Ribosomal synthesis of unnatural peptides

Combinatorial libraries of non-biological polymers and drug-like peptides could in principle be synthesized from unnatural amino acids by exploiting the broad substrate specificity of the ribosome. The ribosomal synthesis of such libraries would allow rare functional molecules to be identified using technologies developed for the in vitro selection of peptides and proteins. Here, we use a reconstituted E. coli translation system to simultaneously re-assign 35 of the 61 sense codons to 12 unnatural amino acid analogues. This reprogrammed genetic code was used to direct the synthesis of a single peptide containing 10 different unnatural amino acids. This system is compatible with mRNA-display, enabling the synthesis of unnatural peptide libraries of 10(14) unique members for the in vitro selection of functional unnatural molecules. We also show that the chemical space sampled by these libraries can be expanded using mutant aminoacyl-tRNA synthetases for the incorporation of additional unnatural amino acids or by the specific posttranslational chemical derivitization of reactive groups with small molecules. This system represents a first step toward a platform for the synthesis by enzymatic tRNA aminoacylation and ribosomal translation of cyclic peptides comprised of unnatural amino acids that are similar to the nonribosomal peptides.     

Expedient parallel synthesis of 2-amino-4-heteroarylpyrimidines

[reaction: see text] An expedient synthesis of diverse 2-amino-4-heteroarylpyrimidines via a 2-chloropyrimidine intermediate is described. A series of potentially biologically active analogues have been synthesized in two parallel steps to afford focused arrays.     

Evidence for specific solvation of two halocarbene amides

Laser flash photolysis (LFP, 308 nm) of endo-10-halo-10'-N,N-dimethylcarboxamidetricyclo[4.3.1.0]-deca-2,4-diene (1Cl and 1F) releases indan and halocarbene amide (2Cl and 2F). Although the carbenes are not UV-vis active, they react rapidly with pyridine to form ylides (4Cl, 4F), which are readily detected in LFP experiments (lambda(max) = 450 nm). Dioxane decreases the observed rate of carbene reaction with pyridine in CF(2)ClCFCl(2). Small amounts of THF decrease the observed rate of reaction of carbene 2F with pyridine but increase the rate of reaction of carbene 2Cl with pyridine. LFP (266 nm) of dienes 1Cl and 1F in CF(2)ClCFCl(2) with IR detection produces carbenes 2Cl and 2F with carbonyl vibrations at 1635 and 1650 cm(-1), respectively. In dioxane or THF solvent, LFP produces the corresponding ether ylides (5Cl, 5F) by capture of carbenes 2Cl and 2F. The ylides have broad carbonyl vibrations between 1560 and 1610 cm(-1). The addition of a small amount of dioxane in CFCl(2)CF(2)Cl extends the lifetime of the carbene. This observation, together with the ether-induced retardation of the rates of carbene capture by tetramethylethylene and pyridine, is evidence for solvation of the carbene by dioxane.     

Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria

Antibiotic resistant infections are projected to cause over 10 million deaths by 2050, yet the development of new antibiotics has slowed. This points to an urgent need for methodologies for the rapid development of antibiotics against emerging drug resistant pathogens. We report on a generalizable combined computational and synthetic approach, called antibody-recruiting protein-catalyzed capture agents (AR-PCCs), to address this challenge. We applied the combinatorial protein catalyzed capture agent (PCC) technology to identify macrocyclic peptide ligands against highly conserved surface protein epitopes of carbapenem-resistant Klebsiella pneumoniae, an opportunistic Gram-negative pathogen with drug resistant strains. Multi-omic data combined with bioinformatic analyses identified epitopes of the highly expressed MrkA surface protein of K. pneumoniae for targeting in PCC screens. The top-performing ligand exhibited high-affinity (EC₅₀ ∼50 nM) to full-length MrkA, and selectively bound to MrkA-expressing K. pneumoniae, but not to other pathogenic bacterial species. AR-PCCs that bear a hapten moiety promoted antibody recruitment to K. pneumoniae, leading to enhanced phagocytosis and phagocytic killing by macrophages. The rapid development of this highly targeted antibiotic implies that the integrated computational and synthetic toolkit described here can be used for the accelerated production of antibiotics against drug resistant bacteria.

Antibody-recruiting protein-catalyzed capture agent (AR-PCCs) are a new class of all-synthetic and highly targeted antibiotics that recruit endogenous immune responses to eliminate drug-resistant microbes.     

C2-symmetric bis(oxazolinato)lanthanide catalysts for enantioselective intramolecular hydroamination/cyclization

C(2)-symmetric bis(oxazolinato)lanthanide complexes of the type [(4R,5S)-Ph(2)Box]La[N(TMS)(2)](2), [(4S,5R)-Ar(2)Box]La[N(TMS)(2)](2), and [(4S)-Ph-5,5-Me(2)Box]La[N(TMS)(2)](2) (Box = 2,2'-bis(2-oxazoline)methylenyl; Ar = 4-tert-butylphenyl, 1-naphthyl; TMS = SiMe(3)) serve as precatalysts for the efficient enantioselective intramolecular hydroamination/cyclization of aminoalkenes and aminodienes. These new catalyst systems are conveniently generated in situ from the known metal precursors Ln[N(TMS)(2)](3) or Ln[CH(TMS)(2)](3) (Ln = La, Nd, Sm, Y, Lu) and 1.2 equiv of commercially available or readily prepared bis(oxazoline) ligands such as (4R,5S)-Ph(2)BoxH, (4S,5R)-Ar(2)BoxH, and (4S)-Ph-5,5-Me(2)BoxH. The X-ray crystal structure of [(4S)-(t)BuBox]Lu[CH(TMS)(2)](2) provides insight into the structure of the in situ generated precatalyst species. Lanthanides having the largest ionic radii exhibit the highest turnover frequencies as well as enantioselectivities. Reaction rates maximize near 1:1 BoxH:Ln ratio (ligand acceleration); however, increasing the ratio to 2:1 BoxH:Ln decreases the reaction rate, while affording enantiomeric excesses similar to the 1:1 BoxH:Ln case. A screening study of bis(oxazoline) ligands reveals that aryl stereodirecting groups at the oxazoline ring 4 position and additional substitution (geminal dimethyl or aryl) at the 5 position are crucial for high turnover frequencies and good enantioselectivities. The optimized precatalyst, in situ generated [(4R,5S)-Ph(2)Box]La[N(TMS)(2)](2), exhibits good rates and enantioselectivities, comparable to or greater than those achieved with chiral C(1)-symmetric organolanthanocene catalysts, even for poorly responsive substrates (up to 67% ee at 23 degrees C). Kinetic studies reveal that hydroamination rates are zero order in [amine substrate] and first order in [catalyst], implicating the same general mechanism for organolanthanide-catalyzed hydroamination/cyclizations (intramolecular turnover-limiting olefin insertion followed by the rapid protonolysis of an Ln-C bond by amine substrate) and implying that the active catalytic species is monomeric.     

The gold(III) tetra­chloride salt of L‐cocaine

The title salt, methyl (1R,2R,3S,5S,8S)‐3‐benzoyl­oxy‐8‐methyl‐8‐aza­bicyclo­[3.2.1]octane‐2‐carboxyl­ate tetra­chloro­aurate(III), (C₁₇H₂₂NO₄)[AuCl₄], has its protonated N atom intra­molecularly hydrogen bonded to the O atom of the methoxy­carbonyl group [N⋯O = 2.755 (6) Å and N—H⋯O = 136°]. Two close inter­molecular C—H⋯O contacts exist, as well as five C—H⋯Cl close contacts. The [AuCl₄]⁻ anion was found to be distorted square planar.     

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides

We studied here the binding of the mastoparan X peptide to a zwitterionic lipid bilayer (POPC) and demonstrated that nitrile-derivatized amino acids can be used to determine the hydration state (or change in hydration state) of specific sites of membrane-interactive peptides (upon binding). We have also shown that polarized ATR-FTIR measurements can further be used to uncover information regarding the spatial orientation of individual side chains as well as their conformational preference within the lipid bilayer.     

Photochemistry of dicyanopyridines

The photochemistry of a variety of dicyanopyridines (2,3-, 2,4-, 2,5-, 2,6-, 3,4- and 3,5-dicyanopyridine) in solution at room temperature was investigated. Pulsed UV (308 nm) laser irradiation in deoxygenated acetonitrile yields the triplet state with lifetimes between 4 and 10 μs and absorption bands in the 400 and 320 nm regions. In the presence of added HCl an air-insensitive transient (τ ≈ 10–12 μs, λ_max ≈ 360–380 nm) was observed, suggesting the formation of a protonated excited state.

Irradiation in the presence of amines resulted in the production of the pyridyl radical anion (τ ≈ 40–80 μs, air sensitive, λ_max ≈ 360–380 nm) formed by electron transfer from the amine to the pyridine triplet excited state. Stern-Volmer analysis gave electron transfer rate constants in the range (1–8) × 10⁻⁸ M⁻¹ s⁻¹.

In methanol solvent, irradiation yielded an air-insensitive transient assigned as the neutral pyridyl radical (τ ≈ 30–200 μs, λ_max ≈ 370–385 nm). The formation of these transients is discussed in the context of previous photochemical electron spin resonance and product studies.     

Comparison of the Bonding of Benzene and C60 to a Metal Cluster: Ru3(CO)9(μ3-η2,η 2,η2-C6H6) and Ru3(CO)9(μ3-η2,η2,η2-C60)

The electron distributions and bonding in Ru₃(CO)₉( ³- ², ², ²-C₆H₆) and Ru₃(CO)₉( ³- ², ², ²-C₆₀) are examined via electronic structure calculations in order to compare the nature of ligation of benzene and buckminsterfullerene to the common Ru₃(CO)₉ inorganic cluster. A fragment orbital approach, which is aided by the relatively high symmetry that these molecules possess, reveals important features of the electronic structures of these two systems. Reported crystal structures show that both benzene and C₆₀ are geometrically distorted when bound to the metal cluster fragment, and our ab initio calculations indicate that the energies of these distortions are similar. The experimental Ru–C_fullerene bond lengths are shorter than the corresponding Ru–C_benzene distances and the Ru–Ru bond lengths are longer in the fullerene-bound cluster than for the benzene-ligated cluster. Also, the carbonyl stretching frequencies are slightly higher for Ru₃(CO)₉( ³- ², ², ²-C₆₀) than for Ru₃(CO)₉( ³- ², ², ²-C₆H₆). As a whole, these observations suggest that electron density is being pulled away from the metal centers and CO ligands to form stronger Ru–C_fullerene than Ru–C_benzene bonds. Fenske-Hall molecular orbital calculations show that an important interaction is donation of electron density in the metal–metal bonds to empty orbitals of C₆₀ and C₆H₆. Bonds to the metal cluster that result from this interaction are the second highest occupied orbitals of both systems. A larger amount of density is donated to C₆₀ than to C₆H₆, thus accounting for the longer metal–metal bonds in the fullerene-bound cluster. The principal metal–arene bonding modes are the same in both systems, but the more band-like electronic structure of the fullerene (i.e., the greater number density of donor and acceptor orbitals in a given energy region) as compared to C₆H₆ permits a greater degree of electron flow and stronger bonding between the Ru₃(CO)₉ and C₆₀ fragments. Of significance to the reduction chemistry of M₃(CO)₉( ³- ², ², ²-C₆₀) molecules, the HOMO is largely localized on the metal–carbonyl fragment and the LUMO is largely localized on the C₆₀ portion of the molecule. The localized C₆₀ character of the LUMO is consistent with the similarity of the first two reductions of this class of molecules to the first two reductions of free C₆₀. The set of orbitals above the LUMO shows partial delocalization (in an antibonding sense) to the metal fragment, thus accounting for the relative ease of the third reduction of this class of molecules compared to the third reduction of free C₆₀.