Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.

Histone deacetylases (HDACs) regulate myriad cellular processes by catalyzing the hydrolysis of acetyl-l-lysine residues in histone and nonhistone proteins. The Zn2+-dependent class IIb enzyme HDAC6 regulates microtubule function by deacetylating α-tubulin, which suppresses microtubule dynamics and leads to cell cycle arrest and apoptosis. Accordingly, HDAC6 is a target for the development of selective inhibitors that might be useful in new therapeutic approaches for the treatment of cancer, neurodegenerative diseases, and other disorders. Here, we present high-resolution structures of catalytic domain 2 from Danio rerio HDAC6 (henceforth simply "HDAC6") complexed with compounds that selectively inhibit HDAC6 while maintaining nanomolar inhibitory potency: N-hydroxy-4-[(N(2-hydroxyethyl)-2-phenylacetamido)methyl)-benzamide)] (HPB), ACY-1215 (Ricolinostat), and ACY-1083. These structures reveal that an unusual monodentate Zn2+ coordination mode is exploited by sterically bulky HDAC6-selective phenylhydroxamate inhibitors. We additionally report the ultrahigh-resolution structure of the HDAC6-trichostatin A complex, which reveals two Zn2+-binding conformers for the inhibitor: a major conformer (70%) with canonical bidentate hydroxamate-Zn2+ coordination geometry and a minor conformer (30%) with monodentate hydroxamate-Zn2+ coordination geometry, reflecting a free energy difference of only 0.5 kcal/mol. The minor conformer is not visible in lower resolution structure determinations. Structural comparisons of HDAC6-inhibitor complexes with class I HDACs suggest active site features that contribute to the isozyme selectivity observed in biochemical assays.

Magnesium pyrophosphates in enzyme mimics of nucleotide synthases and kinases and in their prebiotic chemistry.

Derivatives of ribosyl pyrophosphate have been synthesized, and examined with magnesium salts in the coupling of the ribose unit to various nucleophiles, including pyrazole and 2-chloroimidazole. Only with the magnesium salt present did they generate the ribosyl cation by binding to the leaving group and then couple the ribose derivative with nucleophiles. The role of magnesium salts in phosphorylation of methanol by ATP was also examined. Here a remarkable effect was seen: phosphorylation by ATP was slowed with low concentrations of Mg(2+) but accelerated by higher concentrations. Related effects were also seen in the effect of Mg(2+) on phosphorylation by ADP. The likely mechanisms explain these effects.

Creation of a histone deacetylase 6 inhibitor and its biological effects [corrected].

We report the development of a potent, selective histone deacetylase 6 (HDAC6) inhibitor. This HDAC6 inhibitor blocks growth of normal and transformed cells but does not induce death of normal cells. The HDAC6 inhibitor alone is as effective as paclitaxel in anticancer activity in tumor-bearing mice.

Evidence for tunneling in base-catalyzed isomerization of glyceraldehyde to dihydroxyacetone by hydride shift under formose conditions.

Hydrogen atom transfer reactions between the aldose and ketose are key mechanistic features in formose chemistry by which formaldehyde is converted to higher sugars under credible prebiotic conditions. For one of these transformations, we have investigated whether hydrogen tunneling makes a significant contribution to the mechanism by examining the deuterium kinetic isotope effect associated with the hydrogen transfer during the isomerization of glyceraldehyde to the corresponding dihydroxyacetone. To do this, we developed a quantitative HPLC assay that allowed us to measure the apparent large intrinsic kinetic isotope effect. From the Arrhenius plot of the kinetic isotope effect, the ratio of the preexponential factors AH/AD was 0.28 and the difference in activation energies Ea(D) - Ea(H) was 9.1 kJ·mol(-1). All these results imply a significant quantum-mechanical tunneling component in the isomerization mechanism. This is supported by multidimensional tunneling calculations using POLYRATE with small curvature tunneling.

Novel aromatic and antiaromatic systems.

We contributed to the field of non-benzenoid aromatic compounds by creating the cyclopropenyl cation and various of its derivatives, including cyclopropenone; it was the first aromatic system with other than six pi electrons in a single ring, and the simplest aromatic system. The pioneering work of Tetsuo Nozoe in tropolone chemistry was celebrated with the founding of ISNA, the International Symposium on Non-Benzenoid Aromatic Compounds, where I described our work in the field. It fit the prediction that aromaticity would be found in systems with 4n + 2 pi electrons, where n is an integer. I was also concerned with the properties of monocyclic systems with 4n cyclically conjugated pi electrons. They were expected not to be aromatic, but the interesting question was whether they were actually antiaromatic, especially destabilized by the cyclic conjugation in such 4n species as the cyclopropenyl anion, cyclobutadiene, and cyclopentadienyl cation. The evidence supports antiaromaticity in these cases. We also examined compounds where 4n cyclic pi systems were fused with aromatic systems, and most interestingly systems in which two 4n pi systems were fused. In these cases the periphery of the molecules had 4n + 2 pi electrons, for aromaticity, but the components were antiaromatic. Recently we have studied electrical conductivities in aromatic molecules such as thiophene and saw that aromaticity added resistance to the systems, so non-aromatic compounds are better conductors and antiaromatic compounds are predicted to be the best of all.

Deoxypolypeptides bind and cleave RNA.

We have prepared L- and D-deoxypolypeptides (DOPPs) by selective reduction of appropriately protected polyhistidines with borane, reducing the carbonyl groups to methylenes. The result is a chiral polyamine, not amide, with a mainly protonated backbone and chirally mounted imidazolylmethylene side chains that are mostly unprotonated at neutrality because of the nearby polycationic backbone. We found that, in contrast with the D-octahistidine DOPP, the L-octahistidine DOPP is able to cooperatively bind to a D-polyuridylic acid RNA; this is consistent with results of previous studies showing that, relative to D-histidine, L-histidine is able to more strongly bind to RNA. The L-DOPP was also a better catalyst for cleaving the RNA than the D-DOPP, consistent with evidence that the L-DOPP uses its imidazole groups for catalysis, in addition to the backbone cations, but the D-DOPP does not use the imidazoles. The L-DOPP bifunctional process probably forms a phosphorane intermediate. This is a mechanism we have proposed for models of ribonuclease cleavage and for the ribonuclease A enzyme itself, based on our studies of the cleavage and isomerization of UpU catalyzed by imidazole buffers as well as other relevant studies. This mechanism contrasts with earlier, generally accepted ribonuclease cleavage mechanisms where the proton donor coordinates with the oxygen of the leaving group as the 2-hydroxyl of ribose attacks the unprotonated phosphate.

Deuterium studies reveal a new mechanism for the formose reaction involving hydride shifts.

In the formose reaction, formaldehyde is converted to glycolaldehyde, its dimer, under credible prebiotic conditions. Breslow proposed a mechanism for the process in 1959, but recent studies by Benner showed that it was wrong in detail. Our present studies clarify the mechanism, which involves the original Breslow intermediates but some different connecting steps.

Aromaticity decreases single-molecule junction conductance.

We have measured the conductance of single-molecule junctions created with three different molecular wires using the scanning tunneling microscope-based break-junction technique. Each wire contains one of three different cyclic five-membered rings: cyclopentadiene, furan, or thiophene. We find that the single-molecule conductance of these three wires correlates negatively with the resonance energy of the five-membered ring; the nonaromatic cyclopentadiene derivative has the highest conductance, while the most aromatic of this series, thiophene, has the lowest. Furthermore, we show for another wire structure that the conductance of furan-based wires is consistently higher than for analogous thiophene systems, indicating that the negative correlation between conductance and aromaticity is robust. The best conductance would be for a quinoid structure that diminishes aromaticity. The energy penalty for partly adopting the quinoid structure is less with compounds having lower initial aromatic stabilization. An additional effect may reflect the lower HOMOs of aromatic compounds.

Catalysis of glyceraldehyde synthesis by primary or secondary amino acids under prebiotic conditions as a function of pH.

The synthesis of an excess of D-glyceraldehyde by coupling glycolaldehyde with formaldehyde under prebiotic conditions is catalyzed by L amino acids having primary amino groups at acidic pH's, but at neutral or higher pH's they preferentially form L-glyceraldehyde. L Amino acids having secondary amino groups, such as proline, have the reverse preferences, affording excess L-glyceraldehyde at low pH but excess D-glyceraldehyde at higher pHs. Detailed mechanistic proposals make these preferences understandable. The relevance of these findings to the origin of D sugars on prebiotic Earth is described.

Development of a histone deacetylase 6 inhibitor and its biological effects.

Development of isoform-selective histone deacetylase (HDAC) inhibitors is important in elucidating the function of individual HDAC enzymes and their potential as therapeutic agents. Among the eleven zinc-dependent HDACs in humans, HDAC6 is structurally and functionally unique. Here, we show that a hydroxamic acid-based small-molecule N-hydroxy-4-(2-[(2-hydroxyethyl)(phenyl)amino]-2-oxoethyl)benzamide (HPOB) selectively inhibits HDAC6 catalytic activity in vivo and in vitro. HPOB causes growth inhibition of normal and transformed cells but does not induce cell death. HPOB enhances the effectiveness of DNA-damaging anticancer drugs in transformed cells but not normal cells. HPOB does not block the ubiquitin-binding activity of HDAC6. The HDAC6-selective inhibitor HPOB has therapeutic potential in combination therapy to enhance the potency of anticancer drugs.

Transketolase reaction under credible prebiotic conditions.

A transketolase reaction was catalyzed by cyanide ion under prebiotic conditions instead of its modern catalyst, thiamine pyrophosphate (TPP). Cyanide ion converted fructose plus glyceraldehyde to erythrose plus xylulose, the same products as are formed in modern biochemistry (but without the phosphate groups on the sugars). Cyanide was actually a better catalyst than was TPP in simple solution, where there is a negligible concentration of the C-2 anion of TPP, but of course not with an enzyme in modern biology. The cyanide ion was probably not toxic on prebiotic earth, but only when the oxygen atmosphere developed and iron porphyrin species were needed, which cyanide poisons. Thus, catalyses by TPP that are so important in modern biochemistry in the Calvin cycle for photosynthesis and the gluconic acid pathway for glucose oxidation, among other processes, were probably initially performed instead by cyanide ion until its toxicity with metalloproteins became a problem and primitive enzymes were present to work with TPP, or most likely its primitive precursors.

Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles.

Four polyimidazoles were used in the binding and cleavage studies with poly(U). The two polydisperse polyvinylimidazoles were previously described by others, while the other two new polymers of polyethyleneimines were prepared by cationic polymerization of oxazolines. The latter had imidazole units attached to each nitrogen of the polymers. They were characterized by gel permeation chromatography and had very low polydispersities. When they were partially protonated they bound to the poly(U) and catalyzed its cleavage by a process analogous to that used by the enzyme ribonuclease A. The kinetics of the cleavage were followed by an assay we had previously described using phosphodiesterase I from Crotalus venom after the cleavage processes. Cleavage of poly(U) with Zn(2+) was also examined, with and without the polymers. A scheme is described in which these cleavages could be made sequence selective with various RNAs, particularly with important targets, such as viral RNAs.

Highly conducting π-conjugated molecular junctions covalently bonded to gold electrodes.

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ, resulting in formation of a direct covalent σ bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated π system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the π system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G(0) = 2e(2)/h). Junctions formed with methylene-terminated oligophenyls with two to four phenyl units show a 100-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling, as they exhibit an exponential dependence of conductance on oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission, with a crossover to tunneling for the longer oligomers.

Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections.

Understanding electron transport across π-π-stacked systems will help to answer fundamental questions about biochemical redox processes and benefit the design of new materials and molecular devices. Herein we employed the STM break-junction technique to measure the single-molecule conductance of multiple π-π-stacked aromatic rings. We studied electron transport through up to four stacked benzene rings held together in an eclipsed fashion via a paracyclophane scaffold. We found that the strained hydrocarbons studied herein couple directly to gold electrodes during the measurements; hence, we did not require any heteroatom binding groups as electrical contacts. Density functional theory-based calculations suggest that the gold atoms of the electrodes bind to two neighboring carbon atoms of the outermost cyclophane benzene rings in η(2) fashion. Our measurements show an exponential decay of the conductance with an increasing number of stacked benzene rings, indicating a nonresonant tunneling mechanism. Furthermore, STM tip-substrate displacement data provide additional evidence that the electrodes bind to the outermost benzene rings of the π-π-stacked molecular wires.

A mimic of the pyruvate dehydrogenase complex.

Pyruvic acid undergo decarboxylation catalyzed by a hydrophobic thiazolium salt and reacts with a hydrophobic analog of lipoic acid to form a hydrophobic acylthioester that reacts with aniline to form acetanilide in water, but only in the presence of a hydrophobically modified polyaziridine that acts to gather the reactants just as the enzyme complex does.

The electrical properties of biphenylenes.

The effect of the partial antiaromaticity of biphenylene on its substitution chemistry, its oxidation potential, and its single-molecule conductance is explored. Biphenylene and fluorene molecules with linkers of two amino groups or two cyclic thioether groups were synthesized and their conduction properties were investigated using scanning tunneling microscopy (STM) break-junction techniques and DFT calculations. Despite the partial antiaromaticity of biphenylene, which causes the biphenylenes to be much more easily oxidizable, no significant increase in molecular conductance was found.

L-amino acids catalyze the formation of an excess of D-glyceraldehyde, and thus of other D sugars, under credible prebiotic conditions.

Previous work by us, and others, has shown that the formation of amino acids on prebiotic earth with the geometric arrangement called the L configuration can be understood. Some meteorites of the carbonaceous chondritic type deliver unusual amino acids, with alpha-methyl groups, which have an excess of the L isomers. We previously showed that in decarboxylative transamination reactions under credible prebiotic conditions they produce normal amino acids that also have a preference for the L isomer, as is found in our proteins. We, and others, showed that as little as a 1% excess of the L isomers could be amplified up to a 95/5 ratio of L over D on simple evaporation of a solution, so life could start with such a solution in which the dominant L isomers would be selectively chosen. We now find that the geometry of sugars referred to D, as in D-ribose or D-glucose, is not an independent mystery. D-glyceraldehyde, the simplest sugar with a D center, is the basic unit on which other sugars are built. We find that the synthesis of glyceraldehyde by reaction of formaldehyde with glycolaldehyde is catalyzed under prebiotic conditions to D/L ratios greater than 1, to as much as 60/40, by a representative group of L-amino acids (with the exception of L-proline). The D/L glyceraldehyde ratio in water solution is amplified to 92/8 using simple selective solubilities of the D and the DL forms. This D center would then be carried into the prebiotic syntheses of larger sugars.

Imitating prebiotic homochirality on Earth.

We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids-that have been identified in the Murchison meteorite-with alpha-keto acids under credible prebiotic conditions. When they are simply heated together they perform a process of decarboxylative transamination but with almost no chiral transfer, and that in the wrong direction, producing D-amino acids from the L-alpha-methyl amino acids. With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, producing small enantioexcesses of the normal L-amino acids. We also show how these can be amplified, not by making more of the L form but by increasing its concentration in water solution. The process can start with a miniscule excess and in one step generate water solutions with L/D ratios in the over 90% region. Kinetic processes can exceed the results from equilibria. We have also examined such amplifications with ribonucleosides, and have shown that initial modest excesses of the D-nucleosides can be amplified to afford water solutions with D to L ratios in the high 90's. We have shown that the homochiral compound has two effects on the solubility of the racemate. On one hand it decreases the solubility of the racemate by its role in the solubility product, as a theoretical equation predicts. On the other hand, it increases the solubility of the racemate by changing the nature of the solvent, acting as a cosolvent with the water. This explains why the amplification, while large, is not as large as the simple theoretical equation predicts. Thus when credible examples are produced where small enantioexcesses of D-ribose are created under credible prebiotic conditions, the prerequisites for the RNA world will have been exemplified.

High rates and substrate selectivities in water by polyvinylimidazoles as transaminase enzyme mimics with hydrophobically bound pyridoxamine derivatives as coenzyme mimics.

Free-radical polymers of 4-vinylimidazole and copolymers with 1-dodecyl-4-vinylimidazole were used as enzyme mimics to transaminate pyruvic acid to alanine, phenylpyruvic acid to phenylalanine, and indole-3-pyruvic acid to tryptophan in water at pH 7.5 and 20 degrees C using pyridoxamines carrying hydrophobic side chains as coenzyme mimics. The best enzyme mimic accelerated the transamination of indole-3-pyruvic acid by a factor of 4 million relative to the rate without the polymer, a higher rate ratio than we had previously achieved with a polyaziridine-based enzyme mimic. The properties of various polyvinylimidazoles were compared, including those prepared with the RAFT modification of the polymerization process.