Cyclooctyne-based reagents for uncatalyzed click chemistry: A computational survey

With the goal of identifying alkyne-like reagents for use in click chemistry, but without Cu catalysts, we used B3LYP density function theory (DFT) to investigate the trends in activation barriers for the 1,3-dipolar cycloadditions of azides with various cyclooctyne, dibenzocyclooctyne, and azacyclooctyne compounds. Based on these trends, we find monobenzocyclooctyne-based reagents that are predicted to have dramatically improved reactivity over currently employed reagents

Allosteric modulation of DNA by small molecules

Many human diseases are caused by dysregulated gene expression. The oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell permeable small molecules that can be programmed to disrupt transcription factor-DNA interfaces could silence aberrant gene expression pathways. Pyrrole-imidazole polyamides are DNA minor-groove binding molecules that are programmable for a large repertoire of DNA motifs. A high resolution X-ray crystal structure of an 8-ring cyclic Py/Im polyamide bound to the central 6 bp of the sequence d(5′-CCAGGCCTGG-3′)2 reveals a 4 Å widening of the minor groove and compression of the major groove along with a >18 ° bend in the helix axis toward the major groove. This allosteric perturbation of the DNA helix provides a molecular basis for disruption of transcription factor-DNA interfaces by small molecules, a minimum step in chemical control of gene networks

Solution-phase synthesis of pyrrole-imidazole polyamides

Pyrrole−imidazole polyamides are DNA-binding molecules that are programmable for a large repertoire of DNA sequences. Typical syntheses of this class of heterocyclic oligomers rely on solid-phase methods. Solid-phase methodologies offer rapid assembly on a micromole scale sufficient for biophysical characterizations and cell culture studies. In order to produce gram-scale quantities necessary for efficacy studies in animals, polyamides must be readily synthesized in solution. An 8-ring hairpin polyamide 1, which targets the DNA sequence 5′-WGWWCW-3′, was chosen for our synthesis studies as this oligomer exhibits androgen receptor antagonism in cell culture models of prostate cancer. A convergent solution-phase synthesis of 1 from a small set of commercially available building blocks is presented which highlights principles for preparing gram quantities of pyrrole−imidazole oligomers with minimal chromatography

Oligomerization Route to Py-Im Polyamide Macrocycles

Cyclic eight-ring pyrrole−imidazole polyamides are sequence-specific DNA-binding small molecules that are cell permeable and can regulate endogenous gene expression. Syntheses of cyclic polyamides have been achieved by solid-phase and solution-phase methods. A rapid solution-phase oligomerization approach to eight-ring symmetrical cyclic polyamides yields 12- and 16-membered macrocycles as well. A preference for DNA binding by the 8- and 16-membered oligomers was observed over the 12-ring macrocycle, which we attributed to a conformational constraint not present in the smaller and larger systems

Cyclic pyrrole-imidazole polyamides targeted to the androgen response element

Hairpin pyrrole−imidazole (Py-Im) polyamides are a class of cell-permeable DNA-binding small molecules that can disrupt transcription factor−DNA binding and regulate endogenous gene expression. The covalent linkage of antiparallel Py-Im ring pairs with an γ-amino acid turn unit affords the classical hairpin Py-Im polyamide structure. Closing the hairpin with a second turn unit yields a cyclic polyamide, a lesser-studied architecture mainly attributable to synthetic inaccessibility. We have applied our methodology for solution-phase polyamide synthesis to cyclic polyamides with an improved high-yield cyclization step. Cyclic 8-ring Py-Im polyamides 1−3 target the DNA sequence 5′-WGWWCW-3′, which corresponds to the androgen response element (ARE) bound by the androgen receptor transcription factor to modulate gene expression. We find that cyclic Py-Im polyamides 1−3 bind DNA with exceptionally high affinities and regulate the expression of AR target genes in cell culture studies, from which we infer that the cycle is cell permeable

Fluorescent Sequence-Specific dsDNA Binding Oligomers

Sequence-specific detection methods for double-stranded DNA that obviate the need for denaturation would provide a powerful tool for bioorganic chemistry and genetics. As part of a sustained effort to develop sequence-specific fluorescent DNA detection methods, two programmable oligomers have been synthesized which target their respective sequences 5‘-WTACGW-3‘ and 5‘-WGGGGW-3‘ (W = A or T). The two oligomers were found to fluoresce weakly in the absence of DNA but showed significant fluorescence enhancement by the addition of match DNA. The fluorescence is shown to increase in a concentration-dependent manner, and the intensity varies depending on the number of mismatch sites incorporated into the DNA hairpins. This new class of oligomers provides a method to detect DNA sequences without denaturation and in the absence of conjugation to a dye molecule. This is a first step toward sequence-specific DNA-binding molecules containing a fluorescent switch integrated as part of the recognition modules

Pyrrole-Imidazole Polyamides Distinguish Between Double-Helical DNA and RNA

Groove specificity: Pyrrole-imidazole polyamides are well-known for their specific interactions with the minor groove of DNA (see scheme). However, polyamides do not show similar binding to duplex RNA, and a structural rationale for the molecular-level discrimination of nucleic acid duplexes by minor-groove-binding ligands is presented

SLIDES: The Economic Benefits of Completing Initial Reclamation Successfully for Oil and Gas

Presenters: Joe Schneider and Colby Reid, Western States Reclamation, Inc. 34 slide

SLIDES: The Economic Benefits of Completing Initial Reclamation Successfully for Oil and Gas

Presenters: Joe Schneider and Colby Reid, Western States Reclamation, Inc. 34 slide

Next generation hairpin polyamides with (R)-3,4-diaminobutyric acid turn unit

The characterization of a new class of pyrrole−imidazole hairpin polyamides with β-amino-γ-turn units for recognition of the DNA minor groove is reported. A library of eight hairpins containing (R)- and (S)-3,4-diaminobutyric acid (β-amino-γ-turn) has been synthesized, and the impact of the molecules on DNA-duplex stabilization was studied for comparison with the parent γ-aminobutyric acid (γ-turn) and standard (R)-2,4-diaminobutyric acid (α-amino-γ-turn)-linked eight-ring polyamides. For some, but not all, sequence compositions, melting temperature analyses have revealed that both enantiomeric forms of the β-amino-γ-turn increase the DNA-binding affinity of polyamides relative to the (R)-α-amino-γ-turn. The (R)-β-amine residue may be an attractive alternative for constructing hairpin polyamide conjugates. Biological assays have shown that (R)-β-amino-γ-turn hairpins are able to inhibit androgen receptor-mediated gene expression in cell culture similar to hairpins bearing the standard (R)-α-amino-γ-turn, from which we infer they are cell-permeable