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Bakrim S, El Omari N, Khan EJ, Khalid A, Abdalla AN, Chook JB, Goh KW, Ming LC, Aboulaghras S, Bouyahya A. Phytosterols activating nuclear receptors are involving in steroid hormone-dependent cancers: Myth or fact? Biomed Pharmacother 2023; 169:115783. [PMID: 37944439 DOI: 10.1016/j.biopha.2023.115783] [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: 08/09/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Nuclear receptors (NRs) represent intracellular proteins that function as a signaling network of transcriptional factors to control genes in response to a variety of environmental, dietary, and hormonal stimulations or serve as orphan receptors lacking a recognized ligand. They also play an essential role in normal development, metabolism, cell growth, cell division, physiology, reproduction, and homeostasis and function as biological markers for tumor subclassification and as targets for hormone therapy. NRs, including steroid hormone receptors (SHRs), have been studied as tools to examine the fundamentals of transcriptional regulation within the development of mammals and human physiology, in addition to their links to disturbances. In this regard, it is widely recognized that aberrant NR signaling is responsible for the pathological growth of hormone-dependent tumors in response to SHRs dysregulation and consequently represents a potential therapeutic candidate in a range of diseases, as in the case of prostate cancer and breast cancer. On the other hand, phytosterols are a group of plant-derived compounds that act directly as ligands for NRs and have proven their efficacy in the management of diabetes, heart diseases, and cancers. However, these plants are not suggested in cases of hormone-dependent cancer since a certain group of plants contains molecules with a chemical structure similar to that of estrogens, which are known as phytoestrogens or estrogen-like compounds, such as lignans, coumestans, and isoflavones. Therefore, it remains an open and controversial debate regarding whether consuming a phytosterol-rich diet and adopting a vegetarian lifestyle like the Mediterranean diet may increase the risk of developing steroid hormone-dependent cancers by constitutively activating SHRs and thereby leading to tumor transformation. Overall, the purpose of this review is to better understand the relevant mechanistic pathways and explore epidemiological investigations in order to establish that phytosterols may contribute to the activation of NRs as cancer drivers in hormone-dependent cancers.
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Affiliation(s)
- Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir 80000, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat 10100, Morocco
| | | | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, Khartoum, Sudan.
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Jack Bee Chook
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Malaysia.
| | - Long Chiau Ming
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Sara Aboulaghras
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco.
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2
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Okuyama R. Chronological Analysis of First-in-Class Drugs Approved from 2011 to 2022: Their Technological Trend and Origin. Pharmaceutics 2023; 15:1794. [PMID: 37513981 PMCID: PMC10386398 DOI: 10.3390/pharmaceutics15071794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The discovery and development of first-in-class (FIC) drugs are becoming increasingly important due to increasing reimbursement pressure and personalized medication. To investigate the technological trends and origin of FIC drugs, the FIC drugs approved in the U.S. from January 2011 to December 2022 were analyzed. The analysis shows that previous major target families, viz. enzymes, G-protein coupled receptors, transporters, and transcription factors, are no longer considered major in recent years. Instead, the shares of secreted proteins/peptides and mRNAs have continuously increased from 2011-2014 to 2019-2022, suggesting that the target family of FIC drugs has shifted to molecules previously considered challenging as drug targets. Small molecules were predominant in 2011-2014, followed by a large increase in antibody medicines in 2015-2018 and further diversification of antibody medicine modalities in 2019-2022. Nucleic acid medicine has also continuously increased its share, suggesting that diversifying modalities supports the creation of FIC drugs toward challenging target molecules. Over half of FIC drugs were created by small and medium enterprises (SMEs), especially young companies established in the 1990s and 2000s. All SMEs that produced more than one FIC drug approved in 2019-2022 have the strong technological capability in a specific modality. Investment in modality technologies and facilitating mechanisms to translate academic modality technologies to start-ups might be important for enhancing FIC drug development.
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Affiliation(s)
- Ryo Okuyama
- College of International Management, Ritsumeikan Asia Pacific University, Beppu 874-8577, Japan
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3
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Xu P. Nuclear Receptors in Health and Diseases. Int J Mol Sci 2023; 24:ijms24119153. [PMID: 37298107 DOI: 10.3390/ijms24119153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Nuclear receptors (NRs) are a vital superfamily of transcription factors that play crucial roles in physiology and pharmacology [...].
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Affiliation(s)
- Pengfei Xu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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4
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Parent EE, Fowler AM. Nuclear Receptor Imaging In Vivo-Clinical and Research Advances. J Endocr Soc 2022; 7:bvac197. [PMID: 36655003 PMCID: PMC9838808 DOI: 10.1210/jendso/bvac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Indexed: 01/01/2023] Open
Abstract
Nuclear receptors are transcription factors that function in normal physiology and play important roles in diseases such as cancer, inflammation, and diabetes. Noninvasive imaging of nuclear receptors can be achieved using radiolabeled ligands and positron emission tomography (PET). This quantitative imaging approach can be viewed as an in vivo equivalent of the classic radioligand binding assay. A main clinical application of nuclear receptor imaging in oncology is to identify metastatic sites expressing nuclear receptors that are targets for approved drug therapies and are capable of binding ligands to improve treatment decision-making. Research applications of nuclear receptor imaging include novel synthetic ligand and drug development by quantifying target drug engagement with the receptor for optimal therapeutic drug dosing and for fundamental research into nuclear receptor function in cells and animal models. This mini-review provides an overview of PET imaging of nuclear receptors with a focus on radioligands for estrogen receptor, progesterone receptor, and androgen receptor and their use in breast and prostate cancer.
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Affiliation(s)
- Ephraim E Parent
- Mayo Clinic Florida, Department of Radiology, Jacksonville, Florida 32224, USA
| | - Amy M Fowler
- Correspondence: Amy M. Fowler, MD, PhD, Department of Radiology, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792-3252, USA.
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5
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Sellami A, Réau M, Montes M, Lagarde N. Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns. Front Endocrinol (Lausanne) 2022; 13:986016. [PMID: 36176461 PMCID: PMC9513233 DOI: 10.3389/fendo.2022.986016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Being in the center of both therapeutic and toxicological concerns, NRs are widely studied for drug discovery application but also to unravel the potential toxicity of environmental compounds such as pesticides, cosmetics or additives. High throughput screening campaigns (HTS) are largely used to detect compounds able to interact with this protein family for both therapeutic and toxicological purposes. These methods lead to a large amount of data requiring the use of computational approaches for a robust and correct analysis and interpretation. The output data can be used to build predictive models to forecast the behavior of new chemicals based on their in vitro activities. This atrticle is a review of the studies published in the last decade and dedicated to NR ligands in silico prediction for both therapeutic and toxicological purposes. Over 100 articles concerning 14 NR subfamilies were carefully read and analyzed in order to retrieve the most commonly used computational methods to develop predictive models, to retrieve the databases deployed in the model building process and to pinpoint some of the limitations they faced.
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6
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Nuclear receptors: from molecular mechanisms to therapeutics. Essays Biochem 2021; 65:847-856. [PMID: 34825698 PMCID: PMC8628184 DOI: 10.1042/ebc20210020] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023]
Abstract
Nuclear receptors are classically defined as ligand-activated transcription factors that regulate key functions in reproduction, development, and physiology. Humans have 48 nuclear receptors, which when dysregulated are often linked to diseases. Because most nuclear receptors can be selectively activated or inactivated by small molecules, they are prominent therapeutic targets. The basic understanding of this family of transcription factors was accelerated in the 1980s upon the cloning of the first hormone receptors. During the next 20 years, a deep understanding of hormone signaling was achieved that has translated to numerous clinical applications, such as the development of standard-of-care endocrine therapies for hormonally driven breast and prostate cancers. A 2004 issue of this journal reviewed progress on elucidating the structures of nuclear receptors and their mechanisms of action. In the current issue, we focus on the broad application of new knowledge in this field for therapy across diverse disease states including cancer, cardiovascular disease, various inflammatory diseases, the aging brain, and COVID-19.
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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8
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The journey of multifunctional bone scaffolds fabricated from traditional toward modern techniques. Biodes Manuf 2020. [DOI: 10.1007/s42242-020-00094-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Griesenauer RH, Schillebeeckx C, Kinch MS. CDEK: Clinical Drug Experience Knowledgebase. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5549735. [PMID: 31411687 PMCID: PMC6693031 DOI: 10.1093/database/baz087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
The Clinical Drug Experience Knowledgebase (CDEK) is a database and web platform of active pharmaceutical ingredients with evidence of clinical testing as well as the organizations involved in their research and development. CDEK was curated by disambiguating intervention and organization names from ClinicalTrials.gov and cross-referencing these entries with other prominent drug databases. Approximately 43% of active pharmaceutical ingredients in the CDEK database were sourced from ClinicalTrials.gov and cannot be found in any other prominent compound-oriented database. The contents of CDEK are structured around three pillars: active pharmaceutical ingredients (n = 22 292), clinical trials (n = 127 223) and organizations (n = 24 728). The envisioned use of the CDEK is to support the investigation of many aspects of drug development, including discovery, repurposing opportunities, chemo- and bio-informatics, clinical and translational research and regulatory sciences.
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Affiliation(s)
- Rebekah H Griesenauer
- Center for Research Innovation in Biotechnology, Washington University in St. Louis, MO 63110, USA
| | | | - Michael S Kinch
- Center for Research Innovation in Biotechnology, Washington University in St. Louis, MO 63110, USA
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10
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DuShane JK, Maginnis MS. Human DNA Virus Exploitation of the MAPK-ERK Cascade. Int J Mol Sci 2019; 20:ijms20143427. [PMID: 31336840 PMCID: PMC6679023 DOI: 10.3390/ijms20143427] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
The extracellular signal-regulated kinases (ERKs) comprise a particular branch of the mitogen-activated protein kinase cascades (MAPK) that transmits extracellular signals into the intracellular environment to trigger cellular growth responses. Similar to other MAPK cascades, the MAPK-ERK pathway signals through three core kinases—Raf, MAPK/ERK kinase (MEK), and ERK—which drive the signaling mechanisms responsible for the induction of cellular responses from extracellular stimuli including differentiation, proliferation, and cellular survival. However, pathogens like DNA viruses alter MAPK-ERK signaling in order to access DNA replication machineries, induce a proliferative state in the cell, or even prevent cell death mechanisms in response to pathogen recognition. Differential utilization of this pathway by multiple DNA viruses highlights the dynamic nature of the MAPK-ERK pathway within the cell and the importance of its function in regulating a wide variety of cellular fates that ultimately influence viral infection and, in some cases, result in tumorigenesis.
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Affiliation(s)
- Jeanne K DuShane
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04401, USA
| | - Melissa S Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04401, USA.
- Graduate School in Biomedical Sciences and Engineering, The University of Maine, Orono, ME 04401, USA.
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11
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Kinch MS, Griesenauer RH. 2018 in review: FDA approvals of new molecular entities. Drug Discov Today 2019; 24:1710-1714. [PMID: 31158510 DOI: 10.1016/j.drudis.2019.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/16/2019] [Accepted: 05/28/2019] [Indexed: 11/26/2022]
Abstract
2018 was a remarkable year, both in terms of the number of new molecular entities (NMEs) approved and the organizations developing them. In total, 59 NMEs received a nod from the US Food and Drug Administration (FDA), most of which were approved using a priority or breakthrough designation. Orphan drugs accounted for more than half of new approvals, only the second time in history that level has been achieved. Moreover, the net number of organizations that received an FDA approval and remain active in new drug research surged in 2018, reflecting both an increase in new organizations and lower levels of industry consolidation.
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Affiliation(s)
- Michael S Kinch
- Center for Research Innovation and Biotechnology, Washington University in St Louis, St Louis, MO 63130, USA.
| | - Rebekah H Griesenauer
- Center for Research Innovation and Biotechnology, Washington University in St Louis, St Louis, MO 63130, USA
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12
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Douguet D. Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs. ACS Med Chem Lett 2018. [PMID: 29541361 DOI: 10.1021/acsmedchemlett.7b00462] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Presented here are several data sets that gather information collected from the labels of the FDA approved drugs: their molecular structures and those of the described active metabolites, their associated pharmacokinetics and pharmacodynamics data, and the history of their marketing authorization by the FDA. To date, 1852 chemical structures have been identified with a molecular weight less than 2000 of which 492 are or have active metabolites. To promote the sharing of data, the original web server was upgraded for browsing the database and downloading the data sets (http://chemoinfo.ipmc.cnrs.fr/edrug3d). It is believed that the multidimensional chemistry-oriented collections are an essential resource for a thorough analysis of the current drug chemical space. The data sets are envisioned as being used in a wide range of endeavors that include drug repurposing, drug design, privileged structures analyses, structure-activity relationship studies, and improving of absorption, distribution, metabolism, and elimination predictive models.
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Affiliation(s)
- Dominique Douguet
- Université Côte d’Azur, Inserm, CNRS, IPMC, 660 Route des Lucioles, 06560 Valbonne, France
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13
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Affiliation(s)
- Rebekah H Griesenauer
- Center for Research Innovation in Biotechnology, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Ryan Moore
- Center for Research Innovation in Biotechnology, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Michael S Kinch
- Center for Research Innovation in Biotechnology, Washington University in St. Louis, St Louis, MO 63110, USA.
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14
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GPR88 is a critical regulator of feeding and body composition in mice. Sci Rep 2017; 7:9912. [PMID: 28855710 PMCID: PMC5577241 DOI: 10.1038/s41598-017-10058-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
GPR88 is an orphan G-protein-coupled receptor with predominant expression in reward-related areas in the brain. While the lack of GPR88 has been demonstrated to induce behavioral deficits, the potential function of the receptor in the control of food intake and energy balance remains unexplored. In this work, the role of GPR88 in energy homeostasis was investigated in Gpr88−/− mice fed either standard chow or high fat diet (HFD). Gpr88−/− mice showed significantly reduced adiposity accompanied with suppressed spontaneous food intake, particularly pronounced under HFD treatment. While energy expenditure was likewise lower in Gpr88−/− mice, body weight gain remained unchanged. Furthermore, deregulation in glucose tolerance and insulin responsiveness in response to HFD was attenuated in Gpr88−/− mice. On the molecular level, distinct changes in the hypothalamic mRNA levels of cocaine-and amphetamine-regulated transcript (Cartpt), a neuropeptide involved in the control of feeding and reward, were observed in Gpr88−/− mice. In addition, GPR88 deficiency was associated with altered expressions of the anorectic Pomc and the orexigenic Npy in the arcuate nucleus, especially under HFD condition. Together, our results indicate that GPR88 signalling is not only important for reward processes, but also plays a role in the central regulatory circuits for energy homeostasis.
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15
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Griesenauer RH, Kinch MS. 2016 in review: FDA approvals of new molecular entities. Drug Discov Today 2017; 22:1593-1597. [PMID: 28687460 DOI: 10.1016/j.drudis.2017.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/06/2017] [Accepted: 06/28/2017] [Indexed: 11/16/2022]
Abstract
An overview of drugs approved by FDA in 2016 reveals dramatic disruptions in long-term trends. The number of new molecular entities (NMEs) dropped, reflecting the lowest rate of small-molecule approvals observed in almost five decades. In addition, the pace of industry consolidation slowed substantially. The impact of mergers and acquisitions decreased the total number of organizations with past approval experience and continued research and development (R&D) activities to 102, divided evenly between more established pharmaceutical and newer biotechnology companies. Despite these substantial differences, the industry continued to pursue regulatory incentives, as evidenced by a continued increase in the fraction of NMEs approved using an orphan or priority designation, and almost all oncology drugs approved in 2016 utilized these mechanisms.
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Affiliation(s)
- Rebekah H Griesenauer
- Center for Research Innovation and Biotechnology, Washington University in Saint Louis, St Louis, MO 63130, USA
| | - Michael S Kinch
- Center for Research Innovation and Biotechnology, Washington University in Saint Louis, St Louis, MO 63130, USA.
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16
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First protein drug target’s appraisal of lead-likeness descriptors to unfold the intervening chemical space. J Mol Graph Model 2017; 72:272-282. [DOI: 10.1016/j.jmgm.2016.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
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17
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Haddad Y, Heger Z, Adam V. Targeting Neuroblastoma Cell Surface Proteins: Recommendations for Homology Modeling of hNET, ALK, and TrkB. Front Mol Neurosci 2017; 10:7. [PMID: 28163672 PMCID: PMC5247432 DOI: 10.3389/fnmol.2017.00007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/06/2017] [Indexed: 11/13/2022] Open
Abstract
Targeted therapy is a promising approach for treatment of neuroblastoma as evident from the large number of targeting agents employed in clinical practice today. In the absence of known crystal structures, researchers rely on homology modeling to construct template-based theoretical structures for drug design and testing. Here, we discuss three candidate cell surface proteins that are suitable for homology modeling: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor 2 (NTRK2 or TrkB). When choosing templates, both sequence identity and structure quality are important for homology modeling and pose the first of many challenges in the modeling process. Homology modeling of hNET can be improved using template models of dopamine and serotonin transporters instead of the leucine transporter (LeuT). The extracellular domains of ALK and TrkB are yet to be exploited by homology modeling. There are several idiosyncrasies that require direct attention throughout the process of model construction, evaluation and refinement. Shifts/gaps in the alignment between the template and target, backbone outliers and side-chain rotamer outliers are among the main sources of physical errors in the structures. Low-conserved regions can be refined with loop modeling method. Residue hydrophobicity, accessibility to bound metals or glycosylation can aid in model refinement. We recommend resolving these idiosyncrasies as part of "good modeling practice" to obtain highest quality model. Decreasing physical errors in protein structures plays major role in the development of targeting agents and understanding of chemical interactions at the molecular level.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in BrnoBrno, Czechia; Central European Institute of Technology, Brno University of TechnologyBrno, Czechia
| | - Zbyněk Heger
- Department of Chemistry and Biochemistry, Mendel University in BrnoBrno, Czechia; Central European Institute of Technology, Brno University of TechnologyBrno, Czechia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in BrnoBrno, Czechia; Central European Institute of Technology, Brno University of TechnologyBrno, Czechia
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18
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Ngo T, Kufareva I, Coleman JL, Graham RM, Abagyan R, Smith NJ. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol 2016; 173:2934-51. [PMID: 26837045 PMCID: PMC5341249 DOI: 10.1111/bph.13452] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 11/18/2015] [Accepted: 01/29/2016] [Indexed: 12/26/2022] Open
Abstract
GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.
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Affiliation(s)
- Tony Ngo
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - James Lj Coleman
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Robert M Graham
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Nicola J Smith
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia.
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19
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Mignani S, Huber S, Tomás H, Rodrigues J, Majoral JP. Why and how have drug discovery strategies in pharma changed? What are the new mindsets? Drug Discov Today 2016; 21:239-49. [PMID: 26376356 DOI: 10.1016/j.drudis.2015.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/30/2015] [Accepted: 09/08/2015] [Indexed: 02/08/2023]
Abstract
In the pharmaceutical industry the long-term challenge of drug innovation is the key phrase throughout R&D that refers to increasing the output of original drug candidate molecules. To increase R&D productivity, implementation of new and strategic R&D orientations to develop new approaches or systems to identify hits and leads efficiently has taken place and enabled all scientists working in the drug discovery domain to develop innovative medicines for the 21st century.
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Affiliation(s)
- Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, 45, rue des Saints Peres, 75006, Paris, France.
| | - Scot Huber
- SCYNEXIS Inc., P.O. Box 12878, Research Triangle Park, NC 27709, USA
| | - Helena Tomás
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal
| | - João Rodrigues
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal.
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France.
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Doak BC, Zheng J, Dobritzsch D, Kihlberg J. How Beyond Rule of 5 Drugs and Clinical Candidates Bind to Their Targets. J Med Chem 2015; 59:2312-27. [DOI: 10.1021/acs.jmedchem.5b01286] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bradley C. Doak
- Department of Chemistry—BMC, Uppsala University, Box
576, SE-751 23 Uppsala, Sweden
| | - Jie Zheng
- Department of Chemistry—BMC, Uppsala University, Box
576, SE-751 23 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, Box
576, SE-751 23 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry—BMC, Uppsala University, Box
576, SE-751 23 Uppsala, Sweden
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