1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Mori T, Abe I. Lincosamide Antibiotics: Structure, Activity, and Biosynthesis. Chembiochem 2024; 25:e202300840. [PMID: 38165257 DOI: 10.1002/cbic.202300840] [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: 12/12/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Lincosamides are naturally occurring antibiotics isolated from Streptomyces sp. Currently, lincomycin A and its semisynthetic analogue clindamycin are used as clinical drugs. Due to their unique structures and remarkable biological activities, derivatizations of lincosamides via semi-synthesis and biosynthetic studies have been reported. This review summarizes the structures and biological activities of lincosamides, and the recent studies of lincosamide biosynthetic enzymes.
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Grants
- JP20H00490 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP22H05126 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H00393 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H02641 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JPNP20011 New Energy and Industrial Technology Development Organization
- JP21ak0101164 New Energy and Industrial Technology Development Organization
- JP23ama121027 New Energy and Industrial Technology Development Organization
- JPMJPR20DA Japan Science and Technology Agency
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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3
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Fu C, Liu Y, Walt C, Rasheed S, Bader CD, Lukat P, Neuber M, Haeckl FPJ, Blankenfeldt W, Kalinina OV, Müller R. Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins. Nat Commun 2024; 15:791. [PMID: 38278788 PMCID: PMC10817943 DOI: 10.1038/s41467-024-44953-5] [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: 06/22/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
DNA polymerase III sliding clamp (DnaN) was recently validated as a new anti-tuberculosis target employing griselimycins. Three (2 S,4 R)-4-methylproline moieties of methylgriselimycin play significant roles in target binding and metabolic stability. Here, we identify the mycoplanecin biosynthetic gene cluster by genome mining using bait genes from the 4-methylproline pathway. We isolate and structurally elucidate four mycoplanecins comprising scarce homo-amino acids and 4-alkylprolines. Evaluating mycoplanecin E against Mycobacterium tuberculosis surprisingly reveals an excitingly low minimum inhibition concentration at 83 ng/mL, thus outcompeting griselimycin by approximately 24-fold. We show that mycoplanecins bind DnaN with nanomolar affinity and provide a co-crystal structure of mycoplanecin A-bound DnaN. Additionally, we reconstitute the biosyntheses of the unusual L-homoleucine, L-homonorleucine, and (2 S,4 R)-4-ethylproline building blocks by characterizing in vitro the full set of eight enzymes involved. The biosynthetic study, bioactivity evaluation, and drug target validation of mycoplanecins pave the way for their further development to tackle multidrug-resistant mycobacterial infections.
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Affiliation(s)
- Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
| | - Yunkun Liu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Christine Walt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Sari Rasheed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Chantal D Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Peer Lukat
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Neuber
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Olga V Kalinina
- Medical Faculty, Saarland University, 66421, Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Center for Bioinformatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany.
- German Centre for Infection Research (DZIF), 38124, Braunschweig, Germany.
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4
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Yang G, Wijma HJ, Rozeboom HJ, Mascotti ML, Fraaije MW. Identification and characterization of archaeal and bacterial F 420 -dependent thioredoxin reductases. FEBS J 2023; 290:4777-4791. [PMID: 37403630 DOI: 10.1111/febs.16896] [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: 03/04/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
The thioredoxin pathway is an antioxidant system present in most organisms. Electrons flow from a thioredoxin reductase to thioredoxin at the expense of a specific electron donor. Most known thioredoxin reductases rely on NADPH as a reducing cofactor. Yet, in 2016, a new type of thioredoxin reductase was discovered in Archaea which utilize instead a reduced deazaflavin cofactor (F420 H2 ). For this reason, the respective enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). To have a broader understanding of the biochemistry of DFTRs, we identified and characterized two other archaeal representatives. A detailed kinetic study, which included pre-steady state kinetic analyses, revealed that these two DFTRs are highly specific for F420 H2 while displaying marginal activity with NADPH. Nevertheless, they share mechanistic features with the canonical thioredoxin reductases that are dependent on NADPH (NTRs). A detailed structural analysis led to the identification of two key residues that tune cofactor specificity of DFTRs. This allowed us to propose a DFTR-specific sequence motif that enabled for the first time the identification and experimental characterization of a bacterial DFTR.
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Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | | | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, The Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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5
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Zheng XH, Ye RF, Ding QH, Hu FX, Zhang HZ, Lai S. Simultaneous improvement of lincomycin A production and reduction of lincomycin B levels in Streptomyces lincolnensis using a combined medium optimization approach. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
The current study aimed to optimize the culture and production parameters of industrial production of lincomycin A by Streptomyces lincolnensis using a statistical approach that could also reduce unwanted by-products.
Methods
The Plackett-Burman design, steepest ascent method, and response surface design were used to evaluate different factors that affect lincomycin A production.
Results
Using an optimized S. lincolnensis fermentation medium, lincomycin A production was increased up to 4600 mg/L in shaking flasks, which indicated a 28.3% improvement over previous production in an un-optimized medium (3585 mg/L). Additionally, the concentration of lincomycin B by-product was reduced to 0.8%, which was 82.2% lower than that in the un-optimized medium. Further, quantitative real-time PCR analysis revealed the optimized medium improved lincomycin A production by stimulating key genes in the lincomycin A biosynthesis pathway, as well as an osmotic stress gene.
Conclusions
Based on the results, the sequential optimization strategy in this study provides powerful means for the enhancement of lincomycin A with less by-product. We found that osmotic stress reduced the concentration of lincomycin B, which could also help reduce fermentation by-product yields in other actinobacteria.
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6
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Cofactor F420, an emerging redox power in biosynthesis of secondary metabolites. Biochem Soc Trans 2022; 50:253-267. [PMID: 35191491 DOI: 10.1042/bst20211286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 02/07/2023]
Abstract
Cofactor F420 is a low-potential hydride-transfer deazaflavin that mediates important oxidoreductive reactions in the primary metabolism of archaea and a wide range of bacteria. Over the past decade, biochemical studies have demonstrated another essential role for F420 in the biosynthesis of various classes of natural products. These studies have substantiated reports predating the structural determination of F420 that suggested a potential role for F420 in the biosynthesis of several antibiotics produced by Streptomyces. In this article, we focus on this exciting and emerging role of F420 in catalyzing the oxidoreductive transformation of various imine, ketone and enoate moieties in secondary metabolites. Given the extensive and increasing availability of genomic and metagenomic data, these F420-dependent transformations may lead to the discovery of novel secondary metabolites, providing an invaluable and untapped resource in various biotechnological applications.
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7
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Shimo S, Ushimaru R, Engelbrecht A, Harada M, Miyamoto K, Kulik A, Uchiyama M, Kaysser L, Abe I. Stereodivergent Nitrocyclopropane Formation during Biosynthesis of Belactosins and Hormaomycins. J Am Chem Soc 2021; 143:18413-18418. [PMID: 34710328 DOI: 10.1021/jacs.1c10201] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Belactosins and hormaomycins are peptide natural products containing 3-(2-aminocyclopropyl)alanine and 3-(2-nitrocyclopropyl)alanine residues, respectively, with opposite stereoconfigurations of the cyclopropane ring. Herein we demonstrate that the heme oxygenase-like enzymes BelK and HrmI catalyze the N-oxygenation of l-lysine to generate 6-nitronorleucine. The nonheme iron enzymes BelL and HrmJ then cyclize the nitroalkane moiety to the nitrocyclopropane ring with the desired stereochemistry found in the corresponding natural products. We also show that both cyclopropanases remove the 4-proS-H of 6-nitronorleucine during the cyclization, establishing the inversion and retention of the configuration at C4 during the BelL and HrmJ reactions, respectively. This study reveals the unique strategy for stereocontrolled cyclopropane synthesis in nature.
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Affiliation(s)
- Shotaro Shimo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Alicia Engelbrecht
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mei Harada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, Ueda, 386-8567, Japan
| | - Leonard Kaysser
- Institute for Drug Discovery, Department of Pharmaceutical Biology, University of Leipzig, Eilenburger Str. 14, 04317 Leipzig, Germany
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Koberska M, Vesela L, Vimberg V, Lenart J, Vesela J, Kamenik Z, Janata J, Balikova Novotna G. Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin Biosynthesis. mBio 2021; 12:e0173121. [PMID: 34488446 PMCID: PMC8546547 DOI: 10.1128/mbio.01731-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/05/2021] [Indexed: 12/24/2022] Open
Abstract
In natural environments, antibiotics are important means of interspecies competition. At subinhibitory concentrations, they act as cues or signals inducing antibiotic production; however, our knowledge of well-documented antibiotic-based sensing systems is limited. Here, for the soil actinobacterium Streptomyces lincolnensis, we describe a fundamentally new ribosome-mediated signaling cascade that accelerates the onset of lincomycin production in response to an external ribosome-targeting antibiotic to synchronize antibiotic production within the population. The entire cascade is encoded in the lincomycin biosynthetic gene cluster (BGC) and consists of three lincomycin resistance proteins in addition to the transcriptional regulator LmbU: a lincomycin transporter (LmrA), a 23S rRNA methyltransferase (LmrB), both of which confer high resistance, and an ATP-binding cassette family F (ABCF) ATPase, LmrC, which confers only moderate resistance but is essential for antibiotic-induced signal transduction. Specifically, antibiotic sensing occurs via ribosome-mediated attenuation, which activates LmrC production in response to lincosamide, streptogramin A, or pleuromutilin antibiotics. Then, ATPase activity of the ribosome-associated LmrC triggers the transcription of lmbU and consequently the expression of lincomycin BGC. Finally, the production of LmrC is downregulated by LmrA and LmrB, which reduces the amount of ribosome-bound antibiotic and thus fine-tunes the cascade. We propose that analogous ABCF-mediated signaling systems are relatively common because many ribosome-targeting antibiotic BGCs encode an ABCF protein accompanied by additional resistance protein(s) and transcriptional regulators. Moreover, we revealed that three of the eight coproduced ABCF proteins of S. lincolnensis are clindamycin responsive, suggesting that the ABCF-mediated antibiotic signaling may be a widely utilized tool for chemical communication. IMPORTANCE Resistance proteins are perceived as mechanisms protecting bacteria from the inhibitory effect of their produced antibiotics or antibiotics from competitors. Here, we report that antibiotic resistance proteins regulate lincomycin biosynthesis in response to subinhibitory concentrations of antibiotics. In particular, we show the dual character of the ABCF ATPase LmrC, which confers antibiotic resistance and simultaneously transduces a signal from ribosome-bound antibiotics to gene expression, where the 5' untranslated sequence upstream of its encoding gene functions as a primary antibiotic sensor. ABCF-mediated antibiotic signaling can in principle function not only in the induction of antibiotic biosynthesis but also in selective gene expression in response to any small molecules targeting the 50S ribosomal subunit, including clinically important antibiotics, to mediate intercellular antibiotic signaling and stress response induction. Moreover, the resistance-regulatory function of LmrC presented here for the first time unifies functionally inconsistent ABCF family members involving antibiotic resistance proteins and translational regulators.
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Affiliation(s)
- Marketa Koberska
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Ludmila Vesela
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
- Charles University in Prague, Faculty of Science, Department of Genetics and Microbiology, Prague, Czech Republic
| | - Vladimir Vimberg
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jakub Lenart
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Vesela
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Janata
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czech Republic
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9
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Mascotti ML, Juri Ayub M, Fraaije MW. On the diversity of F 420 -dependent oxidoreductases: A sequence- and structure-based classification. Proteins 2021; 89:1497-1507. [PMID: 34216160 PMCID: PMC8518648 DOI: 10.1002/prot.26170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/30/2021] [Accepted: 06/26/2021] [Indexed: 11/05/2022]
Abstract
The F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although behaves as a nicotinamide cofactor due to its obligate hydride-transfer reactivity and similar low redox potential. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit great structural variability. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of the F420 -dependent oxidoreductases. Five different deazaflavoenzyme Classes (I-V) are described according to their structural folds as follows: Class I encompassing the TIM-barrel F420 -dependent enzymes; Class II including the Rossmann fold F420 -dependent enzymes; Class III comprising the β-roll F420 -dependent enzymes; Class IV which exclusively gathers the SH3 barrel F420 -dependent enzymes and Class V including the three layer ββα sandwich F420 -dependent enzymes. This classification provides a framework for the identification and biochemical characterization of novel deazaflavoenzymes.
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Affiliation(s)
- María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.,IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Maximiliano Juri Ayub
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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10
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Sakaine G, Ture A, Pedroni J, Smits G. Isolation, chemistry, and biology of pyrrolo[1,4]benzodiazepine natural products. Med Res Rev 2021; 42:5-55. [PMID: 33846985 DOI: 10.1002/med.21803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 02/11/2021] [Accepted: 03/23/2021] [Indexed: 11/06/2022]
Abstract
The isolation of the antitumor antibiotic anthramycin in the 1960s prompted extensive research into pyrrolo[1,4]benzodiazepines (PBD) as potential therapeutics for the treatment of cancers. Since then, nearly 60 PBD natural products have been isolated and evaluated with regard to their biological activity. Synthetic studies and total syntheses have enabled access to PBD analogues, culminating in the development of highly potent anticancer agents. This review provides a summary of the occurrence and biological activity of PBD natural products and covers the strategies employed for their total syntheses.
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Affiliation(s)
- Guna Sakaine
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Julia Pedroni
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gints Smits
- Latvian Institute of Organic Synthesis, Riga, Latvia
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11
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Chaithanya Kiran IN, Fujita K, Tanaka S, Kitamura M. Asymmetric Synthesis of Multi‐substituted Prolines via a Catalytic 1,3‐Dipolar Cycloaddition Using a Monocationic Zn
II
OAc Complex of a Chiral Bisamidine Ligand, Naph‐diPIM‐dioxo‐R. ChemCatChem 2020. [DOI: 10.1002/cctc.202001202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kazuki Fujita
- Graduate School of Pharmaceutical Sciences Nagoya University Chikusa Nagoya 464-8601 Japan
| | - Shinji Tanaka
- Research Center for Materials Science Nagoya University Chikusa Nagoya 464-8602 Japan
| | - Masato Kitamura
- Graduate School of Pharmaceutical Sciences Nagoya University Chikusa Nagoya 464-8601 Japan
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12
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Vobruba S, Kamenik Z, Kadlcik S, Janata J. N-Deacetylation in Lincosamide Biosynthesis Is Catalyzed by a TldD/PmbA Family Protein. ACS Chem Biol 2020; 15:2048-2054. [PMID: 32786288 DOI: 10.1021/acschembio.0c00224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lincosamides are clinically important antibiotics originally produced as microbial specialized metabolites. The complex biosynthesis of lincosamides is coupled to the metabolism of mycothiol as a sulfur donor. Here, we elucidated the N-deacetylation of the mycothiol-derived N-acetyl-l-cysteine residue of a lincosamide intermediate, which is comprised of an amino acid and an aminooctose connected via an amide bond. We purified this intermediate from the culture broth of a deletion mutant strain and tested it as a substrate of recombinant lincosamide biosynthetic proteins in the in vitro assays that were monitored via liquid chromatography-mass spectrometry. Our findings showed that the N-deacetylation reaction is catalyzed by CcbIH/CcbQ or LmbIH/LmbQ proteins in celesticetin and lincomycin biosynthesis, respectively. These are the first N-deacetylases from the TldD/PmbA protein family, from which otherwise only several proteases and peptidases were functionally characterized. Furthermore, we present a sequence similarity network of TldD/PmbA proteins, which suggests that the lincosamide N-deacetylases are unique among these widely distributed proteins.
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Affiliation(s)
- Simon Vobruba
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Janata
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
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13
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Steiningerova L, Kamenik Z, Gazak R, Kadlcik S, Bashiri G, Man P, Kuzma M, Pavlikova M, Janata J. Different Reaction Specificities of F 420H 2-Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets. J Am Chem Soc 2020; 142:3440-3448. [PMID: 31944685 DOI: 10.1021/jacs.9b11234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorum-sensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of l-tyrosine- or l-leucine-derived 4-alkyl-l-proline derivatives (APDs) in their structures. Here, we report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420H2-dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosyntheses of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4-substituted Δ1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420H2-dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, our bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated l-proline-like precursors and likely in the microbial central metabolism.
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Affiliation(s)
- Lucie Steiningerova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Department of Genetics and Microbiology, Faculty of Science , Charles University in Prague , Vinicna 5 , 128 00 Praha 2 , Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Radek Gazak
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences , University of Auckland , Auckland 1010 , New Zealand
| | - Petr Man
- Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Marek Kuzma
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Magdalena Pavlikova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Jiri Janata
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
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14
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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15
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Kubyshkin V, Budisa N. The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis. Int J Mol Sci 2019; 20:ijms20215507. [PMID: 31694194 PMCID: PMC6862034 DOI: 10.3390/ijms20215507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 12/13/2022] Open
Abstract
A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg, MB R3T 2N2, Canada
- Correspondence: (V.K.); or (N.B.); Tel.: +1-204-474-9321 or +49-30-314-28821 (N.B.)
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg, MB R3T 2N2, Canada
- Department of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
- Correspondence: (V.K.); or (N.B.); Tel.: +1-204-474-9321 or +49-30-314-28821 (N.B.)
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16
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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17
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Xiao Y, Wu X, Wang H, Sun S, Yu JT, Cheng J. Rhodium-Catalyzed Reaction of Azobenzenes and Nitrosoarenes toward Phenazines. Org Lett 2019; 21:2565-2568. [DOI: 10.1021/acs.orglett.9b00502] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yan Xiao
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Xiaopeng Wu
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Hepan Wang
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Song Sun
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Jin-Tao Yu
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Jiang Cheng
- School of Petrochemical Engineering, and Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Changzhou University, Changzhou 213164, P.R. China
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18
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Structural basis of the nonribosomal codes for nonproteinogenic amino acid selective adenylation enzymes in the biosynthesis of natural products. ACTA ACUST UNITED AC 2019; 46:515-536. [DOI: 10.1007/s10295-018-2084-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023]
Abstract
Abstract
Nonproteinogenic amino acids are the unique building blocks of nonribosomal peptides (NRPs) and hybrid nonribosomal peptide–polyketides (NRP–PKs) and contribute to their diversity of chemical structures and biological activities. In the biosynthesis of NRPs and NRP–PKs, adenylation enzymes select and activate an amino acid substrate as an aminoacyl adenylate, which reacts with the thiol of the holo form of the carrier protein to afford an aminoacyl thioester as the electrophile for the condensation reaction. Therefore, the substrate specificity of adenylation enzymes is a key determinant of the structure of NRPs and NRP–PKs. Here, we focus on nonproteinogenic amino acid selective adenylation enzymes, because understanding their unique selection mechanisms will lead to accurate functional predictions and protein engineering toward the rational biosynthesis of designed molecules containing amino acids. Based on recent progress in the structural analysis of adenylation enzymes, we discuss the nonribosomal codes of nonproteinogenic amino acid selective adenylation enzymes.
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19
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Kamenik Z, Gazak R, Kadlcik S, Steiningerova L, Rynd V, Janata J. C-C bond cleavage in biosynthesis of 4-alkyl-L-proline precursors of lincomycin and anthramycin cannot precede C-methylation. Nat Commun 2018; 9:3167. [PMID: 30093642 PMCID: PMC6085390 DOI: 10.1038/s41467-018-05455-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 07/10/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Radek Gazak
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Lucie Steiningerova
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Vit Rynd
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Jiri Janata
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic.
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20
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Pavlikova M, Kamenik Z, Janata J, Kadlcik S, Kuzma M, Najmanova L. Novel pathway of 3-hydroxyanthranilic acid formation in limazepine biosynthesis reveals evolutionary relation between phenazines and pyrrolobenzodiazepines. Sci Rep 2018; 8:7810. [PMID: 29773836 PMCID: PMC5958127 DOI: 10.1038/s41598-018-26179-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
Natural pyrrolobenzodiazepines (PBDs) form a large and structurally diverse group of antitumour microbial metabolites produced through complex pathways, which are encoded within biosynthetic gene clusters. We sequenced the gene cluster of limazepines and proposed their biosynthetic pathway based on comparison with five available gene clusters for the biosynthesis of other PBDs. Furthermore, we tested two recombinant proteins from limazepine biosynthesis, Lim5 and Lim6, with the expected substrates in vitro. The reactions monitored by LC-MS revealed that limazepine biosynthesis involves a new way of 3-hydroxyanthranilic acid formation, which we refer to as the chorismate/DHHA pathway and which represents an alternative to the kynurenine pathway employed for the formation of the same precursor in the biosynthesis of other PBDs. The chorismate/DHHA pathway is presumably also involved in the biosynthesis of PBD tilivalline, several natural products unrelated to PBDs, and its part is shared also with phenazine biosynthesis. The similarities between limazepine and phenazine biosynthesis indicate tight evolutionary links between these groups of compounds.
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Affiliation(s)
- Magdalena Pavlikova
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jiri Janata
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Lucie Najmanova
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic.
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21
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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