Peptoid
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Peptoids (root from the
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
πεπτός, ''peptós'' "digested"; derived from πέσσειν, ''péssein'' "to digest" and the Greek-derived suffix -oid meaning "like, like that of, thing like a ______," ), or poly-''N''-substituted
glycine Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid (carbamic acid is unstable), with the chemical formula NH2‐ CH2‐ COOH. Glycine is one of the proteinogeni ...
s, are a class of biochemicals known as biomimetics that replicate the behavior of biological molecules.
Peptidomimetic A peptidomimetic is a small protein-like chain designed to mimic a peptide. They typically arise either from modification of an existing peptide, or by designing similar systems that mimic peptides, such as peptoids and Beta-peptide, β-peptides. ...
s are recognizable by side chains that are appended to the nitrogen atom of the
peptide Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...
backbone, rather than to the α-carbons (as they are in
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
s).


Chemical structure and synthesis

In peptoids, the side chain is connected to the nitrogen of the peptide backbone, instead of the α-carbon as in peptides. Notably, peptoids lack the amide hydrogen which is responsible for many of the
secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
elements in peptides and proteins. Peptoids were first invented by Reyna J. Simon, Ronald N. Zuckermann, Paul Bartlett and Daniel V. Santi to mimic protein/peptide products to aid in the discovery of protease-stable small molecule drugs for the East Bay company
Chiron In Greek mythology, Chiron ( ; also Cheiron or Kheiron; ) was held to be the superlative centaur amongst his brethren since he was called the "wisest and justest of all the centaurs". Biography Chiron was notable throughout Greek mythology ...
. Following the sub-monomer protocol originally created by Ron Zuckermann, each residue is installed in two steps:
acylation In chemistry, acylation (or alkanoylation) is the chemical reaction in which an acyl group () is added to a compound. The compound providing the acyl group is called the acylating agent. Because they form a strong electrophile when treated with ...
and displacement. In the acylation step, a haloacetic acid, typically
bromoacetic acid Bromoacetic acid is the chemical compound with the formula CH2BrCO2H. This colorless solid is a relatively strong alkylating agent. Bromoacetic acid and its esters are widely used building blocks in organic synthesis, for example, in pharmaceuti ...
activated by
diisopropylcarbodiimide ''N'',''N′''-Diisopropylcarbodiimide is a carbodiimide used in peptide synthesis. As a liquid, it is easier to handle than the commonly used ''N'',''N′''-dicyclohexylcarbodiimide, a waxy solid. In addition, ''N'',''N′''-diisopr ...
reacts with the amine of the previous residue. In the displacement step (a classical SN2 reaction), an amine displaces the halide to form the ''N''-substituted glycine residue. The submonomer approach allows the use of any commercially available or synthetically accessible amine with great potential for
combinatorial chemistry Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a large number (tens to thousands or even millions) of compounds in a single process. These compound libraries can be made as mixtures, sets of individua ...
.


Unique characteristics

Like D-Peptides and β peptides, peptoids are completely resistant to
proteolysis Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called protease ...
, and are therefore advantageous for therapeutic applications where proteolysis is a major issue. Since secondary structure in peptoids does not involve hydrogen bonding, it is not typically denatured by solvent, temperature, or chemical denaturants such as
urea Urea, also known as carbamide, is an organic compound with chemical formula . This amide has two amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest amide of carbamic acid. Urea serves an important r ...
(see details below). Notably, since the amino portion of the amino acid results from the use of any amine, thousands of commercially available amines can be used to generate unprecedented chemical diversity at each position at costs far lower than would be required for similar peptides or peptidomimetics. To date, at least 230 different amines have been used as side chains in peptoids.


Structure

Peptoid oligomers are known to be conformationally unstable, due to the flexibility of the main-chain methylene groups and the absence of stabilizing
hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...
interactions along the backbone. Nevertheless, through the choice of appropriate side chains it is possible to form specific steric or electronic interactions that favour the formation of stable secondary structures like helices, especially peptoids with C-α-branched side chains are known to adopt structure analogous to
polyproline A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A left-handed polyproline II helix (PPII, poly-Pro II) is formed when sequential residues all adopt (φ,ψ) backbone dihedr ...
I helix. Different strategies have been employed to predict and characterize peptoid secondary structure, with the ultimate goal of developing fully folded peptoid protein structures The cis/trans
amide bond In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is p ...
isomerization still leads to a conformational heterogeneity which doesn’t allow for the formation of homogeneous peptoid
foldamers In chemistry, a foldamer is a discrete chain molecule (oligomer) that folds into a conformationally ordered state in solution. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into w ...
. Nonetheless, scientists were able to find trans-inducer ''N''-Aryl side chains promoting
polyproline A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A left-handed polyproline II helix (PPII, poly-Pro II) is formed when sequential residues all adopt (φ,ψ) backbone dihedr ...
type II helix, and strong cis-inducer such as bulky naphtylethyl and tert-butyl side chains. It was also found that n→π* interactions can modulate the ratio of cis/trans amide bond conformers, until reaching a complete control of the cis conformer in the peptoid backbone using a functionalizable triazolium side chain.


Applications

The first demonstration of the use of peptoids was in screening a combinatorial library of diverse peptoids, which yielded novel high-affinity ligands for 7-transmembrane G-protein-couple receptors. Peptoids have been developed as candidates for a range of different biomedical applications, including antimicrobial agents, synthetic lung surfactants, ligands for various proteins including Src Homology 3 (
SH3 domain The SRC Homology 3 Domain (or SH3 domain) is a small protein domain of about 60 amino acid residues. Initially, SH3 was described as a conserved sequence in the viral adaptor protein v-Crk. This domain is also present in the molecules of phos ...
), Vascular Endothelial Growth Factor (
VEGF Vascular endothelial growth factor (VEGF, ), originally known as vascular permeability factor (VPF), is a signal protein produced by many cells that stimulates the formation of blood vessels. To be specific, VEGF is a sub-family of growth factors, ...
) receptor 2, and antibody
Immunoglobulin G Immunoglobulin G (Ig G) is a type of antibody. Representing approximately 75% of serum antibodies in humans, IgG is the most common type of antibody found in blood circulation. IgG molecules are created and released by plasma B cells. Each IgG a ...
biomarkers for the identification of
Alzheimer's disease Alzheimer's disease (AD) is a neurodegeneration, neurodegenerative disease that usually starts slowly and progressively worsens. It is the cause of 60–70% of cases of dementia. The most common early symptom is difficulty in short-term me ...
. Due to their advantageous characteristics as described above, peptoids are also being actively developed for use in nanotechnology, an area in which they may play an important role.


Antimicrobial agents

Researchers supported by grants from the
NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...
and
NIAID The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services (HHS). NIAID's ...
tested the efficacy of antimicrobial peptoids against antibiotic-resistant strands of
Mycobacterium tuberculosis ''Mycobacterium tuberculosis'' (M. tb) is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, ''M. tuberculosis'' has an unusual, waxy coating on its c ...
. Antimicrobial peptoids demonstrate a non-specific mechanism of action against the bacterial membrane, one that differs from small-molecule antibiotics that bind to specific receptors (and thus are susceptible to mutations or alterations in bacterial structure).Preliminary results suggested "appreciable activity" against drug-sensitive bacterial strands, leading to a call for more research into the viability of peptoids as a new class of tuberculocidal drugs. Researchers at the Barron Lab at Stanford University (supported by a
NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...
Pioneer Award grant) are currently studying whether upregulation of the human host defense peptide LL-37 or application of antimicrobial treatments based on LL-37 may prevent or treat sporadic Alzheimer’s dementia. Lead researcher Annelise Barron discovered that the innate human defense peptide LL-37 binds to the peptide Ab, which is associated with Alzheimer's disease. Barron's insight is that an imbalance between LL-37 and Ab may be a critical factor affecting AD-associated fibrils and plaques. The project extends focus upon the potential relationship between chronic, oral P. gingivalis and herpesvirus (HSV-1) infections to the progression of Alzheimer's dementia.


See also

*
Peptidomimetic A peptidomimetic is a small protein-like chain designed to mimic a peptide. They typically arise either from modification of an existing peptide, or by designing similar systems that mimic peptides, such as peptoids and Beta-peptide, β-peptides. ...
* Beta-peptide *
Peptoid Nanosheet In nanobiotechnology, a peptoid nanosheet is a synthetic protein structure made from peptoids. Peptoid nanosheets have a thickness of about three nanometers and a length of up to 100 micrometers, meaning that they have a two-dimensional, flat sha ...


References

{{Reflist, 2 Peptides