The design and synthesis of mimetics of peptide beta-turns

Design, Synthesis, and Conformational Analysis of Proposed β-Turn Mimics from Isoxazoline-Cyclopentane Aminols

Constrained aminols from oxazanorbornene derivatives have the geometrical features to be used as β-turn inducers. Four different stereoisomers were prepared and spectroscopically characterized (MD calculations, NMR-titration and VT-NMR experiments). Temperature coefficients in DMSO are indicative for the existence of an intramolecular hydrogen bond. Chirooptical properties revealed a β-turn arrangement of all the synthesized compounds, where, depending on the absolute configuration of the cyclopentane spacer, they can be labeled as left- or right-handed turns.

A novel route to synthesize Freidinger lactams by micowave irradiation*

The incorporation of a Freidinger-like lactam structure into the backbone of peptides has been proven to be an useful strategy in the design of a variety of conformationally restricted targets. Several different strategies have been developed toward Freidinger lactams but no one resulted to be completely facile. Here, we report an efficient strategy that involves the iodo-derivatives in side chain of an appropriate amino acid used as electrophilic agent, and the standard solid phase peptide synthesis assisted by microwave irradiation. The methodology developed could be useful to perform Freidinger-like lactams with defined stereochemistry for routine use in solid phase peptide chemistry.

Traveling for the glycosphingolipid path

Our studies on glycosphingolipids (GSLs) were initiated through isolation and structural characterization of lacto-series type 1 and 2 GSLs, and globo-series GSLs. Lacto-series structures included histo-blood group ABH and I/i antigens. Our subsequent studies were focused on GSL changes associated with: (i) ontogenic development and differentiation; (ii) oncogenic transformation and tumor progression. Various novel types of GSLs such as extended globo-series, sialyl-Le(x) (SLe(x)), sialyl-dimeric-Le(x) (SLe(x)-Le(x)), dimeric-Le(x) (Le(x)-Le(x)), Le(y)-on-Le(x), dimeric-Le(a) (Le(a)-Le(a)), Le(b)-on-Le(a), etc. were identified as tumor-associated antigens. These studies provide an essential basis for up- or down-regulation of key glycosyltransferase genes controlling development, differentiation, and oncogenesis. GSL structures established in our laboratory are summarized in Table 1, and structural changes of GSLs associated with ontogenesis and oncogenesis are summarized in Sections 2 and 3. Based on these results, we endeavored to find out the cell biological significance of GSL changes, focused on (i) cell adhesion, e.g., the compaction process of preimplantation embryo in which Le(x)-to-Le(x), Gb4-to-GalGb4 or -nLc4 play major roles; and (ii) modulation of signal transduction through interaction of growth factor receptor tyrosine kinase with ganglioside, e.g., EGF receptor tyrosine kinase with GM3. Recent trends of studies on i and ii lead to the concept that GSL clusters (microdomains) are organized with various signal transducer molecules to form 'glycosignaling domains' (GSD). GSL-dependent adhesion occurs through clustered GSLs, and is coupled with activation of signal transducers (cSrc, Src family kinase, Rho A, etc.). Clustered GSLs involved in cell adhesion are recognized by GSLs on counterpart cells (carbohydrate-to-carbohydrate interaction), or by lectins (e.g., siglecs, selectins). Our major effort in utilization of GSLs in medical science has been for: (i) cancer diagnosis and treatment (vaccine development) based on tumor-associated GSLs and glycoepitopes; (ii) genetically defined phenotype for susceptibility to E. coli infection; (iii) clear identification of physiological E-selectin epitope (myeloglycan) expressed on neutrophils and myelocytes; (iv) characterization of sialyl poly-LacNAc epitopes recognized as male-specific antigens. Utilization of these GSLs or glycoepitopes in development of anti-adhesion approach to prevent tumor metastasis, infection, inflammation, or fertilization (i.e., contraceptive) is discussed. For each approach, development of mimetics of key GSLs or glycoepitopes is an important subject of future study.

A loop-mimetic inhibitor of the HCV-NS3 protease derived from a minibody

We have been interested for some time in establishing a strategy for deriving lead compounds from macromolecule ligands such as minibody variants. A minibody is a minimized antibody variable domain whose two loops are amenable to combinatorial mutagenesis. This approach can be especially useful when dealing with 'difficult' targets. One such target is the NS3 protease of hepatitis C virus (HCV), a human pathogen that is believed to infect about 100 million individuals worldwide and for which an effective therapy is not yet available. Based on known inhibitor specificity (residues P6-P1) of NS3 protease, we screened a number of minibodies from our collection and we were able to identify a competitive inhibitor of this enzyme. We thus validated an aspect of recognition by HCV NS3 protease, namely that an acid anchor is necessary for inhibitor activity. In addition, the characterization of the minibody inhibitor led to the synthesis of a constrained hexapeptide mimicking the bioactive loop of the parent macromolecule. The cyclic peptide is a lead compound prone to rapid optimization through solid phase combinatorial chemistry. We therefore confirmed that the potential of turning a protein ligand into a low molecular weight active compound for lead discovery is achievable and can complement more traditional drug discovery approaches.

The role in cell binding of a beta-bend within the triple helical region in collagen alpha 1 (I) chain: structural and biological evidence for conformational tautomerism on fiber surface

In its physiological solid state, type I collagen serves as a host for many types of cells. Only the molecules on fiber surface are available for interaction. In this interfacial environment, the conformation of a cell binding domain can be expected to fluctuate between the collagen fold and a distinctive non-collagen molecular marker for recognition and allosteric binding. If the cell binding domain can be localized in contiguous residues within the exposed half of a turn of the triple helix (approximately 15 residues), the need for extensive structural modification and unraveling of the triple helix is avoided. We examined the conformational preferences and biological activity of a synthetic 15-residue peptide (P-15), analogous to the sequence 766GTPGPQGIAGQRGVV780 in the alpha 1 (I) chain. Theoretical studies showed a high potential for a stable beta-bend for the central GIAG sequence. The flanking sequences showed facile transition to extended conformations. Circular dichroism of the synthetic peptide in anisotropic solvents confirmed the presence of beta-strand and beta-bend structures. P-15 inhibited fibroblast binding to collagen in a concentration dependent manner, with near maximal inhibition occurring at a concentration of 7.2 x 10(-6) M. The temporal pattern of cell attachment was altered markedly in the presence of P-15. No inhibition was seen with a peptide P-15(AI), an analogue of P-15 with the central IA residues reversed to AI or with collagen-related peptides (Pro-Pro-Gly)10, (Pro-Hyp-Gly)10, and polyproline, and with several unrelated peptides. Our studies suggest a molecular mechanism for cell binding to collagen fibers based on a conformational transition in collagen molecules on the fiber surface. Since the energy barrier between the collagen fold and beta-strand conformation is low, a local conformational change may be possible in molecules on the fiber surface because of their location in an anisotropic environment. Our observations also suggest that the sequence incorporated in P-15 may be a specific ligand for cells. Unlike other reported cell binding peptides, the residues involved in this interaction are non-polar.

Peptidomimetics of the immunoglobulin supergene family--a review

An important goal of structural biochemistry is the reduction of complex molecules to small functional units that are amenable to high-resolution structural analysis and rapid modification. The dissection of multidomain proteins into small synthetic conformationally restricted components is an important step in the design of low-molecular-weight nonpeptides that mimic the activity of the native protein. Mimetics of critical functional domains might possess beneficial properties in comparison to the intact proteinaceous species with regard to specificity and therapeutic potential, and are valuable probes for the study of molecular recognition events.

Loops and Secondary Structure Mimetics: Development and Applications in Basic Science and Rational Drug Design

One goal of protein design and structural biochemistry is the reduction of complex molecules to small functional units that are amenable to high resolution analysis and rapid modification. We have developed a variety of small molecules which biochemically and biologically mimic the combining sites of proteins of the immunoglobulin superfamily. The chemical and biological properties of peptide mimetics suggest that these analogs can be used as indicators for new pharmaceutical agents. Mimetics are powerful tools for the study of molecular recognition since they are small in size, maintain solubility in physiologic fluids and are amenable to detailed structural studies. As such, they represent a step toward the rational design of low molecular weight non-peptide pharmaceutical agents devoid of some of the shortcomings of conventional peptides. Here we discuss the rationale and approaches for the development of these molecules, and their current and future applications.

Discovering peptide ligands using epitope libraries

Epitope libraries are large collections of peptides. Each peptide is displayed on the surface of a bacteriophage particle and is encoded by a randomly mutated region of the phage genome, thus associating each unique peptide with the DNA molecule encoding it. Antibodies and other binding proteins are used to select specifically for rare, phage-bearing peptide ligands; sequencing of the corresponding viral DNA will reveal their amino acid sequences. Relatively high-affinity peptides for a variety of peptide- and non-peptide-binding ligates have been affinity-isolated from epitope libraries. This technology has been used to map epitopes on proteins and to find peptide mimics for non-peptide-binding ligates. The current challenge lies in developing epitope library technology so that tight-binding peptide ligands can be detected for a wider variety of ligates, including those that recognize folded proteins. Should this be accomplished, many powerful applications can be envisioned in the areas of drug design and the development of diagnostic markers and vaccines.

Design and synthesis of nonpeptide mimetics of jaspamide

Jaspamide is a novel metabolite of mixed peptide/polyketide biosynthesis that was isolated from sponges of the genus Jaspis, and that has been reported to exhibit both insecticidal and antifungal activity. We have evaluated three nonpeptide mimetic designs, and have synthesized a nonpeptide mimic of the proposed bioactive region to investigate the structure activity relationship. Structural investigations of potential mimetics, utilizing molecular modeling in conjunction with spectroscopic and crystallographic data, indicate that positioning of the critical functional groups in two mimetics corresponds closely to that observed in jaspamide, and that the flexibility of mimetic 4 approximates that of jaspamide. Initial biological evaluation suggests that lactam mimetic 4 exhibits a biological profile similar to jaspamide.

Conformational constraints: nonpeptide beta-turn mimics

The beta-turn, which has also been referred to as the beta-bend, beta-loop or reverse turn, has been implicated as an important site for molecular recognition in many biologically active peptides and in globular proteins. This small secondary structure therefore makes an attractive target for mimicry by a conformational constraint, because a peptide which is constrained in a biologically active conformation can display a number of advantages over the parent substrate. The less peptide-like such a constraint is, the more potential there is to maximize these advantages. A decade has passed since the first (and highly successful) attempt to mimic the beta-turn with a nonpeptide conformational constraint was disclosed by Freidinger et al. (1980). Since this report, rapidly growing interest in the field of nonpeptide beta-turn mimics has seen a variety of experimental approaches and a mixed bag of results. It is attempted in this review, not only to summarize and critically analyse these approaches, but also to touch on the complexities associated with the conformational mimicry of such a diverse structure as the beta-turn.