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Abdullaziz MA, Takada S, Illarionov B, Pessanha de Carvalho L, Sakamoto Y, Höfmann S, Knak T, Kiffe-Delf AL, Mazzone F, Pfeffer K, Kalscheuer R, Bacher A, Held J, Fischer M, Tanaka N, Kurz T. Reverse N-Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target a Previously Unknown Subpocket of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase (DXR). ACS Infect Dis 2024; 10:1739-1752. [PMID: 38647213 DOI: 10.1021/acsinfecdis.4c00100] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Reverse analogs of the phosphonohydroxamic acid antibiotic fosmidomycin are potent inhibitors of the nonmevalonate isoprenoid biosynthesis enzyme 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR, IspC) of Plasmodium falciparum. Some novel analogs with large phenylalkyl substituents at the hydroxamic acid nitrogen exhibit nanomolar PfDXR inhibition and potent in vitro growth inhibition of P. falciparum parasites coupled with good parasite selectivity. X-ray crystallographic studies demonstrated that the N-phenylpropyl substituent of the newly developed lead compound 13e is accommodated in a subpocket within the DXR catalytic domain but does not reach the NADPH binding pocket of the N-terminal domain. As shown for reverse carba and thia analogs, PfDXR selectively binds the S-enantiomer of the new lead compound. In addition, some representatives of the novel inhibitor subclass are nanomolar Escherichia coli DXR inhibitors, whereas the inhibition of Mycobacterium tuberculosis DXR is considerably weaker.
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Affiliation(s)
- Mona A Abdullaziz
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstr. 1, 40225 Düsseldorf, Germany
- National Research Centre (NRC), 33 El Buhouth St, Ad Doqi, Dokki, Cairo 12622, Egypt
| | - Sana Takada
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Boris Illarionov
- Hamburg School of Food Science, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Lais Pessanha de Carvalho
- Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstr. 27, 72074 Tübingen, Germany
| | - Yasumitsu Sakamoto
- School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Stefan Höfmann
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Talea Knak
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Anna-Lene Kiffe-Delf
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Flaminia Mazzone
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, University Hospital Düsseldorf, Germany, 40225 Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, University Hospital Düsseldorf, Germany, 40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Adelbert Bacher
- Hamburg School of Food Science, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- TUM School of Natural Sciences, Technical University of Munich, Boltzmannstr. 10, 85748 Garching, Germany
| | - Jana Held
- Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstr. 27, 72074 Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, 72074 Tübingen, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nobutada Tanaka
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Thomas Kurz
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Yu MC, Yang F, Ding XY, Sun NN, Jiang ZY, Huang YF, Yan YR, Zhu C, Xie Q, Chen ZF, Guo SQ, Jiang HL, Chen KX, Luo C, Luo XM, Chen SJ, Wang YH. Crystallography-guided discovery of carbazole-based retinoic acid-related orphan receptor gamma-t (RORγt) modulators: insights into different protein behaviors with "short" and "long" inverse agonists. Acta Pharmacol Sin 2021; 42:1524-1534. [PMID: 33239687 PMCID: PMC8379218 DOI: 10.1038/s41401-020-00552-w] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
A series of 6-substituted carbazole-based retinoic acid-related orphan receptor gamma-t (RORγt) modulators were discovered through 6-position modification guided by insights from the crystallographic profiles of the "short" inverse agonist 6. With the increase in the size of the 6-position substituents, the "short" inverse agonist 6 first reversed its function to agonists and then to "long" inverse agonists. The cocrystal structures of RORγt complexed with the representative "short" inverse agonist 6 (PDB: 6LOB), the agonist 7d (PDB: 6LOA) and the "long" inverse agonist 7h (PDB: 6LO9) were revealed by X-ray analysis. However, minor differences were found in the binding modes of "short" inverse agonist 6 and "long" inverse agonist 7h. To further reveal the molecular mechanisms of different RORγt inverse agonists, we performed molecular dynamics simulations and found that "short" or "long" inverse agonists led to different behaviors of helixes H11, H11', and H12 of RORγt. The "short" inverse agonist 6 destabilizes H11' and dislocates H12, while the "long" inverse agonist 7h separates H11 and unwinds H12. The results indicate that the two types of inverse agonists may behave differently in downstream signaling, which may help identify novel inverse agonists with different regulatory mechanisms.
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Affiliation(s)
- Ming-Cheng Yu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Feng Yang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Yu Ding
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Nan-Nan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zheng-Yuan Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ya-Fei Huang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu-Rong Yan
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Chen Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Fudan Zhangjiang Institute, Shanghai, 201203, China
| | - Zhi-Feng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Si-Qi Guo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hua-Liang Jiang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Kai-Xian Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Cheng Luo
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Xiao-Min Luo
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Shi-Jie Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Yong-Hui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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Guzik K, Tomala M, Muszak D, Konieczny M, Hec A, Błaszkiewicz U, Pustuła M, Butera R, Dömling A, Holak TA. Development of the Inhibitors that Target the PD-1/PD-L1 Interaction-A Brief Look at Progress on Small Molecules, Peptides and Macrocycles. Molecules 2019; 24:E2071. [PMID: 31151293 DOI: 10.3390/molecules24112071] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [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: 05/13/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 01/22/2023] Open
Abstract
Cancer immunotherapy based on antibodies targeting the immune checkpoint PD-1/PD-L1 pathway has seen unprecedented clinical responses and constitutes the new paradigm in cancer therapy. The antibody-based immunotherapies have several limitations such as high production cost of the antibodies or their long half-life. Small-molecule inhibitors of the PD-1/PD-L1 interaction have been highly anticipated as a promising alternative or complementary therapeutic to the monoclonal antibodies (mAbs). Currently, the field of developing anti-PD-1/PD-L1 small-molecule inhibitors is intensively explored. In this paper, we review anti-PD-1/PD-L1 small-molecule and peptide-based inhibitors and discuss recent structural and preclinical/clinical aspects of their development. Discovery of the therapeutics based on small-molecule inhibitors of the PD-1/PD-L1 interaction represents a promising but challenging perspective in cancer treatment.
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van Haren MJ, Marechal N, Troffer-Charlier N, Cianciulli A, Sbardella G, Cavarelli J, Martin NI. Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1. Proc Natl Acad Sci U S A 2017; 114:3625-30. [PMID: 28330993 DOI: 10.1073/pnas.1618401114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics. These constructs were found to be potent CARM1 inhibitors and also formed stable complexes with the enzyme. High-resolution crystal structures of CARM1 in complex with these compounds confirm a mode of binding that is indeed reflective of the transition state at the CARM1 active site. Given the transient nature of PRMT-substrate complexes, such transition state mimics represent valuable chemical tools for structural studies aimed at deciphering the regulation of arginine methylation mediated by the family of arginine methyltransferases.
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Olsson RI, Xue Y, von Berg S, Aagaard A, McPheat J, Hansson EL, Bernström J, Hansson P, Jirholt J, Grindebacke H, Leffler A, Chen R, Xiong Y, Ge H, Hansson TG, Narjes F. Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor RORγ. ChemMedChem 2015; 11:207-16. [PMID: 26553345 DOI: 10.1002/cmdc.201500432] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 09/21/2015] [Indexed: 12/20/2022]
Abstract
RORγt, an isoform of the retinoic acid-related orphan receptor gamma (RORc, RORγ), has been identified as the master regulator of T-helper 17 (TH 17) cell function and development, making it an attractive target for the treatment of autoimmune diseases. Validation for this target comes from antibodies targeting interleukin-17 (IL-17), the signature cytokine produced by TH 17 cells, which have shown impressive results in clinical trials. Through focused screening of our compound collection, we identified a series of N-sulfonylated benzoxazepines, which displayed micromolar affinity for the RORγ ligand-binding domain (LBD) in a radioligand binding assay. Optimization of these initial hits resulted in potent binders, which dose-dependently decreased the ability of the RORγ-LBD to interact with a peptide derived from steroid receptor coactivator 1, and inhibited the release of IL-17 secretion from isolated and cultured human TH 17 cells with nanomolar potency. A cocrystal structure of inverse agonist 15 (2-chloro-6-fluoro-N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3,4,5-tetrahydro-1,4-benzoxazepin-7-yl)benzamide) bound to the RORγ-LBD illustrated that both hydrophobic interactions, leading to an induced fit around the substituted benzamide moiety of 15, as well as a hydrogen bond from the amide NH to His479 seemed to be important for the mechanism of action. This structure is compared with the structure of agonist 25 (N-(2-fluorophenyl)-4-[(4-fluorophenyl)sulfonyl]-2,3,4,5-tetrahydro-1,4-benzoxazepin-6-amine ) and structures of other known RORγ modulators.
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Affiliation(s)
- Roine I Olsson
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Yafeng Xue
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Stefan von Berg
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Anna Aagaard
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Jane McPheat
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Eva L Hansson
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Jenny Bernström
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Pia Hansson
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Johan Jirholt
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Hanna Grindebacke
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Agnes Leffler
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Rongfeng Chen
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Yao Xiong
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Hongbin Ge
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Thomas G Hansson
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Frank Narjes
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden.
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