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Bongard RD, Lepley M, Thakur K, Talipov MR, Nayak J, Lipinski RAJ, Bohl C, Sweeney N, Ramchandran R, Rathore R, Sem DS. Serendipitous discovery of light-induced (In Situ) formation of an Azo-bridged dimeric sulfonated naphthol as a potent PTP1B inhibitor. BMC Biochem 2017; 18:10. [PMID: 28569147 PMCID: PMC5452347 DOI: 10.1186/s12858-017-0083-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 05/10/2017] [Indexed: 02/03/2023]
Abstract
Background Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Furthermore, drug screening for targets like PTPs often produce false positive and false negative results. Results Studies presented herein provide important insights into: (a) how to detect such artifacts, (b) the importance of compound re-synthesis and verification, and (c) how in situ chemical reactivity of compounds, when diagnosed and characterized, can actually lead to serendipitous discovery of valuable new lead molecules. Initial docking of compounds from the National Cancer Institute (NCI), followed by experimental testing in enzyme inhibition assays, identified an inhibitor of DUSP5. Subsequent control experiments revealed that this compound demonstrated time-dependent inhibition, and also a time-dependent change in color of the inhibitor that correlated with potency of inhibition. In addition, the compound activity varied depending on vendor source. We hypothesized, and then confirmed by synthesis of the compound, that the actual inhibitor of DUSP5 was a dimeric form of the original inhibitor compound, formed upon exposure to light and oxygen. This compound has an IC50 of 36 μM for DUSP5, and is a competitive inhibitor. Testing against PTP1B, for selectivity, demonstrated the dimeric compound was actually a more potent inhibitor of PTP1B, with an IC50 of 2.1 μM. The compound, an azo-bridged dimer of sulfonated naphthol rings, resembles previously reported PTP inhibitors, but with 18-fold selectivity for PTP1B versus DUSP5. Conclusion We report the identification of a potent PTP1B inhibitor that was initially identified in a screen for DUSP5, implying common mechanism of inhibitory action for these scaffolds. Electronic supplementary material The online version of this article (doi:10.1186/s12858-017-0083-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert D Bongard
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, USA
| | - Michael Lepley
- Department of Pediatrics, Division of Neonatology, Department of Obstetrics and Gynecology, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, 8701 Watertown Plank Road, P.O. Box 26509, Milwaukee, WI, 53226, USA
| | - Khushabu Thakur
- Department of Chemistry, Marquette University, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI, 53201, USA
| | - Marat R Talipov
- Department of Chemistry, Marquette University, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI, 53201, USA
| | - Jaladhi Nayak
- Department of Pediatrics, Division of Neonatology, Department of Obstetrics and Gynecology, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, 8701 Watertown Plank Road, P.O. Box 26509, Milwaukee, WI, 53226, USA
| | - Rachel A Jones Lipinski
- Department of Pediatrics, Division of Neonatology, Department of Obstetrics and Gynecology, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, 8701 Watertown Plank Road, P.O. Box 26509, Milwaukee, WI, 53226, USA.,Department of Chemistry, Marquette University, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI, 53201, USA
| | - Chris Bohl
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, USA
| | - Noreena Sweeney
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, USA
| | - Ramani Ramchandran
- Department of Pediatrics, Division of Neonatology, Department of Obstetrics and Gynecology, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, 8701 Watertown Plank Road, P.O. Box 26509, Milwaukee, WI, 53226, USA.
| | - Rajendra Rathore
- Department of Chemistry, Marquette University, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI, 53201, USA.
| | - Daniel S Sem
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, USA.
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Neumann TS, Span EA, Kalous KS, Bongard R, Gastonguay A, Lepley MA, Kutty RG, Nayak J, Bohl C, Lange RG, Sarker MI, Talipov MR, Rathore R, Ramchandran R, Sem DS. Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets. BMC Biochem 2015; 16:19. [PMID: 26286528 PMCID: PMC4545774 DOI: 10.1186/s12858-015-0048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/04/2015] [Indexed: 12/02/2022]
Abstract
BACKGROUND Dual-specificity phosphatase-5 (DUSP5) plays a central role in vascular development and disease. We present a p-nitrophenol phosphate (pNPP) based enzymatic assay to screen for inhibitors of the phosphatase domain of DUSP5. METHODS pNPP is a mimic of the phosphorylated tyrosine on the ERK2 substrate (pERK2) and binds the DUSP5 phosphatase domain with a Km of 7.6 ± 0.4 mM. Docking followed by inhibitor verification using the pNPP assay identified a series of polysulfonated aromatic inhibitors that occupy the DUSP5 active site in the region that is likely occupied by the dual-phosphorylated ERK2 substrate tripeptide (pThr-Glu-pTyr). Secondary assays were performed with full length DUSP5 with ERK2 as substrate. RESULTS The most potent inhibitor has a naphthalene trisulfonate (NTS) core. A search for similar compounds in a drug database identified suramin, a dimerized form of NTS. While suramin appears to be a potent and competitive inhibitor (25 ± 5 μM), binding to the DUSP5 phosphatase domain more tightly than the monomeric ligands of which it is comprised, it also aggregates. Further ligand-based screening, based on a pharmacophore derived from the 7 Å separation of sulfonates on inhibitors and on sulfates present in the DUSP5 crystal structure, identified a disulfonated and phenolic naphthalene inhibitor (CSD (3) _2320) with IC₅₀ of 33 μM that is similar to NTS and does not aggregate. CONCLUSIONS The new DUSP5 inhibitors we identify in this study typically have sulfonates 7 Å apart, likely positioning them where the two phosphates of the substrate peptide (pThr-Glu-pTyr) bind, with one inhibitor also positioning a phenolic hydroxyl where the water nucleophile may reside. Polysulfonated aromatic compounds do not commonly appear in drugs and have a tendency to aggregate. One FDA-approved polysulfonated drug, suramin, inhibits DUSP5 and also aggregates. Docking and modeling studies presented herein identify polysulfonated aromatic inhibitors that do not aggregate, and provide insights to guide future design of mimics of the dual-phosphate loops of the ERK substrates for DUSPs.
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Affiliation(s)
- Terrence S Neumann
- Department of Chemistry and Biochemistry, Texas Wesleyan University, 1201 Wesleyan Ave., Fort Worth, TX, 76105, USA.
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Elise A Span
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Kelsey S Kalous
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Robert Bongard
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Adam Gastonguay
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Michael A Lepley
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Raman G Kutty
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Jaladhi Nayak
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Chris Bohl
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA
| | - Rachel G Lange
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA
| | - Majher I Sarker
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Marat R Talipov
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Rajendra Rathore
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Ramani Ramchandran
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Daniel S Sem
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
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Bongard R, Neumann T, Span E, Kalous K, Gastonguay A, Kutty R, Nayak J, Lepley M, Bohl C, Lange R, Sarker M, Talipov M, Rathore R, Ramchandran R, Sem D. Identification of Polysulfonated Inhibitors that Target Dual Specificity Phosphatase 5 and Provide New Insights into the Binding Requirements for Dual‐Phosphate Substrate Pockets. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.1022.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert Bongard
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Terrence Neumann
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Elise Span
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Kelsey Kalous
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Adam Gastonguay
- Dept. of PediatricsMedical College of WisconsinMilwaukeeWIUnited States
| | - Raman Kutty
- Dept. of PediatricsMedical College of WisconsinMilwaukeeWIUnited States
| | - Jaladhi Nayak
- Dept. of PediatricsMedical College of WisconsinMilwaukeeWIUnited States
| | - Michael Lepley
- Dept. of PediatricsMedical College of WisconsinMilwaukeeWIUnited States
| | - Chris Bohl
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Rachel Lange
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
| | - Majher Sarker
- Dept. of ChemistryMarquette UniversityMilwaukeeWIUnited States
| | - Marat Talipov
- Dept. of ChemistryMarquette UniversityMilwaukeeWIUnited States
| | | | | | - Daniel Sem
- School of PharmacyConcordia UniversityWisconsinMequon WIUnited States
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