1
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Kostyusheva A, Brezgin S, Ponomareva N, Frolova A, Lunin A, Bayurova E, Tikhonov A, Slatinskaya O, Demina P, Kachanov A, Babayeva G, Khan I, Khochenkov D, Khochenkova Y, Sokolova D, Silachev D, Maksimov G, Khaydukov E, Pokrovsky VS, Zamyatnin AA, Parodi A, Gordeychuk I, Chulanov V, Kostyushev D. Biologics-based technologies for highly efficient and targeted RNA delivery. Mol Ther 2025; 33:168-183. [PMID: 39511888 DOI: 10.1016/j.ymthe.2024.11.004] [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: 05/05/2024] [Revised: 09/26/2024] [Accepted: 11/04/2024] [Indexed: 11/15/2024] Open
Abstract
The demand for RNA-based therapeutics is increasing globally. However, their use is hampered by the lack of safe and effective delivery vehicles. Here, we developed technologies for highly efficient delivery of RNA cargo into programmable extracellular vesicle-mimetic nanovesicles (EMNVs) by fabricating hybrid EMNV-liposomes (Hybs). Tissue targeting is endowed by highly efficient genetic platforms based on truncated CD63 (ΔCD63) or PTGFRN proteins. For the first time we reveal their efficiency in functionalizing EMNVs, resulting in >10-fold enhancement of nanoparticle internalization in vitro and >2-fold in vivo. RNA delivery using Hybs demonstrated efficiency of >85% in human and mouse cell lines. Comparative analysis of EMNVs and Hyb lysosome colocalization and stability suggested that Hybs enter the lysosomal compartment and escape over time, whereas EMNVs primarily avoid it. Finally, we used these technologies to generate liver-targeting Hybs loaded with therapeutic small interfering RNA and demonstrated the robust efficiency of this system in vitro and in vivo. These technologies can be adapted for manufacturing a wide range of next-generation vehicles for highly efficient, safe delivery of RNA into desired organs and tissues for therapeutic and prophylactic applications.
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Affiliation(s)
- Anastasiya Kostyusheva
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
| | - Sergey Brezgin
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia; Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Natalia Ponomareva
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia; Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Anastasiia Frolova
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia; Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Alexander Lunin
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences (Polio Institute), Moscow 142782, Russia
| | - Ekaterina Bayurova
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences (Polio Institute), Moscow 142782, Russia
| | - Andrey Tikhonov
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
| | - Olga Slatinskaya
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Polina Demina
- Moscow Pedagogical State University, Moscow 119435, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Artyom Kachanov
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
| | - Gulalek Babayeva
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia; RUDN University, Moscow 117198, Russia
| | - Irina Khan
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia; RUDN University, Moscow 117198, Russia
| | - Dmitry Khochenkov
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia; Togliatti State University, Togliatti 445020, Russia
| | - Yulia Khochenkova
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia
| | - Darina Sokolova
- Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia; Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia; RUDN University, Moscow 117198, Russia
| | - Denis Silachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Georgy Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Evgeny Khaydukov
- Moscow Pedagogical State University, Moscow 119435, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Vadim S Pokrovsky
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia; RUDN University, Moscow 117198, Russia
| | - Andrey A Zamyatnin
- Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119192, Russia
| | - Alessandro Parodi
- Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Ilya Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences (Polio Institute), Moscow 142782, Russia
| | - Vladimir Chulanov
- Department of Infectious Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia
| | - Dmitry Kostyushev
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), Moscow 119435, Russia; Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119192, Russia.
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2
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Zdravkova K, Mijanovic O, Brankovic A, Ilicheva PM, Jakovleva A, Karanovic J, Pualic M, Pualic D, Rubel AA, Savvateeva LV, Parodi A, Zamyatnin AA. Unveiling the Roles of Cysteine Proteinases F and W: From Structure to Pathological Implications and Therapeutic Targets. Cells 2024; 13:917. [PMID: 38891048 PMCID: PMC11171618 DOI: 10.3390/cells13110917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Cysteine cathepsins F and W are members of the papain-like cysteine protease family, which have distinct structural features and functional roles in various physiological and pathological processes. This review provides a comprehensive overview of the current understanding of the structure, biological functions, and pathological implications of cathepsins F and W. Beginning with an introduction to these proteases, we delve into their structural characteristics and elucidate their unique features that dictate their enzymatic activities and substrate specificity. We also explore the intricate involvement of cathepsins F and W in malignancies, highlighting their role as potential biomarkers and therapeutic targets in cancer progression. Furthermore, we discuss the emerging roles of these enzymes in immune response modulation and neurological disorders, shedding light on their implications in autoimmune and neurodegenerative diseases. Finally, we review the landscape of inhibitors targeting these proteases, highlighting their therapeutic potential and challenges in clinical translation. This review brings together the diverse facets of cysteine cathepsins F and W, providing insights into their roles in health and disease and guiding future investigations for therapeutic advances.
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Affiliation(s)
- Kristina Zdravkova
- AD Alkaloid Skopje, Boulevard Alexander the Great 12, 1000 Skopje, North Macedonia;
| | - Olja Mijanovic
- Dia-M, LCC, 7 b.3 Magadanskaya Str., 129345 Moscow, Russia;
| | - Ana Brankovic
- Department of Forensic Sciences, Faculty of Forensic Sciences and Engineering, University of Criminal Investigation and Police Studies, Cara Dusana 196, 11000 Belgrade, Serbia;
| | - Polina M. Ilicheva
- Institute of Chemistry, Saratov State University, Astrakhanskaya Street 83, 410012 Saratov, Russia;
| | | | - Jelena Karanovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444A, 11000 Belgrade, Serbia;
| | - Milena Pualic
- Institute Cardiovascular Diseases Dedinje, Heroja Milana Tepica 1, 11000 Belgrade, Serbia;
| | - Dusan Pualic
- Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Lyudmila V. Savvateeva
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alessandro Parodi
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Andrey A. Zamyatnin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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3
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Liu F, Zhou T, Zhang S, Li Y, Chen Y, Miao Z, Wang X, Yang G, Li Q, Zhang L, Liu Y. Cathepsin B: The dawn of tumor therapy. Eur J Med Chem 2024; 269:116329. [PMID: 38508117 DOI: 10.1016/j.ejmech.2024.116329] [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: 11/10/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Cathepsin B (CTSB) is a key lysosomal protease that plays a crucial role in the development of cancer. This article elucidates the relationship between CTSB and cancer from the perspectives of its structure, function, and role in tumor growth, migration, invasion, metastasis, angiogenesis and autophagy. Further, we summarized the research progress of cancer treatment related drugs targeting CTSB, as well as the potential and advantages of Traditional Chinese medicine in treating tumors by regulating the expression of CTSB.
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Affiliation(s)
- Fuxian Liu
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Ting Zhou
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; Experimental & Training Teaching Centers, Gansu University of Chinese Medicine, Lanzhou, China
| | - Shangzu Zhang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yangyang Li
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yan Chen
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Zhiming Miao
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xin Wang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Gengqiang Yang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Qiyang Li
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Liying Zhang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China.
| | - Yongqi Liu
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China; Key Laboratory of Dunhuang Medicine and Transformation at Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou, China.
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4
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Parodi A, Voronina MV, Zamyatnin AA. The Importance of Nanocarriers' Intra- and Extracellular Degradation: What we Know and Should Know About it? Curr Med Chem 2024; 31:128-132. [PMID: 36924098 DOI: 10.2174/0929867330666230315144546] [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: 12/16/2022] [Revised: 01/20/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023]
Affiliation(s)
- Alessandro Parodi
- Scientific Center for Translation Medicine, Sochi State University, Sochi, 354340, Russia
| | - Maya V Voronina
- Scientific Center for Translation Medicine, Sochi State University, Sochi, 354340, Russia
| | - Andrey A Zamyatnin
- Scientific Center for Translation Medicine, Sochi State University, Sochi, 354340, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7X, UK
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5
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Frolova AS, Tikhomirova NK, Kireev II, Zernii EY, Parodi A, Ivanov KI, Zamyatnin AA. Expression, Intracellular Localization, and Maturation of Cysteine Cathepsins in Renal Embryonic and Cancer Cell Lines. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1034-1044. [PMID: 37751872 DOI: 10.1134/s0006297923070143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 09/28/2023]
Abstract
Cysteine cathepsins play an important role in tumor development and metastasis. The expression of these enzymes is often increased in many types of tumor cells. Cysteine cathepsins contribute to carcinogenesis through a number of mechanisms, including proteolysis of extracellular matrix and signaling molecules on the cell surface, as well as degradation of transcription factors and disruption of signaling cascades in the cell nucleus. Distinct oncogenic functions have been reported for several members of the cysteine cathepsin family in various types of cancer, but a comparative study of all eleven cysteine cathepsins in one experimental model is still missing. In this work, we assessed and compared the expression, localization, and maturation of all eleven cysteine cathepsins in embryonic kidney cells HEK293 and kidney cancer cell lines 769-P and A-498. We found that the expression of cathepsins V, B, Z, L, and S was 3- to 9-fold higher in kidney tumor cells than in embryonic cells. We also showed that all cysteine cathepsins were present in varying amounts in the nucleus of both embryonic and tumor cells. Notably, more than half of the cathepsin Z or K and over 88% of cathepsin F were localized in tumor cell nuclei. Moreover, mature forms of cysteine cathepsins were more prevalent in tumor cells than in embryonic cells. These results can be further used to develop novel diagnostic tools and may assist in the investigation of cysteine cathepsins as potential therapeutic targets.
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Affiliation(s)
- Anastasia S Frolova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Natalia K Tikhomirova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Igor I Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alessandro Parodi
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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6
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Egorova VS, Kolesova EP, Lopus M, Yan N, Parodi A, Zamyatnin AA. Smart Delivery Systems Responsive to Cathepsin B Activity for Cancer Treatment. Pharmaceutics 2023; 15:1848. [PMID: 37514035 PMCID: PMC10386206 DOI: 10.3390/pharmaceutics15071848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Cathepsin B is a lysosomal cysteine protease, contributing to vital cellular homeostatic processes including protein turnover, macroautophagy of damaged organelles, antigen presentation, and in the extracellular space, it takes part in tissue remodeling, prohormone processing, and activation. However, aberrant overexpression of cathepsin B and its enzymatic activity is associated with different pathological conditions, including cancer. Cathepsin B overexpression in tumor tissues makes this enzyme an important target for smart delivery systems, responsive to the activity of this enzyme. The generation of technologies which therapeutic effect is activated as a result of cathepsin B cleavage provides an opportunity for tumor-targeted therapy and controlled drug release. In this review, we summarized different technologies designed to improve current cancer treatments responsive to the activity of this enzyme that were shown to play a key role in disease progression and response to the treatment.
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Affiliation(s)
- Vera S Egorova
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Ekaterina P Kolesova
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Manu Lopus
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai Kalina Campus, Vidyanagari, Mumbai 400098, India
| | - Neng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Alessandro Parodi
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, Sochi 354340, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Andrey A Zamyatnin
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, Sochi 354340, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
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7
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Kolesova EP, Egorova VS, Syrocheva AO, Frolova AS, Kostyushev D, Kostyusheva A, Brezgin S, Trushina DB, Fatkhutdinova L, Zyuzin M, Demina PA, Khaydukov EV, Zamyatnin AA, Parodi A. Proteolytic Resistance Determines Albumin Nanoparticle Drug Delivery Properties and Increases Cathepsin B, D, and G Expression. Int J Mol Sci 2023; 24:10245. [PMID: 37373389 DOI: 10.3390/ijms241210245] [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: 05/16/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Proteolytic activity is pivotal in maintaining cell homeostasis and function. In pathological conditions such as cancer, it covers a key role in tumor cell viability, spreading to distant organs, and response to the treatment. Endosomes represent one of the major sites of cellular proteolytic activity and very often represent the final destination of internalized nanoformulations. However, little information about nanoparticle impact on the biology of these organelles is available even though they represent the major location of drug release. In this work, we generated albumin nanoparticles with a different resistance to proteolysis by finely tuning the amount of cross-linker used to stabilize the carriers. After careful characterization of the particles and measurement of their degradation in proteolytic conditions, we determined a relationship between their sensitivity to proteases and their drug delivery properties. These phenomena were characterized by an overall increase in the expression of cathepsin proteases regardless of the different sensitivity of the particles to proteolytic degradation.
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Affiliation(s)
- Ekaterina P Kolesova
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Vera S Egorova
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasiia O Syrocheva
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasiia S Frolova
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Dmitry Kostyushev
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Anastasiia Kostyusheva
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey Brezgin
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Daria B Trushina
- Department of Biomedical Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Federal Scientific Research Center "Crystallography and Photonics", Russian Academy of Sciences, 119333 Moscow, Russia
| | | | - Mikhail Zyuzin
- School of Physics, ITMO University, Lomonosova 9, 191002 St. Petersburg, Russia
| | - Polina A Demina
- Federal Scientific Research Center "Crystallography and Photonics", Russian Academy of Sciences, 119333 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Evgeny V Khaydukov
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Federal Scientific Research Center "Crystallography and Photonics", Russian Academy of Sciences, 119333 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey A Zamyatnin
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7X, UK
| | - Alessandro Parodi
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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8
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Kutumova EO, Akberdin IR, Kiselev IN, Sharipov RN, Egorova VS, Syrocheva AO, Parodi A, Zamyatnin AA, Kolpakov FA. Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools. Int J Mol Sci 2022; 23:12560. [PMID: 36293410 PMCID: PMC9604366 DOI: 10.3390/ijms232012560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022] Open
Abstract
Cancer treatment and pharmaceutical development require targeted treatment and less toxic therapeutic intervention to achieve real progress against this disease. In this scenario, nanomedicine emerged as a reliable tool to improve drug pharmacokinetics and to translate to the clinical biologics based on large molecules. However, the ability of our body to recognize foreign objects together with carrier transport heterogeneity derived from the combination of particle physical and chemical properties, payload and surface modification, make the designing of effective carriers very difficult. In this scenario, physiologically based pharmacokinetic modeling can help to design the particles and eventually predict their ability to reach the target and treat the tumor. This effort is performed by scientists with specific expertise and skills and familiarity with artificial intelligence tools such as advanced software that are not usually in the "cords" of traditional medical or material researchers. The goal of this review was to highlight the advantages that computational modeling could provide to nanomedicine and bring together scientists with different background by portraying in the most simple way the work of computational developers through the description of the tools that they use to predict nanoparticle transport and tumor targeting in our body.
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Affiliation(s)
- Elena O. Kutumova
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU, Ltd., 630058 Novosibirsk, Russia
| | - Ilya R. Akberdin
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU, Ltd., 630058 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ilya N. Kiselev
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU, Ltd., 630058 Novosibirsk, Russia
| | - Ruslan N. Sharipov
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU, Ltd., 630058 Novosibirsk, Russia
- Specialized Educational Scientific Center, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vera S. Egorova
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasiia O. Syrocheva
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Alessandro Parodi
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Andrey A. Zamyatnin
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Fedor A. Kolpakov
- Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU, Ltd., 630058 Novosibirsk, Russia
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9
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Rudzinska-Radecka M, Frolova AS, Balakireva AV, Gorokhovets NV, Pokrovsky VS, Sokolova DV, Korolev DO, Potoldykova NV, Vinarov AZ, Parodi A, Zamyatnin AA. In Silico, In Vitro, and Clinical Investigations of Cathepsin B and Stefin A mRNA Expression and a Correlation Analysis in Kidney Cancer. Cells 2022; 11:1455. [PMID: 35563761 PMCID: PMC9101197 DOI: 10.3390/cells11091455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
The cysteine protease Cathepsin B (CtsB) plays a critical role in multiple signaling pathways, intracellular protein degradation, and processing. Endogenous inhibitors regulate its enzymatic activity, including stefins and other cystatins. Recent data proved that CtsB is implicated in tumor extracellular matrix remodeling, cell invasion, and metastasis: a misbalance between cathepsins and their natural inhibitors is often considered a sign of disease progression. In the present study, we investigated CtsB and stefin A (StfA) expression in renal cell carcinoma (RCC). mRNA analysis unveiled a significant CTSB and STFA increase in RCC tissues compared to adjacent non-cancerogenic tissues and a higher CtsB expression in malignant tumors than in benign renal neoplasms. Further analysis highlighted a positive correlation between CtsB and StfA expression as a function of patient sex, age, tumor size, grade, lymph node invasion, metastasis occurrence, and survival. Alternative overexpression and silencing of CtsB and StfA confirmed the correlation expression between these proteins in human RCC-derived cells through protein analysis and fluorescent microscopy. Finally, the ectopic expression of CtsB and StfA increased RCC cell proliferation. Our data strongly indicated that CtsB and StfA expression play an important role in RCC development by mutually stimulating their expression in RCC progression.
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Affiliation(s)
- Magdalena Rudzinska-Radecka
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Anastasia S. Frolova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
| | - Anastasia V. Balakireva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Neonila V. Gorokhovets
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
| | - Vadim S. Pokrovsky
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, 115478 Moscow, Russia
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Darina V. Sokolova
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, 115478 Moscow, Russia
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Dmitry O. Korolev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Natalia V. Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Andrey Z. Vinarov
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Alessandro Parodi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Immunology, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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10
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Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example. MATHEMATICS 2022. [DOI: 10.3390/math10071176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here we describe a toolkit for presenting physiologically based pharmacokinetic (PBPK) models in a modular graphical view in the BioUML platform. Firstly, we demonstrate the BioUML capabilities for PBPK modeling tested on an existing model of nanoparticles delivery to solid tumors in mice. Secondly, we provide guidance on the conversion of the PBPK model code from a text modeling language like Berkeley Madonna to a visual modular diagram in the BioUML. We give step-by-step explanations of the model transformation and demonstrate that simulation results from the original model are exactly the same as numerical results obtained for the transformed model. The main advantage of the proposed approach is its clarity and ease of perception. Additionally, the modular representation serves as a simplified and convenient base for in silico investigation of the model and reduces the risk of technical errors during its reuse and extension by concomitant biochemical processes. In summary, this article demonstrates that BioUML can be used as an alternative and robust tool for PBPK modeling.
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11
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Machulkin AE, Uspenskaya AA, Zyk NU, Nimenko EA, Ber AP, Petrov SA, Polshakov VI, Shafikov RR, Skvortsov DA, Plotnikova EA, Pankratov AA, Smirnova GB, Borisova YA, Pokrovsky VS, Kolmogorov VS, Vaneev AN, Khudyakov AD, Chepikova OE, Kovalev S, Zamyatnin AA, Erofeev A, Gorelkin P, Beloglazkina EK, Zyk NV, Khazanova ES, Majouga AG. Synthesis, Characterization, and Preclinical Evaluation of a Small-Molecule Prostate-Specific Membrane Antigen-Targeted Monomethyl Auristatin E Conjugate. J Med Chem 2021; 64:17123-17145. [PMID: 34797052 DOI: 10.1021/acs.jmedchem.1c01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prostate cancer is the second most common type of cancer among men. Its main method of treatment is chemotherapy, which has a wide range of side effects. One of the solutions to this challenge is targeted delivery to prostate cancer cells. Here we synthesized a novel small-molecule PSMA-targeted conjugate based on the monomethyl auristatin E. Its structure and conformational properties were investigated by NMR spectroscopy. Cytotoxicity, intracellular reactive oxygen species induction, and stability under liver microsomes and P450-cytochrome species were investigated for this conjugate. The conjugate demonstrated 77-85% tumor growth inhibition levels on 22Rv1 (PSMA (+)) xenografts, compared with a 37% inhibition level on PC-3 (PSMA (-)) xenografts, in a single dose of 0.3 mg/kg and a sufficiently high therapeutic index of 21. Acute, chronic, and subchronic toxicities and pharmacokinetics have shown that the synthesized conjugate is a promising potential agent for the chemotherapy of prostate cancer.
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Affiliation(s)
- Aleksei E Machulkin
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Anastasia A Uspenskaya
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Nikolay U Zyk
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Ekaterina A Nimenko
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Anton P Ber
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Stanislav A Petrov
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Radik R Shafikov
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, Moscow 117997, Russian Federation
| | - Dmitry A Skvortsov
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Ekaterina A Plotnikova
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 2 Botkinskiy Proezd, 3, Moscow 125284, Russian Federation
| | - Andrei A Pankratov
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 2 Botkinskiy Proezd, 3, Moscow 125284, Russian Federation
| | - Galina B Smirnova
- N.N. Blokhin Russian Cancer Research Center, 24 Kashirskoye Shosse, Moscow 115478, Russian Federation
| | - Yulia A Borisova
- N.N. Blokhin Russian Cancer Research Center, 24 Kashirskoye Shosse, Moscow 115478, Russian Federation
| | - Vadim S Pokrovsky
- N.N. Blokhin Russian Cancer Research Center, 24 Kashirskoye Shosse, Moscow 115478, Russian Federation.,RUDN University, Miklukho-Maklaya Street 6, Moscow 117198, Russian Federation
| | - Vasilii S Kolmogorov
- National University of Science and Technology MISiS, 9 Leninskiy Prospekt, Moscow 119049, Russian Federation
| | - Alexander N Vaneev
- National University of Science and Technology MISiS, 9 Leninskiy Prospekt, Moscow 119049, Russian Federation
| | - Alexander D Khudyakov
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Olga E Chepikova
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russian Federation
| | - Sergey Kovalev
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Andrey A Zamyatnin
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russian Federation.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya Street 8-2, Moscow 119991, Russian Federation.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119992, Russian Federation.,Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, U.K
| | - Alexander Erofeev
- National University of Science and Technology MISiS, 9 Leninskiy Prospekt, Moscow 119049, Russian Federation
| | - Petr Gorelkin
- National University of Science and Technology MISiS, 9 Leninskiy Prospekt, Moscow 119049, Russian Federation
| | - Elena K Beloglazkina
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Nikolay V Zyk
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation
| | - Elena S Khazanova
- LLC Izvarino-Pharma, v. Vnukovskoe, Vnukovskoe Shosse, Fifth km., Building 1, Moscow 108817, Russian Federation
| | - Alexander G Majouga
- Chemistry Department, Lomonosov Moscow State University, Building 1/3, GSP-1, Leninskie Gory, Moscow 119991, Russian Federation.,National University of Science and Technology MISiS, 9 Leninskiy Prospekt, Moscow 119049, Russian Federation.,Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, Moscow 125047, Russian Federation
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12
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Gureeva TA, Timoshenko OS, Kugaevskaya EV, Solovyova NI. [Cysteine cathepsins: structure, physiological functions and their role in carcinogenesis]. BIOMEDITSINSKAIA KHIMIIA 2021; 67:453-464. [PMID: 34964439 DOI: 10.18097/pbmc20216706453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cysteine cathepsins (Cts) also known as thiol proteinases belong to the superfamily of cysteine proteinases (EC 3.4.22). Cts are known as lysosomal proteases responsible for the intracellular proteins degradation. All Cts are synthesized as zymogens, activation of which occurs autocatalytically. Their activity is regulated by endogenous inhibitors. Cts can be secreted into the extracellular environment, which is of particular importance in tumor progression. Extracellular Cts not only hydrolyze extracellular matrix (ECM) proteins, but also contribute to ECM remodeling, processing and/or release of cell adhesion molecules, growth factors, cytokines and chemokines. In cancer, the expression and activity of Cts sharply increase both in cell lysosomes and in the intercellular space, which correlates with neoplastic transformation, invasion, metastasis and leads to further tumor progression. It has been shown that Cts expression depends on the cells type, therefore, their role in the tumor development differs depending on their cellular origin. The mechanism of Cts action in cancer is not limited only by their proteolytic action. The Cts influence on signal transduction pathways associated with cancer development, including the pathway involving growth factors, which is mediated through receptors tyrosine kinases (RTK) and various signaling mitogen-activated protein kinases (MAPK), has been proven. In addition, Cts are able to promote the epithelial-mesenchymal transition (EMT) by activating signal transduction pathways such as Wnt, Notch, and the pathway involving TGF-β. So, Ctc perform specific both destructive and regulatory functions, carrying out proteolysis, both inside and outside the cell.
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Affiliation(s)
- T A Gureeva
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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Rudzinska M, Czarnecka-Chrebelska KH, Kuznetsova EB, Maryanchik SV, Parodi A, Korolev DO, Potoldykova N, Svetikova Y, Vinarov AZ, Nemtsova MV, Zamyatnin AA. Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness. Noncoding RNA 2021; 7:25. [PMID: 33920185 PMCID: PMC8167775 DOI: 10.3390/ncrna7020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can be specifically expressed in different tissues and cancers. By controlling the gene expression at the transcriptional and translational levels, lncRNAs have been reported to be involved in tumor growth and metastasis. Recent data demonstrated that multiple lncRNAs have a crucial role in renal cell carcinoma (RCC) progression-the most common malignant urogenital tumor. In the present study, we found a trend towards increased PROX1 antisense RNA 1 (PROX1-AS1) expression in RCC specimens compared to non-tumoral margins. Next, we found a positive correlation between PROX1-AS1 expression and the occurrence of distant and lymph node metastasis, higher tumor stage (pT1 vs. pT2 vs. pT3-T4) and high-grade (G1/G2 vs. G3/G4) clear RCC. Furthermore, global demethylation in RCC-derived cell lines (769-P and A498) and human embryonic kidney 293 (HEK293) cells induced a significant increase of PROX1-AS1 expression level, with the most remarkable change in HEK293 cells. In line with this evidence, bisulfite sequencing analysis confirmed the specific demethylation of bioinformatically selected CpG islands on the PROX1-AS1 promoter sequence in the HEK293 cell line but not in the tumor cells. Additionally, the human specimen analysis showed the hemimethylated state of CG dinucleotides in non-tumor kidney tissues, whereas the tumor samples presented the complete, partial, or no demethylation of CpG-islands. In conclusion, our study indicated that PROX1-AS1 could be associated with RCC progression, and further investigations may define its role as a new diagnostic marker and therapeutic target.
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Affiliation(s)
- Magdalena Rudzinska
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | | | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia
| | - Sofya V. Maryanchik
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | - Alessandro Parodi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
| | - Dmitry O. Korolev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Nataliya Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Yulia Svetikova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Andrey Z. Vinarov
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.P.); (Y.S.); (A.Z.V.)
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.B.K.); (S.V.M.); (A.P.); (M.V.N.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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14
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Rudzińska M, Daglioglu C, Savvateeva LV, Kaci FN, Antoine R, Zamyatnin AA. Current Status and Perspectives of Protease Inhibitors and Their Combination with Nanosized Drug Delivery Systems for Targeted Cancer Therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:9-20. [PMID: 33442233 PMCID: PMC7797289 DOI: 10.2147/dddt.s285852] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
In cancer treatments, many natural and synthetic products have been examined; among them, protease inhibitors are promising candidates for anti-cancer agents. Since dysregulated proteolytic activities can contribute to tumor development and metastasis, antagonization of proteases with tailored inhibitors is an encouraging approach. Although adverse effects of early designs of these inhibitors disappeared after the introduction of next-generation agents, most of the proposed inhibitors did not pass the early stages of clinical trials due to their nonspecific toxicity and lack of pharmacological effects. Therefore, new applications that modulate proteases more specifically and serve their programmed way of administration are highly appreciated. In this context, nanosized drug delivery systems have attracted much attention because preliminary studies have demonstrated that the therapeutic capacity of inhibitors has been improved significantly with encapsulated formulation as compared to their free forms. Here, we address this issue and discuss the current application and future clinical prospects of this potential combination towards targeted protease-based cancer therapy.
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Affiliation(s)
- Magdalena Rudzińska
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Cenk Daglioglu
- Biotechnology and Bioengineering Application and Research Center, Integrated Research Centers, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Fatma Necmiye Kaci
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Yakutiye, Erzurum 25050, Turkey
| | - Rodolphe Antoine
- CNRS, Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, Lyon F-69622, France
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Department of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
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15
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Petushkova AI, Zamyatnin AA. Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations. Pharmaceuticals (Basel) 2020; 13:E277. [PMID: 32998368 PMCID: PMC7601131 DOI: 10.3390/ph13100277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022] Open
Abstract
Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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16
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Peptidyl Fluoromethyl Ketones and Their Applications in Medicinal Chemistry. Molecules 2020; 25:molecules25174031. [PMID: 32899354 PMCID: PMC7504820 DOI: 10.3390/molecules25174031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/29/2022] Open
Abstract
Peptidyl fluoromethyl ketones occupy a pivotal role in the current scenario of synthetic chemistry, thanks to their numerous applications as inhibitors of hydrolytic enzymes. The insertion of one or more fluorine atoms adjacent to a C-terminal ketone moiety greatly modifies the physicochemical properties of the overall substrate, especially by increasing the reactivity of this functionalized carbonyl group toward nucleophiles. The main application of these peptidyl α-fluorinated ketones in medicinal chemistry relies in their ability to strongly and selectively inhibit serine and cysteine proteases. These compounds can be used as probes to study the proteolytic activity of the aforementioned proteases and to elucidate their role in the insurgence and progress on several diseases. Likewise, if the fluorinated methyl ketone moiety is suitably connected to a peptidic backbone, it may confer to the resulting structure an excellent substrate peculiarity and the possibility of being recognized by a specific subclass of human or pathogenic proteases. Therefore, peptidyl fluoromethyl ketones are also currently highly exploited for the target-based design of compounds for the treatment of topical diseases such as various types of cancer and viral infections.
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