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A report on the design, synthesis, and solution structure of a highly functionalized saddle-shaped macrocyclic scaffold, constrained by scaffolds and thiazoles, supporting two short peptide loops projecting orthogonally from the same face of the scaffold is presented. The structural mimetic of two interhelical loops of cytochrome b(sub 562) illustrates an approach to structurally mimicking discontinuous loops of proteins.

Cyclopropylmethyltrimethylstannanes undergo electrophilic cyclopropane cleavage in chloroform with simple inorganic electrophiles in a homologous reaction to the S(sub E) cleavage of allylic stannanes. The sigma-sigma conjugation between the carbon-tin bond and cyclopropane orbitals observed spectroscopically in the parent cyclopropylmethyltrimethylstannane is responsible for a rate enhancement of ca. 10(super 2) toward iodinolysis, relative to comparable alkyl stannanes.

Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the chromatin accessibility and transcriptome dynamics of zinc-containing HDACs during cell differentiation in vitro coupled with chemical perturbation to identify the role of HDACs in mesendoderm cell fate specification. Single-cell RNA sequencing analyses of HDAC expression during human pluripotent stem cell (hPSC) differentiation in vitro and mouse gastrulation in vivo reveal a unique association of HDAC1 and -3 with mesendoderm gene programs during exit from pluripotency. Functional perturbation with small molecules reveals that inhibition of HDAC1 and -3, but not HDAC2, induces mesoderm while impeding endoderm and early cardiac progenitor specification. These data identify unique biological functions of the structurally homologous enzymes HDAC1–3 in influencing hPSC differentiation from pluripotency toward mesendodermal and cardiac progenitor populations. [Display omitted] • Single-cell transcriptomics find HDAC1–3 to be regulators of cardiac differentiation • Inhibition of HDAC1–3 activity results in dynamic chromatin accessibility changes • Loss of HDAC1 and -3, but not HDAC2, impairs cardiac progenitor specification • HDAC1 and -3 are required during early stages of mesendoderm specification Sinniah et al. identify HDAC1 and -3 as required for early mesendoderm and cardiac progenitor specification during human pluripotent stem cell differentiation. Changes to chromatin accessibility and transcriptome dynamics upon perturbation of HDAC activity reveal distinct roles of HDAC1–3 in germ-layer and cardiac-lineage commitment following exit from pluripotency. [ABSTRACT FROM AUTHOR]

Cyclopropylmethyltrimethylstannanes undergo electrophilic cyclopropane cleavage in chloroform with simple inorganic electrophiles (H+, SO2, I2) in a homologous reaction to the SE′ cleavage of allylic stannanes. The σ-σ conjugation between the carbon-tin bond and cyclopropane orbitals observed spectroscopically in the parent cyclopropylmethyltrimethylstannane is responsible for a rate enhancement of ca. 102 toward iodinolysis, relative to comparable alkyl stannanes. This acceleration is considerably less, however, than the ca. 109-fold rate enhancement provided by the corresponding σ-π conjugation in allylic stannanes. Methanol-tin coordination appears to reduce the activating influence of the metal, promoting methyl cleavage over cyclopropane fission with acid and iodine. Decreased σ-σ conjugation can also explain the decreased reactivity of cyclopropyltriphenylstannane compared with its trimethyltin counterpart. Cyclopropylmethylstannanes do not undergo the synthetically useful addition of aldehydes under conditions that facilitate the corresponding reaction of allylic stannanes. [ABSTRACT FROM AUTHOR]

A major chemical challenge is the structural mimicry of discontinuous protein surfaces brought into close proximity through polypeptide folding. We report the design, synthesis, and solution structure of a highly functionalized saddle-shaped macrocyclic scaffold, constrained by oxazoles and thiazoles, supporting two short peptide loops projecting orthogonally from the same face of the scaffold. This structural mimetic of two interhelical loops of cytochrome b562 illustrates a promising approach to structurally mimicking discontinuous loops of proteins. [ABSTRACT FROM AUTHOR]

Transformation of proteins and peptides to fibrillar aggregates rich in β sheets underlies many diseases, but mechanistic details of these structural transitions are poorly understood. To simulate aggregation, four equivalents of a water-soluble, α-helical (65 %) amphipathic peptide (AEQLLQEAEQLLQEL) were assembled in parallel on an oxazole-containing macrocyclic scaffold. The resulting 4α-helix bundle is monomeric and even more α helical (85 %), but it is also unstable at pH 4 and undergoes concentration-dependent conversion to β-sheet aggregates and amyloid fibrils. Fibrils twist and grow with time, remaining flexible like rope (>1 μm long, 5-50 nm wide) with multiple strings (2 nm), before ageing to matted fibers. At pH 7 the fibrils revert back to soluble monomeric 4α-helix bundles. During α→β folding we were able to detect soluble 3(10) helices in solution by using 2D-NMR, CD and FTIR spectroscopy. This intermediate satisfies the need for peptide elongation, from the compressed α helix to the fully extended β strand/sheet, and is driven here by 3(10) -helix aggregation triggered in this case by template-promoted helical bundling and by hydrogen-bonding glutamic acid side chains. A mechanism involving α⇌α(4) ⇌(3(10) )(4) ⇌(3(10) )(n) ⇌(β)(n) ⇋m(β)(n) equilibria is plausible for this peptide and also for peptides lacking hydrogen-bonding side chains, with unfavourable equilibria slowing the α→β conversion., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Chemotherapy in the last century was characterized by cytotoxic drugs that did not discriminate between cancerous and normal cell types and were consequently accompanied by toxic side effects that were often dose limiting. The ability of differentiating agents to selectively kill cancer cells or transform them to a nonproliferating or normal phenotype could lead to cell- and tissue-specific drugs without the side effects of current cancer chemotherapeutics. This may be possible for a new generation of histone deacetylase inhibitors derived from amino acids. Structure-activity relationships are now reported for 43 compounds derived from 2-aminosuberic acid that kill a range of cancer cells, 26 being potent cytotoxins against MM96L melanoma cells (IC50 20 nM-1 microM), while 17 were between 5- and 60-fold more selective in killing MM96L melanoma cells versus normal (neonatal foreskin fibroblasts, NFF) cells. This represents a 10- to 100-fold increase in potency and up to a 10-fold higher selectivity over previously reported compounds derived from cysteine (J. Med. Chem. 2004, 47, 2984). Selectivity is also an underestimate, because the normal cells, NFF, are rarely all killed by the drugs that also induce selective blockade of the cell cycle for normal but not cancer cells. Selected compounds were tested against a panel of human cancer cell lines (melanomas, prostate, breast, ovarian, cervical, lung, and colon) and found to be both selective and potent cytotoxins (IC50 20 nM-1 microM). Compounds in this class typically inhibit human histone deacetylases, as evidenced by hyperacetylation of histones in both normal and cancer cells, induce expression of p21, and differentiate surviving cancer cells to a nonproliferating phenotype. These compounds may be valuable leads for the development of new chemotherapeutic agents.

A major chemical challenge is the structural mimicry of discontinuous protein surfaces brought into close proximity through polypeptide folding. We report the design, synthesis, and solution structure of a highly functionalized saddle-shaped macrocyclic scaffold, constrained by oxazoles and thiazoles, supporting two short peptide loops projecting orthogonally from the same face of the scaffold. This structural mimetic of two interhelical loops of cytochrome b(562) illustrates a promising approach to structurally mimicking discontinuous loops of proteins.