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Zuo Z, Mu Y, Qi F, Zhang H, Li Z, Zhou T, Guo W, Guo K, Hu X, Yao Z. Influenza Vaccination Mediates SARS-CoV-2 Spike Protein Peptide-Induced Inflammatory Response via Modification of Histone Acetylation. Vaccines (Basel) 2024; 12:731. [PMID: 39066369 PMCID: PMC11281326 DOI: 10.3390/vaccines12070731] [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: 04/29/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 07/28/2024] Open
Abstract
The effectiveness of coronavirus disease 2019 (COVID-19) vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain rapidly wanes over time. Growing evidence from epidemiological studies suggests that influenza vaccination is associated with a reduction in the risk of SARS-CoV-2 infection and COVID-19 severity. However, the underlying mechanisms remain elusive. Here, we investigate the cross-reactive immune responses of influenza vaccination to SARS-CoV-2 spike protein peptides based on in vitro study. Our data indicate enhanced activation-induced-marker (AIM) expression on CD4+ T cells in influenza-vaccination (IV)-treated peripheral blood mononuclear cells (PBMCs) upon stimulation with spike-protein-peptide pools. The fractions of other immune cell subtypes, including CD8+ T cells, monocytes, NK cells, and antigen-presenting cells, were not changed between IV-treated and control PBMCs following ex vivo spike-protein-peptide stimulation. However, the classical antiviral (IFN-γ) and anti-inflammatory (IL-1RA) cytokine responses to spike-protein-peptide stimulation were still enhanced in PBMCs from both IV-immunized adult and aged mice. Decreased expression of proinflammatory IL-1β, IL-12p40, and TNF-α is associated with inhibited levels of histone acetylation in PBMCs from IV-treated mice. Remarkably, prior immunity to SARS-CoV-2 does not result in modification of histone acetylation or hemagglutinin-protein-induced cytokine responses. This response is antibody-independent but can be mediated by manipulating the histone acetylation of PBMCs. These data experimentally support that influenza vaccination could induce modification of histone acetylation in immune cells and reveal the existence of potential cross-reactive immunity to SARS-CoV-2 antigens, which may provide insights for the adjuvant of influenza vaccine to limit COVID-19-related inflammatory responses.
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Affiliation(s)
- Zejie Zuo
- Department of Rehabilitation Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China; (Z.Z.)
| | - Yating Mu
- Department of Rehabilitation Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China; (Z.Z.)
| | - Fangfang Qi
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hongyang Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhihui Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Tuo Zhou
- Guangzhou Women and Children’s Medical Center, Guangzhou 510620, China
| | - Wenhai Guo
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Kaihua Guo
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiquan Hu
- Department of Rehabilitation Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China; (Z.Z.)
| | - Zhibin Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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2
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Alkhofash NF, Ali BR. The Evaluation of Drugs as Potential Modulators of the Trafficking and Maturation of ACE2, the SARS-CoV-2 Receptor. Biomolecules 2024; 14:764. [PMID: 39062478 PMCID: PMC11274373 DOI: 10.3390/biom14070764] [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: 05/18/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
ACE2, part of the angiotensin-converting enzyme family and the renin-angiotensin-aldosterone system (RAAS), plays vital roles in cardiovascular and renal functions. It is also the primary receptor for SARS-CoV-2, enabling its entry into cells. This project aimed to study ACE2's cellular trafficking and maturation to the cell surface and assess the impact of various drugs and compounds on these processes. We used cellular and biochemical analyses to evaluate these compounds as potential leads for COVID-19 therapeutics. Our screening assay focused on ACE2 maturation levels and subcellular localization with and without drug treatments. Results showed that ACE2 maturation is generally fast and robust, with certain drugs having a mild impact. Out of twenty-three tested compounds, eight significantly reduced ACE2 maturation levels, and three caused approximately 20% decreases. Screening trafficking inhibitors revealed significant effects from most molecular modulators of protein trafficking, mild effects from most proposed COVID-19 drugs, and no effects from statins. This study noted that manipulating ACE2 levels could be beneficial or harmful, depending on the context. Thus, using this approach to uncover leads for COVID-19 therapeutics requires a thorough understanding ACE2's biogenesis and biology.
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Affiliation(s)
- Nesreen F. Alkhofash
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
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3
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Verma A, Bhagchandani T, Rai A, Nikita, Sardarni UK, Bhavesh NS, Gulati S, Malik R, Tandon R. Short-Chain Fatty Acid (SCFA) as a Connecting Link between Microbiota and Gut-Lung Axis-A Potential Therapeutic Intervention to Improve Lung Health. ACS OMEGA 2024; 9:14648-14671. [PMID: 38585101 PMCID: PMC10993281 DOI: 10.1021/acsomega.3c05846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 04/09/2024]
Abstract
The microbiome is an integral part of the human gut, and it plays a crucial role in the development of the immune system and homeostasis. Apart from the gut microbiome, the airway microbial community also forms a distinct and crucial part of the human microbiota. Furthermore, several studies indicate the existence of communication between the gut microbiome and their metabolites with the lung airways, called "gut-lung axis". Perturbations in gut microbiota composition, termed dysbiosis, can have acute and chronic effects on the pathophysiology of lung diseases. Microbes and their metabolites in lung stimulate various innate immune pathways, which modulate the expression of the inflammatory genes in pulmonary leukocytes. For instance, gut microbiota-derived metabolites such as short-chain fatty acids can suppress lung inflammation through the activation of G protein-coupled receptors (free fatty acid receptors) and can also inhibit histone deacetylase, which in turn influences the severity of acute and chronic respiratory diseases. Thus, modulation of the gut microbiome composition through probiotic/prebiotic usage and fecal microbiota transplantation can lead to alterations in lung homeostasis and immunity. The resulting manipulation of immune cells function through microbiota and their key metabolites paves the way for the development of novel therapeutic strategies in improving the lung health of individuals affected with various lung diseases including SARS-CoV-2. This review will shed light upon the mechanistic aspect of immune system programming through gut and lung microbiota and exploration of the relationship between gut-lung microbiome and also highlight the therapeutic potential of gut microbiota-derived metabolites in the management of respiratory diseases.
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Affiliation(s)
- Anjali Verma
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tannu Bhagchandani
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ankita Rai
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nikita
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Urvinder Kaur Sardarni
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Neel Sarovar Bhavesh
- Transcription
Regulation Group, International Centre for
Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Sameer Gulati
- Department
of Medicine, Lady Hardinge Medical College
(LHMC), New Delhi 110058, India
| | - Rupali Malik
- Department
of Medicine, Vardhman Mahavir Medical College
and Safdarjung Hospital, New Delhi 110029, India
| | - Ravi Tandon
- Laboratory
of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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4
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Naik N, Patel M, Sen R. Developmental Impacts of Epigenetics and Metabolism in COVID-19. J Dev Biol 2024; 12:9. [PMID: 38390960 PMCID: PMC10885083 DOI: 10.3390/jdb12010009] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Developmental biology is intricately regulated by epigenetics and metabolism but the mechanisms are not completely understood. The situation becomes even more complicated during diseases where all three phenomena are dysregulated. A salient example is COVID-19, where the death toll exceeded 6.96 million in 4 years, while the virus continues to mutate into different variants and infect people. Early evidence during the pandemic showed that the host's immune and inflammatory responses to COVID-19 (like the cytokine storm) impacted the host's metabolism, causing damage to the host's organs and overall physiology. The involvement of angiotensin-converting enzyme 2 (ACE2), the pivotal host receptor for the SARS-CoV-2 virus, was identified and linked to epigenetic abnormalities along with other contributing factors. Recently, studies have revealed stronger connections between epigenetics and metabolism in COVID-19 that impact development and accelerate aging. Patients manifest systemic toxicity, immune dysfunction and multi-organ failure. Single-cell multiomics and other state-of-the-art high-throughput studies are only just beginning to demonstrate the extent of dysregulation and damage. As epigenetics and metabolism directly impact development, there is a crucial need for research implementing cutting-edge technology, next-generation sequencing, bioinformatics analysis, the identification of biomarkers and clinical trials to help with prevention and therapeutic interventions against similar threats in the future.
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Affiliation(s)
- Noopur Naik
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Mansi Patel
- Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Rwik Sen
- Active Motif, Inc., Carlsbad, CA 92008, USA
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Banks JM, Capistrano KJ, Brandini DA, Zaidi F, Thakkar P, Rahat R, Schwartz J, Naqvi AR. Herpesviruses and SARS-CoV-2: Viral Association with Oral Inflammatory Diseases. Pathogens 2024; 13:58. [PMID: 38251365 PMCID: PMC10819702 DOI: 10.3390/pathogens13010058] [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: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The oral cavity is a niche for diverse microbes, including viruses. Members of the Herpesviridae family, comprised of dsDNA viruses, as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an ssRNA virus, are among the most prevalent viruses infecting the oral cavity, and they exhibit clinical manifestations unique to oral tissues. Viral infection of oral mucosal epithelia triggers an immune response that results in prolonged inflammation. The clinical and systemic disease manifestations of HHV have been researched extensively, and several recent studies have illuminated the relationship between HHV and oral inflammatory diseases. Burgeoning evidence suggests the oral manifestation of SARS-CoV-2 infection includes xerostomia, dysgeusia, periodontal disease, mucositis, and opportunistic viral and bacterial infections, collectively described as oral post-acute sequelae of COVID-19 (PASC). These diverse sequelae could be a result of intensified immune responses initially due to the copious production of proinflammatory cytokines: the so-called "cytokine storm syndrome", facilitating widespread oral and non-oral tissue damage. This review explores the interplay between HHV, SARS-CoV-2, and oral inflammatory diseases such as periodontitis, endodontic disease, and peri-implantitis. Additionally, the review discusses proper diagnostic techniques for identifying viral infection and how viral diagnostics can lead to improved overall patient health.
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Affiliation(s)
- Jonathan M. Banks
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Kristelle J. Capistrano
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Daniela A. Brandini
- Department of Diagnosis and Surgery, School of Dentistry, São Paulo State University (UNESP), Araçatuba 16015-050, SP, Brazil;
| | - Filza Zaidi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Rani Rahat
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Joel Schwartz
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Afsar R. Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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Ayeldeen G, Shaker OG, Amer E, Zaafan MA, Herzalla MR, Keshk MA, Abdelhamid AM. The Impact of lncRNA-GAS5/miRNA-200/ACE2 Molecular Pathway on the Severity of COVID-19. Curr Med Chem 2024; 31:1142-1151. [PMID: 37190816 DOI: 10.2174/0929867330666230515144133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2), which is responsible for coronavirus disease (COVID-19), potentially has severe adverse effects, leading to public health crises worldwide. In COVID-19, deficiency of ACE-2 is linked to increased inflammation and cytokine storms via increased angiotensin II levels and decreased ACE-2/Mas receptor axis activity. MiRNAs are small sequences of noncoding RNAs that regulate gene expression by binding to the targeted mRNAs. MiR-200 dysfunction has been linked to the development of ARDS following acute lung injury and has been proposed as a key regulator of ACE2 expression. LncRNA growth arrest-specific transcript 5 (GAS5) has been recently studied for its modulatory effect on the miRNA-200/ACE2 axis. OBJECTIVE The current study aims to investigate the role of lncRNA GAS5, miRNA-200, and ACE2 as new COVID-19 diagnostic markers capable of predicting the severity of SARS-CoV-2 complications. METHODS A total of 280 subjects were classified into three groups: COVID-19-negative controls (n = 80), and COVID-19 patients (n=200) who required hospitalization were classified into two groups: group (2) moderate cases (n = 112) and group (3) severe cases (n = 88). RESULTS The results showed that the serum GAS5 expression was significantly down-expressed in COVID-19 patients; as a consequence, the expression of miR-200 was reported to be overexpressed and its targeted ACE2 was down-regulated. The ROC curve was drawn to examine the diagnostic abilities of GAS5, miR-200, and ACE2, yielding high diagnostic accuracy with high sensitivity and specificity. CONCLUSION lncRNA-GAS5, miRNA-200, and ACE2 panels presented great diagnostic potential as they demonstrated the highest diagnostic accuracy for discriminating moderate COVID-19 and severe COVID-19 cases.
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Affiliation(s)
- Ghada Ayeldeen
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eman Amer
- Biochemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Egypt
| | - Mai A Zaafan
- Pharmacology & Toxicology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October City, Egypt
| | - Mohamed R Herzalla
- Internal Medicine Department, Endocrinology & Diabetes Unit, Zagazig University, 6th of October City, Egypt
| | - Mofida A Keshk
- Department of Molecular Diagnostics and Therapeutics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), El-Sadat City, Egypt
| | - Amr M Abdelhamid
- Biochemistry Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October City, Egypt
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7
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Trionfetti F, Alonzi T, Bontempi G, Terri M, Battistelli C, Montaldo C, Repele F, Rotili D, Valente S, Zwergel C, Matusali G, Maggi F, Goletti D, Tripodi M, Mai A, Strippoli R. HDAC1-3 inhibition increases SARS-CoV-2 replication and productive infection in lung mesothelial and epithelial cells. Front Cell Infect Microbiol 2023; 13:1257683. [PMID: 38162580 PMCID: PMC10757821 DOI: 10.3389/fcimb.2023.1257683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024] Open
Abstract
Background Despite the significant progress achieved in understanding the pathology and clinical management of SARS-CoV-2 infection, still pathogenic and clinical issues need to be clarified. Treatment with modulators of epigenetic targets, i.e., epidrugs, is a current therapeutic option in several cancers and could represent an approach in the therapy of viral diseases. Results Aim of this study was the analysis of the role of histone deacetylase (HDAC) inhibition in the modulation of SARS-CoV-2 infection of mesothelial cells (MCs).MeT5A cells, a pleura MC line, were pre-treated with different specific class I and IIb HDAC inhibitors. Unexpectedly, treatment with HDAC1-3 inhibitors significantly increased ACE2/TMPRSS2 expression, suggesting a role in favoring SARS-CoV-2 infection. We focused our analysis on the most potent ACE2/TMPRSS2 inducer among the inhibitors analysed, MS-275, a HDAC1-3 inhibitor. ACE2/TMPRSS2 expression was validated by Western Blot (WB) and immunofluorescence. The involvement of HDAC inhibition in receptor induction was confirmed by HDAC1/HDAC2 silencing. In accordance to the ACE2/TMPRSS2 expression data, MS-275 increased SARS-CoV-2 replication and virus propagation in Vero E6 cells.Notably, MS-275 was able to increase ACE2/TMPRSS2 expression and SARS-CoV-2 production, although to a lesser extent, also in the lung adenocarcinoma cell line Calu-3 cells.Mechanistically, treatment with MS-275 increased H3 and H4 histone acetylation at ACE2/TMPRSS2 promoters, increasing their transcription. Conclusion This study highlights a previously unrecognized effect of HDAC1-3 inhibition in increasing SARS-CoV-2 cell entry, replication and productive infection correlating with increased expression of ACE2 and TMPRSS2. These data, while adding basic insight into COVID-19 pathogenesis, warn for the use of HDAC inhibitors in SARS-CoV-2 patients.
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Affiliation(s)
- Flavia Trionfetti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Tonino Alonzi
- Translational Research Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Rome, Italy
| | - Giulio Bontempi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Michela Terri
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Claudia Montaldo
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Federica Repele
- Translational Research Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Rome, Italy
| | - Marco Tripodi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Raffaele Strippoli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
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8
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Dey A, Vaishak K, Deka D, Radhakrishnan AK, Paul S, Shanmugam P, Daniel AP, Pathak S, Duttaroy AK, Banerjee A. Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review. Infection 2023; 51:1603-1618. [PMID: 36906872 PMCID: PMC10008189 DOI: 10.1007/s15010-023-02017-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023]
Abstract
PURPOSE The COVID-19 pandemic caused by the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has put the world in a medical crisis for the past three years; nearly 6.3 million lives have been diminished due to the virus outbreak. This review aims to update the recent findings on COVID-19 infections from an epigenetic scenario and develop future perspectives of epi-drugs to treat the disease. METHODS Original research articles and review studies related to COVID-19 were searched and analyzed from the Google Scholar/PubMed/Medline databases mainly between 2019 and 2022 to brief the recent work. RESULTS Numerous in-depth studies of the mechanisms used by SARS-CoV-2 have been going on to minimize the consequences of the viral outburst. Angiotensin-Converting Enzyme 2 receptors and Transmembrane serine protease 2 facilitate viral entry to the host cells. Upon internalization, it uses the host machinery to replicate viral copies and alter the downstream regulation of the normal cells, causing infection-related morbidities and mortalities. In addition, several epigenetic regulations such as DNA methylation, acetylation, histone modifications, microRNA, and other factors (age, sex, etc.) are responsible for the regulations of viral entry, its immune evasion, and cytokine responses also play a major modulatory role in COVID-19 severity, which has been discussed in detail in this review. CONCLUSION Findings of epigenetic regulation of viral pathogenicity open a new window for epi-drugs as a possible therapeutical approach against COVID-19.
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Affiliation(s)
- Amit Dey
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - K Vaishak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Dikshita Deka
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Arun Kumar Radhakrishnan
- Department of Pharmacology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, India
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No.500 Fracc., CP 76130, San Pablo, Querétaro, Mexico
| | - Priyadarshini Shanmugam
- Department of Microbiology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, 603103, India
| | - Alice Peace Daniel
- Department of Microbiology, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chennai, TN, 603103, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, TN, 603103, India.
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9
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Man E, Evran S. Deacetylation of Histones and Non-histone Proteins in Inflammatory Diseases and Cancer Therapeutic Potential of Histone Deacetylase Inhibitors. Curr Genomics 2023; 24:136-145. [PMID: 38178983 PMCID: PMC10761333 DOI: 10.2174/0113892029265046231011100327] [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: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/26/2023] [Indexed: 01/06/2024] Open
Abstract
Epigenetic changes play an important role in the pathophysiology of autoimmune diseases such as allergic asthma, multiple sclerosis, lung diseases, diabetes, cystic fibrosis, atherosclerosis, rheumatoid arthritis, and COVID-19. There are three main classes of epigenetic alterations: post-translational modifications of histone proteins, control by non-coding RNA and DNA methylation. Since histone modifications can directly affect chromatin structure and accessibility, they can regulate gene expression levels. Abnormal expression and activity of histone deacetylases (HDACs) have been reported in immune mediated diseases. Increased acetylated levels of lysine residues have been suggested to be related to the overexpression of inflammatory genes. This review focuses on the effect of HDAC modifications on histone and non-histone proteins in autoimmune diseases. Furthermore, we discuss the potential therapeutic effect of HDAC inhibitors (HDACi) used in these diseases.
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Affiliation(s)
- Ezgi Man
- Department of Biochemistry, Faculty of Science, Ege University, 35100, İzmir, Türkiye
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, 35100, Bornova-Izmir, Türkiye
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, 35100, İzmir, Türkiye
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10
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Fišere I, Groma V, Svirskis Š, Strautmane E, Gardovskis A. Evaluation of Clinical Manifestations of Hemorrhoidal Disease, Carried Out Surgeries and Prolapsed Anorectal Tissues: Associations with ABO Blood Groups of Patients. J Clin Med 2023; 12:5119. [PMID: 37568521 PMCID: PMC10420034 DOI: 10.3390/jcm12155119] [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: 06/19/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Hemorrhoidal disease (HD) is a chronic multifactorial disease. Increased abdominal pressure, along with hyperperfusion, neovascularization, overexpression of inflammatory mediators, and dysbiosis, contributes to the development of HD. The deterioration of the anchoring connective tissue with reduced collagen content and altered collagen ratios, dilatation of blood vessels and thrombosis, muscle injury, and inflammation gradually lead to clinically manifesting prolapse and bleeding from hemorrhoids. The associations of the ABO blood types with a disease have been investigated for the upper gastrointestinal tract only. This study aimed to evaluate HD clinical manifestations, surgeries carried out, and the status of prolapsed anorectal tissues by exploring the associations with the patients' ABO blood groups. Clinical and various morphological methods, combined with extensive bioinformatics, were used. The blood type 0, grade III and IV HD individuals constituted the largest group in a moderately-sized cohort of equally represented males and females studied and submitted to surgical treatment of hemorrhoids. There were significantly more complaints reported by HD females compared to males (p = 0.0094). The Longo technique appeared mostly used, and there were proportionally more surgeries performed below the dentate line for HD individuals with blood type 0 compared to other blood type patients (24% vs. 11%). HD males were found to present with significantly more often inflamed rectal mucosa (p < 0.05). Loosening and weakening of collagenous components of the rectal wall combined with vascular dilation and hemorrhage was found to differ in 0 blood type HD individuals compared to other types. HD males were demonstrated to develop the ruptures of vascular beds significantly more often when compared to HD females (p = 0.0165). Furthermore, 0 blood type HD males were significantly more often affected by a disease manifested with tissue hemorrhage compared to the 0 blood type HD females (p = 0.0081). Collectively, the local status of chronically injured anorectal tissue should be considered when applying surgical techniques. Future studies could include patients with HD grades I and II to gain a comprehensive understanding of the disease progression, allowing for a comparison of tissue changes at different disease stages.
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Affiliation(s)
- Inese Fišere
- Department of Doctoral Studies, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
- Surgery Clinic, Pauls Stradins Clinical University Hospital, Pilsonu Street 13, LV-1002 Riga, Latvia;
| | - Valērija Groma
- Institute of Anatomy and Anthropology, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
| | - Šimons Svirskis
- Institute of Microbiology and Virology, Rīga Stradiņš University, Ratsupītes Street 5, LV-1067 Riga, Latvia;
| | - Estere Strautmane
- Medical Faculty, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia;
| | - Andris Gardovskis
- Surgery Clinic, Pauls Stradins Clinical University Hospital, Pilsonu Street 13, LV-1002 Riga, Latvia;
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11
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Zahid S, Ali Y, Rashid S. Structural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection. J Biomol Struct Dyn 2023; 41:14566-14581. [PMID: 36841549 DOI: 10.1080/07391102.2023.2183037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for about 672 million infections and 6.85 million deaths worldwide. Upon SARS-CoV-2 infection, Histone deacetylases (HDACs) hyperactivate the pro-inflammatory response resulting in stimulation of Acetyl-Coenzyme A and cholesterol for viral entry. HDAC3 inhibition results in the anti-inflammatory activity and reduction of pro-inflammatory cytokines that may restrict COVID-19 progression. Here, we have designed 44 conformational ensembles of previously known HD-TAC7 by enumerating torsions of dihedral angles tested for their binding preferences against HDAC3. Through scrutinizing their placements at active site and binding affinities, three hits were isolated. Cereblon (CRBN) is a well-known E3 ligase that facilitates Proteolysis Targeting Chimeras (PROTACs) targeting. Three entities, including HDAC3-binding moiety (4-acetamido-N-(2-amino-4 fluorophenyl) benzamide), a 6-carbon linker, and CRBN binding ligand (pomalidomide) were assembled to design 4 PROTACs followed by energy minimization and docking against HDAC3 and CRBN, respectively. Subsequent molecular dynamics (MD) and free energy analyses corroborated similar binding trends and favorable energy values. Among all cases, Met88, GLu106, Pro352, Trp380 and Trp388 residues of CRBN, and Pro23, Arg28, Lys194, Phe199, Leu266, Thr299 and Ile346 residues of HDAC3 were engaged in PROTAC binding. Thus, conformational dynamics of both HDAC3 and CRBN moieties are essential for the placement of PROTAC, resulting in target degradation. Overall, the proposed bifunctional small molecules may effectively target HDAC3, stimulating innate immune response to restrict COVID-19 hyperinflammation. This study supports the basis for designing new PROTACs by limiting the conformational search space that may prove more efficient for targeting the protein of interest.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sana Zahid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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12
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Capistrano KJ, Richner J, Schwartz J, Mukherjee SK, Shukla D, Naqvi AR. Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166612. [PMID: 36481486 PMCID: PMC9721271 DOI: 10.1016/j.bbadis.2022.166612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
A significant number of SARS-CoV-2-infected individuals naturally overcome viral infection, suggesting the existence of a potent endogenous antiviral mechanism. As an innate defense mechanism, microRNA (miRNA) pathways in mammals have evolved to restrict viruses, besides regulating endogenous mRNAs. In this study, we systematically examined the complete repertoire of human miRNAs for potential binding sites on SARS-CoV-2 Wuhan-Hu-1, Beta, Delta, and Omicron. Human miRNA and viral genome interaction were analyzed using RNAhybrid 2.2 with stringent parameters to identify highly bonafide miRNA targets. Using publicly available data, we filtered for miRNAs expressed in lung epithelial cells/tissue and oral keratinocytes, concentrating on the miRNAs that target SARS-CoV-2 S protein mRNAs. Our results show a significant loss of human miRNA and SARS-CoV-2 interactions in Omicron (130 miRNAs) compared to Wuhan-Hu-1 (271 miRNAs), Beta (279 miRNAs), and Delta (275 miRNAs). In particular, hsa-miR-3150b-3p and hsa-miR-4784 show binding affinity for S protein of Wuhan strain but not Beta, Delta, and Omicron. Loss of miRNA binding sites on N protein was also observed for Omicron. Through Ingenuity Pathway Analysis (IPA), we examined the experimentally validated and highly predicted functional role of these miRNAs. We found that hsa-miR-3150b-3p and hsa-miR-4784 have several experimentally validated or highly predicted target genes in the Toll-like receptor, IL-17, Th1, Th2, interferon, and coronavirus pathogenesis pathways. Focusing on the coronavirus pathogenesis pathway, we found that hsa-miR-3150b-3p and hsa-miR-4784 are highly predicted to target MAPK13. Exploring miRNAs to manipulate viral genome/gene expression can provide a promising strategy with successful outcomes by targeting specific VOCs.
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Affiliation(s)
- Kristelle J Capistrano
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Justin Richner
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Joel Schwartz
- Molecular Pathology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sunil K Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepak Shukla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA; Department of Ophthalmology and Visual Sciences, Ocular Virology Laboratory, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA.
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13
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Bałaban J, Wierzbicki M, Zielińska-Górska M, Sosnowska M, Daniluk K, Jaworski S, Koczoń P, Cysewski D, Chwalibog A, Sawosz E. Graphene Oxide Decreases Pro-Inflammatory Proteins Production in Skeletal Muscle Cells Exposed to SARS-CoV-2 Spike Protein. Nanotechnol Sci Appl 2023; 16:1-18. [PMID: 36699443 PMCID: PMC9869801 DOI: 10.2147/nsa.s391761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
Aim The experiments aimed to document the presence of the ACE2 receptor on human muscle cells and the effects of the interaction of these cells with the spike protein of the SARS-CoV-2 virus in terms of induction of pro-inflammatory proteins, as well as to assess the possibility of reducing the pool of these proteins with the use of graphene oxide (GO) flakes. Methods Human Skeletal Myoblast (HSkM), purchased from Gibco were maintained in standard condition according to the manufacturer's instruction. The cells were divided into 4 groups; 1. C-control, 2. S-with addition of spike protein, 3. GO-with the addition of graphene oxide, 4. GO-S-with addition of GO followed by the addition of S protein. Protein S (PX-COV-P049) was purchased from ProteoGenix (France). GO was obtained from Advanced Graphene Products (Zielona Gora, Poland). The influence of all the factors on the morphology of cells was investigated using light and confocal microscopy. ACE2 protein expression on muscle cells was visualized and 40 pro-inflammatory cytokines were investigated using the membrane antibody array method. The protein profile of the lysate of cells from individual groups was also analyzed by mass spectrometry. Conclusion The experiments confirmed the presence of the ACE2 receptor in human skeletal muscle cells. It has also been documented that the SARS-CoV-2 virus spike protein influences the activation of selected pro-inflammatory proteins that promote cytokine storm and oxidative stress in muscle cells. The use of low levels of graphene oxide does not adversely affect muscle cells, reducing the levels of most proteins, including pro-inflammatory proteins. It can be assumed that GO may support anti-inflammatory therapy in muscles by scavenging proteins that activate cytokine storm.
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Affiliation(s)
- Jaśmina Bałaban
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Mateusz Wierzbicki
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Marlena Zielińska-Górska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Malwina Sosnowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Karolina Daniluk
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Sławomir Jaworski
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Piotr Koczoń
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
| | - André Chwalibog
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark,Correspondence: André Chwalibog, University of Copenhagen, Groennegaardsvej 3, Frederiksberg, 1870, Denmark, Tel +45 40963573, Email
| | - Ewa Sawosz
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
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14
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Yang Z, Liu J, Zhu X, Yang F, Zhang Q, Shah HA. FragDPI: a novel drug-protein interaction prediction model based on fragment understanding and unified coding. FRONTIERS OF COMPUTER SCIENCE 2022; 17:175903. [PMID: 36532946 PMCID: PMC9745276 DOI: 10.1007/s11704-022-2163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/11/2022] [Indexed: 06/17/2023]
Abstract
UNLABELLED Prediction of drug-protein binding is critical for virtual drug screening. Many deep learning methods have been proposed to predict the drug-protein binding based on protein sequences and drug representation sequences. However, most existing methods extract features from protein and drug sequences separately. As a result, they can not learn the features characterizing the drug-protein interactions. In addition, the existing methods encode the protein (drug) sequence usually based on the assumption that each amino acid (atom) has the same contribution to the binding, ignoring different impacts of different amino acids (atoms) on the binding. However, the event of drug-protein binding usually occurs between conserved residue fragments in the protein sequence and atom fragments of the drug molecule. Therefore, a more comprehensive encoding strategy is required to extract information from the conserved fragments. In this paper, we propose a novel model, named FragDPI, to predict the drug-protein binding affinity. Unlike other methods, we encode the sequences based on the conserved fragments and encode the protein and drug into a unified vector. Moreover, we adopt a novel two-step training strategy to train FragDPI. The pre-training step is to learn the interactions between different fragments using unsupervised learning. The fine-tuning step is for predicting the binding affinities using supervised learning. The experiment results have illustrated the superiority of FragDPI. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available for this article at 10.1007/s11704-022-2163-9 and is accessible for authorized users.
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Affiliation(s)
- Zhihui Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Juan Liu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Xuekai Zhu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Feng Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Qiang Zhang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Hayat Ali Shah
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
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15
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Sakamuru S, Huang R, Xia M. Use of Tox21 Screening Data to Evaluate the COVID-19 Drug Candidates for Their Potential Toxic Effects and Related Pathways. Front Pharmacol 2022; 13:935399. [PMID: 35910344 PMCID: PMC9333127 DOI: 10.3389/fphar.2022.935399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
Currently, various potential therapeutic agents for coronavirus disease-2019 (COVID-19), a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are being investigated worldwide mainly through the drug repurposing approach. Several anti-viral, anti-bacterial, anti-malarial, and anti-inflammatory drugs were employed in randomized trials and observational studies for developing new therapeutics for COVID-19. Although an increasing number of repurposed drugs have shown anti-SARS-CoV-2 activities in vitro, so far only remdesivir has been approved by the US FDA to treat COVID-19, and several other drugs approved for Emergency Use Authorization, including sotrovimab, tocilizumab, baricitinib, paxlovid, molnupiravir, and other potential strategies to develop safe and effective therapeutics for SARS-CoV-2 infection are still underway. Many drugs employed as anti-viral may exert unwanted side effects (i.e., toxicity) via unknown mechanisms. To quickly assess these drugs for their potential toxicological effects and mechanisms, we used the Tox21 in vitro assay datasets generated from screening ∼10,000 compounds consisting of approved drugs and environmental chemicals against multiple cellular targets and pathways. Here we summarize the toxicological profiles of small molecule drugs that are currently under clinical trials for the treatment of COVID-19 based on their in vitro activities against various targets and cellular signaling pathways.
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16
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Swati, Rishi P, Chadha VD. Understanding the Epigenetic Mechanisms in SARS CoV-2 Infection and Potential Therapeutic Approaches. Virus Res 2022; 318:198853. [PMID: 35777502 PMCID: PMC9236910 DOI: 10.1016/j.virusres.2022.198853] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/14/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 pandemic caused by the Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) has inflicted a global health challenge. Although the overwhelming escalation of mortality seen during the initial phase of the pandemic has reduced, emerging variants of SARS-CoV-2 continue to impact communities worldwide. Several studies have highlighted the association of gene specific epigenetic modifications in host cells with the pathogenesis and severity of the disease. Therefore, alongside the investigations into the virology and pathogenesis of SARS-CoV-2 infection, understanding the epigenetic mechanisms related to the disease is crucial for the rational design of effective targeted therapies. Here, we discuss the interaction of SARS-CoV-2 with the various epigenetic regulators and their subsequent contribution to the risk of disease severity and dysfunctional immune responses. Finally, we also highlight the use of epigenetically targeted drugs for the potential therapeutic interventions capable of eliminating viral infection and/or build effective immunity against it.
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Affiliation(s)
- Swati
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
| | - Praveen Rishi
- Department of Microbiology, South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
| | - Vijayta D Chadha
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, India-160014.
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Ripamonti C, Spadotto V, Pozzi P, Stevenazzi A, Vergani B, Marchini M, Sandrone G, Bonetti E, Mazzarella L, Minucci S, Steinkühler C, Fossati G. HDAC Inhibition as Potential Therapeutic Strategy to Restore the Deregulated Immune Response in Severe COVID-19. Front Immunol 2022; 13:841716. [PMID: 35592335 PMCID: PMC9111747 DOI: 10.3389/fimmu.2022.841716] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/01/2022] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has had a devastating impact worldwide and has been a great challenge for the scientific community. Vaccines against SARS-CoV-2 are now efficiently lessening COVID-19 mortality, although finding a cure for this infection is still a priority. An unbalanced immune response and the uncontrolled release of proinflammatory cytokines are features of COVID-19 pathophysiology and contribute to disease progression and worsening. Histone deacetylases (HDACs) have gained interest in immunology, as they regulate the innate and adaptative immune response at different levels. Inhibitors of these enzymes have already proven therapeutic potential in cancer and are currently being investigated for the treatment of autoimmune diseases. We thus tested the effects of different HDAC inhibitors, with a focus on a selective HDAC6 inhibitor, on immune and epithelial cells in in vitro models that mimic cells activation after viral infection. Our data indicate that HDAC inhibitors reduce cytokines release by airway epithelial cells, monocytes and macrophages. This anti-inflammatory effect occurs together with the reduction of monocytes activation and T cell exhaustion and with an increase of T cell differentiation towards a T central memory phenotype. Moreover, HDAC inhibitors hinder IFN-I expression and downstream effects in both airway epithelial cells and immune cells, thus potentially counteracting the negative effects promoted in critical COVID-19 patients by the late or persistent IFN-I pathway activation. All these data suggest that an epigenetic therapeutic approach based on HDAC inhibitors represents a promising pharmacological treatment for severe COVID-19 patients.
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Affiliation(s)
- Chiara Ripamonti
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Valeria Spadotto
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Pietro Pozzi
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Andrea Stevenazzi
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Barbara Vergani
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Mattia Marchini
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Giovanni Sandrone
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Emanuele Bonetti
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | | | - Gianluca Fossati
- New Drug Incubator Department, Italfarmaco Group, Cinisello Balsamo, Italy
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18
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Sixto-López Y, Correa-Basurto J. HDAC inhibition as neuroprotection in COVID-19 infection. Curr Top Med Chem 2022; 22:1369-1378. [PMID: 35240959 DOI: 10.2174/1568026622666220303113445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
The SARS-CoV-2 virus is responsible of COVID-19 affecting millions of humans around the world. COVID-19 shows diverse clinical symptoms (fever, cough, fatigue, diarrhea, body aches, headaches, anosmia and hyposmia). Approximately 30% of the patients with COVID-19 showed neurological symptoms, these going from mild to severe manifestations including headache, dizziness, impaired consciousness, encephalopathy, anosmia, hypogeusia, hyposmia, psychology and psychiatry among others. The neurotropism of SARS-CoV-2 virus explains its neuroinvasion provoking neurological damage as acute demyelination, neuroinflammation etc. At molecular level, the COVID-19 patients had higher levels of cytokines and chemokines known as cytokines storms which disrupt the blood brain barrier allowing the entrance of monocytes and lymphocytes causing neuroinflammation, neurodegeneration and demyelination. In addition, ischemic, hemorrhagic strokes, seizures and encephalopathy have been observed due to the proinflammatory cytokines. In this sense, to avoid or decrease neurological damage due to SARS-CoV-2 infection, an early neuroprotective management should be adopted. Several approaches can be used; one of them includes the use of HDAC inhibitors (HDACi) due to their neuroprotective effects. Also, the HDACi down regulates the pro-inflammatory cytokines (IL-6 and TNF- decreasing the neurotoxicity. HDACi can also avoid and prevent the entrance of the virus into the Central nervous System (CNS) as well as decrease the virus replication by downregulating the virus receptors. Here we review the mechanisms that could explain how the SARS-CoV-2 virus could reach the CNS, induce the neurological damage and symptoms, as well as the possibility to use HDACi as neuroprotective therapy.
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Affiliation(s)
- Yudibeth Sixto-López
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México. Plan de San Luis y Díaz Mirón S/N, Casco de Santo Tomas, Miguel Hidalgo, Mexico City, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México. Plan de San Luis y Díaz Mirón S/N, Casco de Santo Tomas, Miguel Hidalgo, Mexico City, Mexico
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19
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Akhmedov VA. Correction of intestinal microbial composition disturbances as a potential link in complex therapy of patients with COVID-19. TERAPEVT ARKH 2022; 94:277-282. [DOI: 10.26442/00403660.2022.02.201388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022]
Abstract
The article reflects the potential for correcting intestinal microbiota disorders in the complex therapy of patients with COVID-19. It has been noted that the inclusion of dietary fiber in the diet contributes to protection against disruption of the integrity of the intestinal barrier and may limit bacterial translocation into the systemic circulation. The possibility of using psyllium (Mucofalk) is reflected, the action of which is realized both through its sorption, cytoprotective and anti-inflammatory properties in viral lesions of the gastrointestinal tract, and through stimulation of the own beneficial intestinal microbiota. The paper presents studies of the prospects for the use of probiotics, synbiotics in the complex therapy of patients with COVID-19. Detailed data are provided on the mechanisms of the positive effect of short-chain fatty acid preparations on reducing the severity of the disease in patients with COVID-19. It was noted that taking the drug Zacofalk leads to a significant increase in its own butyrate-producing microbiota (Faecalibacterium prausnitzii) and suppression of the growth of opportunistic flora with pro-inflammatory activity. The results of a recent study are presented showing that in patients with a mild course of COVID infection with respiratory and intestinal symptoms, the administration of Zakofalk for 30 days (3 tablets per day) led to significantly faster stool normalization (by day 7), persistent normalization of the frequency and consistency of stools by the 21st day and a significantly more pronounced regression of bloating and abdominal pain, as well as a decrease in the risk of developing post-infectious irritable bowel syndrome.
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20
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Zannella C, Rinaldi L, Boccia G, Chianese A, Sasso FC, De Caro F, Franci G, Galdiero M. Regulation of m6A Methylation as a New Therapeutic Option against COVID-19. Pharmaceuticals (Basel) 2021; 14:ph14111135. [PMID: 34832917 PMCID: PMC8625908 DOI: 10.3390/ph14111135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022] Open
Abstract
The rapid spread of SARS-CoV-2 and the resulting pandemic has led to a spasmodic search for approaches able to limit the diffusion of the disease. The epigenetic machinery has aroused considerable interest in the last decades, and much evidence has demonstrated that this type of modification could regulate the early stages of viral infection. Recently it was reported that N6-methyladenosine (m6A) influences SARS-CoV-2 replication, although its role remains to be further investigated. The knockdown of enzymes involved in the m6A pathway could represent an optimal strategy to deepen the epigenetic mechanism. In the present study, we blocked the catalytic activity of the fat mass and obesity-associated protein (FTO) by using the selective inhibitor rhein. We observed a strong broad-spectrum reduction of infectivity caused by various coronaviruses, including SARS-CoV-2. This effect could be due to the modulation of m6A levels and could allow identification of this modification as a new therapeutic target to treat SARS-CoV-2 infection.
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Affiliation(s)
- Carla Zannella
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (M.G.)
| | - Luca Rinaldi
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (L.R.); (F.C.S.)
| | - Giovanni Boccia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (G.B.); (F.D.C.)
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (M.G.)
| | - Ferdinando Carlo Sasso
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (L.R.); (F.C.S.)
| | - Francesco De Caro
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (G.B.); (F.D.C.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (G.B.); (F.D.C.)
- Correspondence:
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.Z.); (A.C.); (M.G.)
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21
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Saiz ML, DeDiego ML, López-García D, Corte-Iglesias V, Baragaño Raneros A, Astola I, Asensi V, López-Larrea C, Suarez-Alvarez B. Epigenetic targeting of the ACE2 and NRP1 viral receptors limits SARS-CoV-2 infectivity. Clin Epigenetics 2021; 13:187. [PMID: 34635175 PMCID: PMC8504098 DOI: 10.1186/s13148-021-01168-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1) receptors for entry into cells, and the serine protease TMPRSS2 for S protein priming. Inhibition of protease activity or the engagement with ACE2 and NRP1 receptors has been shown to be an effective strategy for blocking infectivity and viral spreading. Valproic acid (VPA; 2-propylpentanoic acid) is an epigenetic drug approved for clinical use. It produces potent antiviral and anti-inflammatory effects through its function as a histone deacetylase (HDAC) inhibitor. Here, we propose VPA as a potential candidate to tackle COVID-19, in which rapid viral spread and replication, and hyperinflammation are crucial elements. RESULTS We used diverse cell lines (HK-2, Huh-7, HUVEC, Caco-2, and BEAS-2B) to analyze the effect of VPA and other HDAC inhibitors on the expression of the ACE-2 and NRP-1 receptors and their ability to inhibit infectivity, viral production, and the inflammatory response. Treatment with VPA significantly reduced expression of the ACE2 and NRP1 host proteins in all cell lines through a mechanism mediated by its HDAC inhibitory activity. The effect is maintained after SARS-CoV-2 infection. Consequently, the treatment of cells with VPA before infection impairs production of SARS-CoV-2 infectious viruses, but not that of other ACE2- and NRP1-independent viruses (VSV and HCoV-229E). Moreover, the addition of VPA 1 h post-infection with SARS-CoV-2 reduces the production of infectious viruses in a dose-dependent manner without significantly modifying the genomic and subgenomic messenger RNAs (gRNA and sg mRNAs) or protein levels of N protein. The production of inflammatory cytokines (TNF-α and IL-6) induced by TNF-α and SARS-CoV-2 infection is diminished in the presence of VPA. CONCLUSIONS Our data showed that VPA blocks three essential processes determining the severity of COVID-19. It downregulates the expression of ACE2 and NRP1, reducing the infectivity of SARS-CoV-2; it decreases viral yields, probably because it affects virus budding or virions stability; and it dampens the triggered inflammatory response. Thus, administering VPA could be considered a safe treatment for COVID-19 patients until vaccines have been rolled out across the world.
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Affiliation(s)
- Maria Laura Saiz
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta L DeDiego
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Darío López-García
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Viviana Corte-Iglesias
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Aroa Baragaño Raneros
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ivan Astola
- Intensive Care Department, Hospital Universitario Central de Asturias, Oviedo, Spain.,Translational Microbiology Research Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Victor Asensi
- Infectious Diseases Unit, Translational Research in Infectious Diseases Group, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos López-Larrea
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. .,Department of Immunology, Hospital Universitario Central De Asturias, Oviedo, Spain.
| | - Beatriz Suarez-Alvarez
- Translational Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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22
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Kgatle MM, Lawal IO, Mashabela G, Boshomane TMG, Koatale PC, Mahasha PW, Ndlovu H, Vorster M, Rodrigues HG, Zeevaart JR, Gordon S, Moura-Alves P, Sathekge MM. COVID-19 Is a Multi-Organ Aggressor: Epigenetic and Clinical Marks. Front Immunol 2021; 12:752380. [PMID: 34691068 PMCID: PMC8531724 DOI: 10.3389/fimmu.2021.752380] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
The progression of coronavirus disease 2019 (COVID-19), resulting from a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, may be influenced by both genetic and environmental factors. Several viruses hijack the host genome machinery for their own advantage and survival, and similar phenomena might occur upon SARS-CoV-2 infection. Severe cases of COVID-19 may be driven by metabolic and epigenetic driven mechanisms, including DNA methylation and histone/chromatin alterations. These epigenetic phenomena may respond to enhanced viral replication and mediate persistent long-term infection and clinical phenotypes associated with severe COVID-19 cases and fatalities. Understanding the epigenetic events involved, and their clinical significance, may provide novel insights valuable for the therapeutic control and management of the COVID-19 pandemic. This review highlights different epigenetic marks potentially associated with COVID-19 development, clinical manifestation, and progression.
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Affiliation(s)
- Mankgopo Magdeline Kgatle
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Ismaheel Opeyemi Lawal
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Gabriel Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tebatso Moshoeu Gillian Boshomane
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
- Nuclear and Oncology Division, AXIM Medical (Pty), Midrand
| | - Palesa Caroline Koatale
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Phetole Walter Mahasha
- Precision Medicine and SAMRC Genomic Centre, Grants, Innovation, and Product Development (GIPD) Unit, South African Medical Research Council, Pretoria, South Africa
| | - Honest Ndlovu
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Mariza Vorster
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Hosana Gomes Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Campinas, Brazil
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- South African Nuclear Energy Corporation, Radiochemistry and NuMeRI PreClinical Imaging Facility, Mahikeng, South Africa
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mike Machaba Sathekge
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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23
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Cellular host factors for SARS-CoV-2 infection. Nat Microbiol 2021; 6:1219-1232. [PMID: 34471255 DOI: 10.1038/s41564-021-00958-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has claimed millions of lives and caused a global economic crisis. No effective antiviral drugs are currently available to treat infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The medical need imposed by the pandemic has spurred unprecedented research efforts to study coronavirus biology. Every virus depends on cellular host factors and pathways for successful replication. These proviral host factors represent attractive targets for antiviral therapy as they are genetically more stable than viral targets and may be shared among related viruses. The application of various 'omics' technologies has led to the rapid discovery of proviral host factors that are required for the completion of the SARS-CoV-2 life cycle. In this Review, we summarize insights into the proviral host factors that are required for SARS-CoV-2 infection that were mainly obtained using functional genetic and interactome screens. We discuss cellular processes that are important for the SARS-CoV-2 life cycle, as well as parallels with non-coronaviruses. Finally, we highlight host factors that could be targeted by clinically approved molecules and molecules in clinical trials as potential antiviral therapies for COVID-19.
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24
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Pushparaj PN, Abdulkareem AA, Naseer MI. Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. Front Pharmacol 2021; 12:688227. [PMID: 34531741 PMCID: PMC8438179 DOI: 10.3389/fphar.2021.688227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is the causative agent for coronavirus disease-19 (COVID-19) and belongs to the family Coronaviridae that causes sickness varying from the common cold to more severe illnesses such as severe acute respiratory syndrome, sudden stroke, neurological complications (Neuro-COVID), multiple organ failure, and mortality in some patients. The gene expression profiles of COVID-19 infection models can be used to decipher potential therapeutics for COVID-19 and related pathologies, such as Neuro-COVID. Here, we used the raw RNA-seq reads (Single-End) in quadruplicates derived using Illumina Next Seq 500 from SARS-CoV-infected primary human bronchial epithelium (NHBE) and mock-treated NHBE cells obtained from the Gene Expression Omnibus (GEO) (GSE147507), and the quality control (QC) was evaluated using the CLC Genomics Workbench 20.0 (Qiagen, United States) before the RNA-seq analysis using BioJupies web tool and iPathwayGuide for gene ontologies (GO), pathways, upstream regulator genes, small molecules, and natural products. Additionally, single-cell transcriptomics data (GSE163005) of meta clusters of immune cells from the cerebrospinal fluid (CSF), such as T-cells/natural killer cells (NK) (TcMeta), dendritic cells (DCMeta), and monocytes/granulocyte (monoMeta) cell types for comparison, namely, Neuro-COVID versus idiopathic intracranial hypertension (IIH), were analyzed using iPathwayGuide. L1000 fireworks display (L1000FWD) and L1000 characteristic direction signature search engine (L1000 CDS2) web tools were used to uncover the small molecules that could potentially reverse the COVID-19 and Neuro-COVID-associated gene signatures. We uncovered small molecules such as camptothecin, importazole, and withaferin A, which can potentially reverse COVID-19 associated gene signatures. In addition, withaferin A, trichostatin A, narciclasine, camptothecin, and JQ1 have the potential to reverse Neuro-COVID gene signatures. Furthermore, the gene set enrichment analysis (GSEA) preranked method and Metascape web tool were used to decipher and annotate the gene signatures that were potentially reversed by these small molecules. In conclusion, our study unravels a rapid approach for applying next-generation knowledge discovery (NGKD) platforms to discover small molecules with therapeutic potential against COVID-19 and its related disease pathologies.
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Affiliation(s)
- Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angham Abdulrahman Abdulkareem
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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25
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Al-Saleem J, Granet R, Ramakrishnan S, Ciancetta NA, Saveson C, Gessner C, Zhou Q. Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19. J Chem Inf Model 2021; 61:4058-4067. [PMID: 34297570 PMCID: PMC8340579 DOI: 10.1021/acs.jcim.1c00642] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has motivated researchers all over the world in trying to find effective drugs and therapeutics for treating this disease. To save time, much effort has focused on repurposing drugs known for treating other diseases than COVID-19. To support these drug repurposing efforts, we built the CAS Biomedical Knowledge Graph and identified 1350 small molecules as potentially repurposable drugs that target host proteins and disease processes involved in COVID-19. A computer algorithm-driven drug-ranking method was developed to prioritize those identified small molecules. The top 50 molecules were analyzed according to their molecular functions and included 11 drugs in clinical trials for treating COVID-19 and new candidates that may be of interest for clinical investigation. The CAS Biomedical Knowledge Graph provides researchers an opportunity to accelerate innovation and streamline the investigative process not just for COVID-19 but also in many other diseases.
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Affiliation(s)
- Jacob Al-Saleem
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
| | - Roger Granet
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
| | | | - Natalie A. Ciancetta
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
| | - Catherine Saveson
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
| | - Chris Gessner
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
| | - Qiongqiong Zhou
- CAS, A division of the American Chemical Society,
Columbus, Ohio 43202, United States
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26
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Jardou M, Lawson R. Supportive therapy during COVID-19: The proposed mechanism of short-chain fatty acids to prevent cytokine storm and multi-organ failure. Med Hypotheses 2021; 154:110661. [PMID: 34385045 PMCID: PMC8339546 DOI: 10.1016/j.mehy.2021.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 02/06/2023]
Abstract
The world is currently facing the COVID-19 pandemic that is taking a heavy toll on several countries. While many infected patients have a good prognosis, in some cases the progression can be serious and even lead to death. The commonly seen complications are a cytokine storm and multi-organ failure that require intensive care. The mortality of critically ill patients depends on age, sex, immune state or co-morbidities. There is an urgent need to discover a biomarker to identify early on patients at risk of developing serious complications and to find an effective treatment that could prevent disease progression and critical states. Recent investigations have pointed to the possible contribution of intestinal dysbiosis to the pathophysiology of COVID-19. Herein, we hypothesize that butyrate, a short-chain fatty acid initially produced by the gut microbiota, could be administered as supportive therapy to prevent immune system activation and disease progression.
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Affiliation(s)
- M Jardou
- INSERM, Univ. Limoges, Pharmacology & Transplantation, U1248, F-87000 Limoges, France
| | - R Lawson
- INSERM, Univ. Limoges, Pharmacology & Transplantation, U1248, F-87000 Limoges, France.
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27
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Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-1119. [PMID: 34280732 PMCID: PMC8253661 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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28
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Pham MT, Yang AJ, Kao MS, Gankhuyag U, Zayabaatar E, Jin SLC, Huang CM. Gut probiotic Lactobacillus rhamnosus attenuates PDE4B-mediated interleukin-6 induced by SARS-CoV-2 membrane glycoprotein. J Nutr Biochem 2021; 98:108821. [PMID: 34271099 PMCID: PMC8277543 DOI: 10.1016/j.jnutbio.2021.108821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023]
Abstract
Membrane glycoprotein is the most abundant protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but its role in coronavirus disease 2019 (COVID-19) has not been fully characterized. Mice intranasally inoculated with membrane glycoprotein substantially increased the interleukin (IL)-6, a hallmark of the cytokine storm, in bronchoalveolar lavage fluid (BALF), compared to mice inoculated with green fluorescent protein (GFP). The high level of IL-6 induced by membrane glycoprotein was significantly diminished in phosphodiesterase 4 (PDE4B) knockout mice, demonstrating the essential role of PDE4B in IL-6 signaling. Mycelium fermentation of Lactobacillus rhamnosus (L. rhamnosus) EH8 strain yielded butyric acid, which can down-regulate the PDE4B expression and IL-6 secretion in macrophages. Feeding mice with mycelia increased the relative abundance of commensal L. rhamnosus. Two-week supplementation of mice with L. rhamnosus plus mycelia considerably decreased membrane glycoprotein-induced PDE4B expression and IL-6 secretion. The probiotic activity of L. rhamnosus plus mycelia against membrane glycoprotein was abolished in mice treated with GLPG-0974, an antagonist of free fatty acid receptor 2 (Ffar2). Activation of Ffar2 in the gut-lung axis for down-regulation of the PDE4B-IL-6 signalling may provide targets for development of modalities including probiotics for treatment of the cytokine storm in COVID-19.
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Affiliation(s)
- Minh Tan Pham
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Albert Jackson Yang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Ming-Shan Kao
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Uuganbayar Gankhuyag
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | - Enkhbat Zayabaatar
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan
| | | | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, 32001, Taiwan; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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29
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Chen J, Vitetta L. Modulation of Gut Microbiota for the Prevention and Treatment of COVID-19. J Clin Med 2021; 10:2903. [PMID: 34209870 PMCID: PMC8268324 DOI: 10.3390/jcm10132903] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota is well known to exert multiple benefits on human health including protection from disease causing pathobiont microbes. It has been recognized that healthy intestinal microbiota is of great importance in the pathogenesis of COVID-19. Gut dysbiosis caused by various reasons is associated with severe COVID-19. Therefore, the modulation of gut microbiota and supplementation of commensal bacterial metabolites could reduce the severity of COVID-19. Many approaches have been studied to improve gut microbiota in COVID-19 including probiotics, bacterial metabolites, and prebiotics, as well as nutraceuticals and trace elements. So far, 19 clinical trials for testing the efficacy of probiotics and synbiotics in COVID-19 prevention and treatment are ongoing. In this narrative review, we summarize the effects of various approaches on the prevention and treatment of COVID-19 and discuss associated mechanisms.
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Affiliation(s)
- Jiezhong Chen
- Medlab Clinical, Research Department, Sydney 2015, Australia;
| | - Luis Vitetta
- Medlab Clinical, Research Department, Sydney 2015, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia
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30
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K NK, Patil P, Bhandary SK, Haridas V, N SK, E S, Shetty P. Is butyrate a natural alternative to dexamethasone in the management of CoVID-19? F1000Res 2021; 10:273. [PMID: 34046165 PMCID: PMC8108555 DOI: 10.12688/f1000research.51786.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (CoVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 has affected more than 100 million lives. Severe CoVID-19 infection may lead to acute respiratory distress syndrome and death of the patient, and is associated with hyperinflammation and cytokine storm. The broad spectrum immunosuppressant corticosteroid, dexamethasone, is being used to manage the cytokine storm and hyperinflammation in CoVID-19 patients. However, the extensive use of corticosteroids leads to serious adverse events and disruption of the gut-lung axis. Various micronutrients and probiotic supplementations are known to aid in the reduction of hyperinflammation and restoration of gut microbiota. The attenuation of the deleterious immune response and hyperinflammation could be mediated by short chain fatty acids produced by the gut microbiota. Butyric acid, the most extensively studied short chain fatty acid, is known for its anti-inflammatory properties. Additionally, butyric acid has been shown to ameliorate hyperinflammation and reduce oxidative stress in various pathologies, including respiratory viral infections. In this review, the potential anti-inflammatory effects of butyric acid that aid in cytokine storm depletion, and its usefulness in effective management of critical illness related to CoVID-19 have been discussed.
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Affiliation(s)
- Nithin K. K
- Division of Proteomics and Cancer Biology, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
| | - Prakash Patil
- Central Research Laboratory, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
| | - Satheesh Kumar Bhandary
- Department of ENT, Justice K S Hegde Charitable Hospital, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
| | - Vikram Haridas
- Arthritis Superspeciality Center, Hublic, Karnataka, 580020, India
| | - Suchetha Kumari N
- Department of Biochemistry/Central Research Laboratory, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
| | - Sarathkumar E
- Division of Proteomics and Cancer Biology, Nitte University Center for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
| | - Praveenkumar Shetty
- Department of Biochemistry/Central Research Laboratory, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, 575018, India
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