Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm

Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by ¹H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible.

Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.     

Existence of doubly charged lead monohydrate: experimental evidence and theoretical examination

Despite reports to the contrary, doubly charged lead monohydrate is a stable species against both proton and charge transfers. [Pb(H(2)O)](2+) has been observed as a minor product in the ligand-exchange reaction of [Pb(CH(3)CN)](2+) with H(2)O after collisional activation. Density functional theory has been used to examine reaction profiles of [Pb(H(2)O)(n)](2+) where n = 1, 2, and 3.     

Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains

Specific coiled-coil heterotrimers result from steric matching of hydrophobic core side chains. A 2:1 heterotrimer is formed by peptides containing alanine or cyclohexylalanine, respectively, at a central core residue. Detailed thermodynamic analysis reveals that the designed complex is considerably more stable than the corresponding alanine homotrimer (deltaT(m) = 25 degrees C, deltadeltaG(unf) = 4.5 kcal/mol), while control complexes with naphthylalanine or cyclopropylalanine peptides are much less stable. However, the cyclohexylalanine homotrimer is of comparable stability to the 2:1 complex, prompting an investigation of multiply substituted peptides. A specific 1:1:1 heterotrimer is formed from three independent peptide strands, each bearing one large (cyclohexylalanine) and two small (alanine) side chains at the same three core positions but in different order. The combined impact of three substitutions improves specificity to the point where each pure peptide and all pairwise equimolar mixtures form significantly less stable complexes (deltaTm = 22-24 degrees C). The capacity for specific complex formation governed by multiple unnatural core side chains should facilitate design of numerous new peptide assemblies.     

Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program

Summary In the preceding paper we reported on a docking study with the SYSDOC program for predicting the binding sites of huperzine A in acetylcholinesterase (AChE) [Pang, Y.-P. and Kozikowski, A.P., J. Comput.-Aided Mol. Design, 8 (1994) 669]. Here we present a prediction of the binding sites of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (E2020) in AChE by the same method. E2020 is one of the most potent and selective reversible inhibitors of AChE, and this molecule has puzzled researchers, partly due to its flexible structure, in understanding how it binds to AChE. Based on the results of docking 1320 different conformers of E2020 into 69 different conformers of AChE and on the pharmacological data reported for E2020 and its analogs, we predict that both the R- and the S-isomer of E2020 span the whole binding cavity of AChE, with the ammonium group interacting mainly with Trp⁸⁴, Phe³³⁰ and Asp⁷², the phenyl group interacting mainly with Trp⁸⁴ and Phe³³⁰, and the indanone moiety interacting mainly with Tyr⁷⁰ and Trp²⁷⁹. The topography of the calculated E2020 binding sites provides insights into understanding the high potency of E2020 in the inhibition of AChE and provides hints as to possible structural modifications for identifying improved AChE inhibitors as potential therapeutics for the palliative treatment of Alzheimer's disease.     

Applications of benzotriazole methodology in heterocycle ring synthesis and substituent introduction and modification

Applications of benzotriazole methodology for the preparation of heterocyclic compounds are reviewed. The characteristic advantages of benzotriazole as a synthetic auxiliary are first briefly considered. This is followed by a summary of its use in ring synthesis in which the construction of small; five-membered; six-membered; and larger heterocyclic rings using benzotriazole methodology are each examined separately. Finally, consideration of the use of benzotriazole in the ring annulation - particularly benzannulation - of heterocycles. Subsequent sections deal with the introduction of substituents into aromatic heterocycles; the ring substitution of saturated heterocycles; and benzotriazole assisted modification of heterocyclic substituents. The present review supplements a recent comprehensive review of benzotriazole chemistry [1] which covers the literature through 1996.     

CORRELATION BETWEEN THE BINDING OF FORMATE AND DECREASED RATES OF CHARGE TRANSFER THROUGH THE PHOTOSYSTEM II QUINONES

Abstract— The binding parameters of bicarbonate to the thylakoid membrane at different formate concentrations have been established [Stemler and Murphy (1983) Photochem. Phorobiol. 38, 701–707]. Based on these parameters, predictions could be made concerning the effects of bicarbonate and formate on photosynthetic electron flow. In this work these effects of various concentrations of bicarbonate and formate are measured and compared to predictions from the binding study. Electron flow is measured between Q_A and Q_B (the primary and secondary quinone acceptors) and Q_B and the plastoquinone pool. Also, these same concentration effects are determined for silicomolybdate supported oxygen evolution. It is found that the results of the bicarbonate binding study are in good agreement with the concentration dependence determined for the quinone reactions, as well as the silicomolybdate reaction. The bicarbonate concentrations required for half-maximal effects are approximately 100 μM, 300 μM and 1.3 mM in the presence of 0, 20 mM and 100 mM formate, respectively. It is concluded that a hierarchy of possible electron flow rates exist. The slowest rates occur when formate is bound. A substantially higher rate occurs when neither formate nor bicarbonate (< 2 μM) are present, but only chloride is present. The highest rates of electron flow occur when bicarbonate is bound. The Q_A- Q_B→ Qa Qb^? Qa^? Qb^2– PQ → Q_a Q_b- PQ^2–, and the silicomolybdate reactions all have the same concentration dependence on formate and bicarbonate. From this it is concluded that a single binding site for formate and bicarbonate affect all of these reactions. The possibility that multiple sites exist with approximately equal affinities for bicarbonate cannot be excluded.     

HPLC isolation and NMR structure elucidation of the most prominent octabromo isomer in technical octabromo diphenyl ether

The major octabromo isomer of technical octabromo diphenyl ether mixture (technical octaBDE) DE-79 was isolated by RP-HPLC. Three serially coupled columns (each 250 mm long) enabled a good separation of the target compound from other congeners using 100% ACN as eluent. Approximately 100 microg of the target compound was isolated with a purity of >90% and investigated by MS for confirmation of the degree of bromination. 1H-NMR and 2-D 1H-13C correlation NMR spectra unequivocally clarified that the octaBDE in question is 2,2',3,3',4,4',6,6'-octabromodiphenyl ether (BDE 197). Based on annual production rates of technical BDE products (1999/2001), approximately 380 tons of BDE 197 were annually produced which, on the long term, may enter the environment. Compared with other individual BDE congeners, BDE 197 has the seventh highest application rate. Reductive debromination of BDE 197 can lead to four hepta-, 15 hexa-, 23 penta-, and 28 tetra-BDE isomers, respectively. This variety includes all known major BDEs of environmental concern (BDE 47, 85, 99, 100, 153, 154, and 183). The identification of BDE 197 in technical octaBDE DE-79 strongly suggests that research on the environmental fate of BDEs should include this key-BDE congener.     

Pyrrole studies part 41. Reactivity of 3,4-diformyl-2,5-dimethylpyrrole with diaminoalkanes. An unusual formation of 2-azafulvenes

3,4-Diformyl-2,5-dimethylpyrrole (1) reacts with ,ω-diamino-alkanes, NH₂(CH₂)_nNH₂t' to form either the potentially tautomeric 2:2 macrocyclic adduct (7a) (8), when N = 2, or the potentially tautomeric 1:1 bicyclic adduct (18) (19), when N = 4, 5, 6, and 12. ¹H and ¹³C N.m.r. spectral data indicate that the 2-azafulvene structures predominate for both types of cycloadducts. Only polymeric material was obtained when N = 3.