1
|
Pečar Fonović U, Kos J, Mitrović A. Compensational role between cathepsins. Biochimie 2024:S0300-9084(24)00085-3. [PMID: 38663456 DOI: 10.1016/j.biochi.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Cathepsins, a family of lysosomal peptidases, play a crucial role in maintaining cellular homeostasis by regulating protein turnover and degradation as well as many specific regulatory actions that are important for proper cell function and human health. Alterations in the activity and expression of cathepsins have been observed in many diseases such as cancer, inflammation, neurodegenerative disorders, bone remodelling-related conditions and others. These changes are not exclusively harmful, but rather appear to be a compensatory response on the lack of one cathepsin in order to maintain tissue integrity. The upregulation of specific cathepsins in response to the inhibition or dysfunction of other cathepsins suggests a fine-tuned system of proteolytic balance and understanding the compensatory role of cathepsins may improve therapeutic potential of cathepsin's inhibitors. Selectively targeting one cathepsin or modulating their activity could offer new treatment strategies for a number of diseases. This review emphasises the need for comprehensive research into cathepsin biology in the context of disease. The identification of the specific cathepsins involved in compensatory responses, the elucidation of the underlying molecular mechanisms and the development of targeted interventions could lead to innovative therapeutic approaches.
Collapse
Affiliation(s)
- Urša Pečar Fonović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Ana Mitrović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| |
Collapse
|
2
|
Lockwood TD. Coordination chemistry suggests that independently observed benefits of metformin and Zn 2+ against COVID-19 are not independent. Biometals 2024:10.1007/s10534-024-00590-5. [PMID: 38578560 DOI: 10.1007/s10534-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024]
Abstract
Independent trials indicate that either oral Zn2+ or metformin can separately improve COVID-19 outcomes by approximately 40%. Coordination chemistry predicts a mechanistic relationship and therapeutic synergy. Zn2+ deficit is a known risk factor for both COVID-19 and non-infectious inflammation. Most dietary Zn2+ is not absorbed. Metformin is a naked ligand that presumably increases intestinal Zn2+ bioavailability and active absorption by cation transporters known to transport metformin. Intracellular Zn2+ provides a natural buffer of many protease reactions; the variable "set point" is determined by Zn2+ regulation or availability. A Zn2+-interactive protease network is suggested here. The two viral cysteine proteases are therapeutic targets against COVID-19. Viral and many host proteases are submaximally inhibited by exchangeable cell Zn2+. Inhibition of cysteine proteases can improve COVID-19 outcomes and non-infectious inflammation. Metformin reportedly enhances the natural moderating effect of Zn2+ on bioassayed proteome degradation. Firstly, the dissociable metformin-Zn2+ complex could be actively transported by intestinal cation transporters; thereby creating artificial pathways of absorption and increased body Zn2+ content. Secondly, metformin Zn2+ coordination can create a non-natural protease inhibitor independent of cell Zn2+ content. Moderation of peptidolytic reactions by either or both mechanisms could slow (a) viral multiplication (b) viral invasion and (c) the pathogenic host inflammatory response. These combined actions could allow development of acquired immunity to clear the infection before life-threatening inflammation. Nirmatrelvir (Paxlovid®) opposes COVID-19 by selective inhibition the viral main protease by a Zn2+-independent mechanism. Pending safety evaluation, predictable synergistic benefits of metformin and Zn2+, and perhaps metformin/Zn2+/Paxlovid® co-administration should be investigated.
Collapse
Affiliation(s)
- Thomas D Lockwood
- Department Pharmacology and Toxicology, School of Medicine, Wright State University, Dayton, OH, 45435, USA.
| |
Collapse
|
3
|
Yin Y, Wang B, Yang M, Chen J, Li T. Gastric cancer prognosis: unveiling autophagy-related signatures and immune infiltrates. Transl Cancer Res 2024; 13:1479-1492. [PMID: 38617515 PMCID: PMC11009815 DOI: 10.21037/tcr-23-1755] [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: 09/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background Autophagy played a crucial regulatory role in tumor initiation and progression. Therefore, we aimed to comprehensively analyze autophagy-related genes (ARGs) in gastric cancer, focusing on their expression, prognostic value, and potential functions. Methods The gastric cancer gene chip datasets (GSE79973 and GSE54129) were collected from the Gene Expression Omnibus (GEO) database. Subsequently, the Limma package was employed to identify differentially expressed genes (DEGs) between the normal and disease groups. The selected ARGs were further authenticated using the Human Protein Atlas (HPA) database, The Cancer Genome Atlas (TCGA) database, and GSE19826 database. Results A total of 15 autophagy-related DEGs, eight of which were upregulated [FKBP1A, IL24, PEA15, HSP90AB1, cathepsin B (CTSB), ITGB1, SPHK1, HIF1A], while seven were downregulated (DAPK2, EIF2AK3, FKBP1B, PTK6, NKX2-3, NFE2L2, PRKCD). Analysis revealed that CTSB was specifically associated with the prognosis of gastric cancer patients. Gene set enrichment analysis (GSEA) showcased a significant enrichment of CTSB-related genes within immune-related pathways. Moreover, correlation analysis demonstrated a clear association between the expression of CTSB and immune infiltration. The upregulation of CTSB in gastric cancer was linked to poor survival and increased immune infiltration. Conclusions We conjectured that CTSB likely played a critical role in regulating immunity and autophagy in gastric cancer.
Collapse
Affiliation(s)
- Yichen Yin
- School of Clinical Medicine, Ningxia Medical University, Ningxia, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Baozhen Wang
- School of Clinical Medicine, Ningxia Medical University, Ningxia, China
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
| | - Mingzhe Yang
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Jing Chen
- Key Laboratory of Fertility Preservation and Maintenance (Ningxia Medical University), Ministry of Education, Yinchuan, China
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Tao Li
- Department of Surgical Oncology, Tumor Hospital, The General Hospital of Ningxia Medical University, Yinchuan, China
| |
Collapse
|
4
|
Zhang X, Liang B, Huang Y, Meng H, Li Z, Du J, Zhou L, Zhong Y, Wang B, Lin X, Yu G, Chen X, Lu W, Chen Z, Yang X, Huang Z. Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303753. [PMID: 37991139 PMCID: PMC10754125 DOI: 10.1002/advs.202303753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/28/2023] [Indexed: 11/23/2023]
Abstract
The increased use of low-dose computed tomography screening has led to more frequent detection of early stage lung tumors, including minimally invasive adenocarcinoma (MIA). To unravel the intricacies of tumor cells and the immune microenvironment in MIA, this study performs a comprehensive single-cell transcriptomic analysis and profiles the transcriptomes of 156,447 cells from fresh paired MIA and invasive adenocarcinoma (IA) tumor samples, peripheral blood mononuclear cells, and adjacent normal tissue samples from three patients with synchronous multiple primary lung adenocarcinoma. This study highlights a connection and heterogeneity between the tumor ecosystem of MIA and IA. MIA tumor cells exhibited high expression of aquaporin-1 and angiotensin II receptor type 2 and a basal-like molecular character. Furthermore, it identifies that cathepsin B+ tumor-associated macrophages may over-activate CD8+ T cells in MIA, leading to an enrichment of granzyme K+ senescent CD8+ T cells, indicating the possibility of malignant progression behind the indolent appearance of MIA. These findings are further validated in 34 MIA and 35 IA samples by multiplexed immunofluorescence. These findings provide valuable insights into the mechanisms that maintain the indolent nature and prompt tumor progression of MIA and can be used to develop more effective therapeutic targets and strategies for MIA patients.
Collapse
Affiliation(s)
- Xin Zhang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Boxuan Liang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Hao Meng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Lang Zhou
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Bo Wang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xi Lin
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Guangchuang Yu
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Xuewei Chen
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Weixiang Lu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Zhe‐Sheng Chen
- College of Pharmacy and Health SciencesSt. John's UniversityQueensNY11439USA
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| |
Collapse
|
5
|
Zhao S, Jiang M, Qing H, Ni J. Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets. Br J Pharmacol 2023; 180:2455-2481. [PMID: 37403614 DOI: 10.1111/bph.16187] [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: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.
Collapse
Affiliation(s)
- Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| |
Collapse
|
6
|
Bai X, Schountz T, Buckle AM, Talbert JL, Sandhaus RA, Chan ED. Alpha-1-antitrypsin antagonizes COVID-19: a review of the epidemiology, molecular mechanisms, and clinical evidence. Biochem Soc Trans 2023; 51:1361-1375. [PMID: 37294003 PMCID: PMC10317171 DOI: 10.1042/bst20230078] [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: 03/07/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
Alpha-1-antitrypsin (AAT), a serine protease inhibitor (serpin), is increasingly recognized to inhibit SARS-CoV-2 infection and counter many of the pathogenic mechanisms of COVID-19. Herein, we reviewed the epidemiologic evidence, the molecular mechanisms, and the clinical evidence that support this paradigm. As background to our discussion, we first examined the basic mechanism of SARS-CoV-2 infection and contend that despite the availability of vaccines and anti-viral agents, COVID-19 remains problematic due to viral evolution. We next underscored that measures to prevent severe COVID-19 currently exists but teeters on a balance and that current treatment for severe COVID-19 remains grossly suboptimal. We then reviewed the epidemiologic and clinical evidence that AAT deficiency increases risk of COVID-19 infection and of more severe disease, and the experimental evidence that AAT inhibits cell surface transmembrane protease 2 (TMPRSS2) - a host serine protease required for SARS-CoV-2 entry into cells - and that this inhibition may be augmented by heparin. We also elaborated on the panoply of other activities of AAT (and heparin) that could mitigate severity of COVID-19. Finally, we evaluated the available clinical evidence for AAT treatment of COVID-19.
Collapse
Affiliation(s)
- Xiyuan Bai
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, U.S.A
- Department of Academic Affairs, National Jewish Health, Denver, CO, U.S.A
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, U.S.A
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- PTNG Bio, Melbourne, Australia
| | - Janet L. Talbert
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, U.S.A
| | | | - Edward D. Chan
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, U.S.A
- Department of Academic Affairs, National Jewish Health, Denver, CO, U.S.A
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, U.S.A
| |
Collapse
|
7
|
Milan Bonotto R, Mitrović A, Sosič I, Martinez-Orellana P, Dattola F, Gobec S, Kos J, Marcello A. Cathepsin inhibitors nitroxoline and its derivatives inhibit SARS-CoV-2 infection. Antiviral Res 2023:105655. [PMID: 37355023 PMCID: PMC10287183 DOI: 10.1016/j.antiviral.2023.105655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The severity of the SARS-CoV-2 pandemic and the recurring (re)emergence of viruses prompted the development of new therapeutic approaches that target viral and host factors crucial for viral infection. Among them, host peptidases cathepsins B and L have been described as essential enzymes during SARS-CoV-2 entry. In this study, we evaluated the effect of potent selective cathepsin inhibitors as antiviral agents. We demonstrated that selective cathepsin B inhibitors, such as the antimicrobial agent nitroxoline and its derivatives, impair SARS-CoV-2 infection in vitro. Antiviral activity observed at early stage of virus entry was cell-type dependent and correlated well with the intracellular content and enzymatic function of cathepsins B or L. Furthermore, tested inhibitors were effective against the ancestral SARS-CoV-2 D614 as well as against the more recent BA.1_4 (Omicron). Taken together, our results highlight the important role of host cysteine cathepsin B in SARS-CoV-2 virus entry and show that cathepsin-specific inhibitors, such as nitroxoline and its derivatives, could be used to treat COVID-19. Finally, these results also suggest that nitroxoline has potential to be further explored as repurposed drug in antiviral therapy.
Collapse
Affiliation(s)
- Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Pamela Martinez-Orellana
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Federica Dattola
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy.
| |
Collapse
|
8
|
Zulkifli ND, Zulkifle N. Insight from sirtuins interactome: topological prominence and multifaceted roles of SIRT1 in modulating immunity, aging and cancer. Genomics Inform 2023; 21:e23. [PMID: 37557919 PMCID: PMC10326532 DOI: 10.5808/gi.23003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 07/08/2023] Open
Abstract
The mammalian sirtuin family, consisting of SIRT1-SIRT7, plays a vital role in various biological processes, including cancer, diabetes, neurodegeneration, cardiovascular disease, cellular metabolism, and cellular homeostasis maintenance. Due to their involvement in these biological processes, modulating sirtuin activity seems promising to impact immune- and aging-related diseases, as well as cancer pathways. However, more understanding is required regarding the safety and efficacy of sirtuin-targeted therapies due to the complex regulatory mechanisms that govern their activity, particularly in the context of multiple targets. In this study, the interaction landscape of the sirtuin family was analyzed using a systems biology approach. A sirtuin protein-protein interaction network was built using the Cytoscape platform and analyzed using the NetworkAnalyzer and stringApp plugins. The result revealed the sirtuin family's association with numerous proteins that play diverse roles, suggesting a complex interplay between sirtuins and other proteins. Based on network topological and functional analysis, SIRT1 was identified as the most prominent among sirtuin family members, demonstrating that 25 of its protein partners are involved in cancer, 22 in innate immune response, and 29 in aging, with some being linked to a combination of two or more pathways. This study lays the foundation for the development of novel therapies that can target sirtuins with precision and efficacy. By illustrating the various interactions among the proteins in the sirtuin family, we have revealed the multifaceted roles of SIRT1 and provided a framework for their possible roles to be precisely understood, manipulated, and translated into therapeutics in the future.
Collapse
Affiliation(s)
- Nur Diyana Zulkifli
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Nurulisa Zulkifle
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| |
Collapse
|
9
|
Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
Collapse
Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
| |
Collapse
|
10
|
Rivera RG, Regidor PJS, Ruamero Jr EC, Allanigue EJV, Salinas MV. A network pharmacology and molecular docking approach in the exploratory investigation of the biological mechanisms of lagundi (Vitex negundo L.) compounds against COVID-19. Genomics Inform 2023; 21:e4. [PMID: 37037462 PMCID: PMC10085743 DOI: 10.5808/gi.22060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/27/2022] [Accepted: 02/08/2023] [Indexed: 04/03/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available, treatment of the disease is primarily supportive and symptomatic. Several research have suggested the potential of herbal medicines as an adjunctive treatment for the disease. A popular herbal medicine approved in the Philippines for the treatment of acute respiratory disease is Vitex negundo L. In fact, the Department of Science and Technology of the Philippines has funded a clinical trial to establish its potential as an adjunctive treatment for COVID-19. Here, we utilized network pharmacology and molecular docking in determining pivotal targets of Vitex negundo compounds against COVID-19. The results showed that significant targets of Vitex negundo compounds in COVID-19 are CSB, SERPINE1, and PLG which code for cathepsin B, plasminogen activator inhibitor-1, and plasminogen, respectively. Molecular docking revealed that α-terpinyl acetate and geranyl acetate have good binding affinity in cathepsin B; 6,7,4-trimethoxyflavanone, 5,6,7,8,3',4',5'-heptamethoxyflavone, artemetin, demethylnobiletin, gardenin A, geranyl acetate in plasminogen; and 7,8,4-trimethoxyflavanone in plasminogen activator inhibitor-1. While the results are promising, these are bound to the limitations of computational methods and further experimentation are needed to completely establish the molecular mechanisms of Vitex negundo against COVID-19.
Collapse
Affiliation(s)
- Robertson G. Rivera
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Patrick Junard S. Regidor
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Edwin C. Ruamero Jr
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Eric John V. Allanigue
- Department of Pharmacology and Toxicology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Melanie V. Salinas
- Safety and Medical Affairs Department, Clinchoice Inc., Fort Washington, PA 19034, USA
| |
Collapse
|
11
|
Rashidieh B, Bain AL, Tria SM, Sharma S, Stewart CA, Simmons JL, Apaja PM, Duijf PHG, Finnie J, Khanna KK. Alpha-B-Crystallin overexpression is sufficient to promote tumorigenesis and metastasis in mice. Exp Hematol Oncol 2023; 12:4. [PMID: 36624493 PMCID: PMC9830749 DOI: 10.1186/s40164-022-00365-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND αB-Crystallin is a heat shock chaperone protein which binds to misfolded proteins to prevent their aggregation. It is overexpressed in a wide-variety of cancers. Previous studies using human cancer cell lines and human xenograft models have suggested potential tumor promoter (oncogene) roles for αB-Crystallin in a wide-spectrum of cancers. METHODS To determine the causal relationship between CRYAB overexpression and cancer, we generated a Cryab overexpression knock-in mouse model and monitor them for development of spontaneous and carcinogen (DMBA)-induced tumorigenesis. In order to investigate the mechanism of malignancies observed in this model multiple techniques were used such as immunohistochemical characterizations of tumors, bioinformatics analysis of publically available human tumor datasets, and generation of mouse embryonic fibroblasts (MEFs) for in vitro assays (clonogenic survival and migration assays and proteome analysis by mass-spectrometry). RESULTS This model revealed that constitutive overexpression of Cryab results in the formation of a variety of lethal spontaneous primary and metastatic tumors in mice. In vivo, the overexpression of Cryab correlated with the upregulation of epithelial-to-mesenchymal (EMT) markers, angiogenesis and some oncogenic proteins including Basigin. In vitro, using E1A/Ras transformed MEFs, we observed that the overexpression of Cryab led to the promotion of cell survival via upregulation of Akt signaling and downregulation of pro-apoptotic pathway mediator JNK, with subsequent attenuation of apoptosis as assessed by cleaved caspase-3 and Annexin V staining. CONCLUSIONS Overall, through the generation and characterization of Cryab overexpression model, we provide evidence supporting the role of αB-Crystallin as an oncogene, where its upregulation is sufficient to induce tumors, promote cell survival and inhibit apoptosis.
Collapse
Affiliation(s)
- Behnam Rashidieh
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1003.20000 0000 9320 7537School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4006 Australia
| | - Amanda Louise Bain
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Simon Manuel Tria
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, Brisbane, QLD 4111 Australia
| | - Sowmya Sharma
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Cameron Allan Stewart
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, Brisbane, QLD 4111 Australia
| | - Jacinta Ley Simmons
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Pirjo M. Apaja
- grid.430453.50000 0004 0565 2606South Australian Health and Medical Research Institute, Lifelong Health, Organelle Proteostasis Diseases, Adelaide, SA 5000 Australia ,grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA 5000 Australia ,grid.1014.40000 0004 0367 2697College of Public Health and Medicine, Flinders University, Bedford Park, SA 5042 Australia
| | - Pascal H. G. Duijf
- grid.1024.70000000089150953School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia ,grid.1024.70000000089150953Centre for Data Science, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia ,grid.1024.70000000089150953Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4000 Australia ,grid.1024.70000000089150953Cancer and Aging Research Program, Queensland University of Technology, Brisbane, QLD 4000 Australia ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway
| | - John Finnie
- grid.1010.00000 0004 1936 7304Discipline of Anatomy and Pathology, Adelaide Medical School, University of Adelaide, Adelaide, SA 5000 Australia
| | - Kum Kum Khanna
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| |
Collapse
|
12
|
Zhou L, Hou W, Wang Y, Lin X, Hu J, Li J, Liu C, Liu H, Li H. An extracellular matrix biosensing mimetic for evaluating cathepsin as a host target for COVID-19. Anal Chim Acta 2022; 1225:340267. [PMID: 36038228 PMCID: PMC9380907 DOI: 10.1016/j.aca.2022.340267] [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: 07/08/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/25/2022]
Abstract
To combat the new virus currently ravaging the whole world, every possible anti-virus strategy should be explored. As the main strategy of targeting the virus itself is being frustrated by the rapid mutation of the virus, people are seeking an alternative "host targeting" strategy: neutralizing proteins in the human body that cooperate with the virus. The cathepsin family is such a group of promising host targets, the main biological function of which is to digest the extracellular matrix (ECM) to clear a path for virus spreading. To evaluate the potential of cathepsin as a host target, we have constructed a biosensing interface mimicking the ECM, which can detect cathepsin from 3.3 pM to 33 nM with the limit of detection of 1 pM. Based on our quantitative analysis enabled by this biosensing interface, it is clear that patients with background diseases such as chronic inflammation and tumor, tend to have higher cathepsin activity, confirming the potential of cathepsin to serve as a host target for combating COVID-19 virus.
Collapse
Affiliation(s)
- Lei Zhou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China; Shandong Keyuan Pharmaceutical Co., Ltd, 250022, China.
| | - Wenmin Hou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China
| | - Ying Wang
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China
| | - Xia Lin
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China
| | - Jianguo Hu
- Department of Food Science and Nutrition, College of Culture and Tourism, University of Jinan, 13#, Shungeng Road, Jinan, 250000, China
| | - Jinlong Li
- Department of Laboratory Medicine, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Chen Liu
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China.
| | - Hongkai Liu
- Department of Food Science and Nutrition, College of Culture and Tourism, University of Jinan, 13#, Shungeng Road, Jinan, 250000, China.
| | - Hao Li
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China.
| |
Collapse
|
13
|
Jain M, Bouilloux J, Borrego I, Cook S, van den Bergh H, Lange N, Wagnieres G, Giraud MN. Cathepsin B-Cleavable Polymeric Photosensitizer Prodrug for Selective Photodynamic Therapy: In Vitro Studies. Pharmaceuticals (Basel) 2022; 15:564. [PMID: 35631388 PMCID: PMC9146285 DOI: 10.3390/ph15050564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
Cathepsin B is a lysosomal cysteine protease that plays an important role in cancer, atherosclerosis, and other inflammatory diseases. The suppression of cathepsin B can inhibit tumor growth. The overexpression of cathepsin B can be used for the imaging and photodynamic therapy (PDT) of cancer. PDT targeting of cathepsin B may have a significant potential for selective destruction of cells with high cathepsin B activity. We synthesized a cathepsin B-cleavable polymeric photosensitizer prodrug (CTSB-PPP) that releases pheophorbide a (Pha), an efficient photosensitizer upon activation with cathepsin B. We determined the concentration dependant uptake in vitro, the safety, and subsequent PDT-induced toxicity of CTSB-PPP, and ROS production. CTSB-PPP was cleaved in bone marrow cells (BMCs), which express a high cathepsin B level. We showed that the intracellular fluorescence of Pha increased with increasing doses (3-48 µM) and exerted significant dark toxicity above 12 µM, as assessed by MTT assay. However, 6 µM showed no toxicity on cell viability and ex vivo vascular function. Time-dependent studies revealed that cellular accumulation of CTSB-PPP (6 µM) peaked at 60 min of treatment. PDT (light dose: 0-100 J/cm2, fluence rate: 100 mW/cm2) was applied after CTSB-PPP treatment (6 µM for 60 min) using a special frontal light diffuser coupled to a diode laser (671 nm). PDT resulted in a light dose-dependent reduction in the viability of BMCs and was associated with an increased intracellular ROS generation. Fluorescence and ROS generation was significantly reduced when the BMCs were pre-treated with E64-d, a cysteine protease inhibitor. In conclusion, we provide evidence that CTSB-PPP showed no dark toxicity at low concentrations. This probe could be utilized as a potential imaging agent to identify cells or tissues with cathepsin B activity. CTSB-PPP-based PDT results in effective cytotoxicity and thus, holds great promise as a therapeutic agent for achieving the selective destruction of cells with high cathepsin B activity.
Collapse
Affiliation(s)
- Manish Jain
- Department EMC, Faculty of Sciences and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland; (M.J.); (I.B.); (S.C.)
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh 160014, India
| | - Jordan Bouilloux
- School of Pharmaceutical Sciences, Laboratory of Pharmaceutical Technology, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, CH-1211 Genève, Switzerland; (J.B.); (N.L.)
| | - Ines Borrego
- Department EMC, Faculty of Sciences and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland; (M.J.); (I.B.); (S.C.)
| | - Stéphane Cook
- Department EMC, Faculty of Sciences and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland; (M.J.); (I.B.); (S.C.)
- HFR Hôpital Fribourgeois, CH-1708 Fribourg, Switzerland
| | - Hubert van den Bergh
- Medical Photonics Group, LCOM-ISIC, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland;
| | - Norbert Lange
- School of Pharmaceutical Sciences, Laboratory of Pharmaceutical Technology, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, CH-1211 Genève, Switzerland; (J.B.); (N.L.)
| | - Georges Wagnieres
- Laboratory for Functional and Metabolic Imaging, LIFMET, Swiss Federal Institute of Technology (EPFL), CH-1105 Lausanne, Switzerland;
| | - Marie-Noelle Giraud
- Department EMC, Faculty of Sciences and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland; (M.J.); (I.B.); (S.C.)
| |
Collapse
|