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Budak B, Tükel EY, Turanlı B, Kiraz Y. Integrated systems biology analysis of acute lymphoblastic leukemia: unveiling molecular signatures and drug repurposing opportunities. Ann Hematol 2024:10.1007/s00277-024-05821-w. [PMID: 38836918 DOI: 10.1007/s00277-024-05821-w] [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: 04/04/2024] [Accepted: 05/27/2024] [Indexed: 06/06/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematological malignancy characterized by aberrant proliferation and accumulation of lymphoid precursor cells within the bone marrow. The tyrosine kinase inhibitor (TKI), imatinib mesylate, has played a significant role in the treatment of Philadelphia chromosome-positive ALL (Ph + ALL). However, the achievement of durable and sustained therapeutic success remains a challenge due to the development of TKI resistance during the clinical course.The primary objective of this investigation is to propose a novel and efficacious treatment approach through drug repositioning, targeting ALL and its Ph + subtype by identifying and addressing differentially expressed genes (DEGs). This study involves a comprehensive analysis of transcriptome datasets pertaining to ALL and Ph + ALL in order to identify DEGs associated with the progression of these diseases to identify possible repurposable drugs that target identified hub proteins.The outcomes of this research have unveiled 698 disease-related DEGs for ALL and 100 for Ph + ALL. Furthermore, a subset of drugs, specifically glipizide for Ph + ALL, and maytansine and isoprenaline for ALL, have been identified as potential candidates for therapeutic intervention. Subsequently, cytotoxicity assessments were performed to confirm the in vitro cytotoxic effects of these selected drugs on both ALL and Ph + ALL cell lines.In conclusion, this study offers a promising avenue for the management of ALL and Ph + ALL through drug repurposed drugs. Further investigations are necessary to elucidate the mechanisms underlying cell death, and clinical trials are recommended to validate the promising results obtained through drug repositioning strategies.
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Affiliation(s)
- Betül Budak
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
- Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Türkiye
| | - Ezgi Yağmur Tükel
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balçova, Izmir, Türkiye
| | - Beste Turanlı
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Türkiye
| | - Yağmur Kiraz
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balçova, Izmir, Türkiye.
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Satish KS, Saraswathy GR, Ritesh G, Saravanan KS, Krishnan A, Bhargava J, Ushnaa K, Dsouza PL. Exploring cutting-edge strategies for drug repurposing in female cancers - An insight into the tools of the trade. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:355-415. [PMID: 38942544 DOI: 10.1016/bs.pmbts.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Female cancers, which include breast and gynaecological cancers, represent a significant global health burden for women. Despite advancements in research pertinent to unearthing crucial pathological characteristics of these cancers, challenges persist in discovering potential therapeutic strategies. This is further exacerbated by economic burdens associated with de novo drug discovery and clinical intricacies such as development of drug resistance and metastasis. Drug repurposing, an innovative approach leveraging existing FDA-approved drugs for new indications, presents a promising avenue to expedite therapeutic development. Computational techniques, including virtual screening and analysis of drug-target-disease relationships, enable the identification of potential candidate drugs. Integration of diverse data types, such as omics and clinical information, enhances the precision and efficacy of drug repurposing strategies. Experimental approaches, including high-throughput screening assays, in vitro, and in vivo models, complement computational methods, facilitating the validation of repurposed drugs. This review highlights various target mining strategies based on analysis of differential gene expression, weighted gene co-expression, protein-protein interaction network, and host-pathogen interaction, among others. To unearth drug candidates, the technicalities of leveraging information from databases such as DrugBank, STITCH, LINCS, and ChEMBL, among others are discussed. Further in silico validation techniques encompassing molecular docking, pharmacophore modelling, molecular dynamic simulations, and ADMET analysis are elaborated. Overall, this review delves into the exploration of individual case studies to offer a wide perspective of the ever-evolving field of drug repurposing, emphasizing the multifaceted approaches and methodologies employed for the same to confront female cancers.
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Affiliation(s)
- Kshreeraja S Satish
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ganesan Rajalekshmi Saraswathy
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.
| | - Giri Ritesh
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kamatchi Sundara Saravanan
- Department of Pharmacognosy, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Aarti Krishnan
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Janhavi Bhargava
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kuri Ushnaa
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Prizvan Lawrence Dsouza
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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Bereketoglu C, Häggblom I, Turanlı B, Pradhan A. Comparative analysis of diisononyl phthalate and di(isononyl)cyclohexane-1,2 dicarboxylate plasticizers in regulation of lipid metabolism in 3T3-L1 cells. ENVIRONMENTAL TOXICOLOGY 2024; 39:1245-1257. [PMID: 37927243 DOI: 10.1002/tox.24010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Diisononyl phthalate (DINP) and di(isononyl)cyclohexane-1,2-dicarboxylate (DINCH) are plasticizers introduced to replace previously used phthalate plasticizers in polymeric products. Exposure to DINP and DINCH has been shown to impact lipid metabolism. However, there are limited studies that address the mechanisms of toxicity of these two plasticizers. Here, a comparative toxicity analysis has been performed to evaluate the impacts of DINP and DINCH on 3T3-L1 cells. The preadipocyte 3T3-L1 cells were exposed to 1, 10, and 100 μM of DINP or DINCH for 10 days and assessed for lipid accumulation, gene expression, and protein analysis. Lipid staining showed that higher concentrations of DINP and DINCH can induce adipogenesis. The gene expression analysis demonstrated that both DINP and DINCH could alter the expression of lipid-related genes involved in adipogenesis. DINP and DINCH upregulated Pparγ, Pparα, C/EBPα Fabp4, and Fabp5, while both compounds significantly downregulated Fasn and Gata2. Protein analysis showed that both DINP and DINCH repressed the expression of FASN. Additionally, we analyzed an independent transcriptome dataset encompassing temporal data on lipid differentiation within 3T3-L1 cells. Subsequently, we derived a gene set that accurately portrays significant pathways involved in lipid differentiation, which we subsequently subjected to experimental validation through quantitative polymerase chain reaction. In addition, we extended our analysis to encompass a thorough assessment of the expression profiles of this identical gene set across 40 discrete transcriptome datasets that have linked to diverse pathological conditions to foreseen any potential association with DINP and DINCH exposure. Comparative analysis indicated that DINP could be more effective in regulating lipid metabolism.
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Affiliation(s)
- Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Isabel Häggblom
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Beste Turanlı
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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Romo-Perez A, Domínguez-Gómez G, Chávez-Blanco AD, González-Fierro A, Correa-Basurto J, Dueñas-González A. PaSTe. Blockade of the Lipid Phenotype of Prostate Cancer as Metabolic Therapy: A Theoretical Proposal. Curr Med Chem 2024; 31:3265-3285. [PMID: 37287286 DOI: 10.2174/0929867330666230607104441] [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: 12/08/2022] [Revised: 04/10/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Prostate cancer is the most frequently diagnosed malignancy in 112 countries and is the leading cause of death in eighteen. In addition to continuing research on prevention and early diagnosis, improving treatments and making them more affordable is imperative. In this sense, the therapeutic repurposing of low-cost and widely available drugs could reduce global mortality from this disease. The malignant metabolic phenotype is becoming increasingly important due to its therapeutic implications. Cancer generally is characterized by hyperactivation of glycolysis, glutaminolysis, and fatty acid synthesis. However, prostate cancer is particularly lipidic; it exhibits increased activity in the pathways for synthesizing fatty acids, cholesterol, and fatty acid oxidation (FAO). OBJECTIVE Based on a literature review, we propose the PaSTe regimen (Pantoprazole, Simvastatin, Trimetazidine) as a metabolic therapy for prostate cancer. Pantoprazole and simvastatin inhibit the enzymes fatty acid synthase (FASN) and 3-hydroxy-3-methylglutaryl- coenzyme A reductase (HMGCR), therefore, blocking the synthesis of fatty acids and cholesterol, respectively. In contrast, trimetazidine inhibits the enzyme 3-β-Ketoacyl- CoA thiolase (3-KAT), an enzyme that catalyzes the oxidation of fatty acids (FAO). It is known that the pharmacological or genetic depletion of any of these enzymes has antitumor effects in prostatic cancer. RESULTS Based on this information, we hypothesize that the PaSTe regimen will have increased antitumor effects and may impede the metabolic reprogramming shift. Existing knowledge shows that enzyme inhibition occurs at molar concentrations achieved in plasma at standard doses of these drugs. CONCLUSION We conclude that this regimen deserves to be preclinically evaluated because of its clinical potential for the treatment of prostate cancer.
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Affiliation(s)
- Adriana Romo-Perez
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Alma D Chávez-Blanco
- Subdirección de Investigación Básica, Instituto Nacional de Cancerologia, Mexico City, Mexico
| | - Aurora González-Fierro
- Subdirección de Investigación Básica, Instituto Nacional de Cancerologia, Mexico City, Mexico
| | - José Correa-Basurto
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Alfonso Dueñas-González
- Subdirección de Investigación Básica, Instituto Nacional de Cancerologia, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Comertpay B, Gov E. Immune cell-specific and common molecular signatures in rheumatoid arthritis through molecular network approaches. Biosystems 2023; 234:105063. [PMID: 37852410 DOI: 10.1016/j.biosystems.2023.105063] [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: 02/19/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disorder and common symptom of RA is chronic synovial inflammation. The pathogenesis of RA is not fully understood. Therefore, we aimed to identify underlying common and distinct molecular signatures and pathways among ten types of tissue and cells obtained from patients with RA. In this study, transcriptomic data including synovial tissues, macrophages, blood, T cells, CD4+T cells, CD8+T cells, natural killer T (NKT), cells natural killer (NK) cells, neutrophils, and monocyte cells were analyzed with an integrative and comparative network biology perspective. Each dataset yielded a list of differentially expressed genes as well as a reconstruction of the tissue-specific protein-protein interaction (PPI) network. Molecular signatures were identified by a statistical test using the hypergeometric probability density function by employing the interactions of transcriptional regulators and PPI. Reporter metabolites of each dataset were determined by using genome-scale metabolic networks. It was defined as the common hub proteins, novel molecular signatures, and metabolites in two or more tissue types while immune cell-specific molecular signatures were identified, too. Importantly, miR-155-5p is found as a common miRNA in all tissues. Moreover, NCOA3, PRKDC and miR-3160 might be novel molecular signatures for RA. Our results establish a novel approach for identifying immune cell-specific molecular signatures of RA and provide insights into the role of common tissue-specific genes, miRNAs, TFs, receptors, and reporter metabolites. Experimental research should be used to validate the corresponding genes, miRNAs, and metabolites.
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Affiliation(s)
- Betul Comertpay
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye.
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Aydin B, Beklen H, Arga KY, Bayrakli F, Turanli B. Epigenomic and transcriptomic landscaping unraveled candidate repositioned therapeutics for non-functioning pituitary neuroendocrine tumors. J Endocrinol Invest 2023; 46:727-747. [PMID: 36306107 DOI: 10.1007/s40618-022-01923-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/12/2022] [Indexed: 10/31/2022]
Abstract
PURPOSE Non-functioning pituitary neuroendocrine tumors are challengingly diagnosed tumors in the clinic. Transsphenoidal surgery remains the first-line treatment. Despite the development of state-of-the-art techniques, no drug therapy is currently approved for the treatment. There are also no randomized controlled trials comparing therapeutic strategies or drug therapy for the management after surgery. Therefore, novel therapeutic interventions for the therapeutically challenging NF-PitNETs are urgently needed. METHODS We integrated epigenome and transcriptome data (both coding and non-coding) that elucidate disease-specific signatures, in addition to biological and pharmacological data, to utilize rational pathway and drug prioritization in NF-PitNETs. We constructed an epigenome- and transcriptome-based PPI network and proposed hub genes. The signature-based drug repositioning based on the integration of multi-omics data was performed. RESULTS The construction of a disease-specific network based on three different biological levels revealed DCC, DLG5, ETS2, FOXO1, HBP1, HMGA2, PCGF3, PSME4, RBPMS, RREB1, SMAD1, SOCS1, SOX2, YAP1, ZFHX3 as hub proteins. Signature-based drug repositioning using hub proteins yielded repositioned drug candidates that were confirmed in silico via molecular docking. As a result of molecular docking simulations, palbociclib, linifanib, trametinib, eplerenone, niguldipine, and zuclopenthixol showed higher binding affinities with hub genes compared to their inhibitors and were proposed as potential repositioned therapeutics for the management of NF-PitNETs. CONCLUSION The proposed systems' biomedicine-oriented multi-omics data integration for drug repurposing to provide promising results for the construction of effective clinical therapeutics. To the best of our knowledge, this is the first study reporting epigenome- and transcriptome-based drug repositioning for NF-PitNETs using in silico confirmations.
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Affiliation(s)
- B Aydin
- Department of Bioengineering, Faculty of Engineering and Architecture, Konya Food and Agriculture University, Konya, Turkey
| | - H Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey
| | - K Y Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul, Turkey
| | - F Bayrakli
- Department of Neurosurgery, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
| | - B Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey.
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Kori M, Turanli B, Arga KY. Drug repositioning via host-pathogen protein-protein interactions for the treatment of cervical cancer. Front Oncol 2023; 13:1096081. [PMID: 36761959 PMCID: PMC9905826 DOI: 10.3389/fonc.2023.1096081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Integrating interaction data with biological knowledge can be a critical approach for drug development or drug repurposing. In this context, host-pathogen-protein-protein interaction (HP-PPI) networks are useful instrument to uncover the phenomena underlying therapeutic effects in infectious diseases, including cervical cancer, which is almost exclusively due to human papillomavirus (HPV) infections. Cervical cancer is one of the second leading causes of death, and HPV16 and HPV18 are the most common subtypes worldwide. Given the limitations of traditionally used virus-directed drug therapies for infectious diseases and, at the same time, recent cancer statistics for cervical cancer cases, the need for innovative treatments becomes clear. Methods Accordingly, in this study, we emphasize the potential of host proteins as drug targets and identify promising host protein candidates for cervical cancer by considering potential differences between HPV subtypes (i.e., HPV16 and HPV18) within a novel bioinformatics framework that we have developed. Subsequently, subtype-specific HP-PPI networks were constructed to obtain host proteins. Using this framework, we next selected biologically significant host proteins. Using these prominent host proteins, we performed drug repurposing analysis. Finally, by following our framework we identify the most promising host-oriented drug candidates for cervical cancer. Results As a result of this framework, we discovered both previously associated and novel drug candidates, including interferon alfacon-1, pimecrolimus, and hyaluronan specifically for HPV16 and HPV18 subtypes, respectively. Discussion Consequently, with this study, we have provided valuable data for further experimental and clinical efforts and presented a novel bioinformatics framework that can be applied to any infectious disease.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye,*Correspondence: Medi Kori,
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye,Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul, Türkiye
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Yilmaz DN, Onluturk Aydogan O, Kori M, Aydin B, Rahman MR, Moni MA, Turanli B. Prospects of integrated multi-omics-driven biomarkers for efficient hair loss therapy from systems biology perspective. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kori M, Arga KY, Mardinoglu A, Turanli B. Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types. Front Pharmacol 2022; 13:884548. [PMID: 35770086 PMCID: PMC9234276 DOI: 10.3389/fphar.2022.884548] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is the fourth most commonly diagnosed cancer worldwide and, in almost all cases is caused by infection with highly oncogenic Human Papillomaviruses (HPVs). On the other hand, inflammation is one of the hallmarks of cancer research. Here, we focused on inflammatory proteins that classify cervical cancer patients by considering individual differences between cancer patients in contrast to conventional treatments. We repurposed anti-inflammatory drugs for therapy of HPV-16 and HPV-18 infected groups, separately. In this study, we employed systems biology approaches to unveil the diagnostic and treatment options from a precision medicine perspective by delineating differential inflammation-associated biomarkers associated with carcinogenesis for both subtypes. We performed a meta-analysis of cervical cancer-associated transcriptomic datasets considering subtype differences of samples and identified the differentially expressed genes (DEGs). Using gene signature reversal on HPV-16 and HPV-18, we performed both signature- and network-based drug reversal to identify anti-inflammatory drug candidates against inflammation-associated nodes. The anti-inflammatory drug candidates were evaluated using molecular docking to determine the potential of physical interactions between the anti-inflammatory drug and inflammation-associated nodes as drug targets. We proposed 4 novels anti-inflammatory drugs (AS-601245, betamethasone, narciclasin, and methylprednisolone) for the treatment of HPV-16, 3 novel drugs for the treatment of HPV-18 (daphnetin, phenylbutazone, and tiaprofenoic acid), and 5 novel drugs (aldosterone, BMS-345541, etodolac, hydrocortisone, and prednisolone) for the treatment of both subtypes. We proposed anti-inflammatory drug candidates that have the potential to be therapeutic agents for the prevention and/or treatment of cervical cancer.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul, Turkey
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- *Correspondence: Beste Turanli, ; Adil Mardinoglu,
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- *Correspondence: Beste Turanli, ; Adil Mardinoglu,
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10
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Aydin B, Yildirim E, Erdogan O, Arga KY, Yilmaz BK, Bozkurt SU, Bayrakli F, Turanli B. Past, Present, and Future of Therapies for Pituitary Neuroendocrine Tumors: Need for Omics and Drug Repositioning Guidance. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:115-129. [PMID: 35172108 DOI: 10.1089/omi.2021.0221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Innovation roadmaps are important, because they encourage the actors in an innovation ecosystem to creatively imagine multiple possible science future(s), while anticipating the prospects and challenges on the innovation trajectory. In this overarching context, this expert review highlights the present unmet need for therapeutic innovations for pituitary neuroendocrine tumors (PitNETs), also known as pituitary adenomas. Although there are many drugs used in practice to treat PitNETs, many of these drugs can have negative side effects and show highly variable outcomes in terms of overall recovery. Building innovation roadmaps for PitNETs' treatments can allow incorporation of systems biology approaches to bring about insights at multiple levels of cell biology, from genes to proteins to metabolites. Using the systems biology techniques, it will then be possible to offer potential therapeutic strategies for the convergence of preventive approaches and patient-centered disease treatment. Here, we first provide a comprehensive overview of the molecular subtypes of PitNETs and therapeutics for these tumors from the past to the present. We then discuss examples of clinical trials and drug repositioning studies and how multi-omics studies can help in discovery and rational development of new therapeutics for PitNETs. Finally, this expert review offers new public health and personalized medicine approaches on cases that are refractory to conventional treatment or recur despite currently used surgical and/or drug therapy.
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Affiliation(s)
- Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Esra Yildirim
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Onur Erdogan
- Department of Neurosurgery, School of Medicine, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Betul Karademir Yilmaz
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
- Department of Biochemistry and School of Medicine, Marmara University, Istanbul, Turkey
| | - Suheyla Uyar Bozkurt
- Department of Medical Pathology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Fatih Bayrakli
- Department of Neurosurgery, School of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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11
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Bahmad HF, Demus T, Moubarak MM, Daher D, Alvarez Moreno JC, Polit F, Lopez O, Merhe A, Abou-Kheir W, Nieder AM, Poppiti R, Omarzai Y. Overcoming Drug Resistance in Advanced Prostate Cancer by Drug Repurposing. Med Sci (Basel) 2022; 10:medsci10010015. [PMID: 35225948 PMCID: PMC8883996 DOI: 10.3390/medsci10010015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is the second most common cancer in men. Common treatments include active surveillance, surgery, or radiation. Androgen deprivation therapy and chemotherapy are usually reserved for advanced disease or biochemical recurrence, such as castration-resistant prostate cancer (CRPC), but they are not considered curative because PCa cells eventually develop drug resistance. The latter is achieved through various cellular mechanisms that ultimately circumvent the pharmaceutical’s mode of action. The need for novel therapeutic approaches is necessary under these circumstances. An alternative way to treat PCa is by repurposing of existing drugs that were initially intended for other conditions. By extrapolating the effects of previously approved drugs to the intracellular processes of PCa, treatment options will expand. In addition, drug repurposing is cost-effective and efficient because it utilizes drugs that have already demonstrated safety and efficacy. This review catalogues the drugs that can be repurposed for PCa in preclinical studies as well as clinical trials.
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Affiliation(s)
- Hisham F. Bahmad
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (J.C.A.M.); (F.P.); (R.P.); (Y.O.)
- Correspondence: or ; Tel.: +1-786-961-0216
| | - Timothy Demus
- Division of Urology, Columbia University, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (T.D.); (A.M.N.)
| | - Maya M. Moubarak
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon; (M.M.M.); (W.A.-K.)
- CNRS, IBGC, UMR5095, Universite de Bordeaux, F-33000 Bordeaux, France
| | - Darine Daher
- Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon;
| | - Juan Carlos Alvarez Moreno
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (J.C.A.M.); (F.P.); (R.P.); (Y.O.)
| | - Francesca Polit
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (J.C.A.M.); (F.P.); (R.P.); (Y.O.)
| | - Olga Lopez
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA;
| | - Ali Merhe
- Department of Urology, Jackson Memorial Hospital, University of Miami, Leonard M. Miller School of Medicine, Miami, FL 33136, USA;
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon; (M.M.M.); (W.A.-K.)
| | - Alan M. Nieder
- Division of Urology, Columbia University, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (T.D.); (A.M.N.)
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA;
| | - Robert Poppiti
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (J.C.A.M.); (F.P.); (R.P.); (Y.O.)
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA;
| | - Yumna Omarzai
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA; (J.C.A.M.); (F.P.); (R.P.); (Y.O.)
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA;
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12
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Aydin B, Arslan S, Bayraklı F, Karademir B, Arga KY. MicroRNA-Mediated Drug Repurposing Unveiled Potential Candidate Drugs for Prolactinoma Treatment. Neuroendocrinology 2022; 112:161-173. [PMID: 33706313 DOI: 10.1159/000515801] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/08/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Prolactinomas, also called lactotroph adenomas, are the most encountered type of hormone-secreting pituitary neuroendocrine tumors in the clinic. The preferred first-line therapy is a medical treatment with dopamine agonists (DAs), mainly cabergoline, to reduce serum prolactin levels, tumor volume, and mass effect. However, in some cases, patients have displayed DA resistance with aggressive tumor behavior or are faced with recurrence after drug withdrawal. Also, currently used therapeutics have notorious side effects and impair the life quality of the patients. METHODS Since the amalgamation of clinical and laboratory data besides tumor histopathogenesis and transcriptional regulatory features of the tumor emerges to exhibit essential roles in the behavior and progression of prolactinomas; in this work, we integrated mRNA- and microRNA (miRNA)-level transcriptome data that exploit disease-specific signatures in addition to biological and pharmacological data to elucidate a rational prioritization of pathways and drugs in prolactinoma. RESULTS We identified 8 drug candidates through drug repurposing based on mRNA-miRNA-level data integration and evaluated their potential through in vitro assays in the MMQ cell line. Seven repurposed drugs including 5-fluorocytosine, nortriptyline, neratinib, puromycin, taxifolin, vorinostat, and zileuton were proposed as potential drug candidates for the treatment of prolactinoma. We further hypothesized possible mechanisms of drug action on MMQ cell viability through analyzing the PI3K/Akt signaling pathway and cell cycle arrest via flow cytometry and Western blotting. DISCUSSION We presented the transcriptomic landscape of prolactinoma through miRNA and mRNA-level data integration and proposed repurposed drug candidates based on this integration. We validated our findings through testing cell viability, cell cycle phases, and PI3K/Akt protein expressions. Effects of the drugs on cell cycle phases and inhibition of the PI3K/Akt pathway by all drugs gave us promising output for further studies using these drugs in the treatment of prolactinoma. This is the first study that reports miRNA-mediated repurposed drugs for prolactinoma treatment via in vitro experiments.
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Affiliation(s)
- Busra Aydin
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Sema Arslan
- Department of Biochemistry, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Fatih Bayraklı
- Department of Neurosurgery, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
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13
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Beklen H, Arslan S, Gulfidan G, Turanli B, Ozbek P, Karademir Yilmaz B, Arga KY. Differential Interactome Based Drug Repositioning Unraveled Abacavir, Exemestane, Nortriptyline Hydrochloride, and Tolcapone as Potential Therapeutics for Colorectal Cancers. FRONTIERS IN BIOINFORMATICS 2021; 1:710591. [PMID: 36303724 PMCID: PMC9581026 DOI: 10.3389/fbinf.2021.710591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
There is a critical requirement for alternative strategies to provide the better treatment in colorectal cancer (CRC). Hence, our goal was to propose novel biomarkers as well as drug candidates for its treatment through differential interactome based drug repositioning. Differentially interacting proteins and their modules were identified, and their prognostic power were estimated through survival analyses. Drug repositioning was carried out for significant target proteins, and candidate drugs were analyzed via in silico molecular docking prior to in vitro cell viability assays in CRC cell lines. Six modules (mAPEX1, mCCT7, mHSD17B10, mMYC, mPSMB5, mRAN) were highlighted considering their prognostic performance. Drug repositioning resulted in eight drugs (abacavir, ribociclib, exemestane, voriconazole, nortriptyline hydrochloride, theophylline, bromocriptine mesylate, and tolcapone). Moreover, significant in vitro inhibition profiles were obtained in abacavir, nortriptyline hydrochloride, exemestane, tolcapone, and theophylline (positive control). Our findings may provide new and complementary strategies for the treatment of CRC.
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Affiliation(s)
- Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Sema Arslan
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Betul Karademir Yilmaz
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- *Correspondence: Kazim Yalcin Arga,
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14
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Chtita S, Belhassan A, Aouidate A, Belaidi S, Bouachrine M, Lakhlifi T. Discovery of Potent SARS-CoV-2 Inhibitors from Approved Antiviral Drugs via Docking and Virtual Screening. Comb Chem High Throughput Screen 2021; 24:441-454. [PMID: 32748740 DOI: 10.2174/1386207323999200730205447] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 07/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Coronavirus Disease 2019 (COVID-19) pandemic continues to threaten patients, societies and healthcare systems around the world. There is an urgent need to search for possible medications. OBJECTIVE This article intends to use virtual screening and molecular docking methods to find potential inhibitors from existing drugs that can respond to COVID-19. METHODS To take part in the current research investigation and to define a potential target drug that may protect the world from the pandemic of corona disease, a virtual screening study of 129 approved drugs was carried out which showed that their metabolic characteristics, dosages used, potential efficacy and side effects are clear as they have been approved for treating existing infections. Especially 12 drugs against chronic hepatitis B virus, 37 against chronic hepatitis C virus, 37 against human immunodeficiency virus, 14 anti-herpesvirus, 11 anti-influenza, and 18 other drugs currently on the market were considered for this study. These drugs were then evaluated using virtual screening and molecular docking studies on the active site of the (SARS-CoV-2) main protease (6lu7). Once the efficacy of the drug is determined, it can be approved for its in vitro and in vivo activity against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which can be beneficial for the rapid clinical treatment of patients. These drugs were considered potentially effective against SARS-CoV-2 and those with high molecular docking scores were proposed as novel candidates for repurposing. The N3 inhibitor cocrystallized with protease (6lu7) and the anti-HIV protease inhibitor Lopinavir were used as standards for comparison. RESULTS The results suggest the effectiveness of Beclabuvir, Nilotinib, Tirilazad, Trametinib and Glecaprevir as potent drugs against SARS-CoV-2 since they tightly bind to its main protease. CONCLUSION These promising drugs can inhibit the replication of the virus; hence, the repurposing of these compounds is suggested for the treatment of COVID-19. No toxicity measurements are required for these drugs since they were previously tested prior to their approval by the FDA. However, the assessment of these potential inhibitors as clinical drugs requires further in vivo tests of these drugs.
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Affiliation(s)
- Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of sciences Ben M'Sik, Hassan II University of Casablanca, B.P. 7955 Sidi Othmane, Casablanca, Morocco
| | - Assia Belhassan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes, Morocco
| | - Adnane Aouidate
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes, Morocco
| | - Salah Belaidi
- Laboratory of Molecular Chemistry and Environment, Group of Computational and pharmaceutical Chemistry, University of Biskra, BP145, 07000, Biskra, Algeria
| | - Mohammed Bouachrine
- High School of Technology of Khenifra, Sultan Slimane University, B.P. 591, Khenifra, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes, Morocco
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15
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Chtita S, Belhassan A, Aouidate A, Belaidi S, Bouachrine M, Lakhlifi T. Discovery of Potent SARS-CoV-2 Inhibitors from Approved Antiviral Drugs via Docking and Virtual Screening. Comb Chem High Throughput Screen 2021. [DOI: 10.2174/1386207323999200730205447 10.1093/glycob/1.6.631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background:
Coronavirus Disease 2019 (COVID-19) pandemic continues to threaten
patients, societies and healthcare systems around the world. There is an urgent need to search for
possible medications.
Objective:
This article intends to use virtual screening and molecular docking methods to find
potential inhibitors from existing drugs that can respond to COVID-19.
Methods:
To take part in the current research investigation and to define a potential target
drug that may protect the world from the pandemic of corona disease, a virtual screening
study of 129 approved drugs was carried out which showed that their metabolic
characteristics, dosages used, potential efficacy and side effects are clear as they have been
approved for treating existing infections. Especially 12 drugs against chronic hepatitis B
virus, 37 against chronic hepatitis C virus, 37 against human immunodeficiency virus, 14
anti-herpesvirus, 11 anti-influenza, and 18 other drugs currently on the market were
considered for this study. These drugs were then evaluated using virtual screening and
molecular docking studies on the active site of the (SARS-CoV-2) main protease (6lu7). Once
the efficacy of the drug is determined, it can be approved for its in vitro and in vivo
activity against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which
can be beneficial for the rapid clinical treatment of patients.
:
These drugs were considered potentially effective against SARS-CoV-2 and those with high
molecular docking scores were proposed as novel candidates for repurposing. The N3 inhibitor cocrystallized
with protease (6lu7) and the anti-HIV protease inhibitor Lopinavir were used as
standards for comparison.
Results:
The results suggest the effectiveness of Beclabuvir, Nilotinib, Tirilazad, Trametinib and
Glecaprevir as potent drugs against SARS-CoV-2 since they tightly bind to its main protease.
Conclusion:
These promising drugs can inhibit the replication of the virus; hence, the repurposing
of these compounds is suggested for the treatment of COVID-19. No toxicity measurements are
required for these drugs since they were previously tested prior to their approval by the FDA.
However, the assessment of these potential inhibitors as clinical drugs requires further in vivo tests
of these drugs.
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Affiliation(s)
- Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of sciences Ben M’Sik, Hassan II University of Casablanca, B.P. 7955 Sidi Othmane, Casablanca,Morocco
| | - Assia Belhassan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes,Morocco
| | - Adnane Aouidate
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes,Morocco
| | - Salah Belaidi
- Laboratory of Molecular Chemistry and Environment, Group of Computational and pharmaceutical Chemistry, University of Biskra, BP145, 07000, Biskra,Algeria
| | - Mohammed Bouachrine
- High School of Technology of Khenifra, Sultan Slimane University, B.P. 591, Khenifra,Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, B.P. 11201 Zitoune, Meknes,Morocco
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16
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Kori M, Aydin B, Gulfidan G, Beklen H, Kelesoglu N, Caliskan Iscan A, Turanli B, Erzik C, Karademir B, Arga KY. The Repertoire of Glycan Alterations and Glycoproteins in Human Cancers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:139-168. [PMID: 33404348 DOI: 10.1089/omi.2020.0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer as the leading cause of death worldwide has many issues that still need to be addressed. Since the alterations on the glycan compositions or/and structures (i.e., glycosylation, sialylation, and fucosylation) are common features of tumorigenesis, glycomics becomes an emerging field examining the structure and function of glycans. In the past, cancer studies heavily relied on genomics and transcriptomics with relatively little exploration of the glycan alterations and glycoprotein biomarkers among individuals and populations. Since glycosylation of proteins increases their structural complexity by several orders of magnitude, glycome studies resulted in highly dynamic biomarkers that can be evaluated for cancer diagnosis, prognosis, and therapy. Glycome not only integrates our genetic background with past and present environmental factors but also offers a promise of more efficient patient stratification compared with genetic variations. Therefore, studying glycans holds great potential for better diagnostic markers as well as developing more efficient treatment strategies in human cancers. While recent developments in glycomics and associated technologies now offer new possibilities to achieve a high-throughput profiling of glycan diversity, we aim to give an overview of the current status of glycan research and the potential applications of the glycans in the scope of the personalized medicine strategies for cancer.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Nurdan Kelesoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ayşegul Caliskan Iscan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey.,Department of Pharmacy, Istinye University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Can Erzik
- Department of Medical Biology and School of Medicine, Marmara University, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey.,Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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17
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Islam T, Rahman MR, Aydin B, Beklen H, Arga KY, Shahjaman M. Integrative transcriptomics analysis of lung epithelial cells and identification of repurposable drug candidates for COVID-19. Eur J Pharmacol 2020; 887:173594. [PMID: 32971089 PMCID: PMC7505772 DOI: 10.1016/j.ejphar.2020.173594] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, more commonly COVID-19 has emerged as a world health pandemic. There are couples of treatment methods for COVID-19, however, well-established drugs and vaccines are urgently needed to treat the COVID-19. The new drug discovery is a tremendous challenge; repurposing of existing drugs could shorten the time and expense compared with de novo drug development. In this study, we aimed to decode molecular signatures and pathways of the host cells in response to SARS-CoV-2 and the rapid identification of repurposable drugs using bioinformatics and network biology strategies. We have analyzed available transcriptomic RNA-seq COVID-19 data to identify differentially expressed genes (DEGs). We detected 177 DEGs specific for COVID-19 where 122 were upregulated and 55 were downregulated compared to control (FDR<0.05 and logFC ≥ 1). The DEGs were significantly involved in the immune and inflammatory response. The pathway analysis revealed the DEGs were found in influenza A, measles, cytokine signaling in the immune system, interleukin-4, interleukin -13, interleukin -17 signaling, and TNF signaling pathways. Protein-protein interaction analysis showed 10 hub genes (BIRC3, ICAM1, IRAK2, MAP3K8, S100A8, SOCS3, STAT5A, TNF, TNFAIP3, TNIP1). The regulatory network analysis showed significant transcription factors (TFs) that target DEGs, namely FOXC1, GATA2, YY1, FOXL1, NFKB1. Finally, drug repositioning analysis was performed with these 10 hub genes and showed that in silico validated three drugs with molecular docking. The transcriptomics signatures, molecular pathways, and regulatory biomolecules shed light on candidate biomarkers and drug targets which have potential roles to manage COVID-19. ICAM1 and TNFAIP3 were the key hubs that have demonstrated good binding affinities with repurposed drug candidates. Dabrafenib, radicicol, and AT-7519 were the top-scored repurposed drugs that showed efficient docking results when they tested with hub genes. The identified drugs should be further evaluated in molecular level wet-lab experiments in prior to clinical studies in the treatment of COVID-19.
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Affiliation(s)
- Tania Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh; Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajganj, Bangladesh.
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur, Bangladesh
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18
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Comertpay B, Gov E. Identification of key biomolecules in rheumatoid arthritis through the reconstruction of comprehensive disease-specific biological networks. Autoimmunity 2020; 53:156-166. [DOI: 10.1080/08916934.2020.1722107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Betul Comertpay
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Esra Gov
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
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19
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Turanli B, Altay O, Borén J, Turkez H, Nielsen J, Uhlen M, Arga KY, Mardinoglu A. Systems biology based drug repositioning for development of cancer therapy. Semin Cancer Biol 2019; 68:47-58. [PMID: 31568815 DOI: 10.1016/j.semcancer.2019.09.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/20/2023]
Abstract
Drug repositioning is a powerful method that can assists the conventional drug discovery process by using existing drugs for treatment of a disease rather than its original indication. The first examples of repurposed drugs were discovered serendipitously, however data accumulated by high-throughput screenings and advancements in computational biology methods have paved the way for rational drug repositioning methods. As chemotherapeutic agents have notorious side effects that significantly reduce quality of life, drug repositioning promises repurposed noncancer drugs with little or tolerable adverse effects for cancer patients. Here, we review current drug-related data types and databases including some examples of web-based drug repositioning tools. Next, we describe systems biology approaches to be used in drug repositioning for effective cancer therapy. Finally, we highlight examples of mostly repurposed drugs for cancer treatment and provide an overview of future expectations in the field for development of effective treatment strategies.
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Affiliation(s)
- Beste Turanli
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-17121, Sweden; Department of Bioengineering, Marmara University, Istanbul, Turkey; Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ozlem Altay
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-17121, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital Gothenburg, Sweden
| | - Hasan Turkez
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25240, Turkey
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-17121, Sweden
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-17121, Sweden; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, United Kingdom.
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20
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Turanli B, Karagoz K, Bidkhori G, Sinha R, Gatza ML, Uhlen M, Mardinoglu A, Arga KY. Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. Front Genet 2019; 10:420. [PMID: 31134131 PMCID: PMC6514249 DOI: 10.3389/fgene.2019.00420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC), which is largely synonymous with the basal-like molecular subtype, is the 5th leading cause of cancer deaths for women in the United States. The overall prognosis for TNBC patients remains poor given that few treatment options exist; including targeted therapies (not FDA approved), and multi-agent chemotherapy as standard-of-care treatment. TNBC like other complex diseases is governed by the perturbations of the complex interaction networks thereby elucidating the underlying molecular mechanisms of this disease in the context of network principles, which have the potential to identify targets for drug development. Here, we present an integrated "omics" approach based on the use of transcriptome and interactome data to identify dynamic/active protein-protein interaction networks (PPINs) in TNBC patients. We have identified three highly connected modules, EED, DHX9, and AURKA, which are extremely activated in TNBC tumors compared to both normal tissues and other breast cancer subtypes. Based on the functional analyses, we propose that these modules are potential drivers of proliferation and, as such, should be considered candidate molecular targets for drug development or drug repositioning in TNBC. Consistent with this argument, we repurposed steroids, anti-inflammatory agents, anti-infective agents, cardiovascular agents for patients with basal-like breast cancer. Finally, we have performed essential metabolite analysis on personalized genome-scale metabolic models and found that metabolites such as sphingosine-1-phosphate and cholesterol-sulfate have utmost importance in TNBC tumor growth.
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Affiliation(s)
- Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul, Turkey.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Kubra Karagoz
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Gholamreza Bidkhori
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, United States
| | - Michael L Gatza
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Faculty of Dentistry, Oral and Craniofacial Sciences, Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom.,Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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21
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Islam T, Rahman R, Gov E, Turanli B, Gulfidan G, Haque A, Arga KY, Haque Mollah N. Drug Targeting and Biomarkers in Head and Neck Cancers: Insights from Systems Biology Analyses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:422-436. [PMID: 29927717 DOI: 10.1089/omi.2018.0048] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world, but robust biomarkers and diagnostics are still not available. This study provides in-depth insights from systems biology analyses to identify molecular biomarker signatures to inform systematic drug targeting in HNSCC. Gene expression profiles from tumors and normal tissues of 22 patients with histological confirmation of nonmetastatic HNSCC were subjected to integrative analyses with genome-scale biomolecular networks (i.e., protein-protein interaction and transcriptional and post-transcriptional regulatory networks). We aimed to discover molecular signatures at RNA and protein levels, which could serve as potential drug targets for therapeutic innovation in the future. Eleven proteins, 5 transcription factors, and 20 microRNAs (miRNAs) came into prominence as potential drug targets. The differential expression profiles of these reporter biomolecules were cross-validated by independent RNA-Seq and miRNA-Seq datasets, and risk discrimination performance of the reporter biomolecules, BLNK, CCL2, E4F1, FOSL1, ISG15, MMP9, MYCN, MYH11, miR-1252, miR-29b, miR-29c, miR-3610, miR-431, and miR-523, was also evaluated. Using the transcriptome guided drug repositioning tool, geneXpharma, several candidate drugs were repurposed, including antineoplastic agents (e.g., gemcitabine and irinotecan), antidiabetics (e.g., rosiglitazone), dermatological agents (e.g., clocortolone and acitretin), and antipsychotics (e.g., risperidone), and binding affinities of the drugs to their potential targets were assessed using molecular docking analyses. The molecular signatures and repurposed drugs presented in this study warrant further attention for experimental studies since they offer significant potential as biomarkers and candidate therapeutics for precision medicine approaches to clinical management of HNSCC.
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Affiliation(s)
- Tania Islam
- 1 Department of Biotechnology and Genetic Engineering, Islamic University , Kushtia, Bangladesh
| | - Rezanur Rahman
- 1 Department of Biotechnology and Genetic Engineering, Islamic University , Kushtia, Bangladesh
| | - Esra Gov
- 2 Department of Bioengineering, Adana Science and Technology University , Adana, Turkey
| | - Beste Turanli
- 3 Department of Bioengineering, Marmara University , Istanbul, Turkey
- 4 Department of Bioengineering, Istanbul Medeniyet University , Istanbul, Turkey
| | - Gizem Gulfidan
- 3 Department of Bioengineering, Marmara University , Istanbul, Turkey
| | - Anwarul Haque
- 1 Department of Biotechnology and Genetic Engineering, Islamic University , Kushtia, Bangladesh
| | - Kazım Yalçın Arga
- 3 Department of Bioengineering, Marmara University , Istanbul, Turkey
| | - Nurul Haque Mollah
- 5 Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi , Rajshahi, Bangladesh
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Rahman MR, Islam T, Gov E, Turanli B, Gulfidan G, Shahjaman M, Banu NA, Mollah MNH, Arga KY, Moni MA. Identification of Prognostic Biomarker Signatures and Candidate Drugs in Colorectal Cancer: Insights from Systems Biology Analysis. ACTA ACUST UNITED AC 2019; 55:medicina55010020. [PMID: 30658502 PMCID: PMC6359148 DOI: 10.3390/medicina55010020] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/23/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022]
Abstract
Background and objectives: Colorectal cancer (CRC) is the second most common cause of cancer-related death in the world, but early diagnosis ameliorates the survival of CRC. This report aimed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) from the Gene Expression Omnibus (GEO) to identify mutual differentially expressed genes (DEGs). We integrated DEGs with protein–protein interaction and transcriptional/post-transcriptional regulatory networks to identify reporter signaling and regulatory molecules; utilized functional overrepresentation and pathway enrichment analyses to elucidate their roles in biological processes and molecular pathways; performed survival analyses to evaluate their prognostic performance; and applied drug repositioning analyses through Connectivity Map (CMap) and geneXpharma tools to hypothesize possible drug candidates targeting reporter molecules. Results: A total of 727 upregulated and 99 downregulated DEGs were detected. The PI3K/Akt signaling, Wnt signaling, extracellular matrix (ECM) interaction, and cell cycle were identified as significantly enriched pathways. Ten hub proteins (ADNP, CCND1, CD44, CDK4, CEBPB, CENPA, CENPH, CENPN, MYC, and RFC2), 10 transcription factors (ETS1, ESR1, GATA1, GATA2, GATA3, AR, YBX1, FOXP3, E2F4, and PRDM14) and two microRNAs (miRNAs) (miR-193b-3p and miR-615-3p) were detected as reporter molecules. The survival analyses through Kaplan–Meier curves indicated remarkable performance of reporter molecules in the estimation of survival probability in CRC patients. In addition, several drug candidates including anti-neoplastic and immunomodulating agents were repositioned. Conclusions: This study presents biomarker signatures at protein and RNA levels with prognostic capability in CRC. We think that the molecular signatures and candidate drugs presented in this study might be useful in future studies indenting the development of accurate diagnostic and/or prognostic biomarker screens and efficient therapeutic strategies in CRC.
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Affiliation(s)
- Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia-7003, Bangladesh.
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj-6751, Bangladesh.
| | - Tania Islam
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia-7003, Bangladesh.
| | - Esra Gov
- Department of Bioengineering, Adana Science and Technology University, Adana-01250, Turkey.
| | - Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul-34722, Turkey.
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul-34700, Turkey.
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul-34722, Turkey.
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh.
| | - Nilufa Akhter Banu
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia-7003, Bangladesh.
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul-34722, Turkey.
| | - Mohammad Ali Moni
- The University of Sydney, Faculty of Medicine and Health, Sydney Medical School, Discipline of Biomedical Science, NSW 2006, Australia.
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Turanli B, Grøtli M, Boren J, Nielsen J, Uhlen M, Arga KY, Mardinoglu A. Drug Repositioning for Effective Prostate Cancer Treatment. Front Physiol 2018; 9:500. [PMID: 29867548 PMCID: PMC5962745 DOI: 10.3389/fphys.2018.00500] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
Drug repositioning has gained attention from both academia and pharmaceutical companies as an auxiliary process to conventional drug discovery. Chemotherapeutic agents have notorious adverse effects that drastically reduce the life quality of cancer patients so drug repositioning is a promising strategy to identify non-cancer drugs which have anti-cancer activity as well as tolerable adverse effects for human health. There are various strategies for discovery and validation of repurposed drugs. In this review, 25 repurposed drug candidates are presented as result of different strategies, 15 of which are already under clinical investigation for treatment of prostate cancer (PCa). To date, zoledronic acid is the only repurposed, clinically used, and approved non-cancer drug for PCa. Anti-cancer activities of existing drugs presented in this review cover diverse and also known mechanisms such as inhibition of mTOR and VEGFR2 signaling, inhibition of PI3K/Akt signaling, COX and selective COX-2 inhibition, NF-κB inhibition, Wnt/β-Catenin pathway inhibition, DNMT1 inhibition, and GSK-3β inhibition. In addition to monotherapy option, combination therapy with current anti-cancer drugs may also increase drug efficacy and reduce adverse effects. Thus, drug repositioning may become a key approach for drug discovery in terms of time- and cost-efficiency comparing to conventional drug discovery and development process.
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Affiliation(s)
- Beste Turanli
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kazim Y. Arga
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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