101
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Singh S, Gajulapati V, Gajulapati K, Goo JI, Park YH, Jung HY, Lee SY, Choi JH, Kim YK, Lee K, Heo TH, Choi Y. Structure–activity relationship study of a series of novel oxazolidinone derivatives as IL-6 signaling blockers. Bioorg Med Chem Lett 2016; 26:1282-6. [DOI: 10.1016/j.bmcl.2016.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/23/2015] [Accepted: 01/08/2016] [Indexed: 12/27/2022]
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102
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Zhao C, Li H, Lin HJ, Yang S, Lin J, Liang G. Feedback Activation of STAT3 as a Cancer Drug-Resistance Mechanism. Trends Pharmacol Sci 2015; 37:47-61. [PMID: 26576830 DOI: 10.1016/j.tips.2015.10.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays crucial roles in several cellular processes such as cell proliferation and survival, and has been found to be aberrantly activated in many cancers. Much research has explored the leading mechanisms for regulating the STAT3 pathway and its role in promoting tumorigenesis. We focus here on recent evidence suggesting that feedback activation of STAT3 plays a prominent role in mediating drug resistance to a broad spectrum of targeted cancer therapies and chemotherapies. We highlight the potential of co-targeting STAT3 and its primary target to overcome drug resistance, and provide perspective on repurposing clinically approved drugs as STAT3 pathway inhibitors, in combination with the FDA-approved receptor tyrosine kinase (RTK) inhibitors, to improve clinical outcome of cancer treatment.
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Affiliation(s)
- Chengguang Zhao
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, People's Republic of China; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA; Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, University Town, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Huameng Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, University Town, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Huey-Jen Lin
- Department of Medical Laboratory Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shulin Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, People's Republic of China.
| | - Jiayuh Lin
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA.
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, University Town, Wenzhou, Zhejiang 325035, People's Republic of China
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103
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The dual epigenetic role of PRMT5 in acute myeloid leukemia: gene activation and repression via histone arginine methylation. Leukemia 2015; 30:789-99. [PMID: 26536822 DOI: 10.1038/leu.2015.308] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 01/13/2023]
Abstract
Changes in the enzymatic activity of protein arginine methyltransferase (PRMT) 5 have been associated with cancer; however, the protein's role in acute myeloid leukemia (AML) has not been fully evaluated. Here, we show that increased PRMT5 activity enhanced AML growth in vitro and in vivo while PRMT5 downregulation reduced it. In AML cells, PRMT5 interacted with Sp1 in a transcription repressor complex and silenced miR-29b preferentially via dimethylation of histone 4 arginine residue H4R3. As Sp1 is also a bona fide target of miR-29b, the miR silencing resulted in increased Sp1. This event in turn led to transcription activation of FLT3, a gene that encodes a receptor tyrosine kinase. Inhibition of PRMT5 via sh/siRNA or a first-in-class small-molecule inhibitor (HLCL-61) resulted in significantly increased expression of miR-29b and consequent suppression of Sp1 and FLT3 in AML cells. As a result, significant antileukemic activity was achieved. Collectively, our data support a novel leukemogenic mechanism in AML where PRMT5 mediates both silencing and transcription of genes that participate in a 'yin-yang' functional network supporting leukemia growth. As FLT3 is often mutated in AML and pharmacologic inhibition of PRMT5 appears feasible, the PRMT5-miR-29b-FLT3 network should be further explored as a novel therapeutic target for AML.
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104
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Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015; 87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While the fragment-based drug design approach continues to gain importance, gaps in the tools and methods available in the identification and accurate utilization of protein subpockets have limited the scope. The importance of these features of small molecule-protein recognition is highlighted with several examples. A generalized solution for the identification of subpockets and corresponding chemical fragments remains elusive, but there are numerous advancements in methods that can be used in combination to address subpockets. Finally, additional examples of approaches that consider the relative importance of small-molecule co-dependence of protein conformations are highlighted to emphasize an increased significance of subpockets, especially at protein interfaces.
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Affiliation(s)
- Matthew Bartolowits
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
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105
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Sheng C, Dong G, Miao Z, Zhang W, Wang W. State-of-the-art strategies for targeting protein-protein interactions by small-molecule inhibitors. Chem Soc Rev 2015; 44:8238-59. [PMID: 26248294 DOI: 10.1039/c5cs00252d] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting protein-protein interactions (PPIs) has emerged as a viable approach in modern drug discovery. However, the identification of small molecules enabling us to effectively interrupt their interactions presents significant challenges. In the recent past, significant advances have been made in the development of new biological and chemical strategies to facilitate the discovery process of small-molecule PPI inhibitors. This review aims to highlight the state-of-the-art technologies and the achievements made recently in this field. The "hot spots" of PPIs have been proved to be critical for small molecules to bind. Three strategies including screening, designing, and synthetic approaches have been explored for discovering PPI inhibitors by targeting the "hot spots". Although the classic high throughput screening approach can be used, fragment screening, fragment-based drug design and newly improved virtual screening are demonstrated to be more effective in the discovery of PPI inhibitors. In addition to screening approaches, design strategies including anchor-based and small molecule mimetics of secondary structures involved in PPIs have become powerful tools as well. Finally, constructing new chemically spaced libraries with high diversity and complexity is becoming an important area of interest for PPI inhibitors. The successful cases from the recent five year studies are used to illustrate how these approaches are implemented to uncover and optimize small molecule PPI inhibitors and notably some of them have become promising therapeutics.
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Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P. R. China.
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106
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Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking. Drug Discov Today 2015; 20:969-77. [DOI: 10.1016/j.drudis.2015.03.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/24/2015] [Accepted: 03/13/2015] [Indexed: 12/24/2022]
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107
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Drug affinity responsive target stability (DARTS) for small-molecule target identification. Methods Mol Biol 2015; 1263:287-98. [PMID: 25618353 DOI: 10.1007/978-1-4939-2269-7_22] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Drug affinity responsive target stability (DARTS) is a relatively quick and straightforward approach to identify potential protein targets for small molecules. It relies on the protection against proteolysis conferred on the target protein by interaction with a small molecule. The greatest advantage of this method is being able to use the native small molecule without having to immobilize or modify it (e.g., by incorporation of biotin, fluorescent, radioisotope, or photoaffinity labels). Here we describe in detail the protocol for performing unbiased DARTS with complex protein lysates to identify binding targets of small molecules and for using DARTS-Western blotting to test, screen, or validate potential small-molecule targets. Although the ideas have mainly been developed from studying molecules in areas of biology that are currently of interest to us and our collaborators, the general principles should be applicable to the analysis of all molecules in nature.
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108
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Understanding of complex protein interactions with respect to anchorage independence. Methods Mol Biol 2015; 1270:205-25. [PMID: 25702120 DOI: 10.1007/978-1-4939-2309-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Anchorage-independent growth of cells in soft agar is one of the hallmark characteristics of cellular transformation and uncontrolled cell growth. It may be considered as one of the most stringent assays for detecting malignant transformation of cells. Here, we describe a retroviral infection of a library of small secretory proteins and the use of the soft agar assay to obtain and study novel interacting protein combinations that cause cell transformation.
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109
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Abstract
Low molecular weight compound competing for the binding of the p53 tumor suppressor to the MDM2 oncoprotein.
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Affiliation(s)
- Didier Rognan
- Laboratory for Therapeutical Innovation
- UMR7200 CNRS-Université de Strasbourg
- MEDALIS Drug Discovery Center
- 67400 Illkirch
- France
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110
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Kuenemann MA, Bourbon LML, Labbé CM, Villoutreix BO, Sperandio O. Which three-dimensional characteristics make efficient inhibitors of protein-protein interactions? J Chem Inf Model 2014; 54:3067-79. [PMID: 25285479 DOI: 10.1021/ci500487q] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The specific properties of protein-protein interactions (PPI) (flat, large and hydrophobic) make them harder to tackle with low-molecular-weight compounds. Learning from the properties of successful examples of PPI interface inhibitors (iPPI) at earlier stages of developments, has been pinpointed as a powerful strategy to circumvent this trend. To this end, we have computationally analyzed the bioactive conformations of iPPI and those of inhibitors of conventional targets (e.g enzymes) to highlight putative iPPI 3D characteristics. Most noticeably, the essential property revealed by this study illustrates how efficiently iPPI manages to bind to the hydrophobic patch often present at the core of protein interfaces. The newly identified properties were further confirmed as characteristics of iPPI using much larger data sets (e.g iPPI-DB, www.ippidb.cdithem.fr ). Interestingly, the absence of correlation of such properties with the hydrophobicity and the size of the compounds opens new ways to design potent iPPI with better pharmacokinetic features.
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Affiliation(s)
- Mélaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm , Paris 75013, France
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111
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Hsu WCJ, Nilsson CL, Laezza F. Role of the axonal initial segment in psychiatric disorders: function, dysfunction, and intervention. Front Psychiatry 2014; 5:109. [PMID: 25191280 PMCID: PMC4139700 DOI: 10.3389/fpsyt.2014.00109] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/06/2014] [Indexed: 12/22/2022] Open
Abstract
The progress of developing effective interventions against psychiatric disorders has been limited due to a lack of understanding of the underlying cellular and functional mechanisms. Recent research findings focused on exploring novel causes of psychiatric disorders have highlighted the importance of the axonal initial segment (AIS), a highly specialized neuronal structure critical for spike initiation of the action potential. In particular, the role of voltage-gated sodium channels, and their interactions with other protein partners in a tightly regulated macromolecular complex has been emphasized as a key component in the regulation of neuronal excitability. Deficits and excesses of excitability have been linked to the pathogenesis of brain disorders. Identification of the factors and regulatory pathways involved in proper AIS function, or its disruption, can lead to the development of novel interventions that target these mechanistic interactions, increasing treatment efficacy while reducing deleterious off-target effects for psychiatric disorders.
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Affiliation(s)
- Wei-Chun Jim Hsu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Graduate Program in Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- M.D.–Ph.D. Combined Degree Program, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Carol Lynn Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Sealy Center for Molecular Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Fernanda Laezza
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Center for Addiction Research, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Center for Biomedical Engineering, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Mitchell Center for Neurodegenerative Diseases, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
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112
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dos Santos ES, de Souza LCV, de Assis PN, de Almeida PF, Ramos-de-Souza E. Souring control in fluid samples of oil industry using a multiple ligand simultaneous docking (MLSD) strategy. J Biomol Struct Dyn 2014; 33:1176-84. [PMID: 24956239 DOI: 10.1080/07391102.2014.937461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We have used docking techniques in order to propose potential inhibitors to the enzymes adenosine phosphosulfate reductase and adenosine triphosphate sulfurylase that are responsible, among other deleterious effects, for causing souring of oil and gas reservoirs. Three candidates selected through molecular docking revealed new and improved polar and hydrophobic interactions with the above-mentioned enzymes. Microbiological laboratory assays performed subsequently corroborated the results of computer modelling that the three compounds can efficiently control the biogenic sulfide production.
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Affiliation(s)
- Elias Silva dos Santos
- a Instituto de Física, Universidade Federal da Bahia , Rua Barão de Geremoabo s/n, Ondina, Salvador , BA , Brazil
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113
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Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA. Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform 2014; 33:414-437. [PMID: 25254076 PMCID: PMC4160817 DOI: 10.1002/minf.201400040] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Abstract
[Formula: see text] Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein-protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein-protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators.
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Affiliation(s)
- Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Melaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Jean-Luc Poyet
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- IUH, Hôpital Saint-LouisParis, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Heriberto Bruzzoni-Giovanelli
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CIC, Clinical investigation center, Hôpital Saint-LouisParis, France
| | - Céline Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
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