Length-Selective Synthesis of Acylglycerol-Phosphates through Energy-Dissipative Cycling.

The main aim of origins of life research is to find a plausible sequence of transitions from prebiotic chemistry to nascent biology. In this context, understanding how and when phospholipid membranes appeared on early Earth is critical to elucidating the prebiotic pathways that led to the emergence of primitive cells. Here we show that exposing glycerol-2-phosphate to acylating agents leads to the formation of a library of acylglycerol-phosphates.

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism.

A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others.

Aryl ethynyl anthraquinones: a useful platform for targeting telomeric G-quadruplex structures.

Aryl ethynyl anthraquinones have been synthesized by Sonogashira cross-coupling and evaluated as telomeric G-quadruplex ligands, by the FRET melting assay, circular dichroism, the DNA synthesis arrest assay and molecular docking. Both the binding properties and G-quadruplex vs. duplex selectivity are controlled by the structures of the aryl ethynyl moieties.

Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process.

Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.

Vinylidene-quinone methides, photochemical generation and β-silicon effect on reactivity.

Irradiation of 2-alkynylphenols resulted in the generation of vinylidene-quinone methides (QMs), which were detected by laser flash photolysis in organic solvents and aqueous acetonitrile. QMs' spectroscopic properties and electrophilicity were both significantly affected by β-silicon effect. The hydration of the alkynyl moiety (22 and 900 M(-1) s(-1)for QM-1 and QM-2, in aqueous acetonitrile) was an acid- and base-catalyzed process.

Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures.

The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4.

Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex.

Selective recognition and alkylation of G-quadruplex oligonucleotides has been achieved by substituted naphathalene diimides (NDIs) conjugated to engineered phenol moieties by alkyl-amido spacers with tunable length and conformational mobility. FRET-melting assays, circular dichroism titrations and gel electrophoresis analysis have been carried out to evaluate both reversible stabilization and alkylation of the G-quadruplex. The NDIs conjugated to a quinone methide precursor (NDI-QMP) and a phenol moiety by the shortest alkyl-amido spacer exhibited a planar and fairly rigid geometry (modelled by DFT computation).

Quinone methide generation via photoinduced electron transfer.

Photochemical activation of water-soluble 1,8-naphthalimide derivatives (NIs) as alkylating agents has been achieved by irradiation at 310 and 355 nm in aqueous acetonitrile. Reactivity in aqueous and neat acetonitrile has been extensively investigated by laser flash photolysis (LFP) at 355 nm, as well as by steady-state preparative irradiation at 310 nm in the presence of water, amines, thiols, and ethyl vinyl ether. Product distribution analysis revealed fairly efficient benzylation of the amines, hydration reaction, and 2-ethoxychromane generation, in the presence of ethyl vinyl ether, resulting from a [4 + 2] cycloaddition onto a transient quinone methide.

Protecting group free synthesis of 6-substituted naphthols and binols.

A straightforward route for the preparation of 6-substituted naphthols and 6,6'-disubstituted binols (binol = 2,2'-dihydroxy-1,1'-binaphthyl) is presented. The synthesis has been accomplished by a one-step procedure starting from 6-bromo derivatives via direct lithiation with n-BuLi, followed by the addition of several electrophiles. This C-C functionalization has been successfully achieved with iodomethane, 3-methoxybenzaldehyde, benzophenone, methyl-2-methylbenzoate, methylbenzoate, dimethyl carbonate, ethyl 2-chloro-2-oxoacetate, and 2,2-dimethyloxirane (E).

Photogeneration and reactivity of naphthoquinone methides as purine selective DNA alkylating agents.

A one-step protecting-group-free synthesis of both 6-hydroxy-naphthalene-2-carbaldehyde and the bifunctional binaphthalenyl derivative afforded 6-hydroxymethylnaphthalen-2-ol, 6-methylaminomethyl-naphthalen-2-ol, [(2-hydroxy-3-naphthyl)methyl]trimethyl ammonium iodide, and a small library of bifunctional binol analogues in good yields. Irradiation of naphthol quaternary ammonium salt and binol-derivatives (X = OH, NHR, NMe(3)(+), OCOCH(3), and L-proline) at 310 and 360 nm resulted in the photogeneration of the 2,6-naphthoquinone-6-methide (NQM) and binol quinone methide analogues (BQMs) by a water-mediated excited-state proton transfer (ESPT). The hydration, the mono- and bis-alkylation reactions of morpholine and 2-ethanethiol, as N and S prototype nucleophiles, by the transient NQM (λ(max) 310, 330 nm) and BQMs (λ(max) 360 nm) were investigated in water by product distribution analysis and laser flash photolysis (LFP).

A computational workflow for the design of irreversible inhibitors of protein kinases.

Design of irreversible inhibitors is an emerging and relatively less explored strategy for the design of protein kinase inhibitors. In this paper, we present a computational workflow that was specifically conceived to assist such design. The workflow takes the form of a multi-step procedure that includes: the creation of a database of already known reversible inhibitors of protein kinases, the selection of the most promising scaffolds that bind one or more desired kinase templates, the modification of the scaffolds by introduction of chemically reactive groups (suitable cysteine traps) and the final evaluation of the reversible and irreversible protein-ligand complexes with molecular dynamics simulations and binding free energy predictions.