Pseudo-peptide amyloid-ß blocking inhibitors: molecular dynamics and single molecule force spectroscopy study.

By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-ß (Aß) inhibitors that bind to the Aß peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aß (13-23). The binding affinities between the inhibitor and Aß as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aß-Aß binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aß toxicity in Alzheimer's disease.

Theoretical study on the ring-opening of 1,3-disilacyclobutane and H2 elimination.

The kinetics and thermochemistry of the decomposition pathways for 1,3-disilacyclobutane (1,3-DSCB) in the gas phase were studied using the second-order Møller-Plesset (MP2) perturbation theory and coupled cluster methods with single, double, and perturbative triple excitations (CCSD(T)). The reactions examined include 2 + 2 cycloreversion to form two silenes by either a concerted or a stepwise mechanism, 1,1-, 1,2-, and 1,3-H(2) elimination, and the ring-opening initiated by 1,2-H shift to form an open-chain 1,3-disilabut-1-ylidene, which undergoes further decomposition to produce two pairs of silene/silylene species. The structures of the transition states for the concerted and the stepwise 2 + 2 cycloreversion pathways are found to resemble closely those reported for the head-to-tail and head-to-head dimerization, respectively. Comparison of the activation barriers demonstrates unambiguously that the stepwise cycloreversion (ΔH(0)(‡) = 66.1 kcal/mol) is favored over the concerted one (ΔH(0)(‡) = 77.3 kcal/mol). A new pathway was established from the 1,4-diradical intermediate in the stepwise cycloreversion to form 1-silylmethylsilene via 1,3-H shift. The concerted 1,1-H(2) elimination is shown to have the lowest activation barrier of all H2 elimination reactions. Overall, the 1,2-H shift in 1,3-DSCB with concerted ring-opening to form 1,3-disilabut-1-ylidene is the most kinetically and thermodynamically favorable decomposition pathway, both at 0 and 298 K.

Cheletropic decomposition of cyclic nitrosoamines revisited: the nature of the transition states and a critical role of the ring strain.

The cheletropic decompositions of 1-nitrosoaziridine (1), 1-nitroso-Delta(3)-pyrroline (2), 7-nitroso-7-azabicyclo[2.2. 1]hepta-2,5-diene (3), and 6-nitroso-6-azabicyclo[2.1.1]hexa-4-ene (4) have been studied theoretically using high level ab initio computations. Activation parameters of the decomposition of nitrosoaziridine 1 were obtained experimentally in heptane (DeltaH()(298) = 18.6 kcal mol(-)(1), DeltaS()(298) = -7.6 cal mol(-)(1) K(-)(1)) and methanol (20.3 kcal mol(-)(1), 0.3 cal mol(-)(1) K(-)(1)). Among employed theoretical methods (B3LYP, MP2, CCD, CCSD(T)//CCD), the B3LYP method in conjunction with 6-31+G, 6-311+G, and 6-311++G(3df,2pd) basis sets gives the best agreement with experimental data. It was found that typical N-nitrosoheterocycles 2-4 which have high N-N bond rotation barriers (>16 kcal mol(-)(1)) extrude nitrous oxide via a highly asynchronous transition state with a planar ring nitrogen atom. Nitrosoaziridine 1, with a low rotation barrier (<9 kcal mol(-)(1)) represents a special case. This compound can eliminate N(2)O via a low energy linear synperiplanar transition state (DeltaH()(298) = 20.6 kcal mol(-)(1), DeltaS()(298) = 2.5 cal mol(-)(1) K(-)(1)). Two higher energy transition states are also available. The B3LYP activation barriers of the cheletropic fragmentation of nitrosoheterocycles 2-4 decrease in the series: 2 (58 kcal mol(-)(1)) >> 3 (18 kcal mol(-)(1)) > 4 (12) kcal mol(-)(1). The relative strain energies increase in the same order: 2 (0 kcal mol(-)(1)) << 3 (39 kcal mol(-)(1)) < 4 (52 kcal mol(-)(1)). Comparison of the relative energies of 2-4 and their transition states on a common scale where the energy of nitrosopyrroline 2 is assumed as reference indicates that the thermal stability of the cyclic nitrosoamines toward cheletropic decomposition is almost entirely determined by the ring strain.

Effects of structure on alpha C-H bond enthalpies of amino acid residues: relevance to H transfers in enzyme mechanisms and in protein oxidation.

The bond dissociation enthalpies (BDE) of all of the amino acid residues, modeled by HC(O)NHCH(R)C(O)NH(2) (PH(res)), were determined at the B3LYP/6-31G//B3LYP/6-31G level, coupled with isodesmic reactions. The results for neutral side chains with phi, psi angles approximately 180 degrees, approximately 180 degrees in ascending order, to an expected accuracy of +/-10 kJ mol(-)(1), are Asn 326; cystine 330; Asp 332; Gln 334; Trp 337; Arg 340; Lys 340; Met 343; His 344; Phe 344; Tyr 344; Leu 344; Ala 345; Cys 346; Ser 349; Gly 350; Ile 351; Val 352; Glu 354; Thr 357; Pro-cis 358; Pro-trans 369. BDEs calculated at the ROMP2/6-31G//B3LYP/6-31G level exhibit the same trends but are approximately 7 kJ mol(-)(1) higher. All BDEs are smaller than those of typical secondary or tertiary C-H bonds due to the phenomenon of captodative stabilization. The stabilization is reduced by changes in the phi,psi angles. As a result the BDEs increase by about 10 kJ mol(-)(1) in beta-sheet and 40 kJ mol(-)(1) in alpha-helical environments, respectively. In effect the alpha C-H BDEs can be "tuned" from about 345 to 400 kJ mol(-)(1) by adjusting the local environment. Some very significant effects of this are seen in the current literature on H-transfer processes in enzyme mechanisms and in oxidative damage to proteins. These observations are discussed in terms of the findings of the present study.

Mechanistic consequences of charge transfer systems in serine proteases and angiotensin: semiempirical computations.

Structures and relative energies for the triads of interacting groups in the serine charge relay system of serine proteases and the proposed tyrosine charge relay system of angiotensin II, respectively, were computed according to the standard MNDOC procedure. The most stable configuration obtained for both systems was one in which the histidine residue was negatively charged. These findings indicate that the histidine ring and not the serine hydroxyl group at the active site of serine proteases would be the nucleophilic center which is acylated by substrate. Similarly, the extreme nucleophilicity of the imidazole anion produced by the proposed triad of interacting groups in angiotensin could provoke the formation of a transient covalent bond (acyl intermediate) between receptor and peptide in the receptor activation mechanism.