Protein-Loop Mimetics: A Diketopiperazine-Based Template to Stabilize Loop Conformations in Cyclic Peptides Containing the NPNA and RGD Motifs

We explore here an approach to mimic the structures and biological functions of protein loops in small synthetic molecules, by grafting the loop of interest onto an organic template comprising a bicyclic diketopiperazine, prepared by the formal coupling of (2S,4S)-4-aminoproline (Pro(NH₂)) and aspartic acid (Asp). The Fmoc-protected template 4 is used to prepare cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵- Ala⁶-Temp-) ( 5 ) and cyclo(-Ala¹-Arg²-Gly³-Asp⁴-Temp-) ( 6 ) (where Temp = template derived from 4 ), containing the Asn-Pro-Asn-Ala (NPNA) and Arg-Gly-Asp (RGD) motifs. The conformational properties of these molecules are studied in aqueous solution by NMR and simulated-annealing methods. The NPNA motif, an immunodominant epitope on the circumsporozoite surface protein of the malaria parasite Plasmodium falciparum, is shown to adopt a stable type-I β-turn in 5 . The template in 5 adopts a preferred conformation with Pro(NH₂)χ₁ ≈? ?35° and the Asp moiety χ₁ ≈? 70°. A different template conformation is inferred for 6 , with Pro(NH₂)χ₁ ≈? 0°, but the ARGD loop appears by NMR to undergo rapid conformational averaging. Solid-phase binding assays reveal that 6 displays modest antagonist activity towards both the integrin α_IIbβ₃ and α_vβ₃ receptors.     

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP)

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.     

L'acide hydroxylamine-O-sulfonique,réactif de choix pour la conversion d'aldéhydes en nitriles

Hydroxylamine-O-sulfonic acid: a convenient reagent for the conversion of aldehydes into nitriles . Hydroxylamine-O-sulfonic acid (HAS) proved to be an excellent reagent for the conversion of aliphatic, aromatic and heteroatomic aldehydes into nitriles. There, aldehydes in the form of suspension in HAS water solution, react rapidely to give the corresponding nitriles in high yield. Only with formylpyridines could the intermediate oxime-O-sulfonic acids be isolated.     

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by L?wdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods.     

Electronic determinants of photoacidity in cyanonaphthols

We present semiempirical AM1 calculations for the ground and excited state of 2-naphthol and some of its cyano derivatives in the gas phase. Following photoexcitation, the Mulliken electron density on the oxygen diminishes slightly for the acid and more conspicuously for the anionic conjugated base. This agrees with the measured solvatochromic parameters for 2-naphthol. In both electronic states, we find a nice correlation with the measured pK values in water. The electronic charge distribution on the distal ring of the anion agrees with the experimental acidity order in both S(0) and S(1). Upon excitation, it increases predominantly in positions 3, 5, and 8. The ring system of the anion assumes an alternate quinoidal structure in the ground state of the anion, which becomes more symmetric in the relaxed excited state. This suggests that the enhanced aromatic character of a 4n electron system in the excited state allows for better delocalization of the oxygen charge within the ring.     

Nickel(II)-komplexe des unsubstituierten cyclobutadiens

cis- and trans-3,4-Dichlorocyclobutene (I) react with Ni(CO)₄ and AlCl₃ to give (C₄H₄)NiCl₂ · AlCl₃ (II), while the bromo- and iodo-substituted cyclobutenes (III) without AlCl₃ yield the complexes (C₄H₄)NiX₂ (IVa, X  Br; IVb, X  I). Properties of II and IV are discussed and the presence of a C₄H₄ ring attached to nickel is likely from the results obtained.     

Pyridazines: (thiényl-2)-3 pyridazine,quelques (thiényl-2)-3 pyridazines substituées en 6 et systèmes à noyaux condensés dérivés

We describe the synthesis of 3-(2-thienyl)pyridazine and of some of its derivatives substituted on the 6 position eg., ethoxy, hydrazino and azido. Some of these compounds have lead to condensed rings systems, namely, triazolo- and tetrazolopyridazines.     

Charge-remote fragmentation and the two-step elimination of alkanols from fast atom bombardment-desorbed (M + H)+, (M + Cat)+, and (M - H)− ions of aromatic β-hydroxyoximes

Aromatic β-hydroxyoximes undergo unusual fragmentation reactions as protonated or cationized species, as radical cations, or as (M - H)^? ions, As protonated species, they expel OH ’ from the oxime functionality in violation of the even electron rule. Parallel eliminations of alkyl radicals follow OH’ loss when the aromatic ring is substituted with an alkyl chain. Alkyl radical losses appear to be characteristic of radical cations that can isomerize to ions in which the alkyl chain bears a radical site and the charged site is the conjugate acid of a basic functionality (e.g., oxime or imine). Evidence for the mechanisms was found in the ion chemistry of oxime and imine radical cations. The imine reference compounds were conveniently generated by fast atom bombardment-induced reduction of oximes, removing the requirement for using conventional chemical synthesis. Protonated imines and the (M - H)^? ions of oximes fragment extensively via charge-remote processes to eliminate the elements of alkanes. This chemistry is not shared by the protonated oximes.     

Discovery of O-GlcNAc transferase inhibitors

O-GlcNAcylation of serine and threonine residues is a dynamic and essential post-translational modification involved in signaling pathways in eukaryotes. Studies of O-GlcNAcylation would be aided by small-molecule inhibitors of O-GlcNAc transferase (OGT), the sole enzyme know to mediate this modification, but discovery of such molecules has been hampered by poor expression of cloned OGT and lack of suitable high-throughput screens. This Communication describes the development an expression system to access large amounts of the catalytic domain of OGT and the implementation of a fluorescence-based substrate analogue displacement assay that has led to the discovery of a set of OGT inhibitors. This work lays the foundation for both structural and functional analysis of the catalytic domain of OGT.     

Squaric acid N-hydroxylamides: synthesis, structure, and properties of vinylogous hydroxamic acid analogues

The synthesis of squaric acid N-hydroxylamide esters 5 and amides 6 from dimethyl squarate 2a is described. These derivatives are analogues of the naturally occurring iron(III) chelator hydroxamic acid. On the basis of a comparative reactivity study, a concerted retro-Cope mechanism for the formation of the N-hydroxylamide esters 5 by reaction of dimethyl squarate with hydroxylamines is proposed. A preliminary iron(III) binding study of these hydroxamic acid analogues is presented, demonstrating binding of iron(III) to amides 6 in aqueous solutions, while the esters 5 did not show any sign of metal ion binding. 13C NMR spectroscopic data (chemical shift and spin-lattice relaxation time determination) of these and related derivatives delineate the resonance structures predominant in these molecules. The resonance structures of the derivatives rationalize their spectroscopic data, chemical reactivity, and iron(III) binding properties. Single-crystal X-ray structure analyses of squaric acid N-hydroxylamide ester 5b and squaric acid N-hydroxylamide amide 6c confirm their connectivity and provide structural evidence supporting the spectroscopically derived conclusions. The squaric acid N-hydroxylamides are potentially useful in the construction of chemosensors for iron(III).