John C. Sherman

EFFICIENT COUPLING OF AMINO ACID DERIVATIVES TO RIGID ORGANIC SCAFFOLDS : MODEL SYNTHESES FOR DE NOVO PROTEINS

Abstract We describe the coupling of amino acid derivatives to four different rigid organic macrocycles. The couplings were achieved in high yields, which augurs well for the coupling of polypeptides to the rigid macrocycles to create a new family of de novo proteins. We discuss the structure of the model compounds based on the hydrogen bonding patterns that are evident from their NMR and IR spectra.

Expanding cavitand chemistry: the preparation and characterization of [n]cavitands with n>=4.

The preparation of cavitands composed of 4, 5, 6, and 7 aromatic subunits ([n]cavitands, n=4-7) is described. The simple, two-step synthetic procedure utilized readily available starting materials (2-methylresorcinol and diethoxymethane). The two cavitand products having 4 and 5 aromatic subunits exhibited highly symmetric cone conformations, while the larger cavitands (n = 6 and 7) adopt conformations of lower symmetry. 1H NMR spectroscopic studies of [6]cavitand and [7]cavitand revealed that these hosts undergo exchange between equivalent conformations at room temperature. The departure of these two cavitands from cone conformations is related to steric crowding on their Ar-O-CH2-OAr bridges and is predicted by simple molecular mechanics calculations (MM2 force field). X-ray diffraction studies on single crystals of the [4]cavitand, [5]cavitand, and [6]cavitand hosts afforded additional experimental support for these conclusions.

Cation-Complexation Behavior of Template-Assembled Synthetic G-Quartets

We report the preparation and solution study of a set of template-assembled synthetic G-quartets (TASQs) bound to different cations. These G-quartet baskets effectively extract cations of different sizes and valencies. They form isolated G-quartets with small cations such as Na+ and Sr(2+), and dimeric assemblies with larger cations such as Cs+. Their structures were determined by using (1)H NMR spectroscopy, and their sizes were evaluated by using a series of pulsed-field gradient NMR experiments. The effect of anion has been studied, and the cation selectivities have been investigated by a series of competition experiments.

Design of proteins using rigid organic macrocycles as scaffolds.

We have designed and synthesized new three-helix template-assembled synthetic proteins (TASPs) 1a-c. The template was the rigid cyclotribenzylene (CTB) macrocycle 2, which has C3 symmetry. Thiol moieties on the CTB template were used to link cysteine-containing peptide strands 3a-c via disulfide bonds. With designed peptide strands of 15 and 18 residues in length, the structure of TASPs 1a-c were determined to be helical in water according to circular dichroism (CD) spectroscopy. The helicities of TASPs 1a-c were unchanged over large ranges of pH (2-12) and salt concentrations (0-2 M KCl). TASPs 1a-c were also extremely resistant to chemical denaturants: it requires a guanidine hydrochloride (GnHCl) concentration of 7.4 M for TASPs 1a-c to lose 50% of their helicity. The major force for stabilization of TASPs 1a-c is the hydrophobic bundling of the helices.

Bis-Capsules: Cooperative Reversible Encapsulation of Two Molecules in Adjacent Separate Chambers.

Unprecedented communication takes place between guests G that are reversibly encapsulated in adjacent, but physically separate, chambers of a side-to-side bis-capsule (shown schematically). This was shown by neighbor-dependent NMR chemical shifts of the identical or nonidentical guest molecules. Furthermore, no 1:1 host - guest species is formed.

Prototype for a new family of De Novo proteins

Abstract We report the design, synthesis, and preliminary structural analysis of a four-helix bundle affixed to a rigid organic macrocycle.

Synthesis of a single G-quartet platform in water.

For over 50 years the G-quartet has been a defining self-assembled structure in biology and non-covalent synthesis. It is shown here for the first time that the G-quartet is isolatable in water in the absence of stabilizing G-quartet stacking or cations through the construction of a phosphate-linked template-assembled synthetic G-quartet. Synthetic design has facilitated preservation of the guanine base, ribose sugar, and phosphate components with correct linkage chemistry relative to G-quadruplex DNA. Thus, a minimal synthetic model of G-quadruplex DNA, as in that associated with human gene promoter or telomere regions, is represented by this system. An application as a probe for interactions between G-quadruplex DNA and potential anticancer therapeutical binding ligands is demonstrated. Binding constants of 10(5)-10(7) M(-1) magnitude and 1:1 stoichiometries for TMPyP4, piper, and azatrux ligands were determined, whereas perturbations in BSU1051 and BRACO19 ligand signal were not observed. These data suggest a unique test for critical end-stacking interactions at the exclusion of intercalative or looping interactions for G-quadruplex binding ligands.

X-ray crystal analysis of a TASP: structural insights of a cavitein dimer.

Cavitein Q4 is a template assembled synthetic protein designed for X-ray crystallographic analysis. It is based on a previous monomeric helical bundle cavitein (N1GG) that consists of four identical parallel helical peptides. Crystals that were grown in the presence of bromide ions were used to solve the initial phases via single-wavelength anomalous dispersion (SAD). A 1.4 A resolution data set was then refined starting with the SAD phases to provide the crystal structure of cavitein Q4. The crystal structure revealed cavitein Q4 as an asymmetric dimer, although the cavitein appears to be largely monomeric in solution. A comparative analysis is carried out to discern any intrinsic differences between Q4 and its parent cavitein N1GG. We present herein the first X-ray crystal structure of a TASP system and relate this structure to the solution data for both Q4 and its parent N1GG.

Synthesis and conformational dynamics of ortho-xylyl-bridged-[4]cavitands

Abstract ortho-Xylyl-[4]cavitands 2 to 6 were synthesized from bromoresorcin[4] arenes 1 . Cavitands 2 to 6 show C4v symmetry in their 1H NMR spectra at higher temperatures. Dynamic 1H NMR studies of 2 to 6 indicate the C4v symmetry is due to fast interconversion of rectangular C2v isomers. This is supported by the crystal structure of 2a , which shows a C2v rectangular structure. The activation energy barriers for 2a and 2b were measured by quantitative 1D NOESY (EXSY) experiments. The results were analyzed by the initial rate approximation and matrix calculations. The activation energy barrier was found to depend strongly on the size of the upper rim group (Br, H, OH, CN). In addition, replacing the phenolic proton of tetrol derivatives 4a and 4b with metal ions raises the energy barrier further, likely via bridging metal cations. The two tetrabromo compounds ( 2a and 2b ) reveal a sensitivity of the activation barrier to the feet of the cavitands. Cavitand 6 may act as a hub for radially expanded cavitands. The advantages of the 1D NOESY experiments over the more commonly used two-dimensional experiments are discussed.

Molecules that can't resist templation

The encapsulation of molecules or ions has captured the interest of a variety of researches, including those using zeolites, fullerenes, micelles, clathrates, and metal coordination complexes. Multiple hemispherical units have been used to create organic cages that can bind guests reversibly or irreversibly. Often such cages will only form in the presence of a guest, which acts as a template. This article summarizes some of the work in this field.