1
|
Banasik M, Napolitano V, Blat A, Abdulkarim K, Plewka J, Czaplewski C, Gieldon A, Kozak M, Wladyka B, Popowicz G, Dubin G. Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma. Int J Biol Macromol 2024:135510. [PMID: 39304044 DOI: 10.1016/j.ijbiomac.2024.135510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/22/2024]
Abstract
Peroxisomal protein import has been identified as a valid target in trypanosomiases, an important health threat in Central and South America. The importomer is built of multiple peroxins (Pex) and structural characterization of these proteins facilitates rational inhibitor development. We report crystal structures of the Trypanosoma brucei and T. cruzi tetratricopeptide repeat domain (TPR) of the cytoplasmic peroxisomal targeting signal 1 (PTS1) receptor Pex5. The structure of the TPR domain of TbPex5 represents an apo-form of the receptor which, together with the previously determined structure of the complex of TbPex5 TPR and PTS1 demonstrate significant receptor dynamics associated with signal peptide recognition. The structure of the complex of TPR domain of TcPex5 with PTS1 provided in this study details the molecular interactions that guide signal peptide recognition at the atomic level in the pathogenic species currently perceived as the most relevant among Trypanosoma. Small - angle X - ray scattering (SAXS) data obtained in solution supports the crystallographic findings on the compaction of the TPR domains of TbPex5 and TcPex5 upon interaction with the cargo.
Collapse
Affiliation(s)
- Michal Banasik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Artur Blat
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Karim Abdulkarim
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Community Health, College of Health Technology, Cihan University-Erbil, 100 Street, 44001 Erbil, Kurdistan Region, Iraq; Department of Biology, College of Science, Salahaddin University-Erbil, Kirkuk Road, 44002 Erbil, Kurdistan Region, Iraq
| | - Jacek Plewka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Maciej Kozak
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland; National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, 30-392 Kraków, Poland
| | - Benedykt Wladyka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | | | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| |
Collapse
|
2
|
Rogacheva E, Kraeva L, Lukin A, Vinogradova L, Komarova K, Chudinov M, Gureev M, Chupakhin E. 5-Nitrofuran-Tagged Oxazolyl Pyrazolopiperidines: Synthesis and Activity against ESKAPE Pathogens. Molecules 2023; 28:6491. [PMID: 37764267 PMCID: PMC10537382 DOI: 10.3390/molecules28186491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
A series of eight 5-nitrofuran-tagged oxazolyl tetrahydropyrazolopyridines (THPPs) has been prepared in six stages with excellent regioselectivity. The testing of these compounds against pathogens of the ESKAPE panel showed a good activity of lead compound 1-(2-methoxyethyl)-5-(5-nitro-2-furoyl)-3-(1,3-oxazol-5-yl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c] pyridine (13g), which is superior to nitrofurantoin. These results confirmed the benefit of combining a THPP scaffold with a nitrofuran warhead. Certain structure-activity relationships were established in the course of this study which were rationalized by the induced-fit docking experiments in silico.
Collapse
Affiliation(s)
- Elizaveta Rogacheva
- Pasteur Institute of Epidemiology and Microbiology, Saint Petersburg 197101, Russia; (E.R.)
| | - Lyudmila Kraeva
- Pasteur Institute of Epidemiology and Microbiology, Saint Petersburg 197101, Russia; (E.R.)
| | - Alexey Lukin
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Moscow 119454, Russia
| | - Lyubov Vinogradova
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Moscow 119454, Russia
| | - Kristina Komarova
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Moscow 119454, Russia
| | - Mikhail Chudinov
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Moscow 119454, Russia
| | - Maxim Gureev
- Laboratory of Bio- and Chemoinformatics, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Molecular Modeling Laboratory, HSE University, Saint-Petersburg 190121, Russia
| | - Evgeny Chupakhin
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236041, Russia
| |
Collapse
|
3
|
Marciniak M, Mróz P, Napolitano V, Kalel VC, Fino R, Pykacz E, Schliebs W, Plettenburg O, Erdmann R, Sattler M, Popowicz GM, Dawidowski M. Development of novel PEX5-PEX14 protein-protein interaction (PPI) inhibitors based on an oxopiperazine template. Eur J Med Chem 2023; 258:115587. [PMID: 37406382 DOI: 10.1016/j.ejmech.2023.115587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Protein-protein interactions (PPIs) constitute an important but challenging class of molecular targets for small molecules. The PEX5-PEX14 PPI has been shown to play a critical role in glycosome biogenesis and its disruption impairs the metabolism in Trpanosoma parasites, eventually leading to their death. Therefore, this PPI is a potential molecular target for new drugs against diseases caused by Trypanosoma infections. Here, we report a new class of peptidomimetic scaffolds to target the PEX5-PEX14 PPI. The molecular design was based on an oxopiperazine template for the α-helical mimetics. A structural simplification along with modifications of the central oxopiperazine scaffold and addressing the lipophilic interactions led to the development of peptidomimetics that inhibit PEX5-TbPEX14 PPI and display cellular activity against T. b. brucei. This approach provides an alternative approach towards the development of trypanocidal agents and may be generally useful for the design of helical mimetics as PPI inhibitors.
Collapse
Affiliation(s)
- Monika Marciniak
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Piotr Mróz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Valeria Napolitano
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Roberto Fino
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Emilia Pykacz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany; Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1b, Hannover, 30167, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland.
| |
Collapse
|
4
|
Gopalswamy M, Zheng C, Gaussmann S, Kooshapur H, Hambruch E, Schliebs W, Erdmann R, Antes I, Sattler M. Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14. Biol Chem 2023; 404:179-194. [PMID: 36437542 DOI: 10.1515/hsz-2022-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
Abstract
The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity. Human PEX5 possesses eight of these conserved motifs distributed within its 320-residue disordered N-terminal region. Here, we combine biophysical (ITC, NMR, CD), biochemical and computational methods to characterize the recognition of these (di)aromatic peptides motifs and identify key features that are recognized by PEX14. Notably, the eight motifs present in human PEX5 exhibit distinct affinities and energetic contributions for the interaction with the PEX14 NTD. Computational docking and analysis of the interactions of the (di)aromatic motifs identify the specific amino acids features that stabilize a helical conformation of the peptide ligands and mediate interactions with PEX14 NTD. We propose a refined consensus motif ExWΦxE(F/Y)Φ for high affinity binding to the PEX14 NTD and discuss conservation of the (di)aromatic peptide recognition by PEX14 in other species.
Collapse
Affiliation(s)
- Mohanraj Gopalswamy
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Chen Zheng
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Stefan Gaussmann
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hamed Kooshapur
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Eva Hambruch
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Iris Antes
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| |
Collapse
|
5
|
Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma. Eur J Med Chem 2022; 243:114778. [DOI: 10.1016/j.ejmech.2022.114778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
|
6
|
Jiang ZY, Huang ZY, Yang H, Zhou L, Li QH, Zhao ZG. Cs 2CO 3 catalyzed direct aza-Michael addition of azoles to α,β-unsaturated malonates. RSC Adv 2022; 12:19265-19269. [PMID: 35865588 PMCID: PMC9248005 DOI: 10.1039/d2ra02314h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022] Open
Abstract
A highly efficient method for the synthesis of azole derivatives via a direct aza-Michael addition of azoles to α,β-unsaturated malonates using Cs2CO3 as a catalyst, has been successfully developed. A series of azole derivatives have been obtained in up to 94% yield and the reaction could be amplified to gram scale in excellent yield in the presence of 10 mol% of Cs2CO3. A highly efficient method for the synthesis of azole derivatives via a direct aza-Michael addition of azoles to α,β-unsaturated malonates has been successfully developed. A series of azole derivatives have been obtained in up to 94% yield.![]()
Collapse
Affiliation(s)
- Zi-Yu Jiang
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| | - Zhe-Yao Huang
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| | - Hong Yang
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| | - Lin Zhou
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| | - Qing-Han Li
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| | - Zhi-Gang Zhao
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University Chengdu 610041 P. R. China
| |
Collapse
|
7
|
Li M, Gaussmann S, Tippler B, Ott J, Popowicz GM, Schliebs W, Sattler M, Erdmann R, Kalel VC. Novel Trypanocidal Inhibitors that Block Glycosome Biogenesis by Targeting PEX3-PEX19 Interaction. Front Cell Dev Biol 2022; 9:737159. [PMID: 34988071 PMCID: PMC8721105 DOI: 10.3389/fcell.2021.737159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Human pathogenic trypanosomatid parasites harbor a unique form of peroxisomes termed glycosomes that are essential for parasite viability. We and others previously identified and characterized the essential Trypanosoma brucei ortholog TbPEX3, which is the membrane-docking factor for the cytosolic receptor PEX19 bound to the glycosomal membrane proteins. Knockdown of TbPEX3 expression leads to mislocalization of glycosomal membrane and matrix proteins, and subsequent cell death. As an early step in glycosome biogenesis, the PEX3–PEX19 interaction is an attractive drug target. We established a high-throughput assay for TbPEX3–TbPEX19 interaction and screened a compound library for small-molecule inhibitors. Hits from the screen were further validated using an in vitro ELISA assay. We identified three compounds, which exhibit significant trypanocidal activity but show no apparent toxicity to human cells. Furthermore, we show that these compounds lead to mislocalization of glycosomal proteins, which is toxic to the trypanosomes. Moreover, NMR-based experiments indicate that the inhibitors bind to PEX3. The inhibitors interfering with glycosomal biogenesis by targeting the TbPEX3–TbPEX19 interaction serve as starting points for further optimization and anti-trypanosomal drug development.
Collapse
Affiliation(s)
- Mengqiao Li
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan Gaussmann
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Bettina Tippler
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Julia Ott
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
8
|
Fino R, Lenhart D, Kalel VC, Softley CA, Napolitano V, Byrne R, Schliebs W, Dawidowski M, Erdmann R, Sattler M, Schneider G, Plettenburg O, Popowicz GM. Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2,3,4,5-Tetrahydrobenzo[F][1,4]oxazepines as Potential New Trypanocidal Agents. J Chem Inf Model 2021; 61:5256-5268. [PMID: 34597510 DOI: 10.1021/acs.jcim.1c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
African and American trypanosomiases are estimated to affect several million people across the world, with effective treatments distinctly lacking. New, ideally oral, treatments with higher efficacy against these diseases are desperately needed. Peroxisomal import matrix (PEX) proteins represent a very interesting target for structure- and ligand-based drug design. The PEX5-PEX14 protein-protein interface in particular has been highlighted as a target, with inhibitors shown to disrupt essential cell processes in trypanosomes, leading to cell death. In this work, we present a drug development campaign that utilizes the synergy between structural biology, computer-aided drug design, and medicinal chemistry in the quest to discover and develop new potential compounds to treat trypanosomiasis by targeting the PEX14-PEX5 interaction. Using the structure of the known lead compounds discovered by Dawidowski et al. as the template for a chemically advanced template search (CATS) algorithm, we performed scaffold-hopping to obtain a new class of compounds with trypanocidal activity, based on 2,3,4,5-tetrahydrobenzo[f][1,4]oxazepines chemistry. The initial compounds obtained were taken forward to a first round of hit-to-lead optimization by synthesis of derivatives, which show activities in the range of low- to high-digit micromolar IC50 in the in vitro tests. The NMR measurements confirm binding to PEX14 in solution, while immunofluorescent microscopy indicates disruption of protein import into the glycosomes, indicating that the PEX14-PEX5 protein-protein interface was successfully disrupted. These studies result in development of a novel scaffold for future lead optimization, while ADME testing gives an indication of further areas of improvement in the path from lead molecules toward a new drug active against trypanosomes.
Collapse
Affiliation(s)
- Roberto Fino
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Dominik Lenhart
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute of Medicinal Chemistry, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz Universität Hannover, Schneiderberg 1b, 30167 Hannover, Germany
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Charlotte A Softley
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Valeria Napolitano
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ryan Byrne
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz Universität Hannover, Schneiderberg 1b, 30167 Hannover, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Biomolecular NMR, Bayerisches NMR Zentrum and Center for Integrated Protein Science Munich at Chemistry Department, Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| |
Collapse
|
9
|
Influence of N-Methylation and Conformation on Almiramide Anti-Leishmanial Activity. Molecules 2021; 26:molecules26123606. [PMID: 34204673 PMCID: PMC8231256 DOI: 10.3390/molecules26123606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
The almiramide N-methylated lipopeptides exhibit promising activity against trypanosomatid parasites. A structure–activity relationship study has been performed to examine the influences of N-methylation and conformation on activity against various strains of leishmaniasis protozoan and on cytotoxicity. The synthesis and biological analysis of twenty-five analogs demonstrated that derivatives with a single methyl group on either the first or fifth residue amide nitrogen exhibited greater activity than the permethylated peptides and relatively high potency against resistant strains. Replacement of amino amide residues in the peptide, by turn inducing α amino γ lactam (Agl) and N-aminoimidazalone (Nai) counterparts, reduced typically anti-parasitic activity; however, peptide amides possessing Agl residues at the second residue retained significant potency in the unmethylated and permethylated series. Systematic study of the effects of methylation and turn geometry on anti-parasitic activity indicated the relevance of an extended conformer about the central residues, and conformational mobility by tertiary amide isomerization and turn geometry at the extremities of the active peptides.
Collapse
|
10
|
Xue J, Zhang Z, Hu H. Prostate Cancer Growth Inhibition by 1-(3,5-Dimethylphenyl)-6-methyl-1H-pyrazolo[4,3-c]pyridin-4(5H)-one via Down-regulation of Phosphorylation PI3K/AKT and STA3/JAK2. DOKL BIOCHEM BIOPHYS 2020; 495:347-353. [PMID: 33368049 DOI: 10.1134/s160767292006006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study, 1-(3,5-dimethylphenyl)-6-methyl-1H-pyrazolo[4,3-c]pyridin-4 (5H)-one (DPMPP) was investigated as an antiproliferative agent for prostate cancer cells and the mechanism of its action was studied. Cell lines 22Rv1 and SGC‑7901 were used as in vitro models of prostate cancer. The DPMPP treatment inhibited proliferation of 22Rv1 and SGC‑7901 cells in dose-depended manner. The viability of 22Rv1 and SGC‑7901 cells was reduced to 21 and 19%, respectively after treatment with 32 µM DPMPP. In DPMPP treated (16 µM) 22Rv1 and SGC‑7901 cells apoptosis increased to 62.78 and 68.51%, respectively. Moreover, DPMPP treatment caused cell cycle arrest in S phase and inhibition of PI3K/AKT activation. In the same time ROS production showed elevation and MMP (Matrix MetalloProteinase) decreased in the cells. Apparently DPMPP induces cytotoxicity through induction of oxidative response and apoptosis in prostate cancer cells in vitro. The PI3K/Akt/ERK phosphorylation was inhibited, while p21 and p53, death receptor, expression was promoted by DPMPP treatment. Therefore, DPMPP has a potential to be used as a therapeutic agent for treatment of prostate cancer.
Collapse
Affiliation(s)
- Jingxin Xue
- Department of Urology, Affiliated Jinan Third Hospital of Jining Medical University, Jining Medical University, 250132, Jinan, Shandong Province, China.
| | - Zhenwei Zhang
- Department of Urology, Affiliated Jinan Third Hospital of Jining Medical University, Jining Medical University, 250132, Jinan, Shandong Province, China
| | - Heyi Hu
- Department of Urology, Affiliated Jinan Third Hospital of Jining Medical University, Jining Medical University, 250132, Jinan, Shandong Province, China
| |
Collapse
|
11
|
Mathieu G, Patel H, Lebel H. Convenient Continuous Flow Synthesis of N-Methyl Secondary Amines from Alkyl Mesylates and Epoxides. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Gary Mathieu
- Department of Chemistry and Center in Green Chemistry and Catalysis (CGCC), Université de Montréal, P.O. Box 6128, Station Downtown, Montréal, QC H3C 3J7, Canada
| | - Heena Patel
- Department of Chemistry and Center in Green Chemistry and Catalysis (CGCC), Université de Montréal, P.O. Box 6128, Station Downtown, Montréal, QC H3C 3J7, Canada
| | - Hélène Lebel
- Department of Chemistry and Center in Green Chemistry and Catalysis (CGCC), Université de Montréal, P.O. Box 6128, Station Downtown, Montréal, QC H3C 3J7, Canada
| |
Collapse
|
12
|
Ratkova EL, Dawidowski M, Napolitano V, Dubin G, Fino R, Ostertag MS, Sattler M, Popowicz G, Tetko IV. Water envelope has a critical impact on the design of protein–protein interaction inhibitors. Chem Commun (Camb) 2020; 56:4360-4363. [DOI: 10.1039/c9cc07714f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We show that a water envelope network plays a critical role in protein–protein interactions (PPI).
Collapse
Affiliation(s)
- Ekaterina L. Ratkova
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Medicinal Chemistry, Cardiovascular, Renal and Metabolic Diseases
| | - Maciej Dawidowski
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Department of Drug Technology and Pharmaceutical Biotechnology
| | - Valeria Napolitano
- Faculty of Biochemistry, Biophysics and Biotechnology and Malopolska Centre of Biotechnology
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology and Malopolska Centre of Biotechnology
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Roberto Fino
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Michael S. Ostertag
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Michael Sattler
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR
| | - Grzegorz Popowicz
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
| | - Igor V. Tetko
- Institute of Structural Biology
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH)
- 85764 Neuherberg
- Germany
- BIGCHEM GmbH
| |
Collapse
|