19 results on '"Renato Ferreira de Freitas"'
Search Results
2. Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors.
- Author
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Wemenes José Lima Silva and Renato Ferreira de Freitas
- Published
- 2023
- Full Text
- View/download PDF
3. A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization
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Marcus A. Cheek, Aiping Dong, Renato Ferreira de Freitas, Dalia Barsyte-Lovejoy, Aliakbar Khalili Yazdi, Jinrong Min, Fengling Li, Victoria Vu, Albina Bolotokova, Lindsey I. James, Jack Greenblatt, Naimee Mehta, Irina K. Popova, David Dilworth, Ming Lei, Raquel Arminda Carvalho Machado, Ronan P Hanley, David Y Nie, Matthieu Schapira, Mengqi Zhou, Elisa Gibson, Cheryl H. Arrowsmith, Michael-Christopher Keogh, Suzanne Ackloo, Matthew R. Marunde, Mona Alqazzaz, Dmitri Kireev, Nathan W. Hall, Peter Brown, Abdellah Allali-Hassani, Sina Kazemzadeh, Edyta Marcon, Tigran M. Abramyan, Dominic D G Owens, Yanli Liu, Magdalena M. Szewczyk, Matthew J. Meiners, Irene Chau, Su Qin, and Masoud Vedadi
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Gene isoform ,Methyltransferase ,Nucleolus ,Lysine ,Methylation ,Article ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Chemistry ,Histone-Lysine N-Methyltransferase ,Cell Biology ,Nucleosomes ,Chromatin ,Cell biology ,Repressor Proteins ,Histone ,Enzyme ,Molecular Probes ,030220 oncology & carcinogenesis ,biology.protein ,Multiple Myeloma ,Cell Nucleolus - Abstract
Nuclear receptor-binding SET domain-containing 2 (NSD2) is the primary enzyme responsible for the dimethylation of lysine 36 of histone 3 (H3K36), a mark associated with active gene transcription and intergenic DNA methylation. In addition to a methyltransferase domain, NSD2 harbors two proline-tryptophan-tryptophan-proline (PWWP) domains and five plant homeodomains (PHDs) believed to serve as chromatin reading modules. Here, we report a chemical probe targeting the N-terminal PWWP (PWWP1) domain of NSD2. UNC6934 occupies the canonical H3K36me2-binding pocket of PWWP1, antagonizes PWWP1 interaction with nucleosomal H3K36me2 and selectively engages endogenous NSD2 in cells. UNC6934 induces accumulation of endogenous NSD2 in the nucleolus, phenocopying the localization defects of NSD2 protein isoforms lacking PWWP1 that result from translocations prevalent in multiple myeloma (MM). Mutations of other NSD2 chromatin reader domains also increase NSD2 nucleolar localization and enhance the effect of UNC6934. This chemical probe and the accompanying negative control UNC7145 will be useful tools in defining NSD2 biology.
- Published
- 2021
4. Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2
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Dalia Barsyte-Lovejoy, Masoud Vedadi, Cheryl H. Arrowsmith, Jinrong Min, Ronan P Hanley, Rima Al-awar, Matthieu Schapira, Lindsey I. James, Renato Ferreira de Freitas, Magdalena M. Szewczyk, Abdellah Allali-Hassani, Naimee Mehta, Fengling Li, Carlos Zepeda-Velázquez, Elisa Gibson, David McLeod, Yanli Liu, Peter Brown, and David Dilworth
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Models, Molecular ,Methyltransferase ,Protein domain ,Drug Evaluation, Preclinical ,Antineoplastic Agents ,Crystallography, X-Ray ,Ligands ,01 natural sciences ,Article ,Small Molecule Libraries ,03 medical and health sciences ,Structure-Activity Relationship ,Protein Domains ,Drug Discovery ,Structure–activity relationship ,Humans ,Computer Simulation ,030304 developmental biology ,0303 health sciences ,Virtual screening ,biology ,Chemistry ,Antagonist ,Histone-Lysine N-Methyltransferase ,Small molecule ,0104 chemical sciences ,3. Good health ,Cell biology ,Molecular Docking Simulation ,Repressor Proteins ,010404 medicinal & biomolecular chemistry ,Histone ,biology.protein ,Molecular Medicine ,Drug Screening Assays, Antitumor - Abstract
Increased activity of the lysine methyltransferase NSD2 driven by translocation and activating mutations is associated with multiple myeloma and acute lymphoblastic leukemia, but no NSD2-targeting chemical probe has been reported to date. Here, we present the first antagonists that block the protein–protein interaction between the N-terminal PWWP domain of NSD2 and H3K36me2. Using virtual screening and experimental validation, we identified the small-molecule antagonist 3f, which binds to the NSD2-PWWP1 domain with a K(d) of 3.4 μM and abrogates histone H3K36me2 binding to the PWWP1 domain in cells. This study establishes an alternative approach to targeting NSD2 and provides a small-molecule antagonist that can be further optimized into a chemical probe to better understand the cellular function of this protein.
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- 2021
5. TP-064, a potent and selective small molecule inhibitor of PRMT4 for multiple myeloma
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Dalia Barsyte-Lovejoy, Yuji Baba, Peter Brown, Atsushi Kiba, Daisuke Tomita, Douglas R. Cary, Aiping Dong, Hong Zeng, Mihoko Kunitomo, Kazuhide Nakayama, Cheryl H. Arrowsmith, Fengling Li, Matthieu Schapira, Mohammad S. Eram, Charles E. Grimshaw, Yasuhiro Imaeda, Carlo C. dela Seña, Kumar Singh Saikatendu, Hong Wu, Akihiro Ohashi, Michiko Tawada, Renato Ferreira de Freitas, Magdalena M. Szewczyk, and Masoud Vedadi
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0301 basic medicine ,crystal structure ,Methyltransferase ,Arginine ,CARM1 ,Chemistry ,Protein subunit ,small molecule inhibitor ,Cell cycle ,TP-064 ,Small molecule ,3. Good health ,multiple myeloma ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Oncology ,Biochemistry ,Cell culture ,030220 oncology & carcinogenesis ,PRMT4 ,IC50 ,Research Paper - Abstract
Protein arginine methyltransferase (PRMT) 4 (also known as coactivator-associated arginine methyltransferase 1; CARM1) is involved in a variety of biological processes and is considered as a candidate oncogene owing to its overexpression in several types of cancer. Selective PRMT4 inhibitors are useful tools for clarifying the molecular events regulated by PRMT4 and for validating PRMT4 as a therapeutic target. Here, we report the discovery of TP-064, a potent, selective, and cell-active chemical probe of human PRMT4 and its co-crystal structure with PRMT4. TP-064 inhibited the methyltransferase activity of PRMT4 with high potency (half-maximal inhibitory concentration, IC50 < 10 nM) and selectivity over other PRMT family proteins, and reduced arginine dimethylation of the PRMT4 substrates BRG1-associated factor 155 (BAF155; IC50= 340 ± 30 nM) and Mediator complex subunit 12 (MED12; IC50 = 43 ± 10 nM). TP-064 treatment inhibited the proliferation of a subset of multiple myeloma cell lines, with affected cells arrested in G1 phase of the cell cycle. TP-064 and its negative control (TP-064N) will be valuable tools to further investigate the biology of PRMT4 and the therapeutic potential of PRMT4 inhibition.
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- 2018
6. Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain
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M.K. Mann, Leanna Smith, Matthieu Schapira, Wolfram Tempel, Renato Ferreira de Freitas, Scott Houliston, Rachel Harding, Cheryl H. Arrowsmith, Masoud Vedadi, and Ivan Franzoni
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Ubiquitin-Specific Proteases ,Magnetic Resonance Spectroscopy ,Ubiquitin binding ,Allosteric regulation ,Protein domain ,Drug Evaluation, Preclinical ,Crystallography, X-Ray ,Chemical library ,Small Molecule Libraries ,03 medical and health sciences ,chemistry.chemical_compound ,Structure-Activity Relationship ,0302 clinical medicine ,Ubiquitin ,Protein Domains ,Drug Discovery ,Endopeptidases ,Structure–activity relationship ,Protease Inhibitors ,030304 developmental biology ,Zinc finger ,0303 health sciences ,Binding Sites ,biology ,Dose-Response Relationship, Drug ,Zinc Fingers ,Surface Plasmon Resonance ,3. Good health ,Cell biology ,chemistry ,biology.protein ,Molecular Medicine ,030217 neurology & neurosurgery - Abstract
USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship, which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signaling pathways in health and disease.
- Published
- 2019
7. Selective, Small-Molecule Co-Factor Binding Site Inhibition of a Su(var)3-9, Enhancer of Zeste, Trithorax Domain Containing Lysine Methyltransferase
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Dafydd R. Owen, Aiping Dong, Martin James Wythes, Steven Kennedy, Dalia Barsyte-Lovejoy, Matthieu Schapira, Hong Wu, Rajiah Aldrin Denny, Viacheslav V. Trush, Mihir D. Parikh, Agustin Casimiro-Garcia, Renato Ferreira de Freitas, Masoud Vedadi, Magdalena Swewczyk, Hong Zeng, Tatlock John H, Fengling Li, Alexandria P. Taylor, Robert Arnold Kumpf, Peter Brown, and Cheryl H. Arrowsmith
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Models, Molecular ,S-Adenosylmethionine ,Methyltransferase ,Lysine ,01 natural sciences ,Small Molecule Libraries ,03 medical and health sciences ,Structure-Activity Relationship ,Drug Discovery ,Structure–activity relationship ,Humans ,Binding site ,Enzyme Inhibitors ,Enhancer ,Cells, Cultured ,030304 developmental biology ,Cell Proliferation ,chemistry.chemical_classification ,0303 health sciences ,Binding Sites ,Dose-Response Relationship, Drug ,Molecular Structure ,Substrate (chemistry) ,Histone-Lysine N-Methyltransferase ,Small molecule ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,Enzyme ,chemistry ,Biochemistry ,Molecular Medicine - Abstract
The first chemical probe to primarily occupy the co-factor binding site of a Su(var)3-9, enhancer of a zeste, trithorax (SET) domain containing protein lysine methyltransferase (PKMT) is reported. Protein methyltransferases require S-adenosylmethionine (SAM) as a co-factor (methyl donor) for enzymatic activity. However, SAM itself represents a poor medicinal chemistry starting point for a selective, cell-active inhibitor given its extreme physicochemical properties and its role in multiple cellular processes. A previously untested medicinal chemistry strategy of deliberate file enrichment around molecules bearing the hallmarks of SAM, but with improved lead-like properties from the outset, yielded viable hits against SET and MYND domain-containing protein 2 (SMYD2) that were shown to bind in the co-factor site. These leads were optimized to identify a highly biochemically potent, PKMT-selective, and cell-active chemical probe. While substrate-based inhibitors of PKMTs are known, this represents a novel, co-factor-derived strategy for the inhibition of SMYD2 which may also prove applicable to lysine methyltransferase family members previously thought of as intractable.
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- 2019
8. Discovery of small molecule antagonists of the USP5 zinc finger ubiquitin-binding domain
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Ivan Franzoni, Cheryl H. Arrowsmith, Rachel Harding, Scott Houliston, M.K. Mann, Matthieu Schapira, Wolfram Tempel, and Renato Ferreira de Freitas
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Zinc finger ,0303 health sciences ,Proteases ,Ubiquitin binding ,biology ,Chemistry ,Allosteric regulation ,Small molecule ,Chemical library ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Ubiquitin ,biology.protein ,030217 neurology & neurosurgery ,Function (biology) ,030304 developmental biology - Abstract
USP5 disassembles unanchored polyubiquitin chains to recycle free mono-ubiquitin, and is one of twelve ubiquitin-specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signalling pathways in health and disease.
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- 2019
9. Identification and characterization of the first fragment hits for SETDB1 Tudor domain
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Steven Kennedy, Sean K. Liew, Matthieu Schapira, Masoud Vedadi, Abdellah Allali-Hassani, Cheryl H. Arrowsmith, Scott Houliston, Andrei K. Yudin, Jinrong Min, Diego B. Diaz, P. Mader, Hong Wu, Aman Iqbal, Aiping Dong, Vijayaratnam Santhakumar, Rodrigo Mendoza-Sanchez, Renato Ferreira de Freitas, Victoria B. Corless, David Smil, Peter Brown, Ludmila Dombrovski, Elena Dobrovetsky, and Carlo C. dela Seña
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Models, Molecular ,Tudor domain ,Methyltransferase ,Clinical Biochemistry ,Pharmaceutical Science ,Peptide binding ,Crystallography, X-Ray ,01 natural sciences ,Biochemistry ,Histones ,Small Molecule Libraries ,03 medical and health sciences ,Structure-Activity Relationship ,0302 clinical medicine ,Drug Discovery ,Transferase ,Humans ,Enzyme Inhibitors ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Dose-Response Relationship, Drug ,Molecular Structure ,Tudor Domain ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Nuclear magnetic resonance spectroscopy ,Histone-Lysine N-Methyltransferase ,Small molecule ,0104 chemical sciences ,3. Good health ,Chromatin ,010404 medicinal & biomolecular chemistry ,Histone ,Acetylation ,030220 oncology & carcinogenesis ,biology.protein ,Molecular Medicine - Abstract
SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase, which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the TTD of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.
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- 2019
10. Discovery of a Potent, Selective, and Cell-Active Dual Inhibitor of Protein Arginine Methyltransferase 4 and Protein Arginine Methyltransferase 6
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H. Ümit Kaniskan, Renato Ferreira de Freitas, David Smil, Dalia Barsyte-Lovejoy, Cheryl H. Arrowsmith, Jian Jin, Matthieu Schapira, Magdalena M. Szewczyk, Jing Liu, Fengling Li, Mohammad S. Eram, Guillermo Senisterra, Masoud Vedadi, Yudao Shen, and Peter Brown
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Models, Molecular ,0301 basic medicine ,Protein-Arginine N-Methyltransferases ,Methyltransferase ,Arginine ,Cell ,Chemical biology ,Crystallography, X-Ray ,Article ,03 medical and health sciences ,Drug Discovery ,medicine ,Humans ,Epigenetics ,Enzyme Inhibitors ,Drug discovery ,Chemistry ,HEK 293 cells ,Dual inhibitor ,Nuclear Proteins ,3. Good health ,HEK293 Cells ,030104 developmental biology ,medicine.anatomical_structure ,Biochemistry ,Molecular Medicine - Abstract
Well-characterized selective inhibitors of protein arginine methyltransferases (PRMTs) are invaluable chemical tools for testing biological and therapeutic hypotheses. Based on 4, a fragment-like inhibitor of type I PRMTs, we conducted structure–activity relationship (SAR) studies and explored three regions of this scaffold. The studies led to the discovery of a potent, selective and cell-active dual inhibitor of PRMT4 and PRMT6, 17 (MS049). As compared to 4, 17 displayed much improved potency for PRMT4 and PRMT6 in both biochemical and cellular assays. It was selective for PRMT4 and PRMT6 over other PRMTs and a broad range of other epigenetic modifiers and non-epigenetic targets. We also developed 46 (MS049N), which was inactive in biochemical and cellular assays, as a negative control for chemical biology studies. Considering possible overlapping substrate specificity of PRMTs, 17 and 46 are valuable chemical tools for dissecting specific biological functions and dysregulation of PRMT4 and PRMT6 in health and disease.
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- 2016
11. Discovery of a Potent and Selective Coactivator Associated Arginine Methyltransferase 1 (CARM1) Inhibitor by Virtual Screening
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Renato Ferreira de Freitas, Masoud Vedadi, David Smil, Steven Kennedy, Matthieu Schapira, Magdalena M. Szewczyk, Mohammad S. Eram, Cheryl H. Arrowsmith, Dalia Barsyte-Lovejoy, Vijayaratnam Santhakumar, and Peter Brown
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Models, Molecular ,0301 basic medicine ,Virtual screening ,Methyltransferase ,Dose-Response Relationship, Drug ,Molecular Structure ,CARM1 ,Arginine ,Chemistry ,HEK 293 cells ,Drug Evaluation, Preclinical ,Ligand (biochemistry) ,CARD Signaling Adaptor Proteins ,Structure-Activity Relationship ,03 medical and health sciences ,HEK293 Cells ,030104 developmental biology ,Biochemistry ,Guanylate Cyclase ,Drug Discovery ,Coactivator ,Humans ,Molecular Medicine ,Structure–activity relationship ,Enzyme Inhibitors - Abstract
Protein arginine methyltransferases (PRMTs) represent an emerging target class in oncology and other disease areas. So far, the most successful strategy to identify PRMT inhibitors has been to screen large to medium-size chemical libraries. Attempts to develop PRMT inhibitors using receptor-based computational methods have met limited success. Here, using virtual screening approaches, we identify 11 CARM1 (PRMT4) inhibitors with ligand efficiencies ranging from 0.28 to 0.84. CARM1 selective hits were further validated by orthogonal methods. Two structure-based rounds of optimization produced 27 (SGC2085), a CARM1 inhibitor with an IC50 of 50 nM and more than hundred-fold selectivity over other PRMTs. These results indicate that virtual screening strategies can be successfully applied to Rossmann-fold protein methyltransferases.
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- 2016
12. Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor
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Holger Steuber, Fengling Li, Marion Hitchcock, Matthieu Schapira, Mohammad S. Eram, Peter Brown, Ursula Egner, Guillermo Senisterra, Cheryl H. Arrowsmith, Christian Stegmann, Dieter Moosmayer, Dalia Barsyte-Lovejoy, Masoud Vedadi, Aiping Dong, Renato Ferreira de Freitas, David Smil, Magdalena M. Szewczyk, and Hong Wu
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Models, Molecular ,0301 basic medicine ,Protein-Arginine N-Methyltransferases ,Methyltransferase ,Arginine ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Drug Discovery ,Humans ,Structure–activity relationship ,Transferase ,Enzyme Inhibitors ,Ligand efficiency ,Dose-Response Relationship, Drug ,Molecular Structure ,Drug discovery ,Chemistry ,Methylation ,3. Good health ,Repressor Proteins ,030104 developmental biology ,Biochemistry ,030220 oncology & carcinogenesis ,Molecular Medicine - Abstract
Protein methyltransferases (PMTs) are a promising target class in oncology and other disease areas. They are composed of SET domain methyltransferases and structurally unrelated Rossman-fold enzymes that include protein arginine methyltransferases (PRMTs). In the absence of a well-defined medicinal chemistry tool-kit focused on PMTs, most current inhibitors were identified by screening large and diverse libraries of leadlike molecules. So far, no successful fragment-based approach was reported against this target class. Here, by deconstructing potent PRMT inhibitors, we find that chemical moieties occupying the substrate arginine-binding site can act as efficient fragment inhibitors. Screening a fragment library against PRMT6 produced numerous hits, including a 300 nM inhibitor (ligand efficiency of 0.56) that decreased global histone 3 arginine 2 methylation in cells, and can serve as a warhead for the development of PRMT chemical probes.
- Published
- 2016
13. Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor
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Renato Ferreira de Freitas, Danton Ivanochko, and Matthieu Schapira
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Models, Molecular ,S-Adenosylmethionine ,Methyltransferase ,methyltransferases ,Druggability ,Chemical biology ,Pharmaceutical Science ,Review ,Crystallography, X-Ray ,Catalysis ,Cofactor ,Epigenesis, Genetic ,Analytical Chemistry ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,inhibitors ,Drug Discovery ,Humans ,Enzyme Inhibitors ,Physical and Theoretical Chemistry ,Binding site ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Cofactor binding ,Binding Sites ,biology ,Drug discovery ,Organic Chemistry ,3. Good health ,Enzyme ,chemistry ,Biochemistry ,Chemistry (miscellaneous) ,030220 oncology & carcinogenesis ,biology.protein ,Molecular Medicine ,mechanism of action - Abstract
Protein methyltransferases (PMTs) are enzymes involved in epigenetic mechanisms, DNA repair, and other cellular machineries critical to cellular identity and function, and are an important target class in chemical biology and drug discovery. Central to the enzymatic reaction is the transfer of a methyl group from the cofactor S-adenosylmethionine (SAM) to a substrate protein. Here we review how the essentiality of SAM for catalysis is exploited by chemical inhibitors. Occupying the cofactor binding pocket to compete with SAM can be hindered by the hydrophilic nature of this site, but structural studies of compounds now in the clinic revealed that inhibitors could either occupy juxtaposed pockets to overlap minimally, but sufficiently with the bound cofactor, or induce large conformational remodeling leading to a more druggable binding site. Rather than competing with the cofactor, other inhibitors compete with the substrate and rely on bound SAM, either to allosterically stabilize the substrate binding site, or for direct SAM-inhibitor interactions.
- Published
- 2019
14. Identification and Structure-Activity Relationship of HDAC6 Zinc-finger Ubiquitin Binding Domain Inhibitors
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Matthieu Schapira, Cheryl H. Arrowsmith, Vijayaratnam Santhakumar, Mani Ravichandran, Ivan Franzoni, Renato Ferreira de Freitas, Hui Ouyang, Mark Lautens, Rachel Harding, and M.K. Mann
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0301 basic medicine ,Models, Molecular ,Ubiquitin binding ,Protein Conformation ,Protein aggregation ,Crystallography, X-Ray ,Histone Deacetylase 6 ,Ligands ,01 natural sciences ,Structure-Activity Relationship ,03 medical and health sciences ,Protein structure ,0302 clinical medicine ,Ubiquitin ,Catalytic Domain ,Drug Discovery ,Humans ,Structure–activity relationship ,Protein Interaction Domains and Motifs ,Binding site ,030304 developmental biology ,Zinc finger ,0303 health sciences ,Virtual screening ,Molecular Structure ,biology ,010405 organic chemistry ,Chemistry ,Zinc Fingers ,0104 chemical sciences ,Histone Deacetylase Inhibitors ,030104 developmental biology ,Biochemistry ,Proteasome ,030220 oncology & carcinogenesis ,Biophysics ,biology.protein ,Molecular Medicine ,Protein Binding - Abstract
HDAC6 plays a central role in the recruitment of protein aggregates for lysosomal degradation, and is a promising target for combination therapy with proteasome inhibitors in multiple myeloma. Pharmacologically displacing ubiquitin from the zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition. Here, we present the discovery of a HDAC6 ZnF-UBD-focused chemical series and its progression from virtual screening hits to low micromolar inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin, and an extended aromatic system stacking with W1182 and R1155 are necessary for activity. One of the compounds induced a conformational remodeling of the binding site where the primary binding pocket opens-up onto a ligand-able secondary pocket that may be exploited to increase potency. The preliminary structure-activity relationship accompanied by nine crystal structures should enable further optimization into a chemical probe to investigate the merit of targeting the ZnF-UBD of HDAC6 in multiple myeloma and other diseases.
- Published
- 2018
- Full Text
- View/download PDF
15. Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin
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Mark Lautens, Cheryl H. Arrowsmith, M. Ravichandran, Frank von Delft, Hui Ouyang, Renato Ferreira de Freitas, Ivan Franzoni, Matthieu Schapira, Kevin A. Juarez-Ornelas, Rachel Harding, Vijayaratnam Santhakumar, and P.M. Collins
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0301 basic medicine ,Ubiquitin binding ,Crystallography, X-Ray ,Histone Deacetylase 6 ,Ligands ,Binding, Competitive ,03 medical and health sciences ,0302 clinical medicine ,Ubiquitin ,Drug Discovery ,Hydrolase ,Humans ,Protein Interaction Domains and Motifs ,Zinc finger ,Binding Sites ,biology ,Chemistry ,Zinc Fingers ,HDAC6 ,Small molecule ,3. Good health ,Cell biology ,030104 developmental biology ,Biochemistry ,030220 oncology & carcinogenesis ,biology.protein ,Molecular Medicine ,Alternative strategy ,Protein Binding - Abstract
Inhibitors of HDAC6 have attractive potential in numerous cancers. HDAC6 inhibitors to date target the catalytic domains, but targeting the unique zinc-finger ubiquitin-binding domain (Zf-UBD) of HDAC6 may be an attractive alternative strategy. We developed X-ray crystallography and biophysical assays to identify and characterize small molecules capable of binding to the Zf-UBD and competing with ubiquitin binding. Our results revealed two adjacent ligand-able pockets of HDAC6 Zf-UBD and the first functional ligands for this domain.
- Published
- 2017
16. A Systematic Analysis of Atomic Protein-Ligand Interactions in the PDB
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Renato Ferreira de Freitas and Matthieu Schapira
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0301 basic medicine ,Stereochemistry ,Stacking ,Protein Data Bank (RCSB PDB) ,Pharmaceutical Science ,010402 general chemistry ,Biochemistry ,01 natural sciences ,Hydrophobic effect ,03 medical and health sciences ,Molecular recognition ,Drug Discovery ,030304 developmental biology ,Pharmacology ,0303 health sciences ,010405 organic chemistry ,Hydrogen bond ,Chemistry ,Organic Chemistry ,Ligand (biochemistry) ,Small molecule ,0104 chemical sciences ,Crystallography ,030104 developmental biology ,Molecular Medicine ,Protein folding ,Protein ligand - Abstract
We compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins representing 750 873 protein–ligand atomic interactions, and analyzed the frequency, geometry and the impact of each interaction type. The most frequent ligand–protein atom pairs can be clustered into seven interaction types., As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins – 6444 of which have experimental binding affinity – representing 750 873 protein–ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C–H···O hydrogen bonds or the relatively frequent amide–π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
- Published
- 2017
17. Correction to Discovery of a Potent and Selective Coactivator Associated Arginine Methyltransferase 1 (CARM1) Inhibitor by Virtual Screening
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Vijayaratnam Santhakumar, Magdalena M. Szewczyk, Dalia Barsyte-Lovejoy, Masoud Vedadi, Peter Brown, Mohammad S. Eram, Steven Kennedy, Matthieu Schapira, Cheryl H. Arrowsmith, Renato Ferreira de Freitas, and David Smil
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Virtual screening ,Biochemistry ,CARM1 ,Chemistry ,Drug Discovery ,Coactivator ,Molecular Medicine ,Arginine methyltransferase - Published
- 2016
18. Systematic analysis of atomic protein–ligand interactions in the PDB
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Renato Ferreira de Freitas and Matthieu Schapira
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Inorganic Chemistry ,Structural Biology ,Stereochemistry ,Chemistry ,Protein Data Bank (RCSB PDB) ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry ,Protein ligand - Published
- 2018
19. Estudo computacional da interação entre inibidores não nucleosídeos da transcriptase reversa do vírus HIV-1 com aminoácidos do sítio inibitório
- Author
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Renato Ferreira de Freitas, Sergio Emanuel Galembeck, Joao Pedro Simon Farah, and Richard Charles Garratt
- Abstract
Os inibidores não nucleosídeos da transcriptase reversa (NNRTI) são substâncias que são usadas no combate ao vírus HIV (Vírus da Imunodeficiência Humana). Quando essas moléculas se ligam a RT elas promovem uma mudança conformacional nessa enzima tornando o sítio ativo catalítico inativo. Embora os NNRTI representem um importante componente da quimioterapia anti-HIV, sua utilidade clínica está ameaçada pela emergência de vírus que apresentam mutações que os tornam resistentes aos NNRTI. Por exemplo, com a mutação Y181C a RT se torna resistente ao inibidor 9 Cl-TIBO, pertencente a classe dos NNRTI. A perda de interações do tipo ??? stacking é apontada como uma das razões para o surgimento de resistência da enzima RT frente aos NNRTI. Embora estas interações exerçam um papel relevante na ação de um inibidor, não existem estudos que buscam analisá-las baseada na mecânica quântica. Em virtude desse fato, o objetivo desse trabalho é empregar as potencialidades do uso das técnicas que analisam a função de onda, como orbitais naturais de ligação (NBO), análise populacional natural (NPA) e a densidade eletrônica, através do método AIM (átomos em moléculas), para obter uma compreensão aprofundada das interações estabilizadoras ou desestabilizadoras entre um NNRTI e os aminoácidos do sítio alostérico em contato com o inibidor. Foi escolhida para esse estudo inibidores da classe TIBO, pois essa classe de moléculas têm sido objeto de estudo em nosso laboratório, onde já foi feita a sua análise conformacional e um estudo QSAR-3D. Além disso, essas substâncias encontram-se complexadas com a enzima HIV-1 RT selvagem e também com essa enzima mutante (Y181C). Uma terceira estrutura cristalina usada no estudo foi a do inibidor 9 Cl-TIBO. Com isso as propostas desse trabalho foram: i) elucidar quais os tipos de interações não covalentes que ocorrem entre o inibidor TIBO e os aminoácidos do seu sítio ativo; ii) quais as possíveis causas da perda de atividade com a mutação Y181C; iii) tentar apontar qual a razão da maior atividade do inibidor 8 Cl-TIBO frente ao 9 Cl-TIBO. Para cumprir esses objetivos foi realizada a análise geométrica, da função de onda, utilizando os métodos NBO, NPA e da densidade eletrônica empregando o método AIM, assim como, a análise da energia de interação de inibidores da família TIBO com os aminoácidos Y181 (C181), K101, Y188 e H235. A análise geométrica dos monômeros TIBO revelou que os dois inibidores (8 e 9 Cl-TIBO) apresentam conformações diferentes. Pelos métodos NBO e AIM foi verificada a existência de interações do tipo C-H???S e C-H???Cl na 8 Cl-TIBO. Apenas a primeira interação foi observada no inibidor 9 Cl-TIBO, o que dá a esta molécula uma maior liberdade conformacional. Além disso, a sobreposição da estrutura dos dímeros TIBO/Y188 revelou que a distância entre o inibidor 8 Cl-TIBO e o aminoácido Y188 (M) é a mais curta. A análise NBO e AIM das interações intermoleculares dos dímeros TIBO/Y181 (C181) e TIBO/Y188 demonstraram que as interações dos inibidores com os aminoácidos são estabilizadas por interações hidrofóbicas do tipo van der Waals, além de ligações de hidrogênio fracas do tipo C-H???N e C-H???O. Os dímeros 8 Cl-TIBO/H235 apresentam apenas uma ligação de hidrogênio fraca do tipo C-H???O. A interação dos dímeros TIBO/K101 é estabilizada, de acordo com as análises NBO e AIM, por duas ligações de hidrogênio do tipo N-H???O e N-H???S. A primeira interação tem sido descrita em vários trabalhos, mas é a primeira vez que segunda é reportada. A análise NPA e a soma das energias eletrônicas de estabilização, ??E(2), ambas obtidas pelo método NBO, juntamente com o valor da densidade no BCP (ponto crítico de ligação), oriunda do método AIM, indicam que a mutação Y181C afeta a interação do inibidor não somente com o aminoácido na posição em que ela ocorre, mas também com os aminoácidos K101, Y188 e H235. O valor de ??E(2) para a interação do inibidor TIBO com os aminoácidos Y181 (C181), K101, Y188 e H235 indicam que o inibidor 8 Cl-TIBO apresenta uma interação mais efetiva com esses aminoácidos do que a 9 Cl-TIBO. Esse resultado é bastante interessante é mostra que ??E(2) pode ser utilizado como um parâmetro qualitativo para analisar as diferenças de atividade biológica observadas para diferentes ligantes que atuam sobre um mesmo sítio ativo. Os inibidores não nucleosídeos da transcriptase reversa (NNRTI) são substâncias que são usadas no combate ao vírus HIV (Vírus da Imunodeficiência Humana). Quando essas moléculas se ligam a RT elas promovem uma mudança conformacional nessa enzima tornando o sítio ativo catalítico inativo. Embora os NNRTI representem um importante componente da quimioterapia anti-HIV, sua utilidade clínica está ameaçada pela emergência de vírus que apresentam mutações que os tornam resistentes aos NNRTI. Por exemplo, com a mutação Y181C a RT se torna resistente ao inibidor 9 Cl-TIBO, pertencente a classe dos NNRTI. A perda de interações do tipo pi-stacking é apontada como uma das razões para o surgimento de resistência da enzima RT frente aos NNRTI. Embora estas interações exerçam um papel relevante na ação de um inibidor, não existem estudos que buscam analisá-las baseada na mecânica quântica. Em virtude desse fato, o objetivo desse trabalho é empregar as potencialidades do uso das técnicas que analisam a função de onda, como orbitais naturais de ligação (NBO), análise populacional natural (NPA) e a densidade eletrônica, através do método AIM (átomos em moléculas), para obter uma compreensão aprofundada das interações estabilizadoras ou desestabilizadoras entre um NNRTI e os aminoácidos do sítio alostérico em contato com o inibidor. Foi escolhida para esse estudo inibidores da classe TIBO, pois essa classe de moléculas têm sido objeto de estudo em nosso laboratório, onde já foi feita a sua análise conformacional e um estudo QSAR-3D. Além disso, essas substâncias encontram-se complexadas com a enzima HIV-1 RT selvagem e também com essa enzima mutante (Y181C). Uma terceira estrutura cristalina usada no estudo foi a do inibidor 9 Cl-TIBO. Com isso as propostas desse trabalho foram: i) elucidar quais os tipos de interações não covalentes que ocorrem entre o inibidor TIBO e os aminoácidos do seu sítio ativo; ii) quais as possíveis causas da perda de atividade com a mutação Y181C; iii) tentar apontar qual a razão da maior atividade do inibidor 8 Cl-TIBO frente ao 9 Cl-TIBO. Para cumprir esses objetivos foi realizada a análise geométrica, da função de onda, utilizando os métodos NBO, NPA e da densidade eletrônica empregando o método AIM, assim como, a análise da energia de interação de inibidores da família TIBO com os aminoácidos Y181 (C181), K101, Y188 e H235. A análise geométrica dos monômeros TIBO revelou que os dois inibidores (8 e 9 Cl-TIBO) apresentam conformações diferentes. Pelos métodos NBO e AIM foi verificada a existência de interações do tipo C-H???S e C-H???Cl na 8 Cl-TIBO. Apenas a primeira interação foi observada no inibidor 9 Cl-TIBO, o que dá a esta molécula uma maior liberdade conformacional. Além disso, a sobreposição da estrutura dos dímeros TIBO/Y188 revelou que a distância entre o inibidor 8 Cl-TIBO e o aminoácido Y188 (M) é a mais curta. A análise NBO e AIM das interações intermoleculares dos dímeros TIBO/Y181 (C181) e TIBO/Y188 demonstraram que as interações dos inibidores com os aminoácidos são estabilizadas por interações hidrofóbicas do tipo van der Waals, além de ligações de hidrogênio fracas do tipo C-H???N e C-H???O. Os dímeros 8 Cl-TIBO/H235 apresentam apenas uma ligação de hidrogênio fraca do tipo C-H???O. A interação dos dímeros TIBO/K101 é estabilizada, de acordo com as análises NBO e AIM, por duas ligações de hidrogênio do tipo N-H???O e N-H???S. A primeira interação tem sido descrita em vários trabalhos, mas é a primeira vez que segunda é reportada. A análise NPA e a soma das energias eletrônicas de estabilização, ambas obtidas pelo método NBO, juntamente com o valor da densidade no BCP (ponto crítico de ligação), oriunda do método AIM, indicam que a mutação Y181C afeta a interação do inibidor não somente com o aminoácido na posição em que ela ocorre, mas também com os aminoácidos K101, Y188 e H235. O valor das energias eletrônicas de estabilização para a interação do inibidor TIBO com os aminoácidos Y181 (C181), K101, Y188 e H235 indicam que o inibidor 8 Cl-TIBO apresenta uma interação mais efetiva com esses aminoácidos do que a 9 Cl-TIBO. Esse resultado é bastante interessante é mostra que energias eletrônicas de estabilização pode ser utilizado como um parâmetro qualitativo para analisar as diferenças de atividade biológica observadas para diferentes ligantes que atuam sobre um mesmo sítio ativo
- Published
- 2006
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