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Füsser FT, Wollenhaupt J, Weiss MS, Kümmel D, Koch O. Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening. Acta Crystallogr D Struct Biol 2023; 79:857-865. [PMID: 37574972 PMCID: PMC10478635 DOI: 10.1107/s2059798323005223] [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: 02/25/2023] [Accepted: 06/12/2023] [Indexed: 08/15/2023] Open
Abstract
The increasing number of people dying from tuberculosis and the existence of extensively drug-resistant strains has led to an urgent need for new antituberculotic drugs with alternative modes of action. As part of the thioredoxin system, thioredoxin reductase (TrxR) is essential for the survival of Mycobacterium tuberculosis (Mtb) and shows substantial differences from human TrxR, making it a promising and most likely selective target. As a model organism for Mtb, crystals of Mycobacterium smegmatis TrxR that diffracted to high resolution were used in crystallographic fragment screening to discover binding fragments and new binding sites. The application of the 96 structurally diverse fragments from the F2X-Entry Screen revealed 56 new starting points for fragment-based drug design of new TrxR inhibitors. Over 200 crystal structures were analyzed using FragMAXapp, which includes processing and refinement by largely automated software pipelines and hit identification via the multi-data-set analysis approach PanDDA. The fragments are bound to 11 binding sites, of which four are positioned at binding pockets or important interaction sites and therefore show high potential for possible inhibition of TrxR.
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Affiliation(s)
- Friederike T. Füsser
- Institute of Pharmaceutical and Medicinal Chemistry, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- German Center of Infection Research, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- Institute of Biochemistry, Münster University, Corrensstrasse 36, 48149 Münster, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, Münster University, Corrensstrasse 36, 48149 Münster, Germany
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- German Center of Infection Research, Münster University, Corrensstrasse 48, 48149 Münster, Germany
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Alzain AA, Makki AA, Ibraheem W. Insights into the Inhibition of Mycolic Acid Synthesis by Cytosporone E Derivatives for Tuberculosis Treatment Via an In Silico Multi-target Approach. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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3
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Lata S, Akif M. Structure-based identification of natural compound inhibitor against M. tuberculosis thioredoxin reductase: insight from molecular docking and dynamics simulation. J Biomol Struct Dyn 2021; 39:4480-4489. [PMID: 32567497 DOI: 10.1080/07391102.2020.1778530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/30/2020] [Indexed: 12/19/2022]
Abstract
Antioxidant systems of M. tuberculosis (Mtb) play an important role in providing resistance in the hostile environment of mononuclear phagocytes. Thioredoxin system is a known antioxidant system that consists of three copies of thioredoxins (Trxs) and a single copy of thioredoxin reductase (TrxR). TrxR has been validated as an essential gene known to be involved in the reduction of peroxides, dinitrobenzenes and hydroperoxides, and is crucial in maintaining the survival of Mtb in macrophages. Recently, it has been demonstrated to be a druggable target. In this study, molecular docking was applied to screen more than 20,000 natural compounds from the Traditional Chinese Medicine database. Theoretical calculation of ΔGbinding by the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) methods indicated two top-hit compounds that bind with a high affinity to the allosteric site, consisting of a hinge region, of TrxR. Further, stability and binding analysis of both compounds were carried out with molecular dynamics simulation. An analysis of conformational variation by principal component analysis (PCA) and protein contact network (PCN) uncovered the conformational changes in the compound-bound forms of protein. The NADPH domain formed many new interactions with the FAD domain in the compound-bound form, signifying that the binding may render an effect on the protein structure and function. Our results suggest that these two compounds could potentially be used for structure-based lead inhibitors against TrxR. The inhibitor selected as lead compound will be used further as a scaffold to optimize as novel anti-tuberculosis therapeutic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Surabhi Lata
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | - Mohd Akif
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
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4
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Relevance of peroxiredoxins in pathogenic microorganisms. Appl Microbiol Biotechnol 2021; 105:5701-5717. [PMID: 34258640 DOI: 10.1007/s00253-021-11360-5] [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: 02/01/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/19/2022]
Abstract
The oxidative and nitrosative responses generated by animals and plants are important defenses against infection and establishment of pathogenic microorganisms such as bacteria, fungi, and protozoa. Among distinct oxidant species, hydroperoxides are a group of chemically diverse compounds that comprise small hydrophilic molecules, such as hydrogen peroxide and peroxynitrite, and bulky hydrophobic species, such as organic hydroperoxides. Peroxiredoxins (Prx) are ubiquitous enzymes that use a highly reactive cysteine residue to decompose hydroperoxides and can also perform other functions, like molecular chaperone and phospholipase activities, contributing to microbial protection against the host defenses. Prx are present in distinct cell compartments and, in some cases, they can be secreted to the extracellular environment. Despite their high abundance, Prx expression can be further increased in response to oxidative stress promoted by host defense systems, by treatment with hydroperoxides or by antibiotics. In consequence, some isoforms have been described as virulence factors, highlighting their importance in pathogenesis. Prx are very diverse and are classified into six different classes (Prx1-AhpC, BCP-PrxQ, Tpx, Prx5, Prx6, and AhpE) based on structural and biochemical features. Some groups are absent in hosts, while others present structural peculiarities that differentiate them from the host's isoforms. In this context, the intrinsic characteristics of these enzymes may aid the development of new drugs to combat pathogenic microorganisms. Additionally, since some isoforms are also found in the extracellular environment, Prx emerge as attractive targets for the production of diagnostic tests and vaccines. KEY POINTS: • Peroxiredoxins are front-line defenses against host oxidative and nitrosative stress. • Functional and structural peculiarities differ pathogen and host enzymes. • Peroxiredoxins are potential targets to microbicidal drugs.
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Chupakhin E, Krasavin M. Thioredoxin reductase inhibitors: updated patent review (2017-present). Expert Opin Ther Pat 2021; 31:745-758. [PMID: 33666133 DOI: 10.1080/13543776.2021.1899160] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Thioredoxin reductase (TrxR) is a selenocysteine-containing enzyme which is responsible - as a part of the thioredoxin system - for maintaining redox homeostasis in cells. It is upregulated in cancerous state as a defense against oxidative stress. TrxR has been mostly considered an anticancer drug target although it has applications in other therapeutic areas such as neurodegeneration, inflammation, microbial infections, and neonatal hyperoxic lung injury.Areas covered: The present review covers the patent literature that appeared in the period 2017-2020, i.e. since the publication of the previous expert opinion patent review on TrxR inhibitors. The recent additions to the following traditional classes of inhibitors are discussed: metal complexes, Michael acceptors as well as arsenic and selenium compounds. At the same time, a novel group of nitro (hetero)aromatic compounds have emerged which likely acts via covalent inhibition mechanism. Several miscellaneous chemotypes are grouped under Miscellaneous subsection.Expert opinion: While specificity over glutathione reductase is achieved easily, TrxR is still moving toward the later stages of development at a very slow rate. Michael acceptors, particularly based on TRXR substrate-mimicking scaffolds, are gaining impetus and so are dual and hybrid compounds. The development prospects of the emerging nitro (hetero)aromatic chemotypes remain uncertain.
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Affiliation(s)
- Evgeny Chupakhin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg Russian Federation.,Institute for Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad Russian Federation
| | - Mikhail Krasavin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg Russian Federation.,Institute for Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad Russian Federation
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Timo GO, Reis RSSVD, Melo AFD, Costa TVL, Magalhães PDO, Homem-de-Mello M. Predictive Power of In Silico Approach to Evaluate Chemicals against M. tuberculosis: A Systematic Review. Pharmaceuticals (Basel) 2019; 12:E135. [PMID: 31527425 PMCID: PMC6789803 DOI: 10.3390/ph12030135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an endemic bacterium worldwide that causes tuberculosis (TB) and involves long-term treatment that is not always effective. In this context, several studies are trying to develop and evaluate new substances active against Mtb. In silico techniques are often used to predict the effects on some known target. We used a systematic approach to find and evaluate manuscripts that applied an in silico technique to find antimycobacterial molecules and tried to prove its predictive potential by testing them in vitro or in vivo. After searching three different databases and applying exclusion criteria, we were able to retrieve 46 documents. We found that they all follow a similar screening procedure, but few studies exploited equal targets, exploring the interaction of multiple ligands to 29 distinct enzymes. The following in vitro/vivo analysis showed that, although the virtual assays were able to decrease the number of molecules tested, saving time and money, virtual screening procedures still need to develop the correlation to more favorable in vitro outcomes. We find that the in silico approach has a good predictive power for in vitro results, but call for more studies to evaluate its clinical predictive possibilities.
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Affiliation(s)
- Giulia Oliveira Timo
- InSiliTox, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | | | - Adriana Françozo de Melo
- InSiliTox, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | | | - Pérola de Oliveira Magalhães
- Laboratory of Natural Products, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil
| | - Mauricio Homem-de-Mello
- InSiliTox, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia 70910-900, Brazil.
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Aher RB, Roy K. Computational Approaches as Rational Decision Support Systems for Discovering Next-Generation Antitubercular Agents: Mini-Review. Curr Comput Aided Drug Des 2019; 15:369-383. [PMID: 30706823 DOI: 10.2174/1573409915666190130153214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/19/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022]
Abstract
Tuberculosis, malaria, dengue, chikungunya, leishmaniasis etc. are a large group of neglected tropical diseases that prevail in tropical and subtropical countries, affecting one billion people every year. Minimal funding and grants for research on these scientific problems challenge many researchers to find a different way to reduce the extensive time and cost involved in the drug discovery cycle of these problems. Computer-aided drug design techniques have already been proved successful in the discovery of new molecules rationally by reducing the time and cost involved in the development of drugs. In the current minireview, we are highlighting on the molecular modeling studies published during 2010-2018 for target specific antitubercular agents. This review includes the studies of Structure-Based (SB) and Ligand-Based (LB) modeling and those involving Machine Learning (ML) techniques against different antitubercular targets such as dihydrofolate reductase (DHFR), enoyl Acyl Carrier Protein (ACP) reductase (InhA), catalase-peroxidase (KatG), enzyme antigen 85C, protein tyrosine phosphatases (PtpA and PtpB), dUTPase, thioredoxin reductase (MtTrxR), etc. The information presented in this review will help the researchers to get acquainted with the recent progress in the modeling studies of antitubercular agents.
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Affiliation(s)
- Rahul Balasaheb Aher
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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8
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Patel H, Brinkjost T, Koch O. PyGOLD: a python based API for docking based virtual screening workflow generation. Bioinformatics 2018; 33:2589-2590. [PMID: 28398502 DOI: 10.1093/bioinformatics/btx197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/05/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD. However, within an automated virtual screening workflow it is not feasible to use the GUI in between every step to change the GOLD configuration file. Thus, a python module called PyGOLD was developed, to parse, edit and write the GOLD configuration file and to automate docking based virtual screening workflows. Availability and Implementation The latest version of PyGOLD, its documentation and example scripts are available at: http://www.ccb.tu-dortmund.de/koch or http://www.agkoch.de. PyGOLD is implemented in Python and can be imported as a standard python module without any further dependencies. Contact oliver.koch@agkoch.de, oliver.koch@tu-dortmund.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Tobias Brinkjost
- Faculty of Chemistry and Chemical Biology.,Department of Computer Science, TU Dortmund University, 44227 Dortmund, Germany
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Krüger DM, Glas A, Bier D, Pospiech N, Wallraven K, Dietrich L, Ottmann C, Koch O, Hennig S, Grossmann TN. Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein-Protein Interactions. J Med Chem 2017; 60:8982-8988. [PMID: 29028171 PMCID: PMC5682607 DOI: 10.1021/acs.jmedchem.7b01221] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Macrocyclic
peptides can interfere with challenging biomolecular
targets including protein–protein interactions. Whereas there
are various approaches that facilitate the identification of peptide-derived
ligands, their evolution into higher affinity binders remains a major
hurdle. We report a virtual screen based on molecular docking that
allows the affinity maturation of macrocyclic peptides taking non-natural
amino acids into consideration. These macrocycles bear large and flexible
substituents that usually complicate the use of docking approaches.
A virtual library containing more than 1400 structures was screened
against the target focusing on docking poses with the core structure
resembling a known bioactive conformation. Based on this screen, a
macrocyclic peptide 22 involving two non-natural amino
acids was evolved showing increased target affinity and biological
activity. Predicted binding modes were verified by X-ray crystallography.
The presented workflow allows the screening of large macrocyclic peptides
with diverse modifications thereby expanding the accessible chemical
space and reducing synthetic efforts.
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Affiliation(s)
- Dennis M Krüger
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - David Bier
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Department of Chemistry, University of Duisburg-Essen , Universitätstr. 7, 45141 Essen, Germany
| | - Nicole Pospiech
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Kerstin Wallraven
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Laura Dietrich
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Christian Ottmann
- Department of Chemistry, University of Duisburg-Essen , Universitätstr. 7, 45141 Essen, Germany.,Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Gustafsson TN, Osman H, Werngren J, Hoffner S, Engman L, Holmgren A. Ebselen and analogs as inhibitors of Bacillus anthracis thioredoxin reductase and bactericidal antibacterials targeting Bacillus species, Staphylococcus aureus and Mycobacterium tuberculosis. Biochim Biophys Acta Gen Subj 2016; 1860:1265-71. [PMID: 26971857 DOI: 10.1016/j.bbagen.2016.03.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/25/2016] [Accepted: 03/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Bacillus anthracis is the causative agent of anthrax, a disease associated with a very high mortality rate in its invasive forms. METHODS We studied a number of ebselen analogs as inhibitors of B. anthracis thioredoxin reductase and their antibacterial activity on Bacillus subtilis, Staphylococcus aureus, Bacillus cereus and Mycobacterium tuberculosis. RESULTS The most potent compounds in the series gave IC(50) values down to 70 nM for the pure enzyme and minimal inhibitory concentrations (MICs) down to 0.4 μM (0.12 μg/ml) for B. subtilis, 1.5 μM (0.64 μg/ml) for S. aureus, 2 μM (0.86 μg/ml) for B. cereus and 10 μg/ml for M. tuberculosis. Minimal bactericidal concentrations (MBCs) were found at 1-1.5 times the MIC, indicating a general, class-dependent, bactericidal mode of action. The combined bacteriological and enzymological data were used to construct a preliminary structure-activity-relationship for the benzoisoselenazol class of compounds. When S. aureus and B. subtilis were exposed to ebselen, we were unable to isolate resistant mutants on both solid and in liquid medium suggesting a high resistance barrier. CONCLUSIONS These results suggest that ebselen and analogs thereof could be developed into a novel antibiotic class, useful for the treatment of infections caused by B. anthracis, S. aureus, M. tuberculosis and other clinically important bacteria. Furthermore, the high barrier against resistance development is encouraging for further drug development. GENERAL SIGNIFICANCE We have characterized the thioredoxin system from B. anthracis as a novel drug target and ebselen and analogs thereof as a potential new class of antibiotics targeting several important human pathogens.
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Affiliation(s)
- Tomas N Gustafsson
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Clinical Bacteriology, Sunderby Research Unit, Umeå University, Umeå, Sweden.
| | - Harer Osman
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, Stockholm, Sweden
| | - Jim Werngren
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sven Hoffner
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Lars Engman
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Arne Holmgren
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, Stockholm, Sweden.
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Mehra R, Sharma R, Khan IA, Nargotra A. Identification and optimization of Escherichia coli GlmU inhibitors: An in silico approach with validation thereof. Eur J Med Chem 2015; 92:78-90. [DOI: 10.1016/j.ejmech.2014.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/21/2014] [Accepted: 12/18/2014] [Indexed: 12/25/2022]
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Björnberg O, Viennet T, Skjoldager N, Ćurović A, Nielsen KF, Svensson B, Hägglund P. Lactococcus lactis thioredoxin reductase is sensitive to light inactivation. Biochemistry 2015; 54:1628-37. [PMID: 25675241 DOI: 10.1021/bi5013639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Thioredoxin, involved in numerous redox pathways, is maintained in the dithiol state by the nicotinamide adenine dinucleotide phosphate-dependent flavoprotein thioredoxin reductase (TrxR). Here, TrxR from Lactococcus lactis is compared with the well-characterized TrxR from Escherichia coli. The two enzymes belong to the same class of low-molecular weight thioredoxin reductases and display similar kcat values (∼25 s(-1)) with their cognate thioredoxin. Remarkably, however, the L. lactis enzyme is inactivated by visible light and furthermore reduces molecular oxygen 10 times faster than E. coli TrxR. The rate of light inactivation under standardized conditions (λmax=460 nm and 4 °C) was reduced at lowered oxygen concentrations and in the presence of iodide. Inactivation was accompanied by a distinct spectral shift of the flavin adenine dinucleotide (FAD) that remained firmly bound. High-resolution mass spectrometric analysis of heat-extracted FAD from light-damaged TrxR revealed a mass increment of 13.979 Da, relative to that of unmodified FAD, corresponding to the addition of one oxygen atom and the loss of two hydrogen atoms. Tandem mass spectrometry confined the increase in mass of the isoalloxazine ring, and the extracted modified cofactor reacted with dinitrophenyl hydrazine, indicating the presence of an aldehyde. We hypothesize that a methyl group of FAD is oxidized to a formyl group. The significance of this not previously reported oxidation and the exceptionally high rate of oxygen reduction are discussed in relation to other flavin modifications and the possible occurrence of enzymes with similar properties.
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Affiliation(s)
- Olof Björnberg
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark , Building 224, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
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15
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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