1
|
Lee HM, Kim Y. Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. SCHIZOPHRENIA RESEARCH AND TREATMENT 2016; 2016:6378137. [PMID: 27073698 PMCID: PMC4814692 DOI: 10.1155/2016/6378137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/24/2016] [Indexed: 01/03/2023]
Abstract
Better the drugs you know than the drugs you do not know. Drug repurposing is a promising, fast, and cost effective method that can overcome traditional de novo drug discovery and development challenges of targeting neuropsychiatric and other disorders. Drug discovery and development targeting neuropsychiatric disorders are complicated because of the limitations in understanding pathophysiological phenomena. In addition, traditional de novo drug discovery and development are risky, expensive, and time-consuming processes. One alternative approach, drug repurposing, has emerged taking advantage of off-target effects of the existing drugs. In order to identify new opportunities for the existing drugs, it is essential for us to understand the mechanisms of action of drugs, both biologically and pharmacologically. By doing this, drug repurposing would be a more effective method to develop drugs against neuropsychiatric and other disorders. Here, we review the difficulties in drug discovery and development in neuropsychiatric disorders and the extent and perspectives of drug repurposing.
Collapse
Affiliation(s)
- Hyeong-Min Lee
- Department of Cell Biology & Physiology, School of Medicine, University of North Carolina, 115 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Yuna Kim
- Department of Pediatrics, School of Medicine, Duke University, 905 S. LaSalle Street, Durham, NC 27710, USA
| |
Collapse
|
2
|
Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
Collapse
Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
| |
Collapse
|
3
|
Mizianty MJ, Fan X, Yan J, Chalmers E, Woloschuk C, Joachimiak A, Kurgan L. Covering complete proteomes with X-ray structures: a current snapshot. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2781-93. [PMID: 25372670 PMCID: PMC4220968 DOI: 10.1107/s1399004714019427] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022]
Abstract
Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.
Collapse
Affiliation(s)
- Marcin J. Mizianty
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Xiao Fan
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Jing Yan
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Eric Chalmers
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Christopher Woloschuk
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Lukasz Kurgan
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| |
Collapse
|
4
|
Grey JL, Thompson DH. Challenges and opportunities for new protein crystallization strategies in structure-based drug design. Expert Opin Drug Discov 2012; 5:1039-45. [PMID: 21116481 DOI: 10.1517/17460441.2010.515583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.
Collapse
Affiliation(s)
- Jessica Lynn Grey
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | | |
Collapse
|
5
|
Moncayo R. Reflections on the theory of "silver bullet" octreotide tracers: implications for ligand-receptor interactions in the age of peptides, heterodimers, receptor mosaics, truncated receptors, and multifractal analysis. EJNMMI Res 2011; 1:9. [PMID: 22214590 PMCID: PMC3251005 DOI: 10.1186/2191-219x-1-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/26/2011] [Indexed: 12/25/2022] Open
Abstract
The classical attitude of Nuclear Medicine practitioners on matters of peptide-receptor interactions has maintained an intrinsic monogamic character since many years. New advances in the field of biochemistry and even in clinical Nuclear Medicine have challenged this type of thinking, which prompted me to work on this review. The central issue of this paper will be the use of somatostatin analogs, i.e., octreotide, in clinical imaging procedures as well as in relation to neuroendocirne tumors. Newly described characteristics of G-protein coupled receptors such as the formation of receptor mosaics will be discussed. A small section will enumerate the regulatory processes found in the cell membrane. Possible new interpretations, other than tumor detection, based on imaging procedures with somatostatin analogs will be presented. The readers will be taken to situations such as inflammation, nociception, mechanosensing, chemosensing, fibrosis, taste, and vascularity where somatostatin is involved. Thyroid-associated orbitopathy will be used as a model for the development of multi-agent therapeutics. The final graphical summary depicts the multifactorial properties of ligand binding.
Collapse
Affiliation(s)
- Roy Moncayo
- Department of Nuclear Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
6
|
Abstract
Aminergic G protein-coupled receptors (GPCRs) have been a major focus of pharmaceutical research for many years. Due partly to the lack of reliable receptor structures, drug discovery efforts have been largely ligand-based. The recently determined X-ray structure of the beta(2)-adrenergic receptor offers an opportunity to investigate the advantages and limitations inherent in a structure-based approach to ligand discovery against this and related GPCR targets. Approximately 1 million commercially available, "lead-like" molecules were docked against the beta(2)-adrenergic receptor structure. On testing of 25 high-ranking molecules, 6 were active with binding affinities <4 microM, with the best molecule binding with a K(i) of 9 nM (95% confidence interval 7-10 nM). Five of these molecules were inverse agonists. The high hit rate, the high affinity of the most potent molecule, the discovery of unprecedented chemotypes among the new inhibitors, and the apparent bias toward inverse agonists among the docking hits, have implications for structure-based approaches against GPCRs that recognize small organic molecules.
Collapse
|
7
|
Enna S, Feuerstein G, Piette J, Williams M. Fifty years of Biochemical Pharmacology: The discipline and the journal. Biochem Pharmacol 2008; 76:1-10. [DOI: 10.1016/j.bcp.2008.03.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 03/31/2008] [Indexed: 01/01/2023]
|
8
|
Wang XS, Tang H, Golbraikh A, Tropsha A. Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F. J Chem Inf Model 2008; 48:997-1013. [DOI: 10.1021/ci700404c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xiang S. Wang
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and Molecular & Cellular Biophysics Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Hao Tang
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and Molecular & Cellular Biophysics Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Alexander Golbraikh
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and Molecular & Cellular Biophysics Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products and Carolina Exploratory Center for Cheminformatics Research, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and Molecular & Cellular Biophysics Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| |
Collapse
|