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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Burchacka E, Pstrowska K, Bryk M, Maciejowski F, Kułażyński M, Chojnacka K. The Properties of Activated Carbons Functionalized with an Antibacterial Agent and a New SufA Protease Inhibitor. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1263. [PMID: 36770271 PMCID: PMC9920905 DOI: 10.3390/ma16031263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
S. aureus is the cause of many diseases, including numerous infections of the skin. One way to help combat skin infections is to use bandages containing activated carbon. Currently, there are no dressings on the market that use the synergistic effect of activated carbon and antibiotics. Thus, in this study, we point out the adsorption level of an antimicrobial substance on three different active carbons of different origins; by examining the inhibition level of the growth of S. aureus bacteria, we determined the number of live cells adsorbed on activated carbons depending on the presence of gentamicin in the solution. In addition, we designed and synthesized a new antibacterial substance with a new mechanism of action to act as a bacterial protease inhibitor, as well as determining the antibacterial properties conducted through adsorption. Our results demonstrate that activated carbons with adsorbed antibiotics show better bactericidal properties than activated carbon alone or the antibiotic itself. The use of properly modified activated carbons may have a beneficial effect on the development and functioning of new starting materials for bacteria elimination, e.g., in wound-healing treatments in the future.
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Affiliation(s)
- Ewa Burchacka
- Department of Chemistry, Wroclaw University of Science and Technology, Wyspiańskiego Str. 27, 50-370 Wroclaw, Poland
| | - Katarzyna Pstrowska
- Department of Chemistry, Wroclaw University of Science and Technology, Wyspiańskiego Str. 27, 50-370 Wroclaw, Poland
| | - Michał Bryk
- Department of Chemistry, Wroclaw University of Science and Technology, Wyspiańskiego Str. 27, 50-370 Wroclaw, Poland
| | - Filip Maciejowski
- Department of Chemistry, Wroclaw University of Science and Technology, Wyspiańskiego Str. 27, 50-370 Wroclaw, Poland
| | - Marek Kułażyński
- Innovation and Implementation Company Ekomotor Ltd., 1A Wyścigowa Street, 53-011 Wroclaw, Poland
| | - Katarzyna Chojnacka
- Department of Chemistry, Wroclaw University of Science and Technology, Wyspiańskiego Str. 27, 50-370 Wroclaw, Poland
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3
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Burchacka E, Pięta P, Łupicka-Słowik A. Recent advances in fungal serine protease inhibitors. Biomed Pharmacother 2021; 146:112523. [PMID: 34902742 DOI: 10.1016/j.biopha.2021.112523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
Four types of antifungal drugs are available that include inhibitors of ergosterol synthesis, of fungal RNA biosynthesis, and of cell wall biosynthesis as well as physiochemical regulators of fungal membrane sterols. Increasing resistance to antifungal drugs can severely limit treatment options of fungal nail infections, vaginal candidiasis, ringworm, blastomycosis, histoplasmosis, and Candida infections of the mouth, throat, and esophagus, among other infections. Development of strategies focused on new fungicides can effectively help tackle troublesome fungal diseases. The virulence and optimal growth of fungi depend on various extracellular secreted factors, among which proteases, such as serine proteases, are of particular interest. A specific extracellular proteolytic system enables fungi to survive and penetrate the tissues. Given the role of fungal proteases in infection, any molecule capable of selectively and specifically inhibiting their activity can lead to the development of potential drugs. Owing to their specific mode of action, fungal protease inhibitors can avoid fungal resistance observed with currently available treatments. Although fungal secreted proteases have been extensively studied as potential virulence factors, our understanding of the substrate specificity of such proteases remains poor. In this review, we summarize the recent advances in the design and development of specific serine protease inhibitors and provide a brief history of the compounds that inhibit fungal serine protease activity.
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Affiliation(s)
- E Burchacka
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St, 50-370 Wrocław, Poland.
| | - P Pięta
- Department of Bionic and Medical Experimental Biology, Poznań University of Medical Sciences, Parkowa 2 St, 60-775 Poznań, Poland
| | - A Łupicka-Słowik
- Faculty of Chemistry, Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St, 50-370 Wrocław, Poland
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4
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Walczak M, Chryplewicz A, Olewińska S, Psurski M, Winiarski Ł, Torzyk K, Oleksyszyn J, Sieńczyk M. Phosphonic Analogs of Alanine as Acylpeptide Hydrolase Inhibitors. Chem Biodivers 2021; 18:e2001004. [PMID: 33427376 DOI: 10.1002/cbdv.202001004] [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: 12/07/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022]
Abstract
Acylpeptide hydrolase is a serine protease, which, together with prolyl oligopeptidase, dipeptidyl peptidase IV and oligopeptidase B, belongs to the prolyl oligopeptidase family. Its primary function is associated with the removal of N-acetylated amino acid residues from proteins and peptides. Although the N-acylation occurs in 50-90 % of eukaryotic proteins, the precise functions of this modification remains unclear. Recent findings have indicated that acylpeptide hydrolase participates in various events including oxidized proteins degradation, amyloid β-peptide cleavage, and response to DNA damage. Considering the protein degradation cycle cross-talk between acylpeptide hydrolase and proteasome, inhibition of the first enzyme resulted in down-regulation of the ubiquitin-proteasome system and induction of cancer cell apoptosis. Acylpeptide hydrolase has been proposed as an interesting target for the development of new potential anticancer agents. Here, we present the synthesis of simple derivatives of (1-aminoethyl)phosphonic acid diaryl esters, phosphonic analogs of alanine diversified at the N-terminus and ester rings, as inhibitors of acylpeptide hydrolase and discuss the ability of the title compounds to induce apoptosis of U937 and MV-4-11 tumor cell lines.
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Affiliation(s)
- Maciej Walczak
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Chryplewicz
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sandra Olewińska
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mateusz Psurski
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wroclaw, Poland
| | - Łukasz Winiarski
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina Torzyk
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Józef Oleksyszyn
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Sieńczyk
- Wroclaw University of Science and Technology, Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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Moreno-Cinos C, Sassetti E, Salado IG, Witt G, Benramdane S, Reinhardt L, Cruz CD, Joossens J, Van der Veken P, Brötz-Oesterhelt H, Tammela P, Winterhalter M, Gribbon P, Windshügel B, Augustyns K. α-Amino Diphenyl Phosphonates as Novel Inhibitors of Escherichia coli ClpP Protease. J Med Chem 2019; 62:774-797. [PMID: 30571121 DOI: 10.1021/acs.jmedchem.8b01466] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increased Gram-negative bacteria resistance to antibiotics is becoming a global problem, and new classes of antibiotics with novel mechanisms of action are required. The caseinolytic protease subunit P (ClpP) is a serine protease conserved among bacteria that is considered as an interesting drug target. ClpP function is involved in protein turnover and homeostasis, stress response, and virulence among other processes. The focus of this study was to identify new inhibitors of Escherichia coli ClpP and to understand their mode of action. A focused library of serine protease inhibitors based on diaryl phosphonate warheads was tested for ClpP inhibition, and a chemical exploration around the hit compounds was conducted. Altogether, 14 new potent inhibitors of E. coli ClpP were identified. Compounds 85 and 92 emerged as most interesting compounds from this study due to their potency and, respectively, to its moderate but consistent antibacterial properties as well as the favorable cytotoxicity profile.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Elisa Sassetti
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany.,Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Irene G Salado
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Gesa Witt
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Siham Benramdane
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Laura Reinhardt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Jurgen Joossens
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
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Boyanova L, Markovska R, Mitov I. Virulence arsenal of the most pathogenic species among the Gram-positive anaerobic cocci, Finegoldia magna. Anaerobe 2016; 42:145-151. [DOI: 10.1016/j.anaerobe.2016.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/09/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
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