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Brennan RJ, Jenkinson S, Brown A, Delaunois A, Dumotier B, Pannirselvam M, Rao M, Ribeiro LR, Schmidt F, Sibony A, Timsit Y, Sales VT, Armstrong D, Lagrutta A, Mittlestadt SW, Naven R, Peri R, Roberts S, Vergis JM, Valentin JP. The state of the art in secondary pharmacology and its impact on the safety of new medicines. Nat Rev Drug Discov 2024; 23:525-545. [PMID: 38773351 DOI: 10.1038/s41573-024-00942-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2024] [Indexed: 05/23/2024]
Abstract
Secondary pharmacology screening of investigational small-molecule drugs for potentially adverse off-target activities has become standard practice in pharmaceutical research and development, and regulatory agencies are increasingly requesting data on activity against targets with recognized adverse effect relationships. However, the screening strategies and target panels used by pharmaceutical companies may vary substantially. To help identify commonalities and differences, as well as to highlight opportunities for further optimization of secondary pharmacology assessment, we conducted a broad-ranging survey across 18 companies under the auspices of the DruSafe leadership group of the International Consortium for Innovation and Quality in Pharmaceutical Development. Based on our analysis of this survey and discussions and additional research within the group, we present here an overview of the current state of the art in secondary pharmacology screening. We discuss best practices, including additional safety-associated targets not covered by most current screening panels, and present approaches for interpreting and reporting off-target activities. We also provide an assessment of the safety impact of secondary pharmacology screening, and a perspective on opportunities and challenges in this rapidly developing field.
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Affiliation(s)
| | | | | | | | | | | | - Mohan Rao
- Janssen Research & Development, San Diego, CA, USA
- Neurocrine Biosciences, San Diego, CA, USA
| | - Lyn Rosenbrier Ribeiro
- UCB Biopharma, Braine-l'Alleud, Belgium
- AstraZeneca, Cambridge, UK
- Grunenthal, Berkshire, UK
| | | | | | - Yoav Timsit
- Novartis Biomedical Research, Cambridge, MA, USA
- Blueprint Medicines, Cambridge, MA, USA
| | | | - Duncan Armstrong
- Novartis Biomedical Research, Cambridge, MA, USA
- Armstrong Pharmacology, Macclesfield, UK
| | | | | | - Russell Naven
- Takeda Pharmaceuticals, Cambridge, MA, USA
- Novartis Biomedical Research, Cambridge, MA, USA
| | - Ravikumar Peri
- Takeda Pharmaceuticals, Cambridge, MA, USA
- Alexion Pharmaceuticals, Wilmington, DE, USA
| | - Sonia Roberts
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - James M Vergis
- Faegre Drinker Biddle and Reath, LLP, Washington, DC, USA
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2
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Kovačević T, Nujić K, Cindrić M, Dragojević S, Vinter A, Hozić A, Mesić M. Different chemical proteomic approaches to identify the targets of lapatinib. J Enzyme Inhib Med Chem 2023; 38:2183809. [PMID: 36856014 PMCID: PMC9980154 DOI: 10.1080/14756366.2023.2183809] [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] [Indexed: 03/02/2023] Open
Abstract
The process of identifying the protein targets and off-targets of a biologically active compound is of great importance in modern drug discovery. Various chemical proteomics approaches have been established for this purpose. To compare the different approaches, and to understand which method would provide the best results, we have chosen the EGFR inhibitor lapatinib as an example molecule. Lapatinib derivatives were designed using linkers with motifs, including amino (amidation), alkyne (click chemistry) and the diazirine group (photo-affinity). These modified lapatinib analogues were validated for their ability to inhibit EGFR activity in vitro and were shown to pull down purified recombinant EGFR protein. In all of the approaches evaluated here, we identified EGFR as the main protein target from the lysate of immortalised cell line expressing EGFR, thus validating its potential use to identify unknown protein targets. Taken together, the results reported here give insight into the cellular activities of lapatinib.
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Affiliation(s)
| | | | | | | | | | | | - Milan Mesić
- Selvita Ltd., Zagreb, Croatia,CONTACT Milan Mesić Selvita Ltd., Zagreb, Croatia
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3
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Van Gool A, Corrales F, Čolović M, Krstić D, Oliver-Martos B, Martínez-Cáceres E, Jakasa I, Gajski G, Brun V, Kyriacou K, Burzynska-Pedziwiatr I, Wozniak LA, Nierkens S, Pascual García C, Katrlik J, Bojic-Trbojevic Z, Vacek J, Llorente A, Antohe F, Suica V, Suarez G, t'Kindt R, Martin P, Penque D, Martins IL, Bodoki E, Iacob BC, Aydindogan E, Timur S, Allinson J, Sutton C, Luider T, Wittfooth S, Sammar M. Analytical techniques for multiplex analysis of protein biomarkers. Expert Rev Proteomics 2020; 17:257-273. [PMID: 32427033 DOI: 10.1080/14789450.2020.1763174] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research. AREAS COVERED We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses. EXPERT COMMENTARY The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.
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Affiliation(s)
- Alain Van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Fernado Corrales
- Functional Proteomics Laboratory, Centro Nacional De Biotecnología , Madrid, Spain
| | - Mirjana Čolović
- Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, University of Belgrade , Belgrade, Serbia
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade , Belgrade, Serbia
| | - Begona Oliver-Martos
- Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga , Malaga, Spain
| | - Eva Martínez-Cáceres
- Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona , Cerdanyola Del Vallès, Spain
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb , Zagreb, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health , Zagreb, Croatia
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE , Grenoble, France
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics , Nicosia, Cyprus
| | - Izabela Burzynska-Pedziwiatr
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Lucyna Alicja Wozniak
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Stephan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - César Pascual García
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST) , Belvaux, Luxembourg
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences , Bratislava, Slovakia
| | - Zanka Bojic-Trbojevic
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy - INEP, University of Belgrade , Belgrade, Serbia
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital , Oslo, Norway
| | - Felicia Antohe
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Viorel Suica
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Guillaume Suarez
- Center for Primary Care and Public Health (Unisanté), University of Lausanne , Lausanne, Switzerland
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC) , Kortrijk, Belgium
| | - Petra Martin
- Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James's Hospital , Dublin, Ireland
| | - Deborah Penque
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ines Lanca Martins
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ede Bodoki
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Bogdan-Cezar Iacob
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Eda Aydindogan
- Department of Chemistry, Graduate School of Sciences and Engineering, Koç University , Istanbul, Turkey
| | - Suna Timur
- Institute of Natural Sciences, Department of Biochemistry, Ege University , Izmir, Turkey
| | | | | | - Theo Luider
- Department of Neurology, Erasmus MC , Rotterdam, The Netherlands
| | | | - Marei Sammar
- Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College , Karmiel, Israel
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4
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Orlando E, Aebersold R. On the contribution of mass spectrometry-based platforms to the field of personalized oncology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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5
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Lyons SP, Jenkins NP, Nasa I, Choy MS, Adamo ME, Page R, Peti W, Moorhead GB, Kettenbach AN. A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans. Mol Cell Proteomics 2018; 17:2448-2461. [PMID: 30228194 DOI: 10.1074/mcp.ra118.000822] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/21/2018] [Indexed: 11/06/2022] Open
Abstract
A "tug-of-war" between kinases and phosphatases establishes the phosphorylation states of proteins. While serine and threonine phosphorylation can be catalyzed by more than 400 protein kinases, the majority of serine and threonine dephosphorylation is carried out by seven phosphoprotein phosphatases (PPPs). The PPP family consists of protein phosphatases 1 (PP1), 2A (PP2A), 2B (PP2B), 4 (PP4), 5 (PP5), 6 (PP6), and 7 (PP7). The imbalance in numbers between serine- and threonine-directed kinases and phosphatases led to the early belief that PPPs are unspecific and that kinases are the primary determinants of protein phosphorylation. However, it is now clear that PPPs achieve specificity through association with noncatalytic subunits to form multimeric holoenzymes, which expands the number of functionally distinct signaling entities to several hundred. Although there has been great progress in deciphering signaling by kinases, much less is known about phosphatases.We have developed a chemical proteomic strategy for the systematic interrogation of endogenous PPP catalytic subunits and their interacting proteins, including regulatory and scaffolding subunits (the "PPPome"). PP1, PP2A, PP4, PP5, and PP6 were captured using an immobilized, specific but nonselective PPP inhibitor microcystin-LR (MCLR), followed by protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a single analysis. Here, we combine this approach of phosphatase inhibitor bead profiling and mass spectrometry (PIB-MS) with label-free and tandem mass tag (TMT) quantification to map the PPPome in human cancer cell lines, mouse tissues, and yeast species, through which we identify cell- and tissue-type-specific PPP expression patterns and discover new PPP interacting proteins.
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Affiliation(s)
- Scott P Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Nicole P Jenkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Meng S Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Mark E Adamo
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Greg B Moorhead
- Department of Biological Science, University of Calgary, Alberta, Canada
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA; Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, NH, USA.
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6
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Luteolin attenuates Wnt signaling via upregulation of FZD6 to suppress prostate cancer stemness revealed by comparative proteomics. Sci Rep 2018; 8:8537. [PMID: 29867083 PMCID: PMC5986741 DOI: 10.1038/s41598-018-26761-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/15/2018] [Indexed: 12/28/2022] Open
Abstract
The mechanisms underlying luteolin-induced inhibition of prostate cancer (PCa) stemness have remained elusive. Here, we report that luteolin suppresses PCa stemness through Wnt signaling by upregulation of FZD6 (frizzled class receptor 6). Luteolin inhibits PCa cell proliferation, migration, self-renewal as well as the expression of prostate cancer stem cell markers in vitro. Through iTRAQ-based quantitative proteomics study, we identified 208 differentially expressed proteins in luteolin-treated PC-3 cells. Subsequent mechanistic analysis revealed that luteolin inhibits Wnt signaling by transcriptional upregulation of FZD6, and thereby suppressing the stemness of PCa cells. Furthermore, we identified FZD6 as a tumor suppressor that can abolish PCa stemness. In summary, our findings demonstrate that suppression of Wnt signaling by upregulation of FZD6 is a mechanism underlying luteolin-induced inhibition of PCa stemness. Our work suggests a new therapeutic strategy against human prostate cancer caused by aberrant activation of Wnt signaling.
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7
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Guo H, Peng H, Emili A. Mass spectrometry methods to study protein-metabolite interactions. Expert Opin Drug Discov 2017; 12:1271-1280. [DOI: 10.1080/17460441.2017.1378178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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8
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Jung HJ. Chemical Proteomic Approaches Targeting Cancer Stem Cells: A Review of Current Literature. Cancer Genomics Proteomics 2017; 14:315-327. [PMID: 28870999 PMCID: PMC5611518 DOI: 10.21873/cgp.20042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/24/2022] Open
Abstract
Cancer stem cells (CSCs) have been proposed as central drivers of tumor initiation, progression, recurrence, and therapeutic resistance. Therefore, identifying stem-like cells within cancers and understanding their properties is crucial for the development of effective anticancer therapies. Recently, chemical proteomics has become a powerful tool to efficiently determine protein networks responsible for CSC pathophysiology and comprehensively elucidate molecular mechanisms of drug action against CSCs. This review provides an overview of major methodologies utilized in chemical proteomic approaches. In addition, recent successful chemical proteomic applications targeting CSCs are highlighted. Future direction of potential CSC research by integrating chemical genomic and proteomic data obtained from a single biological sample of CSCs are also suggested in this review.
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Affiliation(s)
- Hye Jin Jung
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asan, Republic of Korea
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9
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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10
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Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL. A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. JOURNAL OF BIOMOLECULAR SCREENING 2016; 21:521-34. [PMID: 26962875 PMCID: PMC4917453 DOI: 10.1177/1087057116635818] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)-driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point.
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Affiliation(s)
- Andrew M. Stern
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E. Schurdak
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Jeremy M. Berg
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- University of Pittsburgh Institute for Personalized Medicine, Pittsburgh, PA, USA
| | - D. Lansing Taylor
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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11
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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12
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Zhou L, Li Q, Wang J, Huang C, Nice EC. Oncoproteomics: Trials and tribulations. Proteomics Clin Appl 2015; 10:516-31. [PMID: 26518147 DOI: 10.1002/prca.201500081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Qifu Li
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Jiandong Wang
- Department of Biomedical; Chengdu Medical College; Chengdu Sichuan Province P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
| | - Edouard C. Nice
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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Abstract
Osteosarcoma (OS) is the most common primary malignant tumor of bone and the third most common cancer in childhood and adolescence. Nowadays, early diagnosis, drug resistance and recurrence of the disease represent the major challenges in OS treatment. Post-genomics, and in particular proteomic technologies, offer an invaluable opportunity to address the level of biological complexity expressed by OS. Although the main goal of OS oncoproteomics is focused on diagnostic and prognostic biomarker discovery, in this review we describe and discuss global protein profiling approaches to other aspects of OS biology and pathophysiology, or to investigate the mechanism of action of chemotherapeutics. In addition, we present proteomic analyses carried out on OS cell lines as in vitro models for studying osteoblastic cell biology and the attractive opportunity offered by proteomics of OS cancer stem cells.
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Affiliation(s)
- Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, via Fiorentina 1, Università degli Studi di Siena, 53100 Siena, Italy
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14
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Wu J, Shin J, Williams CMM, Geoghegan KF, Wright SW, Limburg DC, Sahasrabudhe P, Bonin PD, Lefker BA, Ramsey SJ. Design and chemoproteomic functional characterization of a chemical probe targeted to bromodomains of BET family proteins. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00259h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selectivity of a PFI-1 based BET bromodomain probe was demonstrated using affinity capture in nuclear extracts from human cells.
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Affiliation(s)
- Jiang Wu
- Structural Biology and Biophysics
- Worldwide Medicinal Chemistry
- Groton
- USA
| | - Julia Shin
- Inflammation and Remodeling Research Unit
- Cambridge
- USA
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15
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Guo S, Zou J, Wang G. Advances in the proteomic discovery of novel therapeutic targets in cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:1259-71. [PMID: 24187485 PMCID: PMC3810204 DOI: 10.2147/dddt.s52216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic approaches are continuing to make headways in cancer research by helping to elucidate complex signaling networks that underlie tumorigenesis and disease progression. This review describes recent advances made in the proteomic discovery of drug targets for therapeutic development. A variety of technical and methodological advances are overviewed with a critical assessment of challenges and potentials. A number of potential drug targets, such as baculoviral inhibitor of apoptosis protein repeat-containing protein 6, macrophage inhibitory cytokine 1, phosphoglycerate mutase 1, prohibitin 1, fascin, and pyruvate kinase isozyme 2 were identified in the proteomic analysis of drug-resistant cancer cells, drug action, and differential disease state tissues. Future directions for proteomics-based target identification and validation to be more translation efficient are also discussed.
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Affiliation(s)
- Shanchun Guo
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Clark Atlanta University, Atlanta, GA, USA
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16
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Abstract
Recent advances in proteomics have facilitated the analysis of the kinome 'en masse'. What these studies have revealed is a surprisingly dynamic network of kinase responses to highly selective kinase inhibitors, thereby illustrating the complex biological responses to these small molecules. Moreover these studies have identified key transcription factors, such as c-Myc and FOXO (forkhead box O), that play pivotal roles in kinome reprogramming in cancer cells. Since many kinase inhibitors fail despite a high efficacy of blocking their intended targets, elucidating kinome changes at a more global level will be essential to understanding the mechanisms of kinase inhibitor pharmacology. The development of technologies to study the kinome, as well as examples of kinome resilience and reprogramming, will be discussed in the present review.
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17
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Lees P, Fink-Gremmels J, Toutain PL. Veterinary pharmacology: history, current status and future prospects. J Vet Pharmacol Ther 2013; 36:105-15. [PMID: 23473264 DOI: 10.1111/jvp.12041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/17/2013] [Indexed: 11/27/2022]
Abstract
Veterinary therapeutics, based on the art of Materia Medica, has been practised for countless centuries, but the science of veterinary pharmacology is of very recent origin. This review traces the contribution of Materia Medica to veterinary therapeutics from the Egyptian period through to the Age of Enlightenment. The first tentative steps in the development of the science of veterinary pharmacology were taken in the 18th century, but it was not until the mid 20th century that the science replaced the art of Materia Medica. This review traces the 20th century developments in veterinary pharmacology, with emphasis on the explosion of knowledge in the 35 year period to 2010. The range of factors which have influenced the current status of the discipline are reviewed. Future developments are considered from the perspectives of what might be regarded as desirable and those innovations that might be anticipated. We end with words of encouragement for young colleagues intent upon pursuing a career in veterinary pharmacology.
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Affiliation(s)
- P Lees
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Herts, UK.
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