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Winter M, Bretschneider T, Kleiner C, Ries R, Hehn JP, Redemann N, Luippold AH, Bischoff D, Büttner FH. Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction. SLAS DISCOVERY 2018; 23:561-573. [DOI: 10.1177/2472555218759267] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.
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Affiliation(s)
- Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jörg P. Hehn
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Norbert Redemann
- Cardio-Metabolic Diseases, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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2
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Kenny PW. Comment on The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:2640-2645. [DOI: 10.1021/acs.jcim.7b00313] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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3
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Strelow JM. A Perspective on the Kinetics of Covalent and Irreversible Inhibition. SLAS DISCOVERY 2016; 22:3-20. [PMID: 27703080 DOI: 10.1177/1087057116671509] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC50 value. In a biochemical assay, the IC50 may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by kinact/KI. The kinact/KI is a rate constant describing the efficiency of covalent bond formation resulting from the potency (KI) of the first reversible binding event and the maximum potential rate (kinact) of inactivation. In this perspective, it is proposed that the kinact/KI should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant kinact/KI and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.
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Affiliation(s)
- John M Strelow
- 1 Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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4
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Madabhushi S, Chinthala N, Kanwal A, Kaur G, Banerjee SK. Synthesis and characterization of 2-(4-((1-alkyl or aryl-1H-1,2,3-triazol-4-yl)methoxy)phenyl)naphtho[1,2-d]oxazoles for protein tyrosine phosphatase 1B inhibitory activity. Med Chem Res 2014. [DOI: 10.1007/s00044-013-0784-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Natural products with protein tyrosine phosphatase inhibitory activity. Methods 2014; 65:229-38. [DOI: 10.1016/j.ymeth.2013.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/04/2013] [Accepted: 09/07/2013] [Indexed: 01/05/2023] Open
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Kim YS, Nagy K, Keyser S, Schneekloth JS. An electrophoretic mobility shift assay identifies a mechanistically unique inhibitor of protein sumoylation. ACTA ACUST UNITED AC 2013; 20:604-13. [PMID: 23601649 DOI: 10.1016/j.chembiol.2013.04.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
Abstract
The dynamic, posttranslational modification of proteins with a small ubiquitin-like modifier (SUMO) tag has been recognized as an important cellular regulatory mechanism relevant to a number of cancers as well as normal embryonic development. As part of a program aimed toward the identification of inhibitors of SUMO-conjugating enzymes, we developed a microfluidic electrophoretic mobility shift assay to monitor sumoylation events in real time. We disclose herein the use of this assay to identify a cell-permeable compound capable of blocking the transfer of SUMO-1 from the E2 enzyme Ubc9 to the substrate. We screened a small collection of compounds and identified an oxygenated flavonoid derivative that inhibits sumoylation in vitro. Next, we carried out an in-depth mechanistic analysis that ruled out many common false-positive mechanisms such as aggregation or alkylation. Furthermore, we report that this flavonoid inhibits a single step in the sumoylation cascade: the transfer of SUMO from the E2 enzyme (Ubc9) thioester conjugate to the substrate. In addition to having a unique mechanism of action, this inhibitor has a discrete structure-activity relationship uncharacteristic of a promiscuous inhibitor. Cell-based studies showed that the flavonoid inhibits the sumoylation of topoisomerase-I in response to camptothecin treatment in two different breast cancer cell lines, while isomeric analogs are inactive. Importantly, this compound blocks sumoylation while not affecting ubiquitylation in cells. This work identifies a point of entry for pharmacologic inhibition of the sumoylation cascade and may serve as the basis for continued study of additional pharmacophores that modulate SUMO-conjugating enzymes such as Ubc9.
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Affiliation(s)
- Yeong Sang Kim
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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8
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Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery. Methods 2013; 65:219-28. [PMID: 23969317 DOI: 10.1016/j.ymeth.2013.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
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Maillard MC, Dominguez C, Gemkow MJ, Krieger F, Park H, Schaertl S, Winkler D, Muñoz-Sanjuán I. A label-free LC/MS/MS-based enzymatic activity assay for the detection of genuine caspase inhibitors and SAR development. JOURNAL OF BIOMOLECULAR SCREENING 2013; 18:868-78. [PMID: 23796689 DOI: 10.1177/1087057113492851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The resurgence of interest in caspases (Csp) as therapeutic targets for the treatment of neurodegenerative diseases prompted us to examine the suitability of published nonpeptidic Csp-3 and Csp-6 inhibitors for our medicinal chemistry programs. To support this effort, fluorescence-based Csp-2, Csp-3, and Csp-6 enzymatic assays were optimized for robustness against apparent enzyme inhibition caused by redox-cycling or aggregating compounds. The data obtained under these improved conditions challenge the validity of previously published data on Csp-3 and Csp-6 inhibitors for all but one series, namely, the isatins. Furthermore, in this series, it was observed that the nature of the rhodamine-labeled substrate, typically used to measure caspase activity, interfered with the pharmacological sensitivity of the Csp-2 assay. As a result, a liquid chromatography/tandem mass spectrometry-based assay that eliminates label-dependent assay interference was developed for Csp-2 and Csp-3. In these label-free assays, the activity values of the Csp-2 and Csp-3 reference inhibitors were in agreement with those obtained with the fluorogenic substrates. However, isatin 10a was 50-fold less potent in the label-free Csp-2 assay compared with the rhodamine-based fluorescence format, thus proving the need for an orthogonal readout to validate inhibitors in this class of targets highly susceptible to artifactual inhibition.
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Davis BJ, Erlanson DA. Learning from our mistakes: the 'unknown knowns' in fragment screening. Bioorg Med Chem Lett 2013; 23:2844-52. [PMID: 23562240 DOI: 10.1016/j.bmcl.2013.03.028] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/01/2013] [Accepted: 03/08/2013] [Indexed: 12/27/2022]
Abstract
In the past 15 years, fragment-based lead discovery (FBLD) has been adopted widely throughout academia and industry. The approach entails discovering very small molecular fragments and growing, merging, or linking them to produce drug leads. Because the affinities of the initial fragments are often low, detection methods are pushed to their limits, leading to a variety of artifacts, false positives, and false negatives that too often go unrecognized. This Digest discusses some of these problems and offers suggestions to avoid them. Although the primary focus is on FBLD, many of the lessons also apply to more established approaches such as high-throughput screening.
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Affiliation(s)
- Ben J Davis
- Vernalis Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, UK.
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11
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Baell JB, Ferrins L, Falk H, Nikolakopoulos G. PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening. Aust J Chem 2013. [DOI: 10.1071/ch13551] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pan assay interference compounds (PAINS) are readily discovered in any bioassay and can appear to give selective and optimisable hits. The most common PAINS can be readily recognised by their structure. However, there are compounds that closely resemble PAINS that are not specifically recognised by the PAINS filters. In addition, highly reactive compounds are not encoded for in the PAINS filters because they were excluded from the high-throughput screening (HTS) library used to develop the filters and so were never present to provide indicting data. A compounding complication in the area is that very occasionally a PAINS compound may serve as a viable starting point for progression. Despite such an occasional example, the literature is littered with an overwhelming number of examples of compounds that fail to progress and were probably not optimisable in the first place, nor useful tool compounds. Thus it is with great caution and diligence that compounds possessing a known PAINS core should be progressed through to medicinal chemistry optimisation, if at all, as the chances are very high that the hits will be found to be non-progressable, often after a significant waste of resources.
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12
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He R, Zeng LF, He Y, Zhang S, Zhang ZY. Small molecule tools for functional interrogation of protein tyrosine phosphatases. FEBS J 2012; 280:731-50. [PMID: 22816879 DOI: 10.1111/j.1742-4658.2012.08718.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The importance of protein tyrosine phosphatases (PTPs) in the regulation of cellular signalling is well established. Malfunction of PTP activity is also known to be associated with cancer, metabolic syndromes and autoimmune disorders, as well as neurodegenerative and infectious diseases. However, a detailed understanding of the roles played by the PTPs in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific small molecule agents. In addition, the therapeutic benefits of modulating this target class are underexplored as a result of a lack of suitable chemical probes. Potent and specific PTP inhibitors could significantly facilitate functional analysis of the PTPs in complex cellular signal transduction pathways and may constitute valuable therapeutics in the treatment of several human diseases. We highlight the current challenges to and opportunities for developing PTP-specific small molecule agents. We also review available selective small molecule inhibitors developed for a number of PTPs, including PTP1B, TC-PTP, SHP2, lymphoid-specific tyrosine phosphatase, haematopoietic protein tyrosine phosphatase, CD45, PTPβ, PTPγ, PTPRO, Vaccinia H1-related phosphatase, mitogen-activated protein kinase phosphatase-1, mitogen-activated protein kinase phosphatase-3, Cdc25, YopH, mPTPA and mPTPB.
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Affiliation(s)
- Rongjun He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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13
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Krishnan N, Fu C, Pappin DJ, Tonks NK. H2S-Induced sulfhydration of the phosphatase PTP1B and its role in the endoplasmic reticulum stress response. Sci Signal 2011; 4:ra86. [PMID: 22169477 DOI: 10.1126/scisignal.2002329] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although originally considered toxic, hydrogen sulfide (H(2)S) has been implicated in mediating various biological processes. Nevertheless, its cellular targets and mode of action are not well understood. Protein tyrosine phosphatases (PTPs), which regulate numerous signal transduction pathways, use an essential cysteine residue at the active site, which is characterized by a low pK(a) and is susceptible to reversible oxidation. Here, we report that PTP1B was reversibly inactivated by H(2)S, in vitro and in cells, through sulfhydration of the active-site cysteine residue. Unlike oxidized PTP1B, the sulfhydrated enzyme was preferentially reduced in vitro by thioredoxin, compared to glutathione or dithiothreitol. Sulfhydration of PTP1B in cells required the presence of cystathionine γ-lyase (CSE), a critical enzyme in H(2)S production, and resulted in inhibition of phosphatase activity. Suppression of CSE decreased H(2)S production and decreased the phosphorylation of tyrosine-619 in PERK [protein kinase-like endoplasmic reticulum (ER) kinase], thus reducing its activation in response to ER stress. PERK, which phosphorylates the eukaryotic translational initiation factor 2, leading to attenuation of protein translation, was a direct substrate of PTP1B. In addition, CSE knockdown led to activation of the nonreceptor tyrosine kinase SRC, previously shown to be mediated by PTP1B. These effects of suppressing H(2)S production on the response to ER stress were abrogated by a small-molecule inhibitor of PTP1B. Together, these data define a signaling function for H(2)S in inhibiting PTP1B activity and thereby promoting PERK activity during the response to ER stress.
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Haque A, Andersen JN, Salmeen A, Barford D, Tonks NK. Conformation-sensing antibodies stabilize the oxidized form of PTP1B and inhibit its phosphatase activity. Cell 2011; 147:185-98. [PMID: 21962515 DOI: 10.1016/j.cell.2011.08.036] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 06/30/2011] [Accepted: 08/15/2011] [Indexed: 01/10/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) plays important roles in downregulation of insulin and leptin signaling and is an established therapeutic target for diabetes and obesity. PTP1B is regulated by reactive oxygen species (ROS) produced in response to various stimuli, including insulin. The reversibly oxidized form of the enzyme (PTP1B-OX) is inactive and undergoes profound conformational changes at the active site. We generated conformation-sensor antibodies, in the form of single-chain variable fragments (scFvs), that stabilize PTP1B-OX and thereby inhibit its phosphatase function. Expression of conformation-sensor scFvs as intracellular antibodies (intrabodies) enhanced insulin-induced tyrosyl phosphorylation of the β subunit of the insulin receptor and its substrate IRS-1 and increased insulin-induced phosphorylation of PKB/AKT. Our data suggest that stabilization of the oxidized, inactive form of PTP1B with appropriate therapeutic molecules may offer a paradigm for phosphatase drug development.
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Affiliation(s)
- Aftabul Haque
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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15
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Gao M, Lu CF, Yang GC, Chen ZX. A novel approach for synthesis of 3-amino-5-aryl-2,5-dihydropyridazines using onium salt as soluble support. CHINESE CHEM LETT 2011. [DOI: 10.1016/j.cclet.2010.12.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Abstract
Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.
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Thareja S, Aggarwal S, Bhardwaj TR, Kumar M. Protein Tyrosine Phosphatase 1B Inhibitors: A Molecular Level Legitimate Approach for the Management of Diabetes Mellitus. Med Res Rev 2010; 32:459-517. [DOI: 10.1002/med.20219] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Suresh Thareja
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | - Saurabh Aggarwal
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | | | - Manoj Kumar
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
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18
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Jacobsson M, Gäredal M, Schultz J, Karlén A. Identification of Plasmodium falciparum Spermidine Synthase Active Site Binders through Structure-Based Virtual Screening. J Med Chem 2008; 51:2777-86. [DOI: 10.1021/jm7016144] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Micael Jacobsson
- iNovacia AB, Lindhagensgatan 133, SE-112 51 Stockholm, Sweden, Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Magnus Gäredal
- iNovacia AB, Lindhagensgatan 133, SE-112 51 Stockholm, Sweden, Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Johan Schultz
- iNovacia AB, Lindhagensgatan 133, SE-112 51 Stockholm, Sweden, Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- iNovacia AB, Lindhagensgatan 133, SE-112 51 Stockholm, Sweden, Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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Myers MC, Napper AD, Motlekar N, Shah PP, Chiu CH, Beavers MP, Diamond SL, Huryn DM, Smith AB. Identification and characterization of 3-substituted pyrazolyl esters as alternate substrates for cathepsin B: the confounding effects of DTT and cysteine in biological assays. Bioorg Med Chem Lett 2007; 17:4761-6. [PMID: 17656088 PMCID: PMC2041802 DOI: 10.1016/j.bmcl.2007.06.091] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/20/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
Substituted pyrazole esters were identified as hits in a high throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR) to identify inhibitors of the enzyme cathepsin B. Members of this class, along with functional group analogs, were synthesized in an effort to define the structural requirements for activity. Analog characterization was hampered by the need to include a reducing agent such as dithiothreitol (DTT) or cysteine in the assay, highlighting the caution required in interpreting biological data gathered in the presence of such nucleophiles. Despite the confounding effects of DTT and cysteine, our studies demonstrate that the pyrazole 1 acts as alternate substrate for cathepsin B, rather than as an inhibitor.
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Affiliation(s)
- Michael C Myers
- Penn Center for Molecular Discovery, University of Pennsylvania, 1024 Vagelos Research Laboratories, Philadelphia, PA 19104-6383, USA
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Aziz SI, Anwar HF, El-Apasery MA, Elnagdi MH. Studies with pyridazines and condensed pyridazines: Routes for synthesis of 3-amino-5-aryl-2,5-dihydro-pyridazine, 10aH-pyridazino[1,6-a]quinazoline and thieno[3,4-d]pyridazinone. J Heterocycl Chem 2007. [DOI: 10.1002/jhet.5570440421] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Cho SY, Baek JY, Han SS, Kang SK, Ha JD, Ahn JH, Lee JD, Kim KR, Cheon HG, Rhee SD, Yang SD, Yon GH, Pak CS, Choi JK. PTP-1B inhibitors: Cyclopenta[d][1,2]-oxazine derivatives. Bioorg Med Chem Lett 2006; 16:499-502. [PMID: 16289879 DOI: 10.1016/j.bmcl.2005.10.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 10/07/2005] [Accepted: 10/19/2005] [Indexed: 11/24/2022]
Abstract
A series of novel cyclopenta[d][1,2]-oxazine derivatives was prepared and evaluated for their inhibitory activity toward protein tyrosine phosphatase 1B (PTP-1B). Compound 6s was found to be an inhibitor of PTP-1B with nanomolar IC(50) value and high level of selectivity over other recombinant phosphatases.
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Affiliation(s)
- Sung Yun Cho
- Bio-Organic Science Division, Korea Research Institute of Chemical Technology, 100 Jang-dong, Yuseong-gu, Daejeon 305-600, Republic of Korea
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22
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Moretto AF, Kirincich SJ, Xu WX, Smith MJ, Wan ZK, Wilson DP, Follows BC, Binnun E, Joseph-McCarthy D, Foreman K, Erbe DV, Zhang YL, Tam SK, Tam SY, Lee J. Bicyclic and tricyclic thiophenes as protein tyrosine phosphatase 1B inhibitors. Bioorg Med Chem 2005; 14:2162-77. [PMID: 16303309 DOI: 10.1016/j.bmc.2005.11.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 10/31/2005] [Accepted: 11/01/2005] [Indexed: 11/26/2022]
Abstract
A novel pyridothiophene inhibitor of PTP1B was discovered by rational screening of phosphotyrosine mimics at high micromolar concentrations. The potency of this lead compound has been improved significantly by medicinal chemistry guided by X-ray crystallography and molecular modeling. Excellent consistency has been observed between structure-activity relationships and structural information from PTP1B-inhibitor complexes.
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Affiliation(s)
- A F Moretto
- Chemical and Screening Science, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
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Huth JR, Mendoza R, Olejniczak ET, Johnson RW, Cothron DA, Liu Y, Lerner CG, Chen J, Hajduk PJ. ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. J Am Chem Soc 2005; 127:217-24. [PMID: 15631471 DOI: 10.1021/ja0455547] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-throughput screening (HTS) of large compound collections typically results in numerous small molecule hits that must be carefully evaluated to identify valid drug leads. Although several filtering mechanisms and other tools exist that can assist the chemist in this process, it is often the case that costly synthetic resources are expended in pursuing false positives. We report here a rapid and reliable NMR-based method for identifying reactive false positives including those that oxidize or alkylate a protein target. Importantly, the reactive species need not be the parent compound, as both reactive impurities and breakdown products can be detected. The assay is called ALARM NMR (a La assay to detect reactive molecules by nuclear magnetic resonance) and is based on monitoring DTT-dependent (13)C chemical shift changes of the human La antigen in the presence of a test compound or mixture. Extensive validation has been performed to demonstrate the reliability and utility of using ALARM NMR to assess thiol reactivity. This included comparing ALARM NMR to a glutathione-based fluorescence assay, as well as testing a collection of more than 3500 compounds containing HTS hits from 23 drug targets. The data show that current in silico filtering tools fail to identify more than half of the compounds that can act via reactive mechanisms. Significantly, we show how ALARM NMR data has been critical in identifying reactive compounds that would otherwise have been prioritized for lead optimization. In addition, a new filtering tool has been developed on the basis of the ALARM NMR data that can augment current in silico programs for identifying nuisance compounds and improving the process of hit triage.
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Affiliation(s)
- Jeffrey R Huth
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064, USA
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Ababou A, Ladbury JE. Survey of the year 2004: literature on applications of isothermal titration calorimetry. J Mol Recognit 2005; 19:79-89. [PMID: 16220545 DOI: 10.1002/jmr.750] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The market for commercially available isothermal titration calorimeters continues to grow as new applications and methodologies are developed. Concomitantly the number of users (and abusers) increases dramatically, resulting in a steady increase in the number of publications in which isothermal titration calorimetry (ITC) plays a role. In the present review, we will focus on areas where ITC is making a significant contribution and will highlight some interesting applications of the technique. This overview of papers published in 2004 also discusses current issues of interest in the development of ITC as a tool of choice in the determination of the thermodynamics of molecular recognition and interaction.
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Affiliation(s)
- Abdessamad Ababou
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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Hooft van Huijsduijnen R, Sauer WHB, Bombrun A, Swinnen D. Prospects for Inhibitors of Protein Tyrosine Phosphatase 1B as Antidiabetic Drugs. J Med Chem 2004; 47:4142-6. [PMID: 15293983 DOI: 10.1021/jm030629n] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rob Hooft van Huijsduijnen
- Serono Pharmaceutical Research Institute, Chemin des Aulx 14, 1228 Plan-les-Ouates, Geneva, Switzerland.
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Liljebris C, Baranczewski P, Björkstrand E, Byström S, Lundgren B, Tjernberg A, Warolén M, James SR. Oxidation of protein tyrosine phosphatases as a pharmaceutical mechanism of action: a study using 4-hydroxy-3,3-dimethyl-2H-benzo[g]indole-2,5(3H)-dione. J Pharmacol Exp Ther 2004; 309:711-9. [PMID: 14747616 DOI: 10.1124/jpet.103.062745] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Growth factor and insulin signal transduction comprise series of protein kinases and protein phosphatases whose combined activities serve to propagate the growth factor signal in a regulated fashion. It was shown previously that such signaling cascades generate hydrogen peroxide inside cells. Recent work has implied that one function of this might be to enhance the feed-forward signal through the reversible oxidation and inhibition of protein tyrosine phosphatases (PTPs). We identified compound 4-hydroxy-3,3-dimethyl-2H-benzo[g]indole-2,5(3H)-dione (BVT.948) as an agent that is able to inhibit PTP activity in vitro noncompetitively, a mechanism involving oxidation of the catalytic cysteine residue. We investigated the pharmaceutical utility of this compound by examining its effects in a series of in vitro cellular and in vivo assays. Results showed that BVT.948 was able to enhance insulin signaling in cells, although it did not increase tyrosine phosphorylation globally. Furthermore, the compound was active in vivo, enhancing insulin tolerance tests in ob/ob mice, therefore apparently enhancing insulin sensitivity. BVT.948 was able to inhibit several other PTPs tested and also was efficient at inhibiting several cytochrome P450 (P450) isoforms in vitro. The data suggest that inhibitors of PTPs that display noncompetitive kinetics must be viewed with caution because they may oxidize the enzyme irreversibly. Furthermore, although such compounds display interesting biological effects in vitro and in vivo, their general pharmaceutical utility may be limited due to undesired effects on P450 enzymes.
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