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Synthetic approach to designed chemical structures

a chemical structure and synthetic approach technology, applied in the direction of chemokines, peptides, drug compositions, etc., can solve the problems of reducing the usefulness of scales in designing de novo -, peptides in the betabellin and betadoublet series show limited solubility in water, and the design of a structurally stable -polypeptide is dealing with the interaction between -polypeptides,

Inactive Publication Date: 2006-08-17
RGT UNIV OF MINNESOTA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

A major challenge in de novo polypeptide design (more often referred to as de novo peptide design), which is the design of polypeptides (or peptides) from scratch, is the engineering of a polypeptide having the folding stability of the native structure of a natural polypeptide.
A major difficulty in designing a structurally stable β polypeptide is dealing with the interactions between β sheets.
However, such scales are generally less useful when designing de novo β-sheet folds in short peptides where considerably more β-sheet and / or side-chain surface (particularly hydrophobic surface) will be exposed to water.
However, peptides in the betabellin and betadoublet series show limited solubility in water and minimal, highly transient β-sheet structure, i.e., nonstable structures.
The best betabellin made thus far, Betabellin peptide 14D, for example, becomes less soluble at pH values above 5.5 making it impractical for use at a physiological pH.
A polypeptide that is not soluble under physiological conditions (i.e., in water at a pH of about 7.0-7.4 and in about 150 mM NaCl or an equivalent physiological salt) is not functional and is therefore not useful.
Neither the betabellin nor the betadoublet strategies for peptide design achieved sufficient solubility, peptide compactness, or peptide self-association under physiological conditions.

Method used

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Examples

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example 1

The Design and Synthesis of Water-Soluble β-Sheet Forming Peptides

[0039] Peptides of 33 amino acid residues in length, called βpep-1, βpep-2, βpep-3 and βpep-4, were synthesized on a Milligen Biosearch 9600 automated peptide synthesizer. The procedures used were based on Merrifield solid phase synthesis utilizing Fmoc-BOP chemistry (Stewart et al., 1984. Solid phase peptide synthesis., 2nd ed. Rockford, Ill., Pierce Chemical Co. pp. 135). After the sequence had been obtained, the peptide support and side chain protection groups were acid cleaved (trifluoroacetic acid and scavanger mixture). Crude peptides were analyzed for purity on a Hewlett-Packard 1090M analytical HPLC using a reverse phase C18 VyDac column. Peptides generally were about 90% pure. Further purification was done on a preparative reverse-phase HPLC C-18 column using an elution gradient of 0-60% acetonitrile with 0.1% trifluoroacetic acid in water. Peptides then were analyzed for amino acid composition on a Beckman ...

example 2

Circular Dichroism (CD) of the β-Peptide Series

[0044] Circular dichroism (CD) is one way to measure formation of a β-sheet structure. CD spectra were measured on a JASCO JA-710 (Jasco, Eastern, Md.) automatic recording spectropolarimeter coupled with a data processor. Curves were recorded digitally and fed through the data processor for signal averaging and baseline subtraction. Spectra were recorded from 5° C. to 65° C. in the presence of 10 mM potassium phosphate, over a 185 nm to 250 nm range using a 0.5 mm path-length, thermally-jacketed quartz cuvette. Temperature was controlled by using a NesLab water bath. Peptide concentration was varied from 0.014 to 0.14 mM. The scan speed was 20 nm / min. Spectra were signal-averaged 8 times, and an equally signal-averaged solvent baseline was subtracted. These experiments are well known in the art.

[0045] For βpep-1, CD data resembled those observed for β-sheet-forming PF4 peptide. Based on CD data alone, βpep-1 appeared not to form any β...

example 3

Nuclear Magnetic Resonance (NMR) of the β-Peptide Series

[0047] Since CD data indicate maximal β-sheet formation at about 40° C., NMR spectra (FIG. 3) were accumulated for all four peptides at pH 6.3, 20 mM NaCl and 40° C. For NMR measurements, freeze-dried peptide was dissolved either in D2O or in H2O / D2O (9:1). Polypeptide concentration normally was in the range of 1 to 5 mM. pH was adjusted by adding μL quantities of NaOD or DCl to the peptide sample. NMR spectra were acquired on a Bruker AMX-600 (Bruker Instrument, Inc., Bruker, Mass.) or AMX-500 NMR spectrometer. For resonance assignments, double quantum filtered COSY (Piantini et al. J. Am. Chem. Soc. 104:6800-6801, 1982) and 2D-homonuclear magnetization transfer (HOHAHA) spectra, obtained by spin-locking with a MLEV-17 sequence with a mixing time of 60 ms, were used to identify spin systems (See Bax, et al. J. Magn. Reson. 65: 355-360, 1985). NOESY experiments (see Jeener et al., J. Chem. Phys. 71:4546-4550, 1979 and Wider et...

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Abstract

This invention relates to the chemical design and production of peptides, peptide structure and three dimensional conformation was assessed using NMR, circular dichroisin and pulsed field gradient NMR.

Description

FIELD OF THE INVENTION [0001] This invention relates to the fields of chemical design and to methods for selecting, modifying, and creating synthetic chemical structures. BACKGROUND [0002] A critical feature of a polypeptide is its ability to fold into a three dimensional conformation or structure. Polypeptides usually have a unique conformation which, in turn, determines their function. The conformation of a polypeptide has several levels of structure. The primary structure is a linear sequence of a series of amino acids linked into a polypeptide chain. The secondary structure describes the path that the polypeptide backbone of the polypeptide follows in space, and the tertiary structure describes the three dimensional organization of all the atoms in the polypeptide chain, including the side groups as well as the polypeptide backbone. [0003] Covalent and noncovalent interactions between amino acids determine the conformation of a polypeptide. The most common covalent bond used in ...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12P21/06A61K38/00A61K31/00A61L27/34A61P31/00A61P31/04A61P39/00A61P39/02A61P43/00C07K1/04C07K1/06C07K14/00C07K14/47C07K14/52C07K14/54C07K14/655
CPCA61K38/00A61L27/34C07K14/001C07K14/4742C07K14/522C07K14/5421C07K14/655C07K2319/00C08L89/00A61P31/00A61P31/04A61P35/00A61P39/00A61P39/02A61P43/00
Inventor GRAY, BEULAHHASEMAH, JUDITHMAYO, KEVINGRIFFIOEN, ARJAN
Owner RGT UNIV OF MINNESOTA
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