Author: Michelle Jennifer WuPublisher:
ISBN:
Category :
Languages : en
Pages : 0
Book Description
Genome Mining Approaches for the Discovery of Novel Lasso Peptides
Author: Michelle Jennifer WuLasso Peptides
Author: Yanyan LiPublisher: Springer
ISBN: 1493910108
Category : Medical
Languages : en
Pages : 113
Book Description
Lasso peptides form a growing family of fascinating ribosomally-synthesized and post-translationally modified peptides produced by bacteria. They contain 15 to 24 residues and share a unique interlocked topology that involves an N-terminal 7 to 9-residue macrolactam ring where the C-terminal tail is threaded and irreversibly trapped. The ring results from the condensation of the N-terminal amino group with a side-chain carboxylate of a glutamate at position 8 or 9, or an aspartate at position 7, 8 or 9. The trapping of the tail involves bulky amino acids located in the tail below and above the ring and/or disulfide bridges connecting the ring and the tail. Lasso peptides are subdivided into three subtypes depending on the absence (class II) or presence of one (class III) or two (class I) disulfide bridges. The lasso topology results in highly compact structures that give to lasso peptides an extraordinary stability towards both protease degradation and denaturing conditions. Lasso peptides are generally receptor antagonists, enzyme inhibitors and/or antibacterial or antiviral (anti-HIV) agents. The lasso scaffold and the associated biological activities shown by lasso peptides on different key targets make them promising molecules with high therapeutic potential. Their application in drug design has been exemplified by the development of an integrin antagonist based on a lasso peptide scaffold. The biosynthesis machinery of lasso peptides is therefore of high biotechnological interest, especially since such highly compact and stable structures have to date revealed inaccessible by peptide synthesis. Lasso peptides are produced from a linear precursor LasA, which undergoes a maturation process involving several steps, in particular cleavage of the leader peptide and cyclization. The post-translational modifications are ensured by a dedicated enzymatic machinery, which is composed of an ATP-dependent cysteine protease (LasB) and a lactam synthetase (LasC) that form an enzymatic complex called lasso synthetase. Microcin J25, produced by Escherichia coli AY25, is the archetype of lasso peptides and the most extensively studied. To date only around forty lasso peptides have been isolated, but genome mining approaches have revealed that they are widely distributed among Proteobacteria and Actinobacteria, particularly in Streptomyces, making available a rich resource of novel lasso peptides and enzyme machineries towards lasso topologies.
Genome Mining, Isolation and Characterization of Novel Lasso Peptides and Their Utilization in Drug Development
Author: Julian David HegemannDevelopment of Synthetic Strategies for Lasso Peptides with Anticancer Activity
Author: Helena Martín GómezPublisher:
ISBN:
Category :
Languages : en
Pages : 326
Book Description
Nowadays, the discovery and development of novel constrained peptides which are likely to combine the advantages of therapeutic proteins with those of small molecules is of special interest. This has partially prompted the re-emergence of peptides as therapeutics. Thus, potentially, these peptides provide both the selectivity and potency of larger protein biologics but with zero or low immunogenicity, and the stability and bioavailability of small molecules. Furthermore, they are smaller than biologics, more accessible and cheaper to manufacture using chemical methods, thus presumably combining the advantages of the two therapeutic approaches. Lasso peptides are a class of ribosomally synthesized and post-translationally modified natural products with a unique three-dimensional structure, in which the C-terminus threads through an N-terminal macrolactam ring in a right-handed conformation. These peptides consist of 15–26 proteinogenic amino acids and share an N-terminal 7- to 9- residue macrolactam ring where the N-terminal amino acid is always glycine or cysteine and the amino acid that closes the ring is aspartic or glutamic acid. The lasso topology is predominantly stabilized by steric interactions, in the case of class II lasso peptides, but sometimes is assisted by the presence of disulfide bridges; two in the case of class I or one in class III lasso peptides. Currently, a total of 43 lasso peptides have been described; 3 belong to class I, 39 to class II and 1 to class III.1 Prior to 2008, most of these lasso peptides were discovered by isolation from bacteria; however, capistruin, the first lasso peptide isolated by a genome mining approach, changed this scenario.2 The diverse functionality of lasso peptides makes these molecules attractive candidates for drug discovery. In addition, given their extraordinary stability against chemical, thermal and proteolytic degradation1 and reduced flexibility, these peptides are suitable scaffolds for drug design and epitope grafting approaches.3,4 Considering this, it is possible to use a rational approach to further improve and optimize such a scaffold toward the generation of more potent and more selective bioactive compounds. Currently, all research into new peptide drugs pursues two main common objectives: development of new compounds resistant to enzymatic degradation and the modulation of peptide topology, since the properties are highly related to the shape.5 In this regard, most lasso peptide synthetic strategies are based on the imitation of the interlocked structure of rotaxanes and catenanes.6,7,8,9 Furthermore, lasso peptide-like bicyclic peptides is also a suitable chemical approach, in which the loop sequence is tied with a covalent bond.10 Sungsanpin is a class II lasso peptide isolated from a Streptomyces sp. strain collected in Korea in 2012.11 It shows an inhibitory effect on the invasion of human non-small cell lung cancer (NSCLC), an effect that has been reported with the A549 cell line. Regarding the previously mentioned, the aim of this project is the synthesis of sungsanpin and analogs with linkages able to maintain the threaded lasso structure. Several characterization techniques have been established for lasso peptides identification. A representative and recent technique that allows rapid structural detection and dynamical features is ion-mobility mass spectrometry (IM-MS). It is a complementary approach to MS/MS experiments that provides information on the global shape of molecules,12 and has proven useful for the structural characterization of many lasso peptides.13,14 To date, no synthetic access to lasso peptides is available due to the difficulty in building and maintaining the threaded lasso structure. The ability to generate lasso peptides synthetically remains a challenging endeavor and it would open the door to the production of lasso peptide analog with unnatural amino acids or other nonproteinogenic building blocks. From a therapeutic point of view, these small and constrained structures would represent a new paradigm in drug discovery. (1)Hegemann, J. D.; Zimmermann, M.; Xie, X.; Marahiel, M. A. Acc. Chem. Res. 2015, 48 (7), 1909. (2)Knappe, T. a.; Linne, U.; Zirah, S.; Rebuffat, S.; Xie, X.; Marahiel, M. a. J. Am. Chem. Soc. 2008, 130 (17), 11446. (3)Knappe, T. A.; Manzenrieder, F.; Mas-Moruno, C.; Linne, U.; Sasse, F.; Kessler, H.; Xie, X.; Marahiel, M. A. Angew. Chemie - Int. Ed. 2011, 50 (37), 8714. (4)Hegemann, J. D.; De Simone, M.; Zimmermann, M.; Knappe, T. A.; Xie, X.; Di Leva, F. S.; Marinelli, L.; Novellino, E.; Zahler, S.; Kessler, H.; Marahiel, M. A. J. Med. Chem. 2014, 57 (13), 5829. (5)Clavel, C.; Fournel-Marotte, K.; Coutrot, F. Molecules 2013, 18 (9), 11553. (6)Mohr, B.; Weck, M.; Sauvage, J.-P.; Grubbs, R. H. Angew. Chem. Int. Ed. Engl. 1997, 36 (12), 1308. (7)Hogg, L.; Leigh, D. A.; Lusby, P. J.; Morelli, A.; Parsons, S.; Wong, J. K. Y. Angew. Chemie - Int. Ed. 2004, 43 (10), 1218. (8)Hänni, K. D.; Leigh, D. A. Chem. Soc. Rev. 2010, 39 (4), 1240. (9)Yan, L. Z.; Dawson, P. E. Angew. Chemie Int. Ed. 2001, 40 (19), 3625. (10)Soudy, R.; Wang, L.; Kaur, K. Bioorganic Med. Chem. 2012, 20 (5), 1794. (11)Um, S.; Kim, Y.-J. J.; Kwon, H. H. C.; Wen, H.; Kim, S.-H. H.; Kwon, H. H. C.; Park, S.; Shin, J.; Oh, D.-C. C. J. Nat. Prod. 2013, 76 (5), 873. (12)Clemmer, D. E.; Jarrold, M. F. J. Mass Spectrom. 1997, 32 (6), 577. (13)Jeanne Dit Fouque, K.; Afonso, C.; Zirah, S.; Hegemann, J. D.; Zimmermann, M.; Marahiel, M. A.; Rebuffat, S.; Lavanant, H. Anal. Chem. 2015, 87 (2), 1166. (14)Fouque, K. J. D.; Lavanant, H.; Zirah, S.; Hegemann, J. D.; Zimmermann, M.; Marahiel, M. A.; Rebuffat, S.; Afonso, C. J. Am. Soc. Mass Spectrom. 2016.
Mass Spectrometry-guided Genome Mining of Peptidic and Glycosylated Microbial Natural Products
Author: Roland David KerstenPublisher:
ISBN: 9781303212000
Category :
Languages : en
Pages : 233
Book Description
Scientific progress in organic synthesis, biochemistry and biology and cures to many infectious diseases and cancer rely on discovery of microbial natural products and their biosynthetic pathways. `Omics' approaches such as genome mining have opened new opportunities for natural product discovery within the last decade as ~90% of pathways in microbial genomes are uncharacterized in their products. Genome mining for natural product discovery can be defined as the connection of a natural product (chemotype) with its biosynthetic genes (genotype) by applied biosynthetic knowledge. Traditional genome mining approaches are in silico-guided approaches in which the isolation of a new natural product is guided by bioinformatic predictions from a target cryptic gene cluster. The problem of in silico-guided genome mining in natural product discovery is its low-throughput rate as only one pathway is characterized per experiment. In this dissertation, mass spectrometry (MS)-guided genome mining approaches are introduced which rapidly connect a natural product with its biosynthetic genes by matching de novo tandem MS structures of biosynthetic building blocks such as amino acids and sugars to metabolite structures predicted from microbial genomes. As MS guided genome mining starts at the chemotype level by e.g. liquid chromatography-tandem mass spectrometry analysis of a microbial extract and subsequently connects putative natural products with their gene clusters, it has the potential for automation. In Chapter 2, peptidogenomics is introduced as a MS-guided genome mining approach for characterization of ribosomal and nonribosomal peptide chemotypes and their corresponding genotypes. Peptidogenomics characterized ten new peptide chemo- and genotypes from Streptomyces cultures including lanthipeptides, lassopeptides, linaridins and lipopeptides. In Chapter 3, a combination of imaging mass spectrometry, tandem MS and genome mining characterized the biosynthetic pathway of the didemnin anti-cancer agents in the marine alpha-proteobacterium Tistrella mobilis. In Chapter 4, glycogenomics is introduced as a MS-guided genome mining approach to connect chemo- and genotypes of glycosylated natural products. Glycogenomics enabled the discovery of putative arenimycin B, a glycosylated aromatic polyketide from the marine actinobacterium Salinispora arenicola and its biosynthetic pathway. In Chapter 5, bioactivity-guided genome mining combined with genetic knockouts and glycogenomics characterized the biosynthetic gene cluster of the lomaiviticins anti cancer agents in the marine actinobacterium Salinispora tropica.
Genome Mining on Fungal Polyketide Natural Products for Discovery of Novel Enzymology
Author: YIU-SUN HUNGPublisher:
ISBN:
Category :
Languages : en
Pages : 144
Book Description
Genome mining is a promising approach to elucidate the biosynthetic origins of natural products. Their structural complexity often originated from intriguing enzymatic reactions, in which understanding in biosynthesis could lead to discoveries of novel enzymology, which can be further utilized as biocatalysts for various biotechnological applications. Throughout my doctoral research, I have applied this methodology in biosynthetic studies for three fungal polyketide natural products of interest, where their synthetically challenging chemical moieties were resolved by enzyme catalysis in a highly regio- and stereospecific manner. The newly characterized enzymes have diverse functions, including isomerase, halogenase, and radical oxidase. Apart from their potential to be further developed into biocatalysts to conduct challenging chemical transformations, new drug analogs can also be developed from their bioactive parenting molecules. As a whole, this document not only aims to illustrate the theoretical and experimental details to arrive at these observations and conclusions, it can hopefully serve as motivation for future optimization and application of this promising concept of genome mining with extended applications, coupled with the rapid technological advancement.
Antimicrobial Therapies
Author: Carlos Barreiro (Editor)Publisher:
ISBN: 9781071613580
Category : Anti-infective agents
Languages : en
Pages : 443
Book Description
Antimicrobial resistance will become a global health threat since antimicrobial treatments continue at the forefront of the defense against microbial infections. To respond to the issue, this detailed book explores vital methodologies currently in use to advance our understanding of antibiotic issues and answer the worldwide demand for novel antibiotics therapies. Beginning with a review chapter that guides the reader through the worldwide demand for novel antibiotics therapies, the volume continues with sections covering new screening procedures and environmental sources, advances in analytical, microbiological, and biotechnological methodologies, antibiotic production and antibiotic resistances, as well as considerations of drug trials and clinical concerns regarding multi-resistant patients. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Antimicrobial Therapies: Methods and Protocols provides a reference source for health, laboratory, and industrial professionals, as well as for graduate students in a number of bio-sanitary disciplines, including medicine, nursery, biotechnology, veterinary, microbiology, genetics, molecular biology, nutrition, farming, and more.
Bacteriocins and Other Ribosomally Synthesised and Post-translationally Modified Peptides (RiPPs) as Alternatives to Antibiotics
Author: Harsh MathurPublisher: Frontiers Media SA
ISBN: 2889711110
Category : Science
Languages : en
Pages : 177
Book Description
Prof Upton is the director of Amprologix, a company developing new bacteriocins; the other editors declare no competing interest in regard to editing this Research Topic.
Genome Mining for Structurally Novel Class II Lanthipeptides and Probing the Conformational Dynamics of PhnZ Using Hydrogen Deuterium Exchange Mass Spectrometry
Author: Sally HamryPublisher:
ISBN:
Category :
Languages : en
Pages :
Book Description
"Nature provides a remarkable suite of natural products and biochemical catalysts (enzymes) that have proven beneficial for medicine and agriculture. This research first employs a genome mining-based approach to identify structurally novel lanthipeptide natural products. Lanthipeptides are a subfamily of genetically encoded ribosomally-synthesized and post-translationally modified peptides (RiPPs) that possess characteristic thioether bridges. The thioether bridges are installed by multifunctional enzymes (lanthipeptide synthetases) and confer biological activity to the peptide. Both the synthetases and the macrocyclized peptide products have drawn interest from the research community for the biocatalytic and biomedical properties, respectively. Using a plethora of bioinformatic tools, we have discovered several unique lanthipeptide biosynthetic gene clusters in the bacterial phylum, Actinobacteria. These include unusual glycine-rich lanthipeptides produced by the human symbiont, Rothia dentocariosa M567, as well as highly macrocyclized lanthipeptides from the soil actinomycete, Micromonospora saelicesensis DSM 44871. Preliminary structural characterization of the enzymatically modified peptides suggests that these peptides possess structurally novel sets of thioether linkages that may allow for novel biological functions. In support of this, the M. saelicesensis DSM 44871lanthipeptides were shown to stimulate plant growth. In a second research project, I investigate PhnZ, a metal ion-dependent phosphohydrolase of the HD superfamily. PhnZ is the second component of a two-enzyme oxidative pathway that works alongside PhnY to generate the nutrients inorganic phosphate and glycine. PhnZ shows extraordinary ability to perform the oxidative cleavage of a highly stable carbon phosphorous (CP)-bond using a mixed valence diiron (II/III) cofactor and O2 to generate glycine and Pi. PhnZ can potentially be exploited to break down glyphosate (Roundup) - an extensively used herbicide that has garnered controversy for contaminating unintended targets. However, the native specificity of PhnZ must be tuned to cleave the CP-bond of glyphosate. Enzyme engineering can successfully manipulate enzyme specificity, but a thorough understanding of the structure and function of PhnZ is required. X-ray crystallography has revealed that PhnZ must undergo extensive conformational changes to accomplish CP-bond cleavage. Yet, this is only a snapshot of the whole story as crystal structures alone cannot provide an accurate description of solution-phase protein structural fluctuations. Here we aim to gain a more detailed understanding of the conformational dynamics of PhnZ and the atomic-scale fluctuations that occurs over multiple timescales. A bottom-up continuous labeling hydrogen deuterium exchange mass spectrometry workflow was implemented to investigate the change in conformational dynamics of PhnZ upon substrate binding to a nonreactive substrate mimic, 1-hydroxyethylphosphonic acid"--
Love and Other Dangerous Chemicals
Author: Anthony CapellaPublisher: Atlantic Books
ISBN: 0857890263
Category : Fiction
Languages : en
Pages : 355
Book Description
Dr. Steven J. Fisher is a young and brilliant biochemist (special subject: the female orgasm). He's invented a Viagra-like pill for women—now he just needs his results to be perfect. Annie is an orgasmically-challenged arts student (special subject: Victorian semicolons). She's just volunteered to be one of Fisher's case studies—but for some reason his miracle treatment isn't working. As scientist and subject bond over romantic meals lit by the flickering glow of a Bunsen burner, Dr. Fisher is surprised to find his feelings taking a most unscientifc turn. . . What if love is one thing science can't explain?