Open access peer-reviewed chapter - ONLINE FIRST

Nonribosomal Peptide Synthesis

Written By

Sadık Dincer, Hatice Aysun Mercimek Takci and Melis Sumengen Ozdenefe

Reviewed: March 28th, 2022 Published: April 30th, 2022

DOI: 10.5772/intechopen.104722

IntechOpen
Molecular Cloning Edited by Sadik Dincer

From the Edited Volume

Molecular Cloning [Working Title]

Prof. Sadik Dincer, Dr. Hatice Aysun Merci̇mek Takci and Associate Prof. Melis Sümengen Özdenefe

Chapter metrics overview

21 Chapter Downloads

View Full Metrics

Abstract

Nonribosomal peptides (NRPs) are a type of secondary metabolite with a wide range of pharmacological and biological activities including cytostatics, immunosuppressants or anticancer agents, antibiotics, pigments, siderophores, toxins. NRPs, unlike other proteins, are synthesized on huge nonribosomal peptide synthetase (NRPS) enzyme complexes that are not dependent on ribosomal machinery. Bacteria and fungi are the most common NRPs producers. Furthermore, the presence of these peptides has been confirmed in marine microbes. Nowadays, many of these peptides are used in the treatments of inflammatory, cancer, neurodegenerative disorders, and infectious disease for the development of new therapeutic agents. The structure, function, and synthesis of NRPs, as well as producer microorganisms and their several application areas, are covered in this chapter.

Keywords

  • biological activity
  • nonribosomal peptide
  • producer microorganisms
  • secondary metabolite
  • synthesis
  • structure

1. Introduction

Bioprocesses, which are consisted of a series of enzymatically catalyzed biochemical reactions in all living things, are necessary for survival. They have a high potential in terms of material synthesis, which has recently been performed by chemical techniques [1]. Furthermore, the advancement of heterologous production systems and genetic engineering techniques has resulted in pioneering initiatives to manufacture usable biomaterials [2]. These advancements also enabled the successful generation of primary and secondary metabolic pathway products in physiologically and genetically well-defined hosts, such as Escherichia coliand Saccharomyces cerevisiae, by precise manipulation of the related genes. In particular, heterologous molecular hosts have been used to successfully synthesize structurally varied secondary metabolites showing unique pharmacological action [1, 2, 3]. Nonribosomal peptides (NRPs) obtained by the most extensive, appealing, and useful actively-studied bioprocesses are included among these metabolites, which are important in the discovery and development of drugs and therapeutic reagents [1, 4].

NRPs are secondary metabolites that are synthesized outside of the ribosomal machinery and have a variety of properties such as cytostatics, immunosuppressants or anticancer agents, antibiotics, pigments, siderophores, toxins [3, 5, 6]. NRPs are typically produced by marine microorganisms and invertebrates, as well as soil-inhabiting microorganisms [5, 7, 8]. The majority of natural products produced by sponges, bryozoans, mollusks, and tunicates are members of the NRP or mixed polyketide–NRP families. Several of NRPs are being used in the development of new medicines for inflammatory, cancer, neurological diseases, and infectious disease nowadays [7].

Non-ribosomal peptide synthetases (NRPSs) enzymes are poly-functional mega-synthases that biosynthesize NRPs [7, 9, 10]. NRPSs, multi-modular enzyme or enzyme complexes from common bacteria, less common eukarya, and rare archaea, are capable of producing a wide range of natural pharmaceutical products (Bacitracin, antibiotics for skin infections; Bleomycin antitumor; Cyclosporin, antifungal, and immunosuppressive drugs; Daptomycin, antibiotics) [5, 7, 11]. NRPSs use both proteinogenic and nonproteinogenic amino acids (not encoded by DNA) as building blocks for the growing peptide chain [1, 7, 11, 12]. They catalyze multiple biosynthetic processes, each of which is responsible for particular one amino acid elongation on the growing peptide chain [10]. This chapter looks at the structure, function, and synthesis of NRPs, as well as producer microorganisms and their various applications.

Advertisement

2. Synthesis, structure, and function of nonribosomal peptide (NRP)

NRPSs are responsible for nonribosomal peptide (NRP) synthesis. These are large multi-enzyme complexes that are modularly organized and serve as biosynthetic machinery and templates [5, 11, 12, 13, 14]. For example, a single NRPS of 1.6 MDa synthesizes the Cyclosporine A (7). In fungal systems, such as in the case of cyclosporine A (7), a single NRPS synthesizes peptides, whereas bacteria frequently use numerous NRPSs with genes grouped in an operon. NRPSs have a modular structure [14, 15].

In a genome mining research of 2699 genomes, Wang et al. found that more than half of the NRPS enzymes were non-modular NRPS enzymes [16]. Nonmodular NRPS enzymes can be found in siderophore biosynthesis pathways, such as EntE and VibH in enterobactin and VibE in vibriobactin, or as a standalone peptidyl carrier protein, such as BlmI from the bleomycin gene cluster. NRPS enzymes are found frequently in bacteria, less frequently in eukaryotes, and infrequently in archaea. Actinobacteria, Cyanobacteria, Firmicutes, and Proteobacteria were the phyla with the greatest number of these enzymes in the bacterial domain. There was a correlation between genome size and the number of NRPS clusters [5, 17].

A module is a part of the NRPS polypeptide chain that is in charge of integrating one amino acid into the final product. Modules can further be separated into domains (Figure 1), which represent enzyme units that catalyze distinct steps of NRP synthesis. On the protein level, domains are defined by distinctive, greatly conserved order of patterns known as “core motifs.” In certain instances, biochemical and structural data were used to confirm the involvement of greatly conserved residues in domain function (Table 1) [14].

Figure 1.

Catalyzed reactions by various NRPS-domains [14].

A-domainsPCP-domains
A1 L(TS)YxEL
A2 LKAGxAYL(VL)P(LI)D
A3 LAYxxYTSG(ST)TGxPKG
A4 FDxS
A5 NxYGPTE
A6 GELxJGx(VL)ARGYL
A7 Y(RK)TGDL
A8 GRxPxQVKIRGxRIELGEIE
A9 LPxYM(IV)P
A10 NGK(VL)DR
T LGG(DH)SL
C-domainsTe-domains
C1 SxAQxR(LM)(WY)xL
C2 RHExLRTxF
C3 MHHxISDG(WV)S
C4 YxD(FY)AVW
C5 (IV)GxFVNT(QL)(CA)xR
C6 HN)QD(YD)PFE
C7 RDxSRNPL
Te GxSxG
E-domainsCy-domains
E1 PIQxWF
E2 HHxISDG(WV)S
E3 DxLLxAxG
E4 EGHGRE
E5 RTVGWFTxxYP(YV)PFE
E6 PxxGxGYG
E7 FNYLG(QR)
Cy1 FPL(TS)xxQxAYxxGR
Cy2 RHx(IM)L(PAL)x(ND)GxQ
C3 D(NLI)xDxxS
Cy3 LPxxPxLPLxxxP
Cy4 (TS)(PA)3x(LAF)6x(IVT)LxxW
Cy5 (GA)DFTxLxLL
Cy6 PVVFTSxL
Cy7 (ST)(QR)TPQVx(LI)D13xWD
Ox-domainsN-Mt-domains
Ox1 KYxYxSxGxxY(PG)VQ
Ox2 GxxxG(LV)xxGxYYY(HD)P
Ox3 IxxxYG
M1 VL(DE)xGxGxG
M2 NELSxYRYxAV
M3 VExSxARQxGxLD
R-domains
R1 V(L)(L)TG(A)TG(F)(L)GxxLL
R2 Vx(L)(L)VR(A)
R3 GPL(G)x(P)x(L)GL
R4 V(Y)PYxYLxx(P)NVxxT
R5 GYxxSKW(A)(A)E
R6 R(P)G
R7 YxxxxG(LF)LxxP

Table 1.

NPRS-domains’ core-motifs [14].

There are three domains in a module. These are 1) the adenylation (A) domain, 2) the peptidyl carrier protein (PCP) or thiolation (T) domain, and 3) the condensation (C) domain, all of which are responsible for the synthesis of NRPs. A module may include additional tailoring or altering domains incorporating epimerization (E), methylation and oxidation domains or a heterocyclization (Cy) domain in place of a C-domain. Finally, most NRPS termination modules have a TE-domain, which is in charge of releasing linear, cyclic, or branching cyclic peptides [5, 9, 10, 11, 15, 18, 19, 20, 21].

The order of the modules is frequently aligned with the sequences of the resulting peptides. NRP synthesis begins at the N-terminus and ends at the C-terminus, yielding peptides that are typically 3–15 amino acids long. The released peptides contain amino acids, that is, imino acids or ornithine and their structures are linear, cyclic-macrocyclic, branched-cyclic, branched-macrocyclic, dimers or trimers of identical structural elements [5].

The A-domain is responsible for the first step in biosynthesis, which involves recognizing and activating the amino acid substrate via adenylation with Mg-ATP, resulting in an aminoacyl adenylated intermediate. Around 550 amino acids make up domain A. It has 10 amino acid residues that serve as NRPS enzyme “codons” and are essential for substrate specificity. The D and L forms of the 20 amino acids used in ribosomal protein synthesis, as well as non-proteinogenic amino acids like imino acids, ornithine, and hydroxy acids like β-butyric acids and α-aminoadipic, are substrates recognized by the A-domain. The PCP-domain, which consists of about 80 amino acids and covalently attaches the activated amino acid to their cofactor 4′-phosphopantetheine (PP) arm via a thioester bond, completes the second step. And also, the active substrate and elongation intermediates are transferred to the C-domain via this domain. In the last step, C-domain, which contains approximately 450 amino acids, catalyzes the formation of peptide bonds between the carboxyl group of the incipiently synthesized peptide and the amino acid transported by the side module [5, 22]. Furthermore, this domain allows the expanding chain to be translocated to the next module. Following this step, the linear intermediate peptide is liberated in bacteria via internal cyclization or hydrolysis with the help of the Thioesterase (TE) domain. On the other hand, it appears less commonly in fungi’s NRPSs. Fungi use a variety of ways to release chains. The first is a thioesterase NADP(H)-dependent reductase domain (R), which catalyzes NADPH reduction to create an aldehyde and the second is a terminal C domain, which catalyzes release by forming intermolecular or intramolecular amide bonds. By N-, C-, and O-methylation, halogenation, acylation, hydroxylation, glycosylation, or heterocyclic ring formation, the primary product of this synthesis can be changed post-synthetically to reach its mature form by additional tailoring enzymes that are not part of the NRPS. The structural diversity of NRPs is formed in part by these enzymes and their reactions [5].

Because of their extensive multidomain organization, NRPS genes are easier to identify using recent genome mining technologies, and they are also relatively easy to detect. Secondary metabolites production genes are frequently found in bacterial and fungal gene clusters. The clusters’ core is thought to be NRPS genes. Nevertheless, they are linked to genes involved in building blocks synthesis, product ornamentation, self-resistance, and peptide export. For the purpose of analyzing and in silico exploration of NRPS pathways, advanced genome sequencing techniques have made genome mining methodologies available, which are assisted by a variety of bioinformatics tools, such as AntiSMASH, PRISM, and SMURF [23].

Nowadays, known NRP structures are divided into various categories, each with its own structural characteristics. Lipocyclopeptides with varied linkage patterns, such as fengycin, iturin, surfactin, and head-to-tail-cyclized peptides of varying ring sizes, such as cyclosporine, gramicidin S, maybe the largest group. There are also a lot of linear peptide configurations. They include tripeptides (such as sevadicin and bialaphos) as well as 20-mer peptides (e.g., alamethicin, peptaibols). The current highest size limit for NRPs is syringopeptin 25A, which has 25 amino acids (syringopeptin 25A). Tailoring enzymes modify the structure of some NRPs. The most structurally complicated molecules are probably bleomycins, ergopeptides, glycopeptide antibiotics, and β-lactams [23].

Figure 2 shows some NRPs with diverse structures and a wide spectrum of activities. ACV-tripeptide (6), for example, is a precursor to antibiotics of the penicillin and cephalosporin families. Gramicidin S (4), tyrocidine A (1), and vancomycin (5) are three other antibiotic-active substances. Cyclosporin A (7), an immunosuppressive drug, is used in the post-transplantation care of patients. Cancer is treated with cytostatic agents, such as bleomycin A2 (8) and epothilone (9). Enterobactin (10), bacillibactin (11), mixochelin A (12), yersiniabactin (13), and vibriobactin (14) are examples of iron chelating agents. These compounds, known as siderophores, are created in iron-deficient environments to provide bacteria with an iron source. Figure 2 also depicts the structures of pigments like indigodin (15), toxins like thaxtomin A (17), and peptides with uncertain functions like anabaenopeptilide 90-A (18) [14].

Figure 2.

Some NRPs with structural diversity [14].

NRPs have a number of structural characteristics that distinguish them from ribosomal peptides. For example, non-proteinogenic amino acids, such as ornithine in 1, 2, and 4, hydroxyphenyl or dihydroxyphenyl-glycine in 5 and (4R)-4-[(E)-2-butenyl]-4-methyl-L. -threonine (Bmt) in 7, are included. Furthermore, the structures are frequently macrocyclic (1), branched macrocyclic (2), or dimers of two (4) or trimers of three (10, 11) structural components. Smaller heterocyclic rings, such as thiazole in 9, thiazoline in 13, or oxazoline in 14, are common structural properties of nonribosomal peptides. In addition, fatty acids (3), glycosylations (5), N-methylations (7), and N-formylations (18) may also be present, as well as the addition of propionate units (8) or acetate [14].

Advertisement

3. Overview of producer microorganisms for NRP

NRPs are typically produced by marine microorganisms, soil-inhabiting microorganisms, including Actinomycetes, Bacilli,and eukaryotic filamentous fungus, and invertebrates, such as sponges, bryozoans, mollusks, and tunicates [5, 7, 11, 13, 24]. Many pharmacologically active NRPs have been effectively generated in heterologous hosts, such as Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae,and Streptomycessp. [2]. Bacteria and fungi are the primary producers of NRPS-based metabolites. Except for bacteria and fungus, NRPS Ebony from Drosophila melanogaster(“fruit fly”) and nemamide synthetase from the worm Caenorhabditis eleganshave been confirmed. The distribution and occurrence of NRPS pathways and products have been discovered, thanks to screening efforts and genome sequencing projects followed by bioinformatics research. NRPS enzymes are found frequently in bacteria, less frequently in eukaryotes, and infrequently in archaea. The phylum Actinobacteria (Mycobacterium, Streptomyces), Firmicutes (Bacillus, Staphylococcus,and Streptococcus), and the alpha-/beta-/gama-Proteobacteria classes (Burkholderia, Escherichia, Erwinia, Photorhabdus, Pseudomonas, Salmonella, Serratia, Vibrio, and Yersinia) are the most important contributors among bacteria. Nonetheless, in recent years, the phylum Cyanobacteria (Microcystis, Planktothrix, Anabaena, Oscillatoria,and Nostoc) and the teta-Proteobacteria (Myxobacterium) class have received greater attention [5, 22, 23]. NPRS genes are found predominantly in the Ascomycota (Tolypocladium, Fusarium, Penicillium, Acremonium, Claviceps,and Trichoderma) and marginally in the Basidiomycota (Ustilago) phylum. NRPS biosynthesis investigations in fungus are less investigated than in bacteria due to greater genome sizes, the existence of scattered introns in gene clusters, and a less established molecular biology toolbox [23].

Advertisement

4. Application areas of NRPs

Novel peptide products’ biological functions are strictly associated with their chemical structure, which is constrained by a peptide sequence that ensures specific interaction with a specific molecular target. Chemical alterations, such as the incorporation of fatty acid chains, D-amino acids, glycosylated amino acids, and heterocyclic rings, as well as cyclization or oxidative cross-linking of side chains, add a lot to these unique interactions. Bacitracin, fengycin, pristinamycin, surfactin, tyrocidine, and vancomycin are examples of novel peptides with antibacterial and antifungal properties [25].

When the ribosomal code was deciphered in the 1960s, Tatum and coworkers discovered that ribosomes had no effect on cell-based tyrocidine production [23, 26]. The first NRPs agent is tyrocidine, a cyclic decapeptide that is biosynthesized outside of the Bacillus brevisribosome. Researchers discovered that ribosome targeting antibiotics had no effect on tyrocidine production. They also discovered that B. breviscan synthesize gramicidin S, a cyclic decapeptide, without the use of tRNA molecules or aminoacyl-tRNA synthetases [13, 27]. Nobel Prize Laureate Fritz Lipmann and Søren Laland contributed to present essential biochemical activity insights into NRPSs, including specific ATP-dependent activation of amino acids, thioester-mediated 4′-phosphopantetheine (Ppant) binding of activated amino acids, and the directionality of the peptide synthesis and have given acceleration to the production of NRPS-based metabolites synthesized by a mechanism distinct from protein synthesis. The NRPs and NRPSs were discovered as a result of these findings associated with the synthesis of tyrocidine and gramicidin S peptides. Surprisingly, the majority of studies investigating nonribosomal NRPS-based metabolites have focused on antibacterial and antifungal action [23]. NRPS-based metabolites with antimalarial, antimicrobial, antiparasitic, antiviral, animal growth promoters, cytostatic, immunosuppressive, and natural insecticides properties are currently available on the market, and several are being studied in clinical research [28]. Table 2 presents a summary of commercialized NRPs-based medications with antibacterial activity.

CompoundBiosynthetic class of agentSourceDisease/Molecular target
BacitracinCyclic peptideBacillus subtilisAntibiotic/dephosphorylation of C55-isoprenyl pyrophosphate
BleomycinHybrid peptideStreptomyces verticillusAntibiotic/inhibition of DNA synthesis
CapreomycinCyclicpeptideStreptomyces capreolusAntibiotic/protein synthesis inhibitor
CarbapenemsSynthetic thienamycinStreptomyces cattleyaAntibacterial (multidrug resistant)/bacterial cell-wall biosynthesis (peptidoglycan;β-lactamase inhibition)
Cephalosporinβ-lactamAcremonium chrysogenumAntibiotic/Alters bacterial outer membrane
ChlorampheniolSynthetic;further derivatives: thiamphenicol [c], florfenicolStreptomyces venezuelaeAntibacterial/inhibition of ribosomal protein synthesis
Colistin (Polymyxin E)Paenibacillus polymyxa var. colistinusAntibacterial/binding to lipopolysaccharide (outer membrane), interaction with the cytoplasmic membrane
DalbavancinSemisynthetic teicoplanin derivativeAntibacterial (Gram-positive)/membrane anchoring; disruption of cell membrane and inhibition of bacterial cell wall biosynthesis
DaptomycinLipopeptideStreptomyces roseosporusAntibiotic (Gram-positive)/disrupts the cell membrane
GramicidinLinear pentadecapeptideBacillus brevisAntibiotic/ion-channel formation, increasing the permeability of the membrane
LincomycinStreptomyces lincolnensisAntibacterial (patients allergic to penicillin) inhibition of the ribosomal protein synthesis (50S-subunit, dissociation of peptidyl-tRNA from the ribosome)
MonobactamsChromobacterium violaceumAntibacterial (Gram-negative)/bacterial cell-wall biosynthesis
OritavancinSemi syntheticAntibiotic/disrupts the cell membrane
Polymyxin BPolypeptidesBacillus polymxyaAntibacterial (Gram-negative)/binding to lipopolysaccharide (outer membrane), interaction with cytoplasmic membrane
PristinamycinDepsipeptideStreptomyces pristinaespiralisAntibacterial (Gram-positive)/ribosomal biosynthesis (50S-subunit, peptidyl transfer, and elongation of protein synthesis)
TeicoplaninGlycopeptideActinoplanes teichomyceticusAntibiotic/inhibit cell wall synthesis
TelavancinAmycolatopsis orientalisAntibacterial (Gram-positive) disruption of cell membrane and inhibition of bacterial cell-wall biosynthesis
TyrothricinBacillus brevisAntibacterial (Gram-positive)/disruption of cell membrane
VancomycinGlycopeptideAmycolatopsis orientalisAntibiotic/inhibit cell wall synthesis
VirginiamycinStreptomyces virginiaeAntibacterial/ribosomal biosynthesis (50S-subunit, peptidyl transfer, and elongation of protein synthesis)

Table 2.

Overview of NRPs-based drugs [7, 23].

As demonstrated in Table 2, systemic and topical antibacterials are the most often used NRPs-based drugs, accounting for billions of dollars in the chemical and pharmaceutical industry sales. Table 3 lists their other applications, which include anticancer agents, antifungals, animal feed additives, immunosuppressants (cyclosporine), obstetrics (ergometrine), and pain management (ergotamine).

AgentOriginProperties and area of application
Actinomycin D (Dactinomycin)Actinomyces antibioticus, Streptomyces chrysomallusAntitumor/DNA intercalator, inhibition of transcription
BialaphosStreptomyces hygroscopicus, Streptomyces viridochromogenesHerbicide/tripeptide prodrug, inhibitor of glutamine synthetase
Bleomycin A2, B2Streptomyces verticillusAntitumor/metal-dependent oxidative cleavage of DNA in presence of molecular oxygen
CapreomycinStreptomyces capreolusAntituberculous/ inhibition of the ribosomal protein synthesis (16S and 23S-rRNA)
CarfilzomibSynthetic derivative of epoxomycin (Actinomycessp.)Anticancer/proteasome inhibitor
CaspofunginGlarea lozoyensis, semisynthetic from pneumocandin; further derivatives: micafungin/anidulafunginAntifungal (candidiasis, aspergillosis) fungal cell-wall integrity ((1-3)-β-D-glucan synthase)
Cyclosporine ATolypocladium inflatumImmunosuppressant/cyclophilin binding, inhibition of IL-2 expression (inhibition of T-cell activation)
EmodepsideMycelia sterilia(F); semisynthetic from PF1022AAnthelmintic/Slo-1 receptor (K+ channel)
Enduracidin (Enramycin)Streptomyces fungicidicusAntibacterial, food additive/inhibition of MurG (essential for cell-wall biosynthesis in Gram positive bacteria), inhibition of the transglycosylation step of peptidoglycan biosynthesis
Enniatins (fusafungine)Fusarium lateritium, Fusarium scirpi, Fusariumsp.Antibacterial (topical), antifungal, anti-inflammatory/ ionophore (NH4+) membrane depolarization
Ergometrine (ergonovine)Claviceps purpureaObstetrics/interaction with a-adrenergic, dopaminergic and serotonin receptors
ErgotamineClaviceps purpureaMigraine vasoconstrictive (5-HT1B receptor, but also dopamine and noradrenaline receptors)
RomidepsinChromobacterium violaceumAntitumor/histone deacetylase inhibitor (inducing apoptosis)
TrabectedinBacterial symbiont of Ecteinascidia turbinata(sea squirt)Antitumor (antiproliferative, treatment of soft tissue sarcoma) DNA binder, blocks binding of transcription factors

Table 3.

Marketed-NRPs agents [23].

In the medical field, NRP-based marketed drugs, such as Cyclosporin A and Bleomycin A2, have high selling prices. The cost of these medicines is $107 for 25 mg of Cyclosporine A (98% purity) obtained from T. inflatumand $847 for 20 mg of Bleomycin A2 (70% purity) isolated from S. verticillus, according to Sigma Chemical Company [5].

The 70% discovery of NRPs with antibacterial, antiviral, cytostatic, immunosuppressive, antimalarial, antiparasitic, animal growth promoters, and natural insecticides activity is mostly attributed to marine organisms [13]. NRPs obtained from marine organisms (sponges, tunicates, and their associated phyla, such as Acidobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Cyanobacteria, Nitrospira, Planctomycetes, Poribacteria, Proteobacteria, Verrucomicrobia, and Archaea) have excellent binding properties, low off-target toxicity, and high stability and these properties make them a promising molecule for the development of new therapeutics pharmacologically active in many clinical searches. Table 4 shows the chemical structure and source of various NRPs isolated from marine sponges and tunicates.

NRPs agentsChemical classOriginTarget
Miraziridine ALinear pentapeptideTheonellaaff. mirabilisCancer/inhibit protease cathepsin B
Haligramides A-BCyclic hexapeptidesHaliclona nigraCancer/A-549 (lung), HCT-15 (colon), SF-539 (CNS), SNB-19 (CNS)
Prepatellamide ACyclic peptideLissoclinum patellaCancer/P388 murine leukemia cell lines
Tamandarins A-BDepsipeptidesDidemnid ascidianCancer/pancreatic carcinoma BX-PC3, prostatic cancer DU-145, head and neck carcinoma UMSCC10b
Microsclerodermins F–ICyclic peptidesMicrosclerodermasp.Cancer/HCT-116 cell line
WainunuamideCyclic hexapeptideStylotella aurantiumCancer/A2780 ovarian, K562 leukemia cancer cells
Leucamide ACyclic hexapeptideLeucetta microraphisCancer/Tumor cell lines HM02, HepG2, Huh7
Axinellin CCyclic octapeptideStylotella aurantiumCancer/A2780 ovarian, K562 leukemia cancer cells
Milnamide DLinearpeptideCymbastelasp.Cancer/HCT-116 cells
Kapakahines E–GCribrochalina olemdaCancer/P388 murine leukemia cells
Didmolamides A-BCyclic hexapeptidesDidemnum molleCancer Tumor cell lines (A549, HT29 and MEL28)
Bistratamides E–JCyclic hexapeptidesLissoclinum bistratumCancer/Human colon tumor (HCT-116) cell line
Milnamide CAulettasp.Cancer/MDA-MB-435cancer cells
Scleritodermin ACyclic peptideScleritoderma nodosumCancer
Microcionamids A-BClathria abietinaCancer/Human breast tumor cell lines MCF-7 and SKBR-3
Kendarimide ALinear peptideHaliclonasp.Cancer/KB-C2 cells
Phakellistatin 14Cyclo heptapeptidePhakelliasp.Cancer/Murine lymphocytic leukemia P388 cell line
Polytheonamides A-BPolypeptidesTheonella swinhoeiCancer/P388 murine leukemia cells
Neopetrosiamides A-BTricyclic peptidesNeopetrosiasp.Cancer
Seragamides A–FDepsipeptidesSuberites japonicusCancer
TheopapuamideCyclic depsipeptideTheonella swinhoeiCancer/CEM-TART, HCT-116 cell lines
Azumamide A-ECyclo tetrapeptidesMycale izuensisCancer
Callyaerin GCyclic peptideCallyspongia aerizusaCancer/Mouselymphoma cell line (L5178Y) and HeLa cells
Stylopeptide 2Cyclo decapeptideStylotellasp.Cancer/BT-549 and HS578T breast cancer cell lines
Ciliatamides A-CLipopeptidesAaptos ciliateCancer/HeLa cells
Diazonamides C–EMacrocyclic peptidesDiazonasp.Cancer/Human tumor cell lines (A549, HT29, MDA-MB231)
Rolloamide A-BCyclic heptapeptidesEurypon laughliniCancer
Euryjanicin ACycloheptapeptideProsuberites laughliniCancer
Callyaerin A–F and HCyclic peptidesCallyspongia aerizusaCancer/L5178Y cell line
Papuamides E-FDepsipeptidesMelophlussp.Cancer/Brine shrimp
Stylissamide XOctapeptideStylissasp.Cancer/HeLa cells
Gombamide AHexapeptideClathria gombawuiensisCancer/K562 and A549 cell lines
MicrospinosamideCyclic depsipeptideSidonops microspinosaHIV
Neamphamide ACyclic depsipeptideNeamphius huxleyiHIV
Mirabamides A-DCyclic depsipeptideSiliquariaspongia mirabilisHIV
Homophymine ACyclodepsipeptideHomophymiasp.HIV/PBMC cell line
Celebeside A-CDepsipeptidesSiliquariaspongia mirabilisHIV/Colon carcinoma (HCT-116) cells
Theopapuamides B–D, Mutremdamide A, Koshikamides C-HCyclic depsipeptideTheonellasp.HIV
CeratospongamideCyclic heptapeptideSigmadocia symbioticaInflammation
Halipeptin A-BCyclic depsipeptideHaliclona sp.Inflammation
Perthamide C-DCyclopeptideTheonella swinhoeiInflammation
Solomonamide A- BCyclic peptideTheonella swinhoeiInflammation
Stylissatin ACyclic peptideStylissa massaMurine macrophage RAW264.7
DicynthaurinHalocynthia aurantiumAntimicrobial
Nagahamide ADepsipeptideTheonella swinhoeiAntibacterial
PlicatamideOctapeptideStyela plicataAntimicrobial
CallipeltinsLatrunculia sp.Antifungal/Candida albicans
Citronamides A- BCitronia astraAntifungal/Saccharomyces cerevisiae
RenieramideCyclic tripeptideRenierasp.
Phoriospongins A-BDepsipeptidePhoriospongiasp. and Callyspongia bilamellataNematocidal/Haemonchus contortus

Table 4.

Agents produced from marine sponges and tunicates which are based on NRPs [7].

In the NCBI database, there are currently about 1.164 distinct non-ribosomal peptides that form over 500 different monomers including both proteinogenic and non-proteinogenic L- and D-amino acids, as well as amines and carboxylic acids. These complex secondary metabolites’ linear, cyclic, branching, or other complicated primary structures are frequently altered to enhance clinical qualities and/or bypass resistance mechanisms. Indeed, the nucleotide sequence modification of a native NRPS gene or mixing modules from multiple NRPSs makes them more efficient with pharmacological properties. Several bioengineering and molecular techniques have been developed during the last few decades to produce modified NRPs with improved physicochemical characteristics and bioactivity [13].

Advertisement

5. Conclusion

In this chapter, we discussed the significance, synthesis, and application areas of NRPs-based agents, which have received a lot of interest as a new source of pharmaceutical agents. NRPs with unique chemical structures and diverse biological actions, such as antibacterials (penicillin, vancomycin), anticancer compounds (bleomycin), and immunosuppressants (cyclosporine), have been researched as novel compounds for new drug discovery and development throughout the last several decades. In vitrobioassays and the transfer of biosynthetic gene clusters of NRPs have been the focus of the majority of these studies. For the development of NRPs drugs with improved pharmacological properties, genetic manipulation and molecular approaches will allow the rapid construction of new NRPSs containing specific point mutations or exchanged domains.

References

  1. 1. Tsuge K, Matsui K, Itaya M. Production of the non-ribosomal peptide plipastatin inBacillus subtilisregulated by three relevant gene blocks assembled in a single movable DNA segment. Journal of Biotechnology. 2007;129:592-603. DOI: 10.1016/j.jbiotec.2007.01.033
  2. 2. Siewers V, San-Bento R, Nielsen J. Implementation of communication-mediating domains for non-ribosomal peptide production inSaccharomyces cerevisiae. Biotechnology and Bioengineering. 2010;106(5):841-844. DOI: 10.1002/bit.22739
  3. 3. Zhang H, Liu Y, Wang X, Hu R, Xu G, Mao C, et al. Gene sequence diversity of the nonribosomal peptide and polyketide natural products in Changbaishan soil correlates with changes in landscape belts. Ecological Indicators. 2021;133:108160. DOI: 10.1016/j.ecolind.2021.108160
  4. 4. Corpuz JC, Sanlley JO, Burkart MD. Protein-protein interface analysis of the non-ribosomal peptide synthetase peptidyl carrier protein and enzymatic domains. Synthetic and Systems Biotechnology. 2022;7(2):677-688. DOI: 10.1016/j.synbio.2022.02.006
  5. 5. Martinez-Nunez MA, López y López VE. Nonribosomal peptides synthetases and their applications in industry. Sustainable Chemical Processes. 2016;4:13. DOI: 10.1186/s40508-016-0057-6
  6. 6. Duban M, Cociancich S, Leclère V. Nonribosomal peptide synthesis definitely working out of the rules. Microorganisms. 2022;10:577. DOI: 10.3390/ microorganisms10030577
  7. 7. Agrawal S, Adholeya A, Deshmukh SK. The pharmacological potential of non-ribosomal peptides from marine sponge and tunicates. Frontiers in Pharmacology. 2016;7:333. DOI: 10.3389/fphar.2016.00333
  8. 8. Tippelt A, Nett M.Saccharomyces cerevisiaeas host for the recombinant production of polyketides and nonribosomal peptides. Microbial Cell Factories. 2021;20(1):161. DOI: 10.1186/s12934-021-01650-y
  9. 9. Izoré T, Candace Ho YT, Kaczmarski JA, Gavriilidou A, Chow KA, Steer DL, et al. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nature Communication. 2021;12(1):2511. DOI: 10.1038/s41467-021-22623-0
  10. 10. Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nature Communications. 2022;13(1):548. DOI: 10.1038/s41467-022-28221-y
  11. 11. Bozhuyuk KAJ, Fleischhacker F, Linck A, Wesche F, Tietze A, Niesert CT, et al. De novo design and engineering of non-ribosomal peptide synthetases. Nature Chemistry. 2018;10:275-281. DOI: 10.1038/NCHEM.2890
  12. 12. Oestreich AM, Suli MI, Gerlach D, Fan R, Czermak P. Media development and process parameter optimization using statistical experimental designs for the production of nonribosomal peptides inEscherichia coli. Electronic Journal of Biotechnology. 2021;52:85-92. DOI: 10.1016/j.ejbt.2021.05.001
  13. 13. Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. Nonribosomal peptides from marine microbes and their antimicrobial and anticancer potential. Frontiers in Pharmacology. 2017;8:828. DOI: 10.3389/fphar.2017.00828
  14. 14. Schwarzer D, Finking R, Marahiel MA. Nonribosomal peptides: From genes to products. Natural Product Reports. 2003;20(3):275-287. DOI: 10.1039/b111145k
  15. 15. Kittilä T, Kittel C, Tailhades J, Butz D, Schoppet M, Büttner A, et al. Halogenation of glycopeptide antibiotics occurs at the amino acid level during non-ribosomal peptide synthesis. Chemical Science. 2017;8(9):5992-6004. DOI: 10.1039/c7sc00460e
  16. 16. Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(25):9259-9264. DOI: 10.1073/pnas.1401734111
  17. 17. Chang Z, Flatt P, Gerwick WH, Nguyen VA, Willis CL, Sherman DH. The barbamide biosynthetic gene cluster: A novel marine cyanobacterial system of mixed polyketide synthase (PKS)-non-ribosomal peptide synthetase (NRPS) origin involving an unusual trichloroleucyl starter unit. Gene. 2002;296(1-2):235-247. DOI: 10.1016/S0378 1119(02)00860-0
  18. 18. Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic zippers as an enabling tool for engineering of non-ribosomal peptide synthetases. Angewandte Chemie International Edition in English. 2021;60(32):17531-17538. DOI: 10.1002/anie.202102859
  19. 19. Kries H, Niquille DL, Hilvert D. A Subdomain swap strategy for reengineering nonribosomal peptides. Chemistry & Biology. 2015;22:640-648. DOI: 10.1016/j.chembiol.2015.04.015
  20. 20. Takahashi H, Kumagai T, Kitani K, Mori M, Matoba Y, Sugiyama M. Cloning and characterization of aStreptomycesSingle module type non-ribosomal peptide synthetase catalyzing a blue pigment synthesis. The Journal of Biological Chemistry. 2007;282(12):9073-9081. DOI: 10.1074/jbc.M611319200
  21. 21. Tooming-Klunderud A, Rohrlack T, Shalchian-Tabrizi K, Kristensen T, Jakobsen KS. Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: Implications for evolution of cyanopeptolins. Microbiology. 2007;153:1382-1393. DOI: 10.1099/mic.0.2006/001123-0
  22. 22. Tapi A, Chollet-Imbert M, Scherens B, Jacques P. New approach for the detection of non-ribosomal peptide synthetase genes in Bacillus strains by polymerase chain reaction. Applied Microbiology and Biotechnology. 2010;85(5):1521-1531. DOI: 10.1007/s00253-009-2176-4
  23. 23. Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angewandte Chemie International Edition in English. 2017;56:3770-3821. DOI: 10.1002/anie.201609079
  24. 24. Zhou K, Zhang X, Zhang F, Li Z. Phylogenetically diverse cultivable fungal community and polyketide synthase (pks), non-ribosomal peptide synthase (nrps) genes associated with the South China Sea sponges. Microbial Ecology. 2011;62:644-654. DOI: 10.1007/s00248-011-9859-y
  25. 25. Sieber SA, Marahiel MA. Molecular mechanisms underlying nonribosomal peptide synthesis: Approaches to new antibiotics. Chemical Reviewes. 2005;105:715-738. DOI: 10.1021/cr0301191
  26. 26. Dell M, Dunbar KL, Hertweck C. Ribosome-independent peptide biosynthesis: The challenge of a unifying nomenclature. Natural Product Reports. 2021:1-7. DOI: 10.1039/d1np00019e
  27. 27. Iacovelli R, Bovenberg RA, Driessen AJ. Nonribosomal peptide synthetases and their biotechnological potential inPenicillium rubens. Journal of Industrial Microbiology and Biotechnology. 2021;48(kuab045). DOI: 10.1093/jimb/kuab045
  28. 28. Vinothkumar S, Parameswaran P. Recent advances in marine drug research. Biotechnology Advances. 2013;31:1826-1845. DOI: 10.1016/j.biotechadv.2013.02.006

Written By

Sadık Dincer, Hatice Aysun Mercimek Takci and Melis Sumengen Ozdenefe

Reviewed: March 28th, 2022 Published: April 30th, 2022