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Firoozbakht F, Rezaeian I, Rueda L, Ngom A. Computationally repurposing drugs for breast cancer subtypes using a network-based approach. BMC Bioinformatics 2022; 23:143. [PMID: 35443626 PMCID: PMC9020161 DOI: 10.1186/s12859-022-04662-6] [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: 06/25/2021] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
‘De novo’ drug discovery is costly, slow, and with high risk. Repurposing known drugs for treatment of other diseases offers a fast, low-cost/risk and highly-efficient method toward development of efficacious treatments. The emergence of large-scale heterogeneous biomolecular networks, molecular, chemical and bioactivity data, and genomic and phenotypic data of pharmacological compounds is enabling the development of new area of drug repurposing called ‘in silico’ drug repurposing, i.e., computational drug repurposing (CDR). The aim of CDR is to discover new indications for an existing drug (drug-centric) or to identify effective drugs for a disease (disease-centric). Both drug-centric and disease-centric approaches have the common challenge of either assessing the similarity or connections between drugs and diseases. However, traditional CDR is fraught with many challenges due to the underlying complex pharmacology and biology of diseases, genes, and drugs, as well as the complexity of their associations. As such, capturing highly non-linear associations among drugs, genes, diseases by most existing CDR methods has been challenging. We propose a network-based integration approach that can best capture knowledge (and complex relationships) contained within and between drugs, genes and disease data. A network-based machine learning approach is applied thereafter by using the extracted knowledge and relationships in order to identify single and pair of approved or experimental drugs with potential therapeutic effects on different breast cancer subtypes. Indeed, further clinical analysis is needed to confirm the therapeutic effects of identified drugs on each breast cancer subtype.
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Affiliation(s)
- Forough Firoozbakht
- School of Computer Science, University of Windsor, 401 Sunset Ave., Windsor, ON, Canada
| | - Iman Rezaeian
- School of Computer Science, University of Windsor, 401 Sunset Ave., Windsor, ON, Canada.,Rocket Innovation Studio, 156 Chatham St W, Windsor, ON, Canada
| | - Luis Rueda
- School of Computer Science, University of Windsor, 401 Sunset Ave., Windsor, ON, Canada.
| | - Alioune Ngom
- School of Computer Science, University of Windsor, 401 Sunset Ave., Windsor, ON, Canada
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2
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Afshari AR, Sanati M, Aminyavari S, Shakeri F, Bibak B, Keshavarzi Z, Soukhtanloo M, Jalili-Nik M, Sadeghi MM, Mollazadeh H, Johnston TP, Sahebkar A. Advantages and drawbacks of dexamethasone in glioblastoma multiforme. Crit Rev Oncol Hematol 2022; 172:103625. [PMID: 35158070 DOI: 10.1016/j.critrevonc.2022.103625] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 12/25/2022] Open
Abstract
The most widespread, malignant, and deadliest type of glial tumor is glioblastoma multiforme (GBM). Despite radiation, chemotherapy, and radical surgery, the median survival of afflicted individuals is about 12 months. Unfortunately, existing therapeutic interventions are abysmal. Dexamethasone (Dex), a synthetic glucocorticoid, has been used for many years to treat brain edema and inflammation caused by GBM. Several investigations have recently shown that Dex also exerts antitumoral effects against GBM. On the other hand, more recent disputed findings have questioned the long-held dogma of Dex treatment for GBM. Unfortunately, steroids are associated with various undesirable side effects, including severe immunosuppression and metabolic changes like hyperglycemia, which may impair the survival of GBM patients. Current ideas and concerns about Dex's effects on GBM cerebral edema, cell proliferation, migration, and its clinical outcomes were investigated in this study.
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Affiliation(s)
- Amir R Afshari
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mehdi Sanati
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
| | - Samaneh Aminyavari
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Shakeri
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Bahram Bibak
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Zakieh Keshavarzi
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Soukhtanloo
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Jalili-Nik
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Montazami Sadeghi
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hamid Mollazadeh
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran.
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; School of Medicine, The University of Western Australia, Perth, Australia; Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Clarke GA, Hartse BX, Niaraki Asli AE, Taghavimehr M, Hashemi N, Abbasi Shirsavar M, Montazami R, Alimoradi N, Nasirian V, Ouedraogo LJ, Hashemi NN. Advancement of Sensor Integrated Organ-on-Chip Devices. SENSORS (BASEL, SWITZERLAND) 2021; 21:1367. [PMID: 33671996 PMCID: PMC7922590 DOI: 10.3390/s21041367] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023]
Abstract
Organ-on-chip devices have provided the pharmaceutical and tissue engineering worlds much hope since they arrived and began to grow in sophistication. However, limitations for their applicability were soon realized as they lacked real-time monitoring and sensing capabilities. The users of these devices relied solely on endpoint analysis for the results of their tests, which created a chasm in the understanding of life between the lab the natural world. However, this gap is being bridged with sensors that are integrated into organ-on-chip devices. This review goes in-depth on different sensing methods, giving examples for various research on mechanical, electrical resistance, and bead-based sensors, and the prospects of each. Furthermore, the review covers works conducted that use specific sensors for oxygen, and various metabolites to characterize cellular behavior and response in real-time. Together, the outline of these works gives a thorough analysis of the design methodology and sophistication of the current sensor integrated organ-on-chips.
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Affiliation(s)
- Gabriel A. Clarke
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Brenna X. Hartse
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Amir Ehsan Niaraki Asli
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Mehrnoosh Taghavimehr
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Niloofar Hashemi
- Department of Materials Science and Engineering, Sharif University of Technology, Tehran 11365, Iran;
| | - Mehran Abbasi Shirsavar
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Reza Montazami
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Nima Alimoradi
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Vahid Nasirian
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Lionel J. Ouedraogo
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
| | - Nicole N. Hashemi
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA; (G.A.C.); (B.X.H.); (A.E.N.A.); (M.T.); (M.A.S.); (R.M.); (N.A.); (V.N.); (L.J.O.)
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
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Yao Q, Guo Y, Xue J, Kong D, Li J, Tian X, Hao C, Zhou T. Development and validation of a LC-MS/MS method for simultaneous determination of six glucocorticoids and its application to a pharmacokinetic study in nude mice. J Pharm Biomed Anal 2020; 179:112980. [DOI: 10.1016/j.jpba.2019.112980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 01/18/2023]
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Pharmacokinetic/Pharmacodynamic Modeling of the Anti-Cancer Effect of Dexamethasone in Pancreatic Cancer Xenografts and Anticipation of Human Efficacious Doses. J Pharm Sci 2019; 109:1169-1177. [PMID: 31655033 DOI: 10.1016/j.xphs.2019.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 11/20/2022]
Abstract
Dexamethasone (DEX), a synthetic glucocorticoid, exhibited anti-cancer efficacy in pancreatic xenografts derived from patient tumor tissue or cancer cell lines. The aim of this study was to establish pharmacokinetic/pharmacodynamic (PK/PD) models to quantitatively characterize the inhibitory effect of DEX on tumor growth as well as its discrepancy among 3 xenograft models. Data of tumor growth profiles were collected from a patient-derived xenograft (PDX) model in NOD/SCID mice and 2 cell line-derived (PANC-1 and SW1990) xenograft models in BALB/c nude mice. Empirical PK/PD models were developed to establish mathematical relationships between plasma concentration of DEX and tumor growth dynamics after integrating PK parameters extracted from literature. Drug effect in each model was well described by a linear inhibitory function with a potency factor of 4.67, 3.14, and 2.35 L/mg for PDX, PANC-1, and SW1990 xenograft, respectively. Human efficacious doses of DEX were preliminarily predicted through model-based simulation, and 60% tumor growth inhibition at clinical exposure corresponded to a daily dose range of 26-52 mg intravenously. This modeling work quantified the preclinical anti-cancer effect of DEX and demonstrated the feasibility of its medication in pancreatic cancer, which would be conductive to future translational research.
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Sivolap YP. Antipsychotics: treatment of schizophrenia and other therapeutic options. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:74-78. [DOI: 10.17116/jnevro201911910174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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