, Prophylactic and Clinical Disciplines, Faculty of Medicine, Transilvania University of Brasov, 500019 Brașov, Romania;
- Research Center for Fundamental Research and Prevention Strategies in Medicine, Research and Development Institute of Transilvania University of Brasov, 500484 Brașov, Romania
| |
Collapse
|
7
|
Gajbhiye KR, Salve R, Narwade M, Sheikh A, Kesharwani P, Gajbhiye V. Lipid polymer hybrid nanoparticles: a custom-tailored next-generation approach for cancer therapeutics. Mol Cancer 2023; 22:160. [PMID: 37784179 PMCID: PMC10546754 DOI: 10.1186/s12943-023-01849-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/23/2023] [Indexed: 10/04/2023] Open
Abstract
Lipid-based polymeric nanoparticles are the highly popular carrier systems for cancer drug therapy. But presently, detailed investigations have revealed their flaws as drug delivery carriers. Lipid polymer hybrid nanoparticles (LPHNPs) are advanced core-shell nanoconstructs with a polymeric core region enclosed by a lipidic layer, presumed to be derived from both liposomes and polymeric nanounits. This unique concept is of utmost importance as a combinable drug delivery platform in oncology due to its dual structured character. To add advantage and restrict one's limitation by other, LPHNPs have been designed so to gain number of advantages such as stability, high loading of cargo, increased biocompatibility, rate-limiting controlled release, and elevated drug half-lives as well as therapeutic effectiveness while minimizing their drawbacks. The outer shell, in particular, can be functionalized in a variety of ways with stimuli-responsive moieties and ligands to provide intelligent holding and for active targeting of antineoplastic medicines, transport of genes, and theragnostic. This review comprehensively provides insight into recent substantial advancements in developing strategies for treating various cancer using LPHNPs. The bioactivity assessment factors have also been highlighted with a discussion of LPHNPs future clinical prospects.
Collapse
Affiliation(s)
- Kavita R Gajbhiye
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Erandwane, Pune, 411038, India
| | - Rajesh Salve
- Nanobioscience, Agharkar Research Institute, Pune, 411038, India
- Savitribai Phule Pune University, Pune, 411007, India
| | - Mahavir Narwade
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Erandwane, Pune, 411038, India
| | - Afsana Sheikh
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
- Center for Global health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
| | - Virendra Gajbhiye
- Nanobioscience, Agharkar Research Institute, Pune, 411038, India.
- Savitribai Phule Pune University, Pune, 411007, India.
| |
Collapse
|
8
|
He S, Du Y, Tao H, Duan H. Advances in aptamer-mediated targeted delivery system for cancer treatment. Int J Biol Macromol 2023; 238:124173. [PMID: 36965552 DOI: 10.1016/j.ijbiomac.2023.124173] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/27/2023]
Abstract
Aptamers with high affinity and specificity for certain targets have rapidly become a novel class of targeted ligands applicated in drug delivery. Based on the excellent characteristics of aptamers, different aptamer-mediated drug delivery systems have been developed, including aptamer-drug conjugate (ApDC), aptamer-siRNA, and aptamer-functionalized nanoparticle systems for the effective treatment of cancer, which can reduce potential toxicity and improve therapeutic efficacy. In this review, we summarize the recent progress of aptamer-mediated delivery systems in cancer therapy, and discuss the application prospects and existing problems of innovative approaches based on aptamer therapy. Overall, this review aims to better understand the current aptamer-based targeted delivery applications through in-depth analysis to improve efficacy and develop new therapeutic methods which can ultimately improve treatment outcomes for cancer patients.
Collapse
Affiliation(s)
- Shiming He
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China.
| | - Yue Du
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongyu Tao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Huaiyu Duan
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| |
Collapse
|
9
|
Song M, Li Y, Gao R, Liu J, Huang Q. De novo design of DNA aptamers that target okadaic acid (OA) by docking-then-assembling of single nucleotides. Biosens Bioelectron 2022; 215:114562. [PMID: 35870338 DOI: 10.1016/j.bios.2022.114562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022]
Abstract
Okadaic acid (OA) is a diarrhetic shellfish poison widespread in ocean, so its detection is of great significance to seafood safety. Because of good sensitivity and low cost, biosensors using nucleic-acid aptamers as the recognition molecules are emerging as an important detection tool. However, the traditional SELEX screening method for acquiring OA high-affinity aptamers is time- and resource-intensive. Alternatively, here we developed a de novo design method based on the 3D structure of a target molecule, such as OA. Without experimental screening, this method designs OA aptamers by a computational approach of docking-then-assembling (DTA) of single nucleotides (A, C, G and T) as: (1) determining the high-affinity nucleotide binding sites of the target molecule via saturated molecular docking; (2) assembling the bound nucleotides into binding units to the target molecule; (3) constructing full-length aptamers by introducing stabilizing units to connect these binding units. In this way, five OA aptamers were designed, and microscale thermophoresis (MST) experiments verified that their Kd values are in the range of 100-600 nM; and one of them (named 9CGAT_4_a) could specifically bind to OA with low affinities for the other three marine biotoxins. Therefore, this study provides high-affinity and specific aptamers for the development of OA biosensors, and presents a promising de novo design method applicable to other target molecules.
Collapse
Affiliation(s)
- Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuanyuan Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Jianping Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China; Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
| |
Collapse
|
10
|
Dong H, You J, Zhao Y, Zheng D, Zhong Y, Li G, Weng Z, Luo H, Jiang S. Study on the Characteristics of Small-Molecule Kinase Inhibitors-Related Drug-Induced Liver Injury. Front Pharmacol 2022; 13:838397. [PMID: 35529445 PMCID: PMC9068902 DOI: 10.3389/fphar.2022.838397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/11/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: More than half of the small-molecule kinase inhibitors (KIs) induced liver injury clinically. Meanwhile, studies have shown a close relationship between mitochondrial damage and drug-induced liver injury (DILI). We aimed to study KIs and the binding between drugs and mitochondrial proteins to find factors related to DILI occurrence. Methods: A total of 1,223 oral FDA-approved drugs were collected and analyzed, including 44 KIs. Fisher’s exact test was used to analyze DILI potential and risk of different factors. A total of 187 human mitochondrial proteins were further collected, and high-throughput molecular docking was performed between human mitochondrial proteins and drugs in the data set. The molecular dynamics simulation was used to optimize and evaluate the dynamic binding behavior of the selected mitochondrial protein/KI complexes. Results: The possibility of KIs to produce DILI is much higher than that of other types (OR = 46.89, p = 9.28E-13). A few DILI risk factors were identified, including molecular weight (MW) between 400 and 600, the defined daily dose (DDD) ≥ 100 mg/day, the octanol–water partition coefficient (LogP) ≥ 3, and the degree of liver metabolism (LM) more than 50%. Drugs that met this combination of rules were found to have a higher DILI risk than controls (OR = 8.28, p = 4.82E-05) and were more likely to cause severe DILI (OR = 8.26, p = 5.06E-04). The docking results showed that KIs had a significant higher affinity with human mitochondrial proteins (p = 4.19E-11) than other drug types. Furthermore, the five proteins with the lowest docking score were selected for molecular dynamics simulation, and the smallest fluctuation of the backbone RMSD curve was found in the protein 5FS8/KI complexes, which indicated the best stability of the protein 5FS8 bound to KIs. Conclusions: KIs were found to have the highest odds ratio of causing DILI. MW was significantly related to the production of DILI, and the average docking scores of KI drugs were found to be significantly different from other classes. Further analysis identified the top binding mitochondrial proteins for KIs, and specific binding sites were analyzed. The optimization of molecular docking results by molecular dynamics simulation may contribute to further studying the mechanism of DILI.
Collapse
Affiliation(s)
- Huiqun Dong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Jia You
- Department of Hepatology, Hepatology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yu Zhao
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Danhua Zheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Yi Zhong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Gaozheng Li
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
| | - Heng Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
- MetaNovas Biotech Inc., Foster City, CA, United States
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
| | - Shan Jiang
- Department of Vascular Thyroid Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, China
- *Correspondence: Zuquan Weng, ; Heng Luo, ; Shan Jiang,
| |
Collapse
|
11
|
Wu C, Wu X, Hou F, Wu L, Liu G. An ultrasensitive electrochemical aptasensor based on Pd@PCN-222 as a signal probe coupled with exonuclease III-assisted cycling amplification for the detection of ochratoxin A. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
12
|
Paskeh MDA, Saebfar H, Mahabady MK, Orouei S, Hushmandi K, Entezari M, Hashemi M, Aref AR, Hamblin MR, Ang HL, Kumar AP, Zarrabi A, Samarghandian S. Overcoming doxorubicin resistance in cancer: siRNA-loaded nanoarchitectures for cancer gene therapy. Life Sci 2022; 298:120463. [DOI: 10.1016/j.lfs.2022.120463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/08/2023]
|
13
|
Zeng Z, Qi J, Wan Q, Zu Y. Aptamers with Self-Loading Drug Payload and pH-Controlled Drug Release for Targeted Chemotherapy. Pharmaceutics 2021; 13:1221. [PMID: 34452182 DOI: 10.3390/pharmaceutics13081221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/23/2022] Open
Abstract
Doxorubicin (DOX) is a common anti-tumor drug that binds to DNA or RNA via non-covalent intercalation between G-C sequences. As a therapeutic agent, DOX has been used to form aptamer–drug conjugates for targeted cancer therapy in vitro and in vivo. To improve the therapeutic potential of aptamer–DOX conjugates, we synthesized trifurcated Newkome-type monomer (TNM) structures with three DOX molecules bound through pH-sensitive hydrazone bonds to formulate TNM-DOX. The aptamer–TNM–DOX conjugate (Apt–TNM-DOX) was produced through a simple self-loading process. Chemical validation revealed that Apt–TNM-DOX stably carried high drug payloads of 15 DOX molecules per aptamer sequence. Functional characterization showed that DOX payload release from Apt–TNM-DOX was pH-dependent and occurred at pH 5.0, which reflects the microenvironment of tumor cell lysosomes. Further, Apt–TNM-DOX specifically targeted lymphoma cells without affecting off-target control cells. Aptamer-mediated cell binding resulted in the uptake of Apt–TNM-DOX into targeted cells and the release of DOX payload within cell lysosomes to inhibit growth of targeted lymphoma cells. The Apt–TNM-DOX provides a simple, non-toxic approach to develop aptamer-based targeted therapeutics and may reduce the non-specific side effects associated with traditional chemotherapy.
Collapse
|
14
|
Rotkrua P, Lohlamoh W, Watcharapo P, Soontornworajit B. A molecular hybrid comprising AS1411 and PDGF-BB aptamer, cholesterol, and doxorubicin for inhibiting proliferation of SW480 cells. J Mol Recognit 2021; 34:e2926. [PMID: 34258818 DOI: 10.1002/jmr.2926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
Cancer treatment commonly relies on chemotherapy. This treatment faces many challenges, including treatment specificity and undesired side effects. To address these, a Dox-loaded Chol-aptamer molecular hybrid (Dox-CAH) was developed. This multivalent interaction system combines the key function of each integrated species: doxorubicin, cholesterol, and two aptamers binding to nucleolin and platelet-derived growth factor BB (PDGF-BB). The study has four stages: preparation of CAH via oligonucleotide hybridization, intercalation of doxorubicin into CAH, verification of CAH binding on SW480 by fluorescence microscopy and flow cytometry, and investigation of effect of Dox-CAH on SW480 proliferation. CAH was successfully prepared, as confirmed by electrophoresis. Flow cytometry and fluorescence microscopy demonstrated CAH binding to SW480, due to the presence of the AS1411 aptamer. This molecular hybrid exhibited specific binding because it did not bind to CCD 841 CoN. CAH binding to PDGF-BB compromises its function, as shown by enzyme-linked immunosorbent assay (ELISA) and cell assay. The DNA duplex in this molecular hybrid reduces the cytotoxicity of the Dox-CAH. Binding and the reduction of Dox-CAH toxicity may improve treatment specificity and minimize side effects. Dox-CAH is a model for more effective anticancer therapy, allowing incorporation of chemotherapeutic drugs and recognition elements.
Collapse
Affiliation(s)
- Pichayanoot Rotkrua
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Walaiporn Lohlamoh
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Paphada Watcharapo
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
| | - Boonchoy Soontornworajit
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
| |
Collapse
|
15
|
Zahiri M, Taghdisi SM, Abnous K, Ramezani M, Alibolandi M. Fabrication of versatile targeted lipopolymersomes for improved camptothecin efficacy against colon adenocarcinoma in vitro and in vivo. Expert Opin Drug Deliv 2021; 18:1309-1322. [PMID: 33970721 DOI: 10.1080/17425247.2021.1928631] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Hybrid vesicular systems (lipopolymersomes) are promising platforms for minimizing the liposomes and polymersomes disadvantages in terms of chemotherapeutic transportation. In this regard, lipopolymersome has been designed to integrate the advantage of both polymersomes and liposomes to enable better structural integrity of the bilayer after encapsulation of hydrophobic drugs while maintaining the soft nature of liposomes, superior serum stability, and high encapsulation efficiency of cargos in the bilayer segment. RESEARCH DESIGN AND METHODS In the present study, we reported preparation and characterization of five camptothecin (CPT)-loaded lipopolymersomal formulations composed of poly (ethylene glycol)-poly (lactic acid) (PEG-PLA) and dipalmitoylphosphatidylcholine (DPPC) at different molar ratios using film rehydration method. Afterward, the preferred formulation was tagged with AS1411 DNA aptamer in order to evaluate the therapeutic index using nucleolin-positive colon cancer cell lines (HT29 and C26). RESULTS The obtained data indicated that the prepared CPT-loaded lipopolymersome at a PEG-PLA: DPPC ratio of 75:25 exhibited superior stability and high loading capacity compared to other systems. Moreover, high cytotoxicity of the aptamer-targeted lipopolymersome and increased tumor accumulation were observed in comparison with non-targeted one. CONCLUSIONS The designed polymer-rich lipopolymersomal platform offers bright future for the development of potent nanomedicine against cancer.
Collapse
Affiliation(s)
- Mahsa Zahiri
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
16
|
Grewal T, Rentero C, Enrich C, Wahba M, Raabe CA, Rescher U. Annexin Animal Models-From Fundamental Principles to Translational Research. Int J Mol Sci 2021; 22:ijms22073439. [PMID: 33810523 PMCID: PMC8037771 DOI: 10.3390/ijms22073439] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Routine manipulation of the mouse genome has become a landmark in biomedical research. Traits that are only associated with advanced developmental stages can now be investigated within a living organism, and the in vivo analysis of corresponding phenotypes and functions advances the translation into the clinical setting. The annexins, a family of closely related calcium (Ca2+)- and lipid-binding proteins, are found at various intra- and extracellular locations, and interact with a broad range of membrane lipids and proteins. Their impacts on cellular functions has been extensively assessed in vitro, yet annexin-deficient mouse models generally develop normally and do not display obvious phenotypes. Only in recent years, studies examining genetically modified annexin mouse models which were exposed to stress conditions mimicking human disease often revealed striking phenotypes. This review is the first comprehensive overview of annexin-related research using animal models and their exciting future use for relevant issues in biology and experimental medicine.
Collapse
Affiliation(s)
- Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
- Correspondence: (T.G.); (U.R.); Tel.: +61-(0)2-9351-8496 (T.G.); +49-(0)251-83-52121 (U.R.)
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain; (C.R.); (C.E.)
- Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, 08036 Barcelona, Spain; (C.R.); (C.E.)
- Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Mohamed Wahba
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
| | - Carsten A. Raabe
- Research Group Regulatory Mechanisms of Inflammation, Center for Molecular Biology of Inflammation (ZMBE) and Cells in Motion Interfaculty Center (CiM), Institute of Medical Biochemistry, University of Muenster, 48149 Muenster, Germany;
| | - Ursula Rescher
- Research Group Regulatory Mechanisms of Inflammation, Center for Molecular Biology of Inflammation (ZMBE) and Cells in Motion Interfaculty Center (CiM), Institute of Medical Biochemistry, University of Muenster, 48149 Muenster, Germany;
- Correspondence: (T.G.); (U.R.); Tel.: +61-(0)2-9351-8496 (T.G.); +49-(0)251-83-52121 (U.R.)
| |
Collapse
|
17
|
Ahmad NA, Mohamed Zulkifli R, Hussin H, Nadri MH. In silico approach for Post-SELEX DNA aptamers: A mini-review. J Mol Graph Model 2021; 105:107872. [PMID: 33765525 DOI: 10.1016/j.jmgm.2021.107872] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.
Collapse
|
18
|
Noé V, Aubets E, Félix AJ, Ciudad CJ. Nucleic acids therapeutics using PolyPurine Reverse Hoogsteen hairpins. Biochem Pharmacol 2020; 189:114371. [PMID: 33338475 DOI: 10.1016/j.bcp.2020.114371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023]
Abstract
PolyPurine Reverse Hoogsteen hairpins (PPRHs) are DNA hairpins formed by intramolecular reverse Hoogsteen bonds which can bind to polypyrimidine stretches in dsDNA by Watson:Crick bonds, thus forming a triplex and displacing the fourth strand of the DNA complex. PPRHs were first described as a gene silencing tool in vitro for DHFR, telomerase and survivin genes. Then, the effect of PPRHs directed against the survivin gene was also determined in vivo using a xenograft model of prostate cancer cells (PC3). Since then, the ability of PPRHs to inhibit gene expression has been explored in other genes involved in cancer (BCL-2, mTOR, topoisomerase, C-MYC and MDM2), in immunotherapy (SIRPα/CD47 and PD-1/PD-L1 tandem) or in replication stress (WEE1 and CHK1). Furthermore, PPRHs have the ability to target the complementary strand of a G-quadruplex motif as a regulatory element of the TYMS gene. PPRHs have also the potential to correct point mutations in the DNA as shown in two collections of CHO cell lines bearing mutations in either the dhfr or aprt loci. Finally, based on the capability of PPRHs to form triplexes, they have been incorporated as probes in biosensors for the determination of the DNA methylation status of PAX-5 in cancer and the detection of mtLSU rRNA for the diagnosis of Pneumocystis jirovecii. Of note, PPRHs have high stability and do not present immunogenicity, hepatotoxicity or nephrotoxicity in vitro. Overall, PPRHs constitute a new economical biotechnological tool with multiple biomedical applications.
Collapse
Affiliation(s)
- Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Eva Aubets
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Alex J Félix
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Carlos J Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain.
| |
Collapse
|