TCDB is operated by the Saier Lab Bioinformatics Group

1.D.24 The Marine Sponge Polytheonamide B (pThB) Family 

Polytheonamide B, from the marine sponge, Theonella swinhoei, forms a β-helix that is stable in membranes (Oiki et al. 1997; Hamada et al. 2005). It forms channels with cation selectivity: H+ > Cs+ > Rb+ > K+ > Na+ (Oiki et al. 1997). Voltage-dependent transitions between brief openings and long closures were observed (Iwamoto et al. 2010; Matsuoka et al. 2011). It has been totally synthesized, and structural permutations have been designed (Ducho 2010; Inoue et al. 2010; Inoue 2011). Derivatives have been characterized with respect to their channel activities (Itoh et al. 2012; Shinohara et al. 2012). The vectorial insertion of polytheonamide B into the membrane has been studied (Kalathingal et al. 2021). This family had previously been described under TC#s 1.D.33 and 1.D.105.

Polytheonamide B (pTB), a highly cytotoxic polypeptide, is one of the most unusual nonribosomal peptides of sponge origin. pTB is a linear 48-residue peptide with alternating D- and L-amino acids and contains a total of eight types of nonproteinogenic amino acids. Hamada et al. 2010 determined the three-dimensional structure of pTB by NMR spectroscopy, structure calculation, and energy minimization. pTB adopts a single right-handed β(6.3)-helical structure in a 1:1 mixture of methanol/chloroform with a length of approximately 45 Å and a hydrophilic pore of ca. 4 Å inner diameter. These features indicate that pTB molecules form transmembrane channels that permeate monovalent cations as gramicidin A channels do. The strong cytotoxicity of pTB can be ascribed to its ability to form single molecule channels through biological membranes.

A cytotoxic peptide, polytheonamide B (pTB or pThB), from a symbiotic bacterium in the marine sponge, Theonella swinhoei, has been examined for the cytotoxic spectrum and specific activity to mammalian cells (Iwamoto et al., 2010). pTB is composed of alternative D- and L-amino acid residues throughout the 48-mer peptide. This suggests the formation of a β-helix similar to gramicidin channels. Planar bilayer experiments revealed that pTB forms monovalent cation-selective channels, being compatible with the inner pore diameter of 4Å for a β-helical structure. pTB penetrated vectorially into the membrane, formed a channel by means of a single molecule, and remained in the membrane. These functional properties may account for specific cytotoxic activity (Iwamoto et al., 2010). Functional analysis of synthetic substructures of polytheonamide B have been reported (Matsuoka et al., 2011). 

pTB has more than half of its residues posttranslationally modified. Epimerization reactions result in alternating L- and D-amino acids that allow the peptide to adopt a helical conformation. Other posttranslational modifications include side chain hydroxylations and C- and N-methylations. N-methylations appear to be crucial for stability in a polar environment. They are the driving force for the formation of stable side chain hydrogen-bond chains that act as an 'exoskeleton' (Renevey and Riniker 2016).

Polytheonamide B (PThB) is a unique peptide natural product with an extremely complex structure, a channel-forming ability in vitro, and an extremely potent cytotoxicity (Hayata et al. 2018). The 48-mer sequence of PThB consists of alternating d,l-amino acids and possesses an array of sterically bulky beta-tetrasubstituted and hydrogen bond forming residues. These unusual structural features are believed to drive it to fold into a 4.5 nm long tube, form a transmembrane ion channel in plasma membranes, and exert cytotoxicity. Synthetic PThB was utilized for analysis of its cellular behavior. Reflecting its ion-channel function, its addition to cells rapidly diminished the potential across the plasma membrane, and it was also internalized into the cells, accumulating in acidic lysosomes, neutralizing the lysosomal pH gradient. Thus, it is capable of exerting two functions upon causing apoptotic cell death of mammalian cells: It induces free cation transport across the plasma as well as lysosomal membranes (Hayata et al. 2018).

The generalized reaction catalyzed by pTB is: 

Monovalent cation (in) ⇌ Monovalent cation (out)

References associated with 1.D.24 family:

Ducho, C. (2010). Convergence leads to success: total synthesis of the complex nonribosomal peptide polytheonamide B. Angew Chem Int Ed Engl 49: 5034-5036. 20572229
Hamada, T., S. Matsunaga, G. Yano, and N. Fusetani. (2005). Polytheonamides A and B, highly cytotoxic, linear polypeptides with unprecedented structural features, from the marine sponge, Theonella swinhoei. J. Am. Chem. Soc. 127: 110-118. 15631460
Hamada, T., S. Matsunaga, M. Fujiwara, K. Fujita, H. Hirota, R. Schmucki, P. Güntert, and N. Fusetani. (2010). Solution structure of polytheonamide B, a highly cytotoxic nonribosomal polypeptide from marine sponge. J. Am. Chem. Soc. 132: 12941-12945. 20795624
Hayata, A., H. Itoh, and M. Inoue. (2018). Solid-Phase Total Synthesis and Dual Mechanism of Action of the Channel-Forming 48-mer Peptide Polytheonamide B. J. Am. Chem. Soc. 140: 10602-10611. 30040396
Inoue, M. (2011). Total synthesis and functional analysis of non-ribosomal peptides. Chem Rec 11: 284-294. 21905205
Inoue, M., N. Shinohara, S. Tanabe, T. Takahashi, K. Okura, H. Itoh, Y. Mizoguchi, M. Iida, N. Lee, and S. Matsuoka. (2010). Total synthesis of the large non-ribosomal peptide polytheonamide B. Nat Chem 2: 280-285. 21124508
Itoh, H., S. Matsuoka, M. Kreir, and M. Inoue. (2012). Design, synthesis and functional analysis of dansylated polytheonamide mimic: an artificial peptide ion channel. J. Am. Chem. Soc. 134: 14011-14018. 22861006
Iwamoto, M., H. Shimizu, I. Muramatsu, and S. Oiki. (2010). A cytotoxic peptide from a marine sponge exhibits ion channel activity through vectorial-insertion into the membrane. FEBS Lett. 584: 3995-3999. 20699099
Kalathingal, M., T. Sumikama, S. Oiki, and S. Saito. (2021). Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B. Biophys. J. [Epub: Ahead of Print] 34555359
Matsuoka, S., N. Shinohara, T. Takahashi, M. Iida, and M. Inoue. (2011). Functional analysis of synthetic substructures of polytheonamide B: a transmembrane channel-forming peptide. Angew Chem Int Ed Engl 50: 4879-4883. 21520376
Oiki, S., I. Muramatsu, S. Matsunaga, and N. Fusetani. (1997). [A channel-forming peptide toxin: polytheonamide from marine sponge (Theonella swinhoei)]. Nihon Yakurigaku Zasshi 110Suppl1: 195P-198P. 9503431
Renevey, A. and S. Riniker. (2016). The importance of N-methylations for the stability of the [Formula: see text]-helical conformation of polytheonamide B. Eur Biophys. J. [Epub: Ahead of Print] 27744521
Shinohara, N., H. Itoh, S. Matsuoka, and M. Inoue. (2012). Selective modification of the N-terminal structure of polytheonamide B significantly changes its cytotoxicity and activity as an ion channel. ChemMedChem 7: 1770-1773. 22489077