Protein-reactive natural products

Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.     

Artificial metalloenzymes: The powerful alliance between protein scaffolds and organometallic catalysts

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Self-selection in olefin cross-metathesis: the effect of remote functionality

Olefin cross-metathesis (CM) is potentially an attractive method for generating dynamic combinatorial libraries (DCLs). In order for the CM reaction to be useful for DCL production, the course of the reaction and product distribution must be relatively insensitive to functionality remote from the reacting centers. We report on the CM of a series of allyl- and homoallylamides that are strongly dependent on remote functionality. This includes an unusual example of a cis-selective CM. [Reaction: see text]     

Further reactions of some bis(vinylidene)diruthenium complexes

Whereas {Ru(dppm)Cp*}₂(μ-CCCC) (2) is the only product formed by deprotonation of [{Ru(dppm)Cp*}₂{μ(CCHCHC)}]⁺ with dbu, a mixture of 2 with Ru{CCCHCH(PPh₂)₂[RuCp*]}(dppm)Cp* (3) and {Cp*Ru(PPh₂CHCCH-)}₂ (4) is obtained with KOBu^t. A similar reaction with [{Ru(dppm)Cp*}₂{μ(CCMeCMeC)}]⁺ (5) gave Ru{CCCMeCH(PPh₂)₂[RuCp*]}(dppm)Cp* (6). X-ray structures of 4, 5 and 6 confirm the presence of the 1-ruthena-2,4-diphosphabicyclo[1.1.1]pentane moiety, which is likely formed by an intramolecular attack of the deprotonated dppm ligand on C(1) of the vinylidene ligand. Protonation of {Ru(dppe)Cp*}₂(μ-CCCC) (8-Ru) regenerates its precursor [{Ru(dppe)Cp*}₂{μ(CCHCHC)}]²⁺ (7-Ru). Ready oxidation of the bis(vinylidene) complex affords the cationic carbonyl [Ru(CO)(dppe)Cp*]PF₆ (9) (X-ray structure).     

Some ruthenium complexes containing cyanocarbon ligands: syntheses, structures and extent of electronic communication in binuclear systems

The preparation of several ruthenium complexes containing cyanocarbon anions is reported. Deprotonation (KOBu^t) of [Ru(NCCH₂CN)(PPh₃)₂Cp]PF₆ (1) gives Ru{NCCH(CN)}(PPh₃)₂Cp (2), which adds a second [Ru(PPh₃)₂Cp]⁺ unit to give [{Ru(PPh₃)₂Cp}₂(μ-NCCHCN)]⁺ (3). Attempted deprotonation of the latter to give the μ-NCCCN complex was unsuccessful. Similar chemistry with tricyanomethanide anion gives Ru{NCC(CN)₂}(PPh₃)₂Cp (4) and [{Ru(PPh₃)₂Cp}₂{μ-NCC(CN)CN}]PF₆ (5), and with pentacyanopropenide, Ru{NCC(CN)C(CN)C(CN)₂}(PPh₃)₂Cp (6) and [{Ru(PPh₃)₂Cp}₂{μ-NCC(CN)C(CN)C(CN)CN}]PF₆ (7). The Ru(dppe)Cp* analogues of 6 and 7 (8 and 9) were also prepared. Thermolysis of 6 (refluxing toluene, 12 h) results in loss of PPh₃ and formation of the binuclear cyclic complex {Ru(PPh₃)Cp[μ-NC{C(CN)C(CN)₂}CN]}₂ (10). The solid-state structures of 2-4 and 8-10 have been determined and the nature of the isomers shown to be present in solutions of the binuclear cations 7 and 9 by NMR studies has been probed using Hartree-Fock and density functional theory.     

Multilayer vesicles and vesicle clusters formed by the fullerene-based surfactant C60(CH3)5K

The self-assembly behavior of a fullerene-based surfactant, C60(CH3)5K, in water was studied using a combination of static and dynamic light scattering, as well as transmission electron microscopy, and compared to that of the compound C60(C6H5)5K. Both fullerene surfactant systems spontaneously assemble into large vesicles consisting of closed spherical shells formed by bilayers, with critical aggregation concentrations (CAC) lower than 10(-6) g ml(-1). At low concentrations, the aggregate sizes of C60(CH3)5K (radius R approximately 26.8 nm) and C60(C6H5)5K (R approximately 17.0 nm) were found to be substantially different from each other, showing that the change of the substituents surrounding the polar cyclopentadienide head group makes it possible to control the size of the resulting aggregates. Furthermore, the C60(CH3)5K vesicles were found to exist in two qualitatively different types of aggregation with a critical reaggregation concentration (CRC) located at 3.30 x 10(-6) g ml(-1). Above the CRC, larger aggregates were observed (R approximately 37.6 nm), showing a more complex form of supramolecular aggregation, e.g., in terms of multi-bilayer vesicles and/or of clusters of bilayer vesicles.     

Capillary electrochromatography of peptides on microfabricated poly(dimethylsiloxane) chips modified by cerium(IV)-catalyzed polymerization

Ceramides are important intracellular second messengers that play a role in the regulation of cell growth, differentiation and programmed cell death. Qualitative and quantitative analysis of these second messengers requires sensitive and specific analytical methods to detect endogenous levels of individual ceramide species and to differentiate between them. Nine synthetic ceramides were separated by liquid chromatography coupled to tandem mass spectrometry on a C18 bonded silica column. The lipids were eluted in gradient elution mode using a mixture of water, acetonitrile and 2-propanol as mobile phase. They were detected by reaction monitoring performed on positive ion electrospray generated ions. Collision-induced fragmentations conducted on ceramides produced a well characteristic product ion at m/z 264, making multiple reaction monitoring (MRM) well suited for various ceramides quantitative measurements. After optimization of the extraction step, the proposed methodology was able to identify and quantify different ceramide species issued from human cancer cells. The method could be validated for C16, C18 and C20 ceramides, quantified at the nanogram level. The validation exhibits good results with respect to linearity, accuracy and precision.     

Ru(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and undergoes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate

The lowest excited state of [Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine) 1 is strongly luminescent, even in water, and very oxidizing. Therefore it is able to oxidise not only guanosine-5'-monophosphate (GMP), as demonstrated by laser flash photolysis, but also guanine-containing polynucleotides such as calf thymus DNA and [poly(dG-dC)]2. The luminescence quenching was found to be faster in H2O than in D2O, as is the back reaction, indicating that both processes probably proceed by proton-coupled electron transfer. These properties, that are controlled by the triplet MLCT state in which the charge has been transferred from the Ru to a TAP ligand, contrast with those of the well known [Ru(phen)2(dppz)]2+ 2.