De novo design of a bolaamphiphilic peptide with only natural amino acids

A new self-assembling bolaamphiphilic peptide has been designed and synthesized using only natural amino acids. This simple peptide is composed of two lysines connected by 4-8 alanines to maintain the characteristics of the traditional bolaamphiphiles. Based on an irregular secondary structure, it can self-assemble into nanospheres, nanorods, or nanofibers with lengths up to micrometers. The long nanofibers can be broken into smaller fragments by sonication, however, they could reassemble into nanofibers after incubation. Furthermore, the nanostructures were shown to have considerable thermostability. This new bolaamphiphilic peptide differs from any other self-assembling peptides or bolaamphiphiles, and possibly provides a new approach to fabricate nanomaterials.     

Fluorinated amino acids in protein design and engineering

Selective incorporation of unnatural amino acids into proteins is a powerful tool for illuminating the principles of protein design. In particular, fluorinated amino acids have recently emerged as valuable building blocks for designing hyperstable protein folds, as well as directing highly specific protein-protein interactions. We review the collagen mimetic and coiled coil peptide systems that exemplify generalizable paradigms for future design. The unique electronic and phase properties of fluorocarbons are discussed, and protein synthesis using unnatural amino acids is briefly reviewed.     

Investigations on imidazoles 98. Reactions of nitrohaloimidazoles with amino acids

The reaction of 5-chloro(bromo)-1-methyl(1,2-dimethyl)-4-nitroimidazoles and 4-chloro-1-methyl-5-nitroimidazole with amino acids has been studied. This has enabled a series of N-(4-nitro-5-imidazolyl)- and N-(5-nitro-4-imidazolyl)-substituted amino acids to be synthesized. Esters of some of these acids have been obtained.For Part 97 see [1].Center for Drug Chemistry, All-Russian Research Institute for Pharmaceutical Chemistry, Moscow 119815. Novokuznetsk Research Institute for Pharmaceutical Chemistry, Novokuznetsk 654034, Russia. Zaporozhye State Medical University, Zaporozhye 330074, Ukraine. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 48–53, January, 1999.     

Interactions of cyclodextrins with aromatic amino acids: a basis for protein interactions

Cyclodextrins (CyD) have proven effects on the stability of proteins and can be used in the formulation of aggregation prone therapeutic proteins. This effect stems from specific interactions between the CyD (preferably β-CyD) and solvent exposed amino acid residues. Here the interaction with hydrophobic aromatic amino acid residues stands out and the interaction between CyDs and these amino acid residues holds the key to understanding the observed effects, which CyDs exerts on proteins and peptides. Here we present a comparative study of the interactions between free and peptide bound aromatic amino acids and their derivatives with α, β and γ-CyDs using NMR spectroscopy. We propose a novel, quantitative means of assessing the penetration depth of guest molecules in CyD cavities, the penetration gauge Π, and apply it to the observed interaction patterns from ROESY NMR spectra. We demonstrate that the penetration depths of the aromatic rings within the CyDs rely highly on the nature of the remainder of the guest molecule. Thus the presence of charges, neighboring amino acids and the specific positioning on the surface of a protein highly influences the penetration depth and geometry of guest–CyD interactions.     

Mini-review: computational structure-based design of inhibitors that target protein surfaces

Finding drugs that inhibit protein-protein interactions is usually difficult. While computer-aided design is used widely to facilitate the drug discovery process for protein targets with well-defined binding pockets, its application to the design of inhibitors targeting a protein surface is very limited. In this mini-review we address two aspects of this issue: firstly, we overview the current state of design methodology for inhibitors specifically targeting protein surfaces, and secondly, we briefly outline recent advances in computational methods for structure-based drug design. These methods are closely related to protein docking and protein recognition, the difference being that in ligand design, ligands are built on a fragment-by-fragment basis. A novel scheme of computational combinatorial ligand design developed for the design of inhibitors that interfere with protein-protein interaction is described in detail. Current applications and limitations of this methodology, as well as its future prospects, are discussed.     

Abc amino acids: design, synthesis, and properties of new photoelastic amino acids

Photoisomerizable amino acids provide a direct avenue to the experimental manipulation of bioactive polypeptides, potentially allowing real-time, remote control of biological systems and enabling useful applications in nanobiotechnology. Herein, we report a new class of photoisomerizable amino acids intended to cause pronounced expansion and contraction in the polypeptide backbone, i.e., to be photoelastic. These compounds, termed Abc amino acids, employ a photoisomerizable azobiphenyl chromophore to control the relative disposition of aminomethyl and carboxyl substituents. Molecular modeling of nine Abc isomers led to the identification of one with particularly attractive properties, including the ability to induce contractions up to 13 A in the backbone upon trans --> cis photoisomerization. This isomer, designated mpAbc, has substituents at meta and para positions on the inner (azo-linked) and outer rings, respectively. An efficient synthesis of Fmoc-protected mpAbc was executed in which the biaryl components were formed via Suzuki couplings and the azo linkage was formed via amine/nitroso condensation; protected forms of three other Abc isomers were prepared similarly. An undecapeptide incorporating mpAbc was synthesized by conventional solid-phase methods and displayed characteristic azobenzene photochemical behavior with optimal conversion to the cis isomer at 360 nm and a thermal cis --> trans half-life of 100 min at 80 degrees C.     

Purification of amino acids and small peptides with hollow fibers

Permeation through hollow fibers made of a perfluorinated ionomer membrane of the Nafion type is shown to be a possible way to separate amino acids and small peptides. The fiber has a surface area to volume ratio of 56 cm² cm^?3. Twenty-six different amino acids and small peptides with up to six amino acid units were used for permeation studies. The results show that the bulk pH is the essential parameter acting on the permeation rates and diffusion coefficients through the tubing wall. The cationic forms of the solutes, at a pH lower than their isoelectric points, were highly retained by the cation-exchange membrane. The anionic forms of the solutes, at a pH higher than the isoelectric point, were less retained. The zwitterionic and non-ionic forms had the highest permeation rates, reaching 2.2 × 10^?3 s^?1. The effect of methanol addition was studied. The permeation rates increased, but the selectivity decreased     

Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

AstexViewer: a visualisation aid for structure-based drug design

AstexViewer is a Java molecular graphics program that can be used for visualisation in many aspects of structure-based drug design. This paper describes its functionality, implementation and examples of its use. The program can run as an Applet in a web browser allowing structures to be displayed without installing additional software. Applications of its use are described for visualisation and as part of a structure based design platform. The software is being made freely available to the community and may be downloaded from http://www.astex-technology.com/AstexViewer.     

Preparation of radioactive enantiomers of amino acids using labelled racemates only

It is shown from experiments on leucine, that is possible to obtain pure enantiomer tracers of amino acids by using radioactive racemates only. The resolution takes place in a single crystallization step after mixing the active racemate with the inactive enantiomer, due to an absolute stereoselection.     

Interaction of urea with amino acids: implications for urea-induced protein denaturation

The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.     

phi-Values beyond the ribosomally encoded amino acids: kinetic and thermodynamic consequences of incorporating trifluoromethyl amino acids in a globular protein

The consequences of the substitution of 4,4,4-trifluorovaline for valine on the folding kinetics and thermodynamics of a globular protein are presented. Variants of the N-terminal domain of L9, a small alpha-beta protein, were prepared in which V3 or V21 was replaced by trifluorovaline. CD and NMR demonstrate that the structure is not perturbed. Both are more stable, the V3 variant by 0.8 kcal mol-1 and the V21 variant by 1.4 kcal mol-1. The increase of stability is significantly larger than that observed in coiled-coils on a per trifluoromethyl group basis. Folding is two-state, and the variants both fold faster than the wild type. The Phi-values are 0.16 and 0.11, respectively.     

Exploring experimental sources of multiple protein conformations in structure-based drug design

Receptor flexibility must be incorporated into structure-based drug design in order to portray a more accurate representation of a protein in solution. Our approach is to generate pharmacophore models based on multiple conformations of a protein and is very similar to solvent mapping of hot spots. Previously, we had success using computer-generated conformations of apo human immunodeficiency virus-1 protease (HIV-1p). Here, we examine the use of an NMR ensemble versus a collection of crystal structures, and we compare back to our previous study based on computer-generated conformations. To our knowledge, this is the first direct comparison of an NMR ensemble and a collection of crystal structures to incorporate protein flexibility in structure-based drug design. To provide an accurate comparison between the experimental sources, we used bound structures for our multiple protein structure (MPS) pharmacophore models. The models from an NMR ensemble and a collection of crystal structures were both able to discriminate known HIV-1p inhibitors from decoy molecules and displayed superior performance over models created from single conformations of the protein. Although the active-site conformations were already predefined by bound ligands, the use of MPS allows us to overcome the cross-docking problem and generate a model that does not simply reproduce the chemical characteristics of a specific ligand class. We show that there is more structural variation between 28 structures in an NMR ensemble than 90 crystal structures bound to a variety of ligands. MPS models from both sources performed well, but the model determined using the NMR ensemble appeared to be the most general yet accurate representation of the active site. This work encourages the use of NMR models in structure-based design.     

Rational structure-based design of a novel carboxypeptidase R inhibitor

A novel carboxypeptidase R (CPR) inhibitor, related to potato carboxypeptidase inhibitor (PCI), was designed using rational structure-based strategies, incorporating two principle facts: CPR has a strong affinity for basic amino acids, and the two lysine and arginine residues of PCI are orientated in the same direction and held in close spatial proximity by three disulfide bonds. Initially, a disulfide-bonded fragment of PCI was synthesized showing weak competitive inhibitory activity against CPR. Subsequently, a smaller linear 9-mer peptide, designated CPI-2KR, was designed/synthesized and found to be a more efficient competitive inhibitor of CPR, without affecting the activity of the other plasma carboxypeptidase, carboxypeptidase N. In vitro studies showed that, together with tissue plasminogen activator, CPI-2KR synergistically accelerated fibrinolysis, representing a lead compound for the design of smaller organic molecules for use in thrombolytic therapy.