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Yang J, Yao Y, Li X, He A, Chen S, Wang Y, Dong X, Chen H, Wang Y, Wang L, Sun H. Nontarget Identification of Novel Organophosphorus Flame Retardants and Plasticizers in Indoor Air and Dust from Multiple Microenvironments in China. Environ Sci Technol 2024; 58:7986-7997. [PMID: 38657129 DOI: 10.1021/acs.est.4c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The indoor environment is a typical source for organophosphorus flame retardants and plasticizers (OPFRs), yet the source characteristics of OPFRs in different microenvironments remain less clear. This study collected 109 indoor air samples and 34 paired indoor dust samples from 4 typical microenvironments within a university in Tianjin, China, including the dormitory, office, library, and information center. 29 target OPFRs were analyzed, and novel organophosphorus compounds (NOPs) were identified by fragment-based nontarget analysis. Target OPFRs exhibited the highest air and dust concentrations of 46.2-234 ng/m3 and 20.4-76.0 μg/g, respectively, in the information center, where chlorinated OPFRs were dominant. Triphenyl phosphate (TPHP) was the primary OPFR in office air, while tris(2-chloroethyl) phosphate dominated in the dust. TPHP was predominant in the library. Triethyl phosphate (TEP) was ubiquitous in the dormitory, and tris(2-butoxyethyl) phosphate was particularly high in the dust. 9 of 25 NOPs were identified for the first time, mainly from the information center and office, such as bis(chloropropyl) 2,3-dichloropropyl phosphate. Diphenyl phosphinic acid, two hydroxylated and methylated metabolites of tris(2,4-ditert-butylphenyl) phosphite (AO168), and a dimer phosphate were newly reported in the indoor environment. NOPs were widely associated with target OPFRs, and their human exposure risk and environmental behaviors warrant further study.
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Affiliation(s)
- Ji Yang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiaoxiao Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Ana He
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shijie Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yulong Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiaoyu Dong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hao Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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2
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Böttcher J, Fuchs JE, Mayer M, Kahmann J, Zak KM, Wunberg T, Woehrle S, Kessler D. Ligandability assessment of the C-terminal Rel-homology domain of NFAT1. Arch Pharm (Weinheim) 2024:e2300649. [PMID: 38396281 DOI: 10.1002/ardp.202300649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024]
Abstract
Transcription factors are generally considered challenging, if not "undruggable", targets but they promise new therapeutic options due to their fundamental involvement in many diseases. In this study, we aim to assess the ligandability of the C-terminal Rel-homology domain of nuclear factor of activated T cells 1 (NFAT1), a TF implicated in T-cell regulation. Using a combination of experimental and computational approaches, we demonstrate that small molecule fragments can indeed bind to this protein domain. The newly identified binder is the first small molecule binder to NFAT1 validated with biophysical methods and an elucidated binding mode by X-ray crystallography. The reported eutomer/distomer pair provides a strong basis for potential exploration of higher potency binders on the path toward degrader or glue modalities.
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Affiliation(s)
- Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simon Woehrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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3
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Zhao M, Yao Y, Dong X, Baqar M, Fang B, Chen H, Sun H. Nontarget Identification of Novel Per- and Polyfluoroalkyl Substances (PFAS) in Soils from an Oil Refinery in Southwestern China: A Combined Approach with TOP Assay. Environ Sci Technol 2023; 57:20194-20205. [PMID: 37991390 DOI: 10.1021/acs.est.3c05859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Oil refinery activity can be an emission source of perfluoroalkyl and polyfluoroalkyl substances (PFAS) to the environment, while the contamination profiles in soils remain unknown. This study investigated 44 target PFAS in soil samples collected from an oil refinery in Southeastern China, identified novel PFAS, and characterized their behaviors by assessing their changes before and after employing advanced oxidation using a combination of nontarget analysis and a total oxidizable precursor (TOP) assay. Thirty-four target PFAS were detected in soil samples. Trifluoroacetic acid (TFA) and hexafluoropropylene oxide dimer acid (HFPO-DA) were the dominant PFAS. Twenty-three novel PFAS of 14 classes were identified, including 8 precursors, 11 products, and 4 stable PFAS characterized by the TOP assay. Particularly, three per-/polyfluorinated alcohols were identified for the first time, and hexafluoroisopropanol (HFIP) quantified up to 657 ng/g dw is a novel precursor for TFA. Bistriflimide (NTf2) potentially associated with an oil refinery was also reported for the first time in the soil samples. This study highlighted the advantage of embedding the TOP assay in nontarget analysis to reveal not only the presence of unknown PFAS but also their roles in environmental processes. Overall, this approach provides an efficient way to uncover contamination profiles of PFAS especially in source-impacted areas.
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Affiliation(s)
- Maosen Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
| | - Xiaoyu Dong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
| | - Mujtaba Baqar
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
- Sustainable Development Study Centre, Government College University, Lahore 54000, Pakistan
| | - Bo Fang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
| | - Hao Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
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Buchholz C, Sneddon MS, McPherson JE, Das S, Gee CT, Grillo MJ, Chai SC, Lee RE, Chen T, Harki DA, Shelat AA, Pomerantz WCK. Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small-Molecule Inhibitors. ACS Med Chem Lett 2023; 14:1441-1447. [PMID: 37849548 PMCID: PMC10577693 DOI: 10.1021/acsmedchemlett.3c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
Methyl lysine readers, specifically PHD fingers, are emerging epigenetic targets in human diseases. For example, several PHD finger fusions are implicated in clinical cases of acute myeloid leukemia, highlighting the potential for PHD inhibitors in disease regulation. However, limited chemical matter targeting PHD fingers exists. Here we report the first fragment-based screen against the BPTF PHD to identify several of the first reported BPTF PHD-targeting small-molecule ligands. We used ligand-observed NMR to first screen a fragment library, followed by biophysical validation to prioritize two scaffolds, pyrrolidine- and pyridazine-containing fragments. Structural predictions show that these respective scaffolds may engage two distinct subpockets on the protein. The demonstrated ligandability of the BPTF PHD supports the future development of methyl lysine reader chemical probes to study their oncogenic functions.
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Affiliation(s)
- Caroline
R. Buchholz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Molly S. Sneddon
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Joseph E. McPherson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sourav Das
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Clifford T. Gee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Michael J. Grillo
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sergio C. Chai
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anang A. Shelat
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - William C. K. Pomerantz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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5
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Fay EM, Newton A, Berney M, El‐Sagheer AH, Brown T, McGouran JF. Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A. Chembiochem 2023; 24:e202200756. [PMID: 36917742 PMCID: PMC10962688 DOI: 10.1002/cbic.202200756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.
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Affiliation(s)
- Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Ailish Newton
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Mark Berney
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Tom Brown
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
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6
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Govindaraj RG, Thangapandian S, Schauperl M, Denny RA, Diller DJ. Recent applications of computational methods to allosteric drug discovery. Front Mol Biosci 2023; 9:1070328. [PMID: 36710877 PMCID: PMC9877542 DOI: 10.3389/fmolb.2022.1070328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Interest in exploiting allosteric sites for the development of new therapeutics has grown considerably over the last two decades. The chief driving force behind the interest in allostery for drug discovery stems from the fact that in comparison to orthosteric sites, allosteric sites are less conserved across a protein family, thereby offering greater opportunity for selectivity and ultimately tolerability. While there is significant overlap between structure-based drug design for orthosteric and allosteric sites, allosteric sites offer additional challenges mostly involving the need to better understand protein flexibility and its relationship to protein function. Here we examine the extent to which structure-based drug design is impacting allosteric drug design by highlighting several targets across a variety of target classes.
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Affiliation(s)
- Rajiv Gandhi Govindaraj
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States,*Correspondence: Rajiv Gandhi Govindaraj,
| | | | - Michael Schauperl
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
| | | | - David J. Diller
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
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7
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Chavda VP, Ertas YN, Walhekar V, Modh D, Doshi A, Shah N, Anand K, Chhabria M. Advanced Computational Methodologies Used in the Discovery of New Natural Anticancer Compounds. Front Pharmacol 2021; 12:702611. [PMID: 34483905 PMCID: PMC8416109 DOI: 10.3389/fphar.2021.702611] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Natural chemical compounds have been widely investigated for their programmed necrosis causing characteristics. One of the conventional methods for screening such compounds is the use of concentrated plant extracts without isolation of active moieties for understanding pharmacological activity. For the last two decades, modern medicine has relied mainly on the isolation and purification of one or two complicated active and isomeric compounds. The idea of multi-target drugs has advanced rapidly and impressively from an innovative model when first proposed in the early 2000s to one of the popular trends for drug development in 2021. Alternatively, fragment-based drug discovery is also explored in identifying target-based drug discovery for potent natural anticancer agents which is based on well-defined fragments opposite to use of naturally occurring mixtures. This review summarizes the current key advancements in natural anticancer compounds; computer-assisted/fragment-based structural elucidation and a multi-target approach for the exploration of natural compounds.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, India
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Vinayak Walhekar
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Dharti Modh
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Avani Doshi
- Department of Chemistry, SAL Institute of Pharmacy, Ahmedabad, India
| | - Nirav Shah
- Department of Pharmaceutics, SAL Institute of Pharmacy, Ahmedabad, India
| | - Krishna Anand
- Faculty of Health Sciences and National Health Laboratory Service, Department of Chemical Pathology, School of Pathology, University of the Free State, Bloemfontein, South Africa
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L.M. College of Pharmacy, Ahmedabad, India
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Abstract
The variety and complexity of drug targets are expanding rapidly. At the same time, there is significant interest in exploring a larger chemical space to identify new candidates. Fragment-based screening (FBS) has emerged as a popular alternative to traditional high-throughput screening campaigns to identify such drug candidates. FBS identifies hit fragments that exhibit weak interactions with the target of interest, thereby enabling the rational design of small-molecule compounds from the identified hit fragments, which serve as building blocks. This strategy reduces the number of molecules to screen while also allowing the exploration of a greater chemical space.Here we use temperature-related intensity change (TRIC) technology to perform FBS against the target MAPK/ERK kinase-1 (Mek1). TRIC describes the change in fluorescence intensity of a fluorescently labeled molecule upon a change in temperature. This intensity variation is dependent on the physicochemical environment in the vicinity of the dye and strongly affected by binding events. Thus, the detection of binding events is independent of mass, making TRIC an ideal tool for FBS.Using only 150 pmol of labeled Mek1, the authors screened 193 fragments from a prescreened library in less than 1 h of measurement time, leading to 66 hits. Among those hits, they identified more than 80% of the published top hits found using orthogonal techniques. Furthermore, TRIC allowed the identification of fragments that were of poor solubility but could be mistaken as false-positive hits in other methods.
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Affiliation(s)
- Semir Jeridi
- Application Team, NanoTemper Technologies GmbH, Munich, Germany
| | - Alexey Rak
- Structure-Design-Informatics, Sanofi R&D, Vitry sur Seine, France
| | - Amit Gupta
- Product Management, NanoTemper Technologies GmbH, Munich, Germany
| | - Pierre Soule
- Application Team, NanoTemper Technologies GmbH, Munich, Germany
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Sprenger J, Lawson CL, von Wachenfeldt C, Lo Leggio L, Carey J. Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan. Acta Crystallogr F Struct Biol Commun 2021; 77:215-225. [PMID: 34196612 PMCID: PMC8248821 DOI: 10.1107/s2053230x21006142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand L-tryptophan (L-Trp) indicate that L-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with L-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it bears a disordered extension of about 20 residues, is accessible in the large solvent channels of the domain-swapped crystal form, as in the structures reported previously in this form for TrpR without N-terminal extensions. These findings inspire the exploration of L-Trp analogs and N-terminal modifications as labels to orient guest proteins that cannot otherwise be crystallized in the solvent channels of crystalline domain-swapped TrpR hosts for potential diffraction analysis.
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Affiliation(s)
- Janina Sprenger
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
| | - Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, NJ 08544, USA
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10
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Baybekov S, Marcou G, Ramos P, Saurel O, Galzi JL, Varnek A. DMSO Solubility Assessment for Fragment-Based Screening. Molecules 2021; 26:3950. [PMID: 34203441 DOI: 10.3390/molecules26133950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, we report comprehensive experimental and chemoinformatics analyses of the solubility of small organic molecules (“fragments”) in dimethyl sulfoxide (DMSO) in the context of their ability to be tested in screening experiments. Here, DMSO solubility of 939 fragments has been measured experimentally using an NMR technique. A Support Vector Classification model was built on the obtained data using the ISIDA fragment descriptors. The analysis revealed 34 outliers: experimental issues were retrospectively identified for 28 of them. The updated model performs well in 5-fold cross-validation (balanced accuracy = 0.78). The datasets are available on the Zenodo platform (DOI:10.5281/zenodo.4767511) and the model is available on the website of the Laboratory of Chemoinformatics.
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11
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Shin WS, Nguyen ME, Bergstrom A, Jennings IR, Crowder MW, Muthyala R, Sham YY. Fragment-based screening and hit-based substructure search: Rapid discovery of 8-hydroxyquinoline-7-carboxylic acid as a low-cytotoxic, nanomolar metallo β-lactamase inhibitor. Chem Biol Drug Des 2021; 98:481-492. [PMID: 34148302 DOI: 10.1111/cbdd.13912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/25/2021] [Accepted: 06/06/2021] [Indexed: 12/13/2022]
Abstract
Metallo-β-lactamases (MBLs) are zinc-containing carbapenemases that inactivate a broad range of β-lactam antibiotics. There is a lack of β-lactamase inhibitors for restoring existing β-lactam antibiotics arsenals against common bacterial infections. Fragment-based screening of a non-specific metal chelator library demonstrates 8-hydroxyquinoline as a broad-spectrum nanomolar inhibitor against VIM-2 and NDM-1. A hit-based substructure search provided an early structure-activity relationship of 8-hydroxyquinolines and identified 8-hydroxyquinoline-7-carboxylic acid as a low-cytotoxic β-lactamase inhibitor that can restore β-lactam activity against VIM-2-expressing E. coli. Molecular modeling further shed structural insight into its potential mode of binding within the dinuclear zinc active site. 8-Hydroxyquinoline-7-carboxylic acid is highly stable in human plasma and human liver microsomal study, making it an ideal lead candidate for further development.
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Affiliation(s)
- Woo Shik Shin
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Megin E Nguyen
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | | | - Isabella R Jennings
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Ramaiah Muthyala
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Yuk Yin Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA.,Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
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Hoarau M, Vanichtanankul J, Srimongkolpithak N, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S. Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem 2021; 36:198-206. [PMID: 33530764 PMCID: PMC8759724 DOI: 10.1080/14756366.2020.1854244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC50 in the 28-695 μM range and selectivity for PfDHFR. In addition to the known pyrimidine, three new anti-PfDHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with PfDHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.
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Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
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13
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Kessler D, Mayer M, Zahn SK, Zeeb M, Wöhrle S, Bergner A, Bruchhaus J, Ciftci T, Dahmann G, Dettling M, Döbel S, Fuchs JE, Geist L, Hela W, Kofink C, Kousek R, Moser F, Puchner T, Rumpel K, Scharnweber M, Werni P, Wolkerstorfer B, Breitsprecher D, Baaske P, Pearson M, McConnell DB, Böttcher J. Getting a Grip on the Undrugged: Targeting β-Catenin with Fragment-Based Methods. ChemMedChem 2021; 16:1420-1424. [PMID: 33275320 PMCID: PMC8247886 DOI: 10.1002/cmdc.202000839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Indexed: 12/20/2022]
Abstract
Aberrant WNT pathway activation, leading to nuclear accumulation of β‐catenin, is a key oncogenic driver event. Mutations in the tumor suppressor gene APC lead to impaired proteasomal degradation of β‐catenin and subsequent nuclear translocation. Restoring cellular degradation of β‐catenin represents a potential therapeutic strategy. Here, we report the fragment‐based discovery of a small molecule binder to β‐catenin, including the structural elucidation of the binding mode by X‐ray crystallography. The difficulty in drugging β‐catenin was confirmed as the primary screening campaigns identified only few and very weak hits. Iterative virtual and NMR screening techniques were required to discover a compound with sufficient potency to be able to obtain an X‐ray co‐crystal structure. The binding site is located between armadillo repeats two and three, adjacent to the BCL9 and TCF4 binding sites. Genetic studies show that it is unlikely to be useful for the development of protein–protein interaction inhibitors but structural information and established assays provide a solid basis for a prospective optimization towards β‐catenin proteolysis targeting chimeras (PROTACs) as alternative modality.
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Affiliation(s)
- Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Stephan K Zahn
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Markus Zeeb
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jens Bruchhaus
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Maike Dettling
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Franziska Moser
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Dennis Breitsprecher
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany.,Leica Microsystems AG, Max Schmidheiny-Strasse 201, 9435, Heerbrugg, Switzerland
| | - Philipp Baaske
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
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14
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Binas O, de Jesus V, Landgraf T, Völklein AE, Martins J, Hymon D, Kaur Bains J, Berg H, Biedenbänder T, Fürtig B, Lakshmi Gande S, Niesteruk A, Oxenfarth A, Shahin Qureshi N, Schamber T, Schnieders R, Tröster A, Wacker A, Wirmer-Bartoschek J, Wirtz Martin MA, Stirnal E, Azzaoui K, Richter C, Sreeramulu S, José Blommers MJ, Schwalbe H. 19 F NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens. Chembiochem 2020; 22:423-433. [PMID: 32794266 PMCID: PMC7436455 DOI: 10.1002/cbic.202000476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Indexed: 11/17/2022]
Abstract
We report here the nuclear magnetic resonance 19F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter‐screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow‐up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low‐micromolar binding affinity without losing binding specificity between two different terminator structures.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Albrecht Eduard Völklein
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hannes Berg
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Santosh Lakshmi Gande
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Niesteruk
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Alix Tröster
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Kamal Azzaoui
- Saverna Therapeutics, Gewerbestrasse 24, 4123, Allschwil, Switzerland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
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15
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Yang Y, Vankayalapati H, Tang M, Zheng Y, Li Y, Ma C, Lai K. Discovery of Novel Inhibitors Targeting Multi-UDP-hexose Pyrophosphorylases as Anticancer Agents. Molecules 2020; 25:E645. [PMID: 32028604 DOI: 10.3390/molecules25030645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
To minimize treatment toxicities, recent anti-cancer research efforts have switched from broad-based chemotherapy to targeted therapy, and emerging data show that altered cellular metabolism in cancerous cells can be exploited as new venues for targeted intervention. In this study, we focused on, among the altered metabolic processes in cancerous cells, altered glycosylation due to its documented roles in cancer tumorigenesis, metastasis and drug resistance. We hypothesize that the enzymes required for the biosynthesis of UDP-hexoses, glycosyl donors for glycan synthesis, could serve as therapeutic targets for cancers. Through structure-based virtual screening and kinetic assay, we identified a drug-like chemical fragment, GAL-012, that inhibit a small family of UDP-hexose pyrophosphorylases-galactose pyro-phosphorylase (GALT), UDP-glucose pyrophosphorylase (UGP2) and UDP-N-acetylglucosamine pyrophosphorylase (AGX1/UAP1) with an IC50 of 30 µM. The computational docking studies supported the interaction of GAL-012 to the binding sites of GALT at Trp190 and Ser192, UGP2 at Gly116 and Lys127, and AGX1/UAP1 at Asn327 and Lys407, respectively. One of GAL-012 derivatives GAL-012-2 also demonstrated the inhibitory activity against GALT and UGP2. Moreover, we showed that GAL-012 suppressed the growth of PC3 cells in a dose-dependent manner with an EC50 of 75 µM with no effects on normal skin fibroblasts at 200 µM. Western blot analysis revealed reduced expression of pAKT (Ser473), pAKT (Thr308) by 77% and 72%, respectively in the treated cells. siRNA experiments against the respective genes encoding the pyrophosphorylases were also performed and the results further validated the proposed roles in cancer growth inhibition. Finally, synergistic relationships between GAL-012 and tunicamycin, as well as bortezomib (BTZ) in killing cultured cancer cells were observed, respectively. With its unique scaffold and relatively small size, GAL-012 serves as a promising early chemotype for optimization to become a safe, effective, multi-target anti-cancer drug candidate which could be used alone or in combination with known therapeutics.
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16
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Vásquez AF, González Barrios A. Pushing the Ligand Efficiency Metrics: Relative Group Contribution (RGC) Model as a Helpful Strategy to Promote a Fragment "Rescue" Effect. Front Chem 2019; 7:564. [PMID: 31482085 PMCID: PMC6710606 DOI: 10.3389/fchem.2019.00564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/24/2019] [Indexed: 12/30/2022] Open
Abstract
The ligand efficiency (LE) indexes have long been used as decision-making criteria in drug discovery and development. However, in the context of fragment-based drug design (FBDD), these metrics often exhibit a strong emphasis toward the selection of highly efficient “core” fragments for potential optimization, which are not usually considered as parts of a larger molecule with a size typical for a drug. In this study, we present a relative group contribution (RGC) model intended to predict the efficiency of a drug-sized compound in terms of its component fragments. This model could be useful not only in rapidly predicting all the possible combinations of promising fragments from an earlier hit discovery stage, but also in enabling a relatively low-LE fragment to become part of a drug-sized compound as long as it is “rescued” by other high-LE fragments.
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Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia.,Laboratorio de Fisiología Molecular, Instituto Nacional de Salud, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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17
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Chilingaryan Z, Headey SJ, Lo ATY, Xu ZQ, Otting G, Dixon NE, Scanlon MJ, Oakley AJ. Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction. Antibiotics (Basel) 2018; 7:E14. [PMID: 29470422 PMCID: PMC5872125 DOI: 10.3390/antibiotics7010014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 12/30/2022] Open
Abstract
In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using 15N-¹H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.
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Affiliation(s)
- Zorik Chilingaryan
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Stephen J Headey
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Martin J Scanlon
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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18
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Egner JM, Jensen DR, Olp MD, Kennedy NW, Volkman BF, Peterson FC, Smith BC, Hill RB. Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR Spectroscopy. Chembiochem 2018; 19:448-458. [PMID: 29239081 DOI: 10.1002/cbic.201700386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/11/2017] [Indexed: 11/08/2022]
Abstract
An academic chemical screening approach was developed by using 2D protein-detected NMR, and a 352-chemical fragment library was screened against three different protein targets. The approach was optimized against two protein targets with known ligands: CXCL12 and BRD4. Principal component analysis reliably identified compounds that induced nonspecific NMR crosspeak broadening but did not unambiguously identify ligands with specific affinity (hits). For improved hit detection, a novel scoring metric-difference intensity analysis (DIA)-was devised that sums all positive and negative intensities from 2D difference spectra. Applying DIA quickly discriminated potential ligands from compounds inducing nonspecific NMR crosspeak broadening and other nonspecific effects. Subsequent NMR titrations validated chemotypes important for binding to CXCL12 and BRD4. A novel target, mitochondrial fission protein Fis1, was screened, and six hits were identified by using DIA. Screening these diverse protein targets identified quinones and catechols that induced nonspecific NMR crosspeak broadening, hampering NMR analyses, but are currently not computationally identified as pan-assay interference compounds. The results established a streamlined screening workflow that can easily be scaled and adapted as part of a larger screening pipeline to identify fragment hits and assess relative binding affinities in the range of 0.3-1.6 mm. DIA could prove useful in library screening and other applications in which NMR chemical shift perturbations are measured.
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Affiliation(s)
- John M Egner
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Davin R Jensen
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Nolan W Kennedy
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
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19
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Delbart F, Brams M, Gruss F, Noppen S, Peigneur S, Boland S, Chaltin P, Brandao-Neto J, von Delft F, Touw WG, Joosten RP, Liekens S, Tytgat J, Ulens C. An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein. J Biol Chem 2017; 293:2534-2545. [PMID: 29237730 PMCID: PMC5818190 DOI: 10.1074/jbc.m117.815316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) belong to the family of pentameric ligand-gated ion channels and mediate fast excitatory transmission in the central and peripheral nervous systems. Among the different existing receptor subtypes, the homomeric α7 nAChR has attracted considerable attention because of its possible implication in several neurological and psychiatric disorders, including cognitive decline associated with Alzheimer's disease or schizophrenia. Allosteric modulators of ligand-gated ion channels are of particular interest as therapeutic agents, as they modulate receptor activity without affecting normal fluctuations of synaptic neurotransmitter release. Here, we used X-ray crystallography and surface plasmon resonance spectroscopy of α7-acetylcholine-binding protein (AChBP), a humanized chimera of a snail AChBP, which has 71% sequence similarity with the extracellular ligand-binding domain of the human α7 nAChR, to investigate the structural determinants of allosteric modulation. We extended previous observations that an allosteric site located in the vestibule of the receptor offers an attractive target for receptor modulation. We introduced seven additional humanizing mutations in the vestibule-located binding site of AChBP to improve its suitability as a model for studying allosteric binding. Using a fragment-based screening approach, we uncovered an allosteric binding site located near the β8-β9 loop, which critically contributes to coupling ligand binding to channel opening in human α7 nAChR. This work expands our understanding of the topology of allosteric binding sites in AChBP and, by extrapolation, in the human α7 nAChR as determined by electrophysiology measurements. Our insights pave the way for drug design strategies targeting nAChRs involved in ion channel-mediated disorders.
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Affiliation(s)
- Florian Delbart
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Marijke Brams
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Fabian Gruss
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Sam Noppen
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Steve Peigneur
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Sandro Boland
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium
| | - Patrick Chaltin
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium.,the Center for Innovation and Stimulation of Drug Discovery Leuven and Center for Drug Design and Discovery, KU Leuven, 3001 Heverlee, Belgium
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Wouter G Touw
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Robbie P Joosten
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Sandra Liekens
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jan Tytgat
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Chris Ulens
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium,
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20
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Dalvit C, Knapp S. 19 F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers. Magn Reson Chem 2017; 55:1091-1095. [PMID: 28762528 DOI: 10.1002/mrc.4640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
Fluorine ligand-based NMR spectroscopy is now an established method for performing binding screening against a macromolecular target. Typically, the transverse relaxation rate of the fluorine signals is monitored in the absence and presence of the target. However, useful structural information can sometimes be obtained from the analysis of the fluorine isotropic chemical shift. This is particularly relevant for molecules that are racemates and/or display multiple conformers. The large difference in fluorine isotropic chemical shift between free and bound state deriving mainly from the breaking and/or making of intramolecular and/or intermolecular hydrogen bonds allows the detection of very weak affinity ligands. According to our experimental results, racemates should always be included in the generation of the fluorinated fragment libraries. The selection or the availability of only one of the enantiomers for the fluorinated screening library could result in missing relevant chemical scaffold motifs.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, 2000, Neuchatel, Switzerland
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, 60438, Frankfurt, Germany
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford University, Oxford, OX3 7DQ, UK
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21
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Dalvit C, Piotto M. 19 F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis. Magn Reson Chem 2017; 55:106-114. [PMID: 27514284 DOI: 10.1002/mrc.4500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Ligand-based 19 F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the 19 F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the 19 F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the 19 F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment-based screening. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, Neuchatel, Switzerland
- IDD/SDI, Sanofi, Vitry-sur-Seine, France
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22
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Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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23
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Pelz NF, Bian Z, Zhao B, Shaw S, Tarr JC, Belmar J, Gregg C, Camper DV, Goodwin CM, Arnold AL, Sensintaffar JL, Friberg A, Rossanese OW, Lee T, Olejniczak ET, Fesik SW. Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods. J Med Chem 2016; 59:2054-66. [PMID: 26878343 PMCID: PMC5565212 DOI: 10.1021/acs.jmedchem.5b01660] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Myeloid cell leukemia-1 (Mcl-1) is a member of the Bcl-2 family of proteins responsible for the regulation of programmed cell death. Amplification of Mcl-1 is a common genetic aberration in human cancer whose overexpression contributes to the evasion of apoptosis and is one of the major resistance mechanisms for many chemotherapies. Mcl-1 mediates its effects primarily through interactions with pro-apoptotic BH3 containing proteins that achieve high affinity for the target by utilizing four hydrophobic pockets in its binding groove. Here we describe the discovery of Mcl-1 inhibitors using fragment-based methods and structure-based design. These novel inhibitors exhibit low nanomolar binding affinities to Mcl-1 and >500-fold selectivity over Bcl-xL. X-ray structures of lead Mcl-1 inhibitors when complexed to Mcl-1 provided detailed information on how these small-molecules bind to the target and were used extensively to guide compound optimization.
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Affiliation(s)
- Nicholas F. Pelz
- Corresponding Author Phone: +1 (615) 322 6303. Fax: +1 (615) 875 3236.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen W. Fesik
- Corresponding Author Phone: +1 (615) 322 6303. Fax: +1 (615) 875 3236.
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24
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Gable JE, Lee GM, Acker TM, Hulce KR, Gonzalez ER, Schweigler P, Melkko S, Farady CJ, Craik CS. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem 2016; 11:862-9. [PMID: 26822284 DOI: 10.1002/cmdc.201500526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 11/11/2022]
Abstract
Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Biophysics Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Timothy M Acker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Kaitlin R Hulce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Chemistry and Chemical Biology Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Eric R Gonzalez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Patrick Schweigler
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Samu Melkko
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Christopher J Farady
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
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25
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Hung AW, Silvestre HL, Wen S, George GPC, Boland J, Blundell TL, Ciulli A, Abell C. Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis. ChemMedChem 2015; 11:38-42. [PMID: 26486566 PMCID: PMC4949533 DOI: 10.1002/cmdc.201500414] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 11/06/2022]
Abstract
Ligand efficiency has proven to be a valuable concept for optimization of leads in the early stages of drug design. Taking this one step further, group efficiency (GE) evaluates the binding efficiency of each appendage of a molecule, further fine‐tuning the drug design process. Here, GE analysis is used to systematically improve the potency of inhibitors of Mycobacterium tuberculosis pantothenate synthetase, an important target in tuberculosis therapy. Binding efficiencies were found to be distributed unevenly within a lead molecule derived using a fragment‐based approach. Substitution of the less efficient parts of the molecule allowed systematic development of more potent compounds. This method of dissecting and analyzing different groups within a molecule offers a rational and general way of carrying out lead optimization, with potential broad application within drug discovery.
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Affiliation(s)
- Alvin W Hung
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Experimental Therapeutic Centre, A-STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - H Leonardo Silvestre
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Shijun Wen
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Guillaume P C George
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Jennifer Boland
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Division of Biological Chemistry & Drug Discovery, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.
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26
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Burke JP, Bian Z, Shaw S, Zhao B, Goodwin CM, Belmar J, Browning CF, Vigil D, Friberg A, Camper DV, Rossanese OW, Lee T, Olejniczak ET, Fesik SW. Discovery of tricyclic indoles that potently inhibit Mcl-1 using fragment-based methods and structure-based design. J Med Chem 2015; 58:3794-805. [PMID: 25844895 PMCID: PMC5565203 DOI: 10.1021/jm501984f] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Myeloid cell leukemia-1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that is overexpressed and amplified in many cancers. Overexpression of Mcl-1 allows cancer cells to evade apoptosis and contributes to the resistance of cancer cells to be effectively treated with various chemotherapies. From an NMR-based screen of a large fragment library, several distinct chemical scaffolds that bind to Mcl-1 were discovered. Here, we describe the discovery of potent tricyclic 2-indole carboxylic acid inhibitors that exhibit single digit nanomolar binding affinity to Mcl-1 and greater than 1700-fold selectivity over Bcl-xL and greater than 100-fold selectivity over Bcl-2. X-ray structures of these compounds when complexed to Mcl-1 provide detailed information on how these small-molecules bind to the target, which was used to guide compound optimization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen W. Fesik
- Corresponding Author, Phone: +1 (615) 322 6303. Fax: +1 (615) 875 3236.
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27
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience.
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Affiliation(s)
- Mary J Harner
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Ave, 607 Light Hall, Nashville, TN 37232-0146, USA
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28
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Friberg A, Vigil D, Zhao B, Daniels RN, Burke JP, Garcia-Barrantes PM, Camper D, Chauder BA, Lee T, Olejniczak ET, Fesik SW. Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design. J Med Chem 2013; 56:15-30. [PMID: 23244564 PMCID: PMC3646517 DOI: 10.1021/jm301448p] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Myeloid cell leukemia 1 (Mcl-1), a member of the Bcl-2 family of proteins, is overexpressed and amplified in various cancers and promotes the aberrant survival of tumor cells that otherwise would undergo apoptosis. Here we describe the discovery of potent and selective Mcl-1 inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified two chemically distinct hit series that bind to different sites on Mcl-1. Members of the two fragment classes were merged together to produce lead compounds that bind to Mcl-1 with a dissociation constant of <100 nM with selectivity for Mcl-1 over Bcl-xL and Bcl-2. Structures of merged compounds when complexed to Mcl-1 were obtained by X-ray crystallography and provide detailed information about the molecular recognition of small-molecule ligands binding Mcl-1. The compounds represent starting points for the discovery of clinically useful Mcl-1 inhibitors for the treatment of a wide variety of cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stephen W. Fesik
- Corresponding author; Phone, +1 (615) 322 6303; Fax, +1 (615) 875 3236
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29
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Cho YS, Angove H, Brain C, Chen CHT, Cheng H, Cheng R, Chopra R, Chung K, Congreve M, Dagostin C, Davis DJ, Feltell R, Giraldes J, Hiscock SD, Kim S, Kovats S, Lagu B, Lewry K, Loo A, Lu Y, Luzzio M, Maniara W, McMenamin R, Mortenson PN, Benning R, O'Reilly M, Rees DC, Shen J, Smith T, Wang Y, Williams G, Woolford AJA, Wrona W, Xu M, Yang F, Howard S. Fragment-Based Discovery of 7-Azabenzimidazoles as Potent, Highly Selective, and Orally Active CDK4/6 Inhibitors. ACS Med Chem Lett 2012; 3:445-9. [PMID: 24900493 DOI: 10.1021/ml200241a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 04/16/2012] [Indexed: 11/28/2022] Open
Abstract
Herein, we describe the discovery of potent and highly selective inhibitors of both CDK4 and CDK6 via structure-guided optimization of a fragment-based screening hit. CDK6 X-ray crystallography and pharmacokinetic data steered efforts in identifying compound 6, which showed >1000-fold selectivity for CDK4 over CDKs 1 and 2 in an enzymatic assay. Furthermore, 6 demonstrated in vivo inhibition of pRb-phosphorylation and oral efficacy in a Jeko-1 mouse xenograft model.
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Affiliation(s)
- Young Shin Cho
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Hayley Angove
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Christopher Brain
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Christine Hiu-Tung Chen
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Hong Cheng
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Robert Cheng
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Rajiv Chopra
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Kristy Chung
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Miles Congreve
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Claudio Dagostin
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Deborah J. Davis
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Ruth Feltell
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - John Giraldes
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Steven D. Hiscock
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Sunkyu Kim
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Steven Kovats
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Bharat Lagu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Kim Lewry
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Alice Loo
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Yipin Lu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Michael Luzzio
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Wiesia Maniara
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Rachel McMenamin
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Paul N. Mortenson
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Rajdeep Benning
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Marc O'Reilly
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - David C. Rees
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Junqing Shen
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Troy Smith
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Yaping Wang
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Glyn Williams
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Alison J.-A. Woolford
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
| | - Wojciech Wrona
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Mei Xu
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Fan Yang
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Steven Howard
- Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge,
CB4 0QA, United Kingdom
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30
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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