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  1. Article: Structure determinants defining the specificity of papain-like cysteine proteases.

    Petushkova, Anastasiia I / Savvateeva, Lyudmila V / Zamyatnin, Andrey A

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 6552–6569

    Abstract: Papain-like cysteine proteases are widely expressed enzymes that mostly regulate protein turnover in the acidic conditions of lysosomes. However, in the last twenty years, these proteases have been evidenced to exert specific functions within different ... ...

    Abstract Papain-like cysteine proteases are widely expressed enzymes that mostly regulate protein turnover in the acidic conditions of lysosomes. However, in the last twenty years, these proteases have been evidenced to exert specific functions within different organelles as well as outside the cell. The most studied proteases of this family are human cysteine cathepsins involved both in physiological and pathological processes. The specificity of each protease to its substrates is mostly defined by the structure of the binding cleft. Different patterns of amino acid motif in this area determine the interaction between the protease and the ligands. Moreover, this specificity can be altered under the specific media conditions and in case other proteins are present. Understanding how this network works would allow researchers to design the diagnostic selective probes and therapeutic inhibitors. Moreover, this knowledge might serve as a key for redesigning and
    Language English
    Publishing date 2022-11-24
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.11.040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Redox-Mediated Post-Translational Modifications of Proteolytic Enzymes and Their Role in Protease Functioning.

    Petushkova, Anastasiia I / Zamyatnin, Andrey A

    Biomolecules

    2020  Volume 10, Issue 4

    Abstract: Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to ...

    Abstract Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to maintain cellular and extracellular homeostasis. The redox regulation of proteolysis provides a flexible dose-dependent mechanism for proteolytic activity control. The excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) in living organisms indicate pathological conditions, so redox-sensitive proteases can swiftly induce pro-survival responses or regulated cell death (RCD). At the same time, severe protein oxidation can lead to the dysregulation of proteolysis, which induces either protein aggregation or superfluous protein hydrolysis. Therefore, oxidative stress contributes to the onset of age-related dysfunction. In the present review, we consider the post-translational modifications (PTMs) of proteolytic enzymes and their impact on homeostasis.
    MeSH term(s) Animals ; Humans ; Oxidation-Reduction ; Peptide Hydrolases/metabolism ; Protein Processing, Post-Translational ; Proteolysis ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism
    Chemical Substances Reactive Nitrogen Species ; Reactive Oxygen Species ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2020-04-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom10040650
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations.

    Petushkova, Anastasiia I / Zamyatnin, Andrey A

    Pharmaceuticals (Basel, Switzerland)

    2020  Volume 13, Issue 10

    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 ... ...

    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.
    Keywords covid19
    Language English
    Publishing date 2020-09-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph13100277
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations

    Petushkova, Anastasiia I. / Zamyatnin, Andrey A.

    Pharmaceuticals

    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 ... ...

    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
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #799734
    Database COVID19

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  5. Article ; Online: Papain-Like Proteases as Coronaviral Drug Targets

    Anastasiia I. Petushkova / Andrey A. Zamyatnin

    Pharmaceuticals, Vol 13, Iss 277, p

    Current Inhibitors, Opportunities, and Limitations

    2020  Volume 277

    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 ... ...

    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.
    Keywords coronavirus ; papain-like proteases ; inhibitor ; outbreak ; Medicine ; R ; Pharmacy and materia medica ; RS1-441 ; covid19
    Subject code 572
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Unravelling the Network of Nuclear Matrix Metalloproteinases for Targeted Drug Design.

    Frolova, Anastasia S / Petushkova, Anastasiia I / Makarov, Vladimir A / Soond, Surinder M / Zamyatnin, Andrey A

    Biology

    2020  Volume 9, Issue 12

    Abstract: Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and ... ...

    Abstract Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and organs. Overexpression of MMPs has been observed to facilitate cellular growth, migration, and metastasis of tumor cells during cancer progression. A growing number of these proteins are being found to exist in the nuclei of both healthy and tumor cells, thus highlighting their localization as having a genuine purpose in cellular homeostasis. The mechanism underlying nuclear transport and the effects of MMP nuclear translocation have not yet been fully elucidated. To date, nuclear MMPs appear to have a unique impact on cellular apoptosis and gene regulation, which can have effects on immune response and tumor progression, and thus present themselves as potential therapeutic targets in certain types of cancer or disease. Herein, we highlight and evaluate what progress has been made in this area of research, which clearly has some value as a specific and unique way of targeting the activity of nuclear matrix metalloproteinases within various cell types.
    Language English
    Publishing date 2020-12-19
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology9120480
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Cathepsin D-Managing the Delicate Balance.

    Mijanovic, Olja / Petushkova, Anastasiia I / Brankovic, Ana / Turk, Boris / Solovieva, Anna B / Nikitkina, Angelina I / Bolevich, Sergey / Timashev, Peter S / Parodi, Alessandro / Zamyatnin, Andrey A

    Pharmaceutics

    2021  Volume 13, Issue 6

    Abstract: Lysosomal proteases play a crucial role in maintaining cell homeostasis. Human cathepsin D manages protein turnover degrading misfolded and aggregated proteins and favors apoptosis in the case of proteostasis disruption. However, when cathepsin D ... ...

    Abstract Lysosomal proteases play a crucial role in maintaining cell homeostasis. Human cathepsin D manages protein turnover degrading misfolded and aggregated proteins and favors apoptosis in the case of proteostasis disruption. However, when cathepsin D regulation is affected, it can contribute to numerous disorders. The down-regulation of human cathepsin D is associated with neurodegenerative disorders, such as neuronal ceroid lipofuscinosis. On the other hand, its excessive levels outside lysosomes and the cell membrane lead to tumor growth, migration, invasion and angiogenesis. Therefore, targeting cathepsin D could provide significant diagnostic benefits and new avenues of therapy. Herein, we provide a brief overview of cathepsin D structure, regulation, function, and its role in the progression of many diseases and the therapeutic potentialities of natural and synthetic inhibitors and activators of this protease.
    Language English
    Publishing date 2021-06-05
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics13060837
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  8. Article ; Online: Unravelling the Network of Nuclear Matrix Metalloproteinases for Targeted Drug Design

    Anastasia S. Frolova / Anastasiia I. Petushkova / Vladimir A. Makarov / Surinder M. Soond / Andrey A. Zamyatnin

    Biology, Vol 9, Iss 480, p

    2020  Volume 480

    Abstract: Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and ... ...

    Abstract Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and organs. Overexpression of MMPs has been observed to facilitate cellular growth, migration, and metastasis of tumor cells during cancer progression. A growing number of these proteins are being found to exist in the nuclei of both healthy and tumor cells, thus highlighting their localization as having a genuine purpose in cellular homeostasis. The mechanism underlying nuclear transport and the effects of MMP nuclear translocation have not yet been fully elucidated. To date, nuclear MMPs appear to have a unique impact on cellular apoptosis and gene regulation, which can have effects on immune response and tumor progression, and thus present themselves as potential therapeutic targets in certain types of cancer or disease. Herein, we highlight and evaluate what progress has been made in this area of research, which clearly has some value as a specific and unique way of targeting the activity of nuclear matrix metalloproteinases within various cell types.
    Keywords matrix metalloproteinase ; extracellular matrix ; nuclei ; cancer ; apoptosis ; immune response ; Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Unravelling the Network of Nuclear Matrix Metalloproteinases for Targeted Drug Design

    Frolova, Anastasia S / Petushkova, Anastasiia I / Makarov, Vladimir A / Soond, Surinder M / Zamyatnin, Andrey A

    Biology. 2020 Dec. 19, v. 9, no. 12

    2020  

    Abstract: Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and ... ...

    Abstract Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and organs. Overexpression of MMPs has been observed to facilitate cellular growth, migration, and metastasis of tumor cells during cancer progression. A growing number of these proteins are being found to exist in the nuclei of both healthy and tumor cells, thus highlighting their localization as having a genuine purpose in cellular homeostasis. The mechanism underlying nuclear transport and the effects of MMP nuclear translocation have not yet been fully elucidated. To date, nuclear MMPs appear to have a unique impact on cellular apoptosis and gene regulation, which can have effects on immune response and tumor progression, and thus present themselves as potential therapeutic targets in certain types of cancer or disease. Herein, we highlight and evaluate what progress has been made in this area of research, which clearly has some value as a specific and unique way of targeting the activity of nuclear matrix metalloproteinases within various cell types.
    Keywords apoptosis ; area ; cell growth ; degradation ; drug design ; extracellular matrix proteins ; genes ; homeostasis ; immune response ; metalloproteinases ; metastasis ; neoplasm cells ; neoplasm progression ; nuclear matrix ; research ; therapeutics ; tissues
    Language English
    Dates of publication 2020-1219
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-light
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology9120480
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Trends and Prospects of Plant Proteases in Therapeutics.

    Balakireva, Anastasia V / Kuznetsova, Natalia V / Petushkova, Anastasiia I / Savvateeva, Lyudmila V / Zamyatnin, Andrey A

    Current medicinal chemistry

    2017  Volume 26, Issue 3, Page(s) 465–486

    Abstract: The main function of proteases in any living organism is the cleavage of proteins resulting in the degradation of damaged, misfolded and potentially harmful proteins and therefore providing the cell with amino acids essential for the synthesis of new ... ...

    Abstract The main function of proteases in any living organism is the cleavage of proteins resulting in the degradation of damaged, misfolded and potentially harmful proteins and therefore providing the cell with amino acids essential for the synthesis of new proteins. Besides this main function, proteases may play an important role as signal molecules and participate in numerous protein cascades to maintain the vital processes of an organism. Plant proteases are no exception to this rule. Moreover, in contrast to humanencoded enzymes, many plant proteases possess exceptional features such as higher stability, unique substrate specificity and a wide pH range for enzymatic activity. These valuable features make plant-derived proteolytic enzymes suitable for many biomedical applications, and furthermore, the plants can serve as factories for protein production. Plant proteases are already applied in the treatment of several pathological conditions in the human organism. Some of the enzymes possess antitumour, antibacterial and antifungal activity. The collagenolytic activity of plant proteases determines important medical applications such as the healing of wounds and burn debridement. Plant proteases may affect blood coagulation processes and can be applied in the treatment of digestive disorders. The present review summarizes recent advances and possible applications for plant proteases in biomedicine, and proposes further development of plant-derived proteolytic enzymes in the biotechnology and pharmaceutical industries.
    MeSH term(s) Humans ; Hydrogen-Ion Concentration ; Peptide Hydrolases/metabolism ; Peptide Hydrolases/therapeutic use ; Plants/enzymology ; Wound Healing
    Chemical Substances Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2017-11-26
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 1319315-6
    ISSN 1875-533X ; 0929-8673
    ISSN (online) 1875-533X
    ISSN 0929-8673
    DOI 10.2174/0929867325666171123204403
    Database MEDical Literature Analysis and Retrieval System OnLINE

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