Biomedical subjects

Bernd Engels

Publications and source records attributed to Bernd Engels.

At least 19 recordsLinked to original sources

PubMed2007

Gradient tabu search.

This paper presents a modification of the tabu search called gradient tabu search (GTS). It uses analytical gradients for a fast minimization to the next local minimum and analytical diagonal elements of the Hessian to escape local minima. For an efficient blocking of already visited areas tabu regions and tabu directions are introduced into the tabu list (TL). Trials with various well-known test functions indicate that the GTS is a very promising approach to determine local and global minima of differentiable functions. Possible application areas could be optimization routines for force field parameters or conformational searches for large molecules.

Journal Article↗

PubMed2007

The importance of the active site histidine for the activity of epoxide- or aziridine-based inhibitors of cysteine proteases.

In the present study the importance of the active site histidine residue (His) for the activity of epoxide- or aziridine-based cysteine protease inhibitors is examined theoretically. To account for all important effects, QM/MM hybrid approaches are employed which combine quantum mechanical (QM) methods that are necessary to describe bond-breaking and formation processes, with molecular mechanics (MM) methods that incorporate the influence of the protein environment. Using various model systems, the computations exclude a direct proton shift from the active site His residue to the inhibitor, but show that one water molecule is sufficient to establish a very efficient relay system. This relay system allows an easy proton transfer from the active site His residue to the inhibitor and is thus essential for the activity of both types of inhibitors. Differences between the epoxides and the aziridines are discussed, along with some implications for the rational design of optimized inhibitors. The work presented herein represents the first QM/MM study into the mode of action of these important inhibitor classes.

Aziridines↗

PubMed2006

Computer-aided design of promising photochemical alkoxy radical precursors.

A computer-aided design of alkoxyl radical precursors is performed. The new precursors should combine the advantages of N-alkoxypyridine-2(1H)thiones (less reactive radicals) and N-alkoxythiazole-2(3H)thiones (stable with respect to daylight). Additionally, the radical liberation process should be initiated by light with a wavelength of around 350 nm. To find promising compounds, 18 test candidates were obtained by a systematic variation of the parent compound N-alkoxythiazole-2(3H)thione. The properties of the test molecules were computed by a protocol that was already successfully used to rationalize the photochemical behavior of N-alkoxypyridine-2(1H)thiones and N-alkoxythiazole-2(3H)thiones. The computations identify two promising new compounds. For N-methoxy-(1,3)dihydro-[1,3]azaphosphole-2-thione (6a), they predict that the fragmentation process will be initiated by an absorption at 348 nm. An analysis of its fragmentation process indicates that the free excess energy of the resulting radicals should more resemble the situation found for N-alkoxypyridine-2(1H)thiones. For N-methoxy-(1,3)dihydro-pyrrole-2-thione (3a), the excitation energy is somewhat higher (330 nm), but the computed fragmentation paths again indicate that the remaining excess energy of the released radicals is quite favorable. The test molecules also contained the experimentally well-known N-methoxypyridine-2(1H)one (1b). For this molecule, our computed data rationalizes nicely the experimental findings.

Alcohols↗

PubMed2006

DIESEL-MP2: a new program to perform large-scale multireference-MP2 computations.

This article presents a new MR-MP2 code (Multi-Reference Møller-Plesset 2nd order) suitable for the computation MR-MP2 energies of extended systems with strong near degeneracy effects (e.g., open shell systems). It is based on the DIESEL program package developed by Hanrath and Engels. Due to improved algorithms the new code is able to handle systems with 400-500 basis functions and more than 100 electrons. The code is made for parallel computers with distributed memory, but can also be run on local machines. It possesses two integral interfaces (MOLCAS, TURBOMOLE). The algorithms are briefly introduced and timings for the Neocarzinostatin chromophore are presented. The efficiencies of the codes obtained with Intel or GNU compilers are compared.

Algorithms↗

PubMed2006

Unsubstituted bicyclo[1.1.0]but-2-ylcarbinyl cations.

A synthesis for the unsubstituted bicyclo[1.1.0]but-2-ylmethanols (endo- and exo-9) from 1,3-butadiene has been developed. Solvolyses of their sulfonates 10 and 11 took entirely different courses, as the endo compound 10 gave rise exclusively to rearranged products such as cyclopent-3-en-1-ol (14), while the exo compound 11 underwent only the substitution of the tosylate group with complete retention of the exo-bicyclo[1.1.0]but-2-ylmethyl skeleton. Under solvolytic conditions, 10 reacted at very similar rates to the corresponding monocyclic substrate, that is, cyclopropylcarbinyl mesylate (19); in contrast, 11 reacted only three times as fast as n-butyl tosylate and about 1000-fold slower than 10. The nature of the bicyclo[1.1.0]but-2-ylcarbinyl cations has been probed by quantum chemical calculations. Whereas, the exo isomer (exo-18) corresponds to a local energy minimum, the endo isomer is only a transition state [endo-18(TS)] for an automerization of the nonclassical cyclopent-3-en-1-yl cation (13) and converts into 13 by a Wagner-Meerwein rearrangement. The most favorable isomerization of exo-18 also leads to 13 but via a transition state resembling the 2-vinylcycloprop-1-yl cation [25(TS)]. On the introduction of methyl groups at positions 1 and 3 of exo-18, the cation is no longer an energy minimum and it becomes a transition state [27(TS)] for an automerization of the nonclassical 1,3-dimethylcyclopent-3-en-1-yl cation (28). The large effect of the methyl substitution rationalizes the puzzling results of the previous product and rate studies, which utilized various substituted derivatives of bicyclo[1.1.0]but-2-ylcarbinyl sulfonates as substrates.

Journal Article↗

PubMed2006

Rational design of aziridine-containing cysteine protease inhibitors with improved potency: studies on inhibition mechanism.

To enable a rational design of improved cysteine protease inhibitors, the present work investigates trends in the inhibition potency of aziridine derivatives with a substituted nitrogen center. To predict the influence of electron-withdrawing substituents, quantum chemical computations of the ring opening of N-formylated, N-methylated, and N-unsubstituted aziridines with thiolate were performed. They revealed that the N-formyl group leads to a strong decrease of the reaction barrier and a considerable increase in exothermicity due to stabilization of the transition state. In contrast, a nucleophilic attack at the carbonyl carbon atom is characterized by very low reaction barriers, suggesting a reversible reaction, thus providing the theoretical background for the reversible inhibition of cysteine proteases by peptidyl aldehydes. Reactions of aziridine building blocks (diethyl aziridine-2,3-dicarboxylate 1, diethyl 1-formyl aziridine-2,3-dicarboxylate 2) with a model thiolate in aqueous solution which were followed by NMR spectroscopy and mass spectrometry, showed the N-formylated compound 2 to readily undergo a ring-opening reaction. In contrast, the reaction of 1 with the thiolate is much slower. Enzyme assays with the cysteine protease cathepsin L showed 2 to be a 5000-fold better enzyme inhibitor than 1. Dialysis assays clearly proved irreversible inhibition. These experiments, together with the results obtained with the model thiolate, indicate that the main inhibition mechanism of the N-formylated aziridine 2 is the ring-opening reaction rather than the reversible attack of the active site cysteine residue at the carbonyl carbon atom.

Aziridines↗

PubMed2006

Aziridide-based inhibitors of cathepsin L: synthesis, inhibition activity, and docking studies.

A comprehensive screening of N-acylated aziridine (aziridide) based cysteine protease inhibitors containing either Boc-Leu-Caa (Caa=cyclic amino acid), Boc-Gly-Caa, or Boc-Phe-Ala attached to the aziridine nitrogen atom revealed Boc-(S)-Leu-(S)-Azy-(S,S)-Azi(OBn)(2) (18 a) as a highly potent cathepsin L (CL) inhibitor (K(i)=13 nM) (Azy=aziridine-2-carboxylate, Azi=aziridine-2,3-dicarboxylate). Docking studies, which also accounted for the unusual bonding situations (the flexibility and hybridization of the aziridides) predict that the inhibitor adopts a Y shape and spans across the entire active site cleft, binding into both the nonprimed and primed sites of CL.

Animals↗

PubMed2005

Geometry and cooperativity effects in adenosine-carboxylic acid complexes.

NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.

Adenosine↗

PubMed2005

"Knock-out" analogues as a tool to quantify supramolecular processes: a theoretical study of molecular interactions in guanidiniocarbonyl pyrrole carboxylate dimers.

It was recently shown experimentally that 5-(guanidiniocarbonyl)-1H-pyrrole-2-carboxylate 1, a self-complementary zwitterion, dimerizes even in water with an unprecedented high association constant of K = 170 M(-1) (J. Am. Chem. Soc. 2003, 125, 452-459). To get an insight into the importance of the various noncovalent binding interactions and of their interplay (electrostatic interactions, hydrogen binding, cooperative effects), we employ density functional theory to study the stability of several "knock-out" analogues in which single hydrogen bonds within these multiple point binding motif are switched off by replacing N-H hydrogen-donor groups with either methylene groups or an oxygen ether bridge. The influence of a highly polar solvent on the dimer stabilities is also examined. These calculations reproduce the experimental data for zwitterion 1. A comparison of 1 with the arginine dimer shows that the energy contents of the monomers also significantly influence the dimer stabilities. The analysis of the various "knock-out" analogues reveals as a main conclusion that simple models either based just on hydrogen-bond counting or on the assumption that the charge interaction by itself is the main and dominant factor fail to explain the stability of such self-assembled dimers. Our computations show that the hydrogen-bond network, the electrostatic attraction, and also their mutual interactions are responsible for the high stability of zwitterion 1.

Journal Article↗

PubMed2005

On the homolytic cleavage of the N,O bond in N-(methoxy)pyridine-2(1H)-thione and N-(methoxy)thiazole-2(3H)-thione in thermally and photochemically induced reactions: a theoretical study.

The accuracy of theoretical approaches to describe electronic absorption spectra of N-(hydroxy)- and N-(methoxy)- derivatives of pyridine-2(1H)-thione and thiazole-2(3H)-thione are examined with the aim to identify methods that are applicable for a rational design of new photochemically active oxyl radical precursors. In addition, the mechanism of the photochemically induced methoxyl radical formation from N-(methoxy)pyridine-2(1H)-thiones and of N-(methoxy)thiazole-2(3H)-thiones is investigated by means of theoretical methods. The results of the study are applied in order to explain differences in photoreactions of N-(alkoxy)pyridine-2(1H)-thiones and the corresponding thiazole-2(3H)-thiones.

Hot Temperature↗

PubMed2005

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

BACKGROUND: A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest. RESULTS: YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL), edit (including support for the SBML format), visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM) activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA) for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at http://yana.bioapps.biozentrum.uni-wuerzburg.de. CONCLUSION: A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user-friendly software for such efforts.

Algorithms↗

PubMed2005

An ab initio study of the vibronic, spin-orbit, and magnetic hyperfine structure in the X2Pi electronic state of NCO.

In the present study we give the results of the ab initio calculations on the vibronic, spin-orbit, and magnetic hyperfine structure in the X (2)Pi electronic state of the NCO radical. The calculations of the potential surfaces and the electronic mean values of the hyperfine coupling constants are carried out by means of the density functional theory approach (B3LYP functional combined with an atomic orbital basis set suitable for calculations of the hyperfine structure). The vibronic levels, spin-orbit splitting, and the vibronic mean values of the components of the hyperfine tensor in the vibronic species are calculated using a variational method. The results of the calculations are in good agreement with the available experimental data.

Journal Article↗

PubMed2005

A combined computational and experimental study of the hydrogen-bonded dimers of xanthine and hypoxanthine.

In addition to uracil, the noncanonical nucleobases xanthine and hypoxanthine are important lesions that are formed from the canonical bases when a cell is under oxidative stress. It is known that they lead to point mutations; however, more detailed information about their ability to form hydrogen-bonded complexes is not available. In the present paper such information is obtained by a combined experimental and theoretical approach. Accurate association constants of xanthosine and inosine dimers are determined by concentration dependent 1H NMR experiments, and a structural characterization of individual complexes formed in solution is performed through measurements under slow exchange conditions at very low temperatures. An interpretation of the experimental data concerning complex geometries becomes possible through a comparison of measured and computed NMR chemical shifts. Further qualitative insights into the hydrogen bonding abilities of xanthine and hypoxanthine are obtained by a theoretical characterization of all possible pairing modes of xanthine and hypoxanthine dimers and by a comparison with simplified model systems. The influence of a polar medium on the bonding properties is also estimated and the importance of the various effects is discussed. Our analysis shows to what extent secondary electronic and electrostatic effects influence the hydrogen bonding properties of xanthine and hypoxanthine in the gas phase and in polar solvents.

Journal Article↗

PubMed2005

Theoretical studies about the influence of different ring substituents on the nucleophilic ring opening of three-membered heterocycles and possible implications for the mechanisms of cysteine protease inhibitors.

Epoxides, aziridines, and thiiranes are electrophilic building blocks that are widely used in synthetic organic chemistry. As a result of their reactivity against nucleophiles they are also used as electrophilic "warheads" for irreversible peptidic or peptidomimetic cysteine protease inhibitors. A general feature of these inhibitors is the remarkable higher inhibition potency of derivatives containing a free carboxylic acid in comparison to corresponding esters. In contrast, experimental investigations about the reaction of methyl thiolate with substituted epoxides revealed a contrary reactivity pattern. These studies also gave information about the regioselectivity of such reactions; however, mechanistic studies were not performed. By analyzing the computed energy profiles of the corresponding reactions we investigate the substituent effects (H vs ester vs carboxylic acid) on the kinetics and thermodynamics of the ring opening by the nucleophile methyl thiolate. Our model computations nicely explain experimental results concerning variations in the reactivities and the regioselectivities and indicate different reasons for the increased inhibition potency of three-membered heterocycles containing an acidic substituent. For aziridines an intramolecular water-mediated acid catalysis seems to be the main reason for the high activity of these inhibitors in acidic media. For epoxides and thiiranes this catalysis is not found, confirming the hypothesis that an ionic interaction between negatively charged carboxylate and the histidinium ion of the active site of the proteases mainly causes the high inhibitory activity of the acids compared to the esters.

Aziridines↗

PubMed2004

An ab initio calculation of the anisotropic hyperfine coupling constants in the low-lying vibronic levels of the X 2Pi electronic state of CCCH.

The results of ab initio calculations of the vibronically averaged components of the anisotropic magnetic hyperfine tensor in the low-lying vibronic species of the X (2)Pi electronic state of CCCH and CCCD are reported. The electronically averaged hyperfine coupling constants for hydrogen and (13)C in (12)C (12)C (12)CH, (13)C (12)C (12)CH, (12)C (13)C (12)CH, (12)C (12)C (13)CH, and (12)C (12)C (12)CD are obtained as functions of two bending vibrational modes by the density functional theory method. The vibronic wave functions are calculated with help of a variational approach which takes into account the Renner-Teller effect and spin-orbit coupling. The results of the present study help to reliably interpret the experimental data previously published and predict the yet unobserved hyperfine structure in excited vibronic states of CCCH and CCCD.

Journal Article↗

PubMed2004

An ab initio study of the hyperfine structure in the X2 Pi electronic state of CCCH.

The results of an ab initio study of the magnetic hyperfine structure in the X (2)Pi electronic state of CCCH are reported. The potential surfaces for two components of the X (2)Pi electronic state were computed by means of an extensive configuration interaction approach. The electronically averaged hyperfine coupling constants of H and (13)C for (12)C (12)C (12)CH, (13)C (12)C (12)CH, (12)C (13)C (12)CH, and (12)C (12)C (13)CH are obtained as functions of two bending vibrational modes by the density functional theory method. The vibronic wave functions are calculated with the help of a variational approach which takes into account the Renner-Teller effect and spin-orbit coupling. The model Hamiltonian is expressed in terms of the normal bending coordinates. It is found that, due to the generally strong geometry dependence of the hyperfine coupling constants, it is necessary to carry out the vibronic averaging of the corresponding functions in order to obtain the values which can be compared to the results of the measurements. The results of the present study help to reliably interpret the experimental data previously published. They also predict the yet unobserved hyperfine structure in excited vibronic states.

Journal Article↗

PubMed2004

Si-E (E = N, O, F) bonding in a hexacoordinated silicon complex: new facts from experimental and theoretical charge density studies.

The concept of hypervalency in molecules, which hold more than eight valence electrons at the central atom, still is a topic of constant debate. There is general interest in silicon compounds with more than four substituents at the central silicon atom. The dispute, whether this silicon is hypervalent or highly coordinated, is enlightened by the first experimental charge density determination and subsequent topological analysis of three different highly polar Si-E (E = N, O, F) bonds in a hexacoordinated compound. The experiment reveals predominantly ionic bonding and much less covalent contribution than commonly anticipated. For comparison gas-phase ab initio calculations were performed on this compound. The results of the theoretical calculations underline the findings of the experiment.

Journal Article↗

PubMed2003

Computational assessment of the electronic structure of 1-azacyclohexa-2,3,5-triene (3 delta 2-1H-pyridine) and its benzo derivative (3 delta 2-1H-quinoline) as well as generation and interception of 1-methyl-3 delta 2-1H-quinoline.

Treatment of a solution of 3-bromo-1-methyl-1,2-dihydroquinoline (9) and [18]crown-6 in furan or styrene with KOtBu followed by hydrolysis afforded a mixture of 1-methyl-1,2-dihydroquinoline (10) and 1-methyl-2-quinolone (11). If the reaction was performed in [D(8)]THF and the mixture was immediately analysed by NMR spectroscopy, 2-tert-butoxy-1-methyl-1,2-dihydroquinoline (17) was shown to be the precursor of 10 and 11. The structure of 17 is evidence for the title cycloallene 7, which arises from 9 by beta elimination of hydrogen bromide and is trapped by KOtBu to give 17 so fast that cycloadditions of 7 with furan or styrene cannot compete. Since this reactivity is unusual compared to the large majority of the known six-membered cyclic allenes, we performed quantum-chemical calculations on 8, which is the parent compound of 7, and the corresponding isopyridine 6 to assess the electronic nature of these species. The ground state of 6 was no longer an allene (6 a) but the zwitterion 6 b. In the case of 8, the allene structure 8 a is more stable than the zwitterionic form 8 b by only approximately 1 kcal mol(-1). These results suggest a high reactivity of 6 and 8 towards nucleophiles and explains the behaviour of 7. In addition to the ground states, the low-lying excited states of 6 and 8 were considered, which are represented by the diradicals 6 c and 8 c and, as singlets, lie above 6 b and 8 a by 19.1-24.8 and 14.4-17.7 kcal mol(-1), respectively.

Journal Article↗