1
|
Umumararungu T, Gahamanyi N, Mukiza J, Habarurema G, Katandula J, Rugamba A, Kagisha V. Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review. Amino Acids 2024; 56:50. [PMID: 39182198 PMCID: PMC11345334 DOI: 10.1007/s00726-024-03410-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/06/2024] [Indexed: 08/27/2024]
Abstract
Proline is a unique amino acid in that its side-chain is cyclised to the backbone, thus giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline forms two well-characterized helical structures: a left-handed polyproline helix (PPII) and a right-handed polyproline helix (PPI). Usually, sequences made only of prolyl residues are in PPII conformation, but even sequences not rich in proline but which are rich in glycine, lysine, glutamate, or aspartate have also a tendency to form PPII helices. Currently, the only way to study unambiguously PPII structure in solution is to use spectroscopies based on optical activity such as circular dichroism, vibrational circular dichroism and Raman optical activity. The importance of the PPII structure is emphasized by its ubiquitous presence in different organisms from yeast to human beings where proline-rich motifs and their binding domains are believed to be involved in vital biological processes. Some of the domains that are bound by proline-rich motifs include SH3 domains, WW domains, GYF domains and UEV domains, etc. The PPII structure has been demonstrated to be essential to biological activities such as signal transduction, transcription, cell motility, and immune response.
Collapse
Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
- Rwanda Biomedical Center, Microbiology Unit, National Reference Laboratory, Kigali, Rwanda
| | - Janvier Mukiza
- Rwanda Food and Drugs Authority, Nyarutarama Plaza, KG 9 Avenue, Kigali, Rwanda
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Alexis Rugamba
- Department of Biochemistry, Molecular Biology and Genetics, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Vedaste Kagisha
- Department of Pharmaceuticals and Biomolecules Analysis, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| |
Collapse
|
2
|
Aquilina JM, Banerjee A, Morais GN, Chen S, Smith MW. Total Synthesis of (-)-Rauvomine B via a Strain-Promoted Intramolecular Cyclopropanation. J Am Chem Soc 2024; 146:22047-22055. [PMID: 39042605 DOI: 10.1021/jacs.4c07669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
We describe the first total synthesis of the unusual cyclopropane-containing indole alkaloid (-)-rauvomine B via a strategy centered upon intramolecular cyclopropanation of a tetracyclic N-sulfonyltriazole. Preparation of this precursor evolved through two generations of synthesis, with the ultimately successful route involving a palladium-catalyzed stereospecific allylic amination, a cis-selective Pictet-Spengler reaction, and ring-closing metathesis as important bond-forming reactions. The key cyclopropanation step was found to be highly dependent on the structure and conformational strain of the indoloquinolizidine N-sulfonyltriazole precursor, the origins of which are explored computationally through DFT studies. Overall, our synthesis proceeds in 11 total steps and 2.4% yield from commercial materials.
Collapse
Affiliation(s)
- Jake M Aquilina
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Ankush Banerjee
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Gabriel N Morais
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland St., Oberlin, Ohio 44074, United States
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland St., Oberlin, Ohio 44074, United States
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States
| |
Collapse
|
3
|
Engelhardt PM, Strippel J, Albat D, Chiha S, Rojas Pión J, Plein L, Kühne R, Müller M, Schmalz HG. C-Terminal Decarboxylation of Proline-Derived Building Blocks for Protein-Binding Peptides. Chemistry 2024; 30:e202401678. [PMID: 38770931 DOI: 10.1002/chem.202401678] [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: 04/29/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
Using a set of conformationally restricted Proline-derived Modules (ProMs), our group has recently succeeded in developing inhibitors for the enabled/vasodilator-stimulated phosphoprotein homology 1 (EVH1) domain, which is a key mediator of cell migration and plays an important role in tumor metastasis. While these (formally) pentapeptidic compounds show nanomolecular binding affinities towards EVH1, their drug-like properties and cell permeability need to be further optimized before they can be clinically tested as therapeutic agents against metastasis. In this study, we sought to improve these properties by removing the C-terminal carboxylic acid function of our peptoids, either by late-stage decarboxylation or by direct synthesis. For late-stage decarboxylation of ProM-like systems, a method for reductive halo decarboxylation was optimized and applied to several proline-derived substrates. In this way, a series of new decarboxy ProMs suitable as building blocks for decarboxy EVH1 inhibitors were obtained. In addition, we incorporated decarboxy-ProM-1 into the pentapeptide-like compound Ac[2ClF][ProM-2][Decarb-ProM-1], which showed similar affinity towards EVH1 as the methyl ester derivative (Ac[2Cl-F][ProM-2][ProM1]OMe). However, despite better calculated drug-like properties, this compound did not inhibit chemotaxis in a cellular assay.
Collapse
Affiliation(s)
- Pascal M Engelhardt
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Julian Strippel
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Dominik Albat
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | - Slim Chiha
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | | | - Laura Plein
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Ronald Kühne
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Matthias Müller
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | - Hans-Günther Schmalz
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| |
Collapse
|
4
|
Klein MT, Krause BM, Neudörfl JM, Kühne R, Schmalz HG. Design and synthesis of a tetracyclic tripeptide mimetic frozen in a polyproline type II (PP2) helix conformation. Org Biomol Chem 2022; 20:9368-9377. [PMID: 36385673 DOI: 10.1039/d2ob01857h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A synthesis of the new tetracyclic scaffold ProM-19, which represents a XPP tripeptide unit frozen in a PPII helix conformation, was developed. As a key building block, N-Boc-protected ethyl (1S,3S,4R)-2-azabicyclo[2.2.1]hept-5-ene-2-carboxylate was prepared through a diastereoselective aza-Diels-Alder reaction and subsequent hydrogenolytic removal of the chiral N-1-phenylethyl substituent under temporary protection of the double bond through dihydroxylation and reconstitution by Corey-Winter olefination. The target compound Boc-[ProM-19]-OMe was then prepared via subsequent peptide coupling and Ru-catalyzed ring-closing metathesis steps employing (S)-N-Boc-allylgylcine and cis-5-vinyl-proline methyl ester as additional building blocks. In addition, Ac-[2-Cl-Phe]-[Pro]-[ProM-19]-OMe was prepared by solution phase peptide synthesis as a potential ligand for the ena-VASP EVH1 domain.
Collapse
Affiliation(s)
- Marco T Klein
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Bernhard M Krause
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Jörg-Martin Neudörfl
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| | - Ronald Kühne
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Hans-Günther Schmalz
- University of Cologne, Department of Chemistry, Greinstrasse 4, 50939 Köln, Germany.
| |
Collapse
|
5
|
Albat D, Köcher A, Witt J, Schmalz HG. On the Asymmetric Ir‐catalyzed N‐Allylation of Amino Acid Esters: Improved Selectivities through Structural Variation of the Chiral Phosphoramidite Ligand. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dominik Albat
- University of Cologne: Universitat zu Koln Department of Chemistry Koeln GERMANY
| | - Alicia Köcher
- University of Cologne: Universitat zu Koln Department of Chemistry Koel GERMANY
| | - Julia Witt
- University of Cologne: Universitat zu Koln Department of Chemistry Koeln GERMANY
| | | |
Collapse
|
6
|
Zhou Y, Chen H, Lei P, Gui C, Wang H, Yan Q, Wang W, Chen F. Palladium-catalyzed base- and solvent-controlled chemoselective allylation of amino acids with allylic carbonates. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Albat D, Reiher M, Neudörfl J, Schmalz H. Improved Synthesis of MediPhos Ligands and Their Use in the Pd‐Catalyzed Enantioselective N‐Allylation of Glycine Esters. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dominik Albat
- Department of Chemistry University of Cologne Greinstrasse 4 50939 Koeln Germany
| | - Martin Reiher
- Department of Chemistry University of Cologne Greinstrasse 4 50939 Koeln Germany
| | - Jörg‐Martin Neudörfl
- Department of Chemistry University of Cologne Greinstrasse 4 50939 Koeln Germany
| | - Hans‐Günther Schmalz
- Department of Chemistry University of Cologne Greinstrasse 4 50939 Koeln Germany
| |
Collapse
|
8
|
Albat D, Neudörfl J, Schmalz H. A General Stereocontrolled Synthesis of Opines through Asymmetric Pd‐Catalyzed N‐Allylation of Amino Acid Esters. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Dominik Albat
- Department of Chemistry University of Cologne Greinstrasse 4 50939 Köln Germany
| | | | | |
Collapse
|
9
|
Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells. Proc Natl Acad Sci U S A 2020; 117:29684-29690. [PMID: 33184177 PMCID: PMC7703624 DOI: 10.1073/pnas.2007213117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein–protein interactions mediated by proline-rich motifs are involved in regulation of many important signaling cascades. These motifs belong to the most abundant recognition motifs in the eukaryotic genome and preferentially adopt a left-handed polyproline helix II, a secondary structure element that has been notoriously difficult to mimic with small molecules. Here, we present a structure-guided design effort yielding a toolkit of chemical entities that enables rational construction of selective small molecule inhibitors for these protein domains. We succeeded in developing an inhibitor for the Ena/VASP protein family that is active in vivo and reduces extravasation of invasive breast cancer cells in a zebrafish model. Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein–protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor (Kd=120 nM,MW=734 Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein–protein interaction involved in actin filament processing and cell migration.
Collapse
|
10
|
Dohmen S, Reiher M, Albat D, Akyol S, Barone M, Neudörfl J, Kühne R, Schmalz H. Pd-Catalyzed Asymmetric N-Allylation of Amino Acid Esters with Exceptional Levels of Catalyst Control: Stereo-Divergent Synthesis of ProM-15 and Related Bicyclic Dipeptide Mimetics. Chemistry 2020; 26:3049-3053. [PMID: 31961029 PMCID: PMC7078984 DOI: 10.1002/chem.202000307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Indexed: 01/09/2023]
Abstract
A general and powerful method for the stereo‐controlled Pd‐catalyzed N‐allylation of amino acid esters is reported, as a previously largely unsolved synthetic challenge. Employing a new class of tartaric acid‐derived C2‐symmetric chiral diphosphane ligands the developed asymmetric amination protocol allows the conversion of various amino acid esters to the N‐allylated products with highest levels of enantio‐ or diastereoselectivity in a fully catalyst‐controlled fashion and predictable configuration. Remarkably, the in situ generated catalysts also exhibit outstanding levels of activity (ligand acceleration). The usefulness of the method was demonstrated in the stereo‐divergent synthesis of a set of new conformationally defined dipeptide mimetics, which represent new modular building blocks for the development of peptide‐inspired bioactive compounds.
Collapse
Affiliation(s)
- Stephan Dohmen
- Department of ChemistryUniversity of CologneGreinstrasse 450939KölnGermany
| | - Martin Reiher
- Department of ChemistryUniversity of CologneGreinstrasse 450939KölnGermany
| | - Dominik Albat
- Department of ChemistryUniversity of CologneGreinstrasse 450939KölnGermany
| | - Sema Akyol
- Department of ChemistryUniversity of CologneGreinstrasse 450939KölnGermany
| | - Matthias Barone
- Leibniz-Institut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | | | - Ronald Kühne
- Leibniz-Institut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | | |
Collapse
|