Computational molecular biology. Software matchmakers help make sense of sequences.
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Algorithms↗
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Results for “Computers, Molecular”
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Pattern recognition display methods for the analysis of computed molecular properties.
Pattern recognition methods, particularly the 'unsupervised learning' techniques, are well suited for the preliminary analysis of the large data sets produced by computer chemistry. The use of linear and non-linear display methods for such exploratory analysis are exemplified with the aid of two data sets of biologically active molecules. Advantages and disadvantages of these techniques are discussed.
Computer Simulation↗
Examination of the computed molecular properties of compounds selected for clinical development.
We have conducted a systematic evaluation of the calculated molecular properties of compounds in clinical development and have found that the development process selects for compounds that have certain computed physical properties. In particular, as the stage of development progresses, compounds that are advanced have lower calculated octanollwater partition coefficient (ClogP), polar surface area, and molecular weight. The findings of this study provide guidance for combinatorial library design and lead selection, which may enhance the chance for ultimate success in lead optimization.
Chemical Phenomena↗
[Molecular computers in cells. I. General considerations and hypotheses].
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Bionics↗
Conformational analysis of the prototype nonclassical cannabinoid CP-47,497, using 2D NMR and computer molecular modeling.
In an effort to determine the stereochemical requirements for pharmacological activity among the series of nonclassical cannabinoids synthesized at Pfizer, we have studied the conformational properties of the parent bicyclic analog CP-47,497. For this study, we have used a combination of solution NMR and theoretical computational approaches. The energetically favored conformation has the phenolic ring almost perpendicular to the cyclohexanol ring which exists in a chair conformation. The OH bond of the phenol is preferentially coplanar with the aromatic ring and points toward the C2 ring proton, while the dimethylheptyl side chain adopts a conformation almost perpendicular to the aromatic ring. The conformational features of this nonclassical cannabinoid analog closely resemble those of its classical counterparts. The only apparent difference is the small dihedral angle (psi 1 = 62 degrees) between the planes of the two rings of CP-47,497 compared to that of the tricyclic tetrahydro- or hexahydrocannabinol analogs (psi 1 = 137 degrees). However, CP-47,497 can be perfectly superimposed over the respective tricyclic analog by rotation around the Ph-cyclohexyl bond (C6-C7 bond) and assume a conformation which is energetically higher than the preferred one by 3.0 kcal/mol. It can be argued that such a conformation may be acquired by the nonclassical analog during its interaction with the active site.
Cannabinoids↗
An ab initio computational molecular orbital study of the conformers of muconaldehyde, and the possible role of 2-formyl-2H-pyran in bringing about the conversion of a (Z,Z)-muconaldehyde structure into an (E,Z)-muconaldehyde structure.
To determine whether conformers of 2-formyl-2H-pyran (2F2HP) can serve as intermediates in the isomerization (Z,Z)-muconaldehyde-->(E,Z)-muconaldehyde--an essential step in the metabolic oxidation of benzene in which (E,E)-muconic acid is formed--we have carried out ab initio molecular orbital calculations at the MP2/6-31G* (frozen core, valence orbitals active) level with full geometry optimization at the RHF/6-31G* level. Taking account of the configuration about the carbon-carbon single bonds as well as that about the double bonds, the six conformers of (Z,Z)-muconaldehyde have been characterized, as well as the eight conformers of (E,Z)-muconaldehyde. Axial and equatorial conformers of 2F2HP have been identified, which exist in stable syn or anti forms depending on the relative position of the pyran and carbonyl O-atoms. Each step in the metabolic pathway is stereospecific. The initial ring opening in 2,3-epoxyoxepin gives (eZzZz)-muconaldehyde, which then undergoes ring closure to give anti-axial-2F2HP (step a). Inversion of the ring gives anti-equatorial-2F2HP, which upon ring opening gives (zEzZz)-muconaldehyde (step b). An alternative pathway links (zZzZz)-muconaldehyde with syn-axial-2F2HP (step a'), and syn-equatorial with (eEzZz)-muconaldehyde (step b'). Half-reaction times, taking into account the fractional representation of each reacting conformer in rapidly established equilibrium mixtures, suggest that the operative pathway is via step a, with little to choose between steps b and b'.
Aldehydes↗
RECOMB98. Computational molecular biology: pre- and post-genomics, March 22-25, 1998, New York.
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Algorithms↗
Cell molecular computers and biological information as the foundation of nature's laws.
It is proposed to unite the principles of new science mathematics, physics and biology for the description of living creatures. Such description is based on four principles: minimal price of action, optimum prediction, minimal irreversibility, and causality. In this new knowledge of nature not only the molecular biological experimental aspects have to be considered, but also the profound 'meaning' of molecular texts of DNA.
Computers↗
Quantum molecular computer model of the neuron and a pathway to the union of the sciences.
Cyclic nucleotide injection in neurons shows that cAMP controls a new type of membrane permeability. The neuron response to cAMP has a short delay, unusual bioenergetics and is blocked by drugs binding with the regulatory subunit of protein kinase. These data are interpreted in terms of the hypothesis that the controlling system of the living cell is a molecular (DNA, RNA, protein operators with complementary addresses), holographic (quick changeable lattice--cytoskeleton), quantum (each phonon examines whole lattice), hypersound (with wave length 100-10,000 A that does not destroy molecules) system with an inner point of view (molecular coding of questions and answers about quantum processing). Neither an electron, nor a macroscopic computer has an inner point of view.
Biology↗
The PRINTS database of protein fingerprints: a novel information resource for computational molecular biology.
PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbors. To date, 650 fingerprints have been constructed and stored in PRINTS, the size of which has doubled in the last 2 years. The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is now accessible via the UCL Bioinformatics Server on http:@ www.biochem.ucl.ac.uk/bsm/dbbrowser/. We describe here progress with the database, its compilation and interrogation software, and its Web interface.
Amino Acid Sequence↗
Genomics and computational molecular biology.
There has been a dramatic increase in the number of completely sequenced bacterial genomes during the past two years as a result of the efforts both of public genome agencies and the pharmaceutical industry. The availability of completely sequenced genomes permits more systematic analyses of genes, evolution and genome function than was otherwise possible. Using computational methods - which are used to identify genes and their functions including statistics, sequence similarity, motifs, profiles, protein folds and probabilistic models - it is possible to develop characteristic genome signatures, assign functions to genes, identify pathogenic genes, identify metabolic pathways, develop diagnostic probes and discover potential drug-binding sites. All of these directions are critical to understanding bacterial growth, pathogenicity and host-pathogen interactions.
Bacterial Proteins↗
Molecular computing for edge-enhanced laser imaging.
In order to illustrate the self-assembly capability, we consider a laser imaging experiment on a wet film that is made of bacteriorhodopsin (BR) molecules suspended in a diffusion-limited viscous medium. BR wet film is similar to a wet photograph film but having a finer resolution and adaptive pixel locations due to laser-induced thermal diffusion. The synergism between thermal diffusion of BR molecules (induced externally by a write-laser) and molecular photochromism (generated internally by a read-laser) is exploited naturally for edge-enhanced image applications.
Bacteriorhodopsins↗
Conformational studies on a diastereoisomeric pair of tricyclic nonclassical cannabinoids by NMR spectroscopy and computer molecular modeling.
Among the nonclassical cannabinoids, CP-55,244 (4), which incorporates an axial 14 beta-hydroxymethyl group, is pharmacologically 30 times more potent than its prototype CP-47,497 (2) and 300 times more potent than delta 9-THC (1). It has a high degree of stereoselectivity (about 120:1) with respect to its diastereoisomer, CP-97,587 (5), which differs structurally by having the 14-hydroxymethyl group equatorial. Conformational studies of 4 and 5 were carried out using 2D NMR spectroscopy and molecular modeling in order to define and compare the similarities and differences between them. Specific structural features of interest are the conformation of the 1',1'-dimethylheptyl (DMH) side chain, the conformation of the cyclohexyl rings, the orientation of the phenolic ring (A ring) relative to the cyclohexyl ring (C ring), and the orientation of the hydroxymethyl group as well as the formation of intramolecular hydrogen bonding. Our results show that the conformations of the phenolic hydroxyl (Ph-OH) and DMH side chain for 4 are similar to those of 2. The proton of the phenolic hydroxyl is pointing away from the C ring while the DMH chain randomly adopts one of four dynamically averaged conformers in which it is almost perpendicular to the plane of the aromatic ring. The relative orientation of the A and C rings is such that the two rings interconvert between two low-energy conformations. Compound 5 prefers the conformer with the Ph-OH pointing toward the alpha-face of the cyclohexyl ring, while for 4, there is an increased preference for the conformer where the Ph-OH is directed toward the beta face. This may be due to intramolecular H-bonding between the Ph-OH and the axial 14 beta-hydroxymethyl group of 4 that stabilizes this conformation. Hydrogen bonding between the Ph-OH and the equatorial-14 alpha-hydroxymethyl of 5 was not detected. Thus, the orientation of the aliphatic hydroxyl group with respect to the D ring in 4 and 5 may play an important role with regard to the pharmacophoric requirements of the two analogs for the cannabinoid receptor and provide an explanation for the observed differences in their biological properties.
Cannabinoids↗
Molecular computation: RNA solutions to chess problems.
We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.
Algorithms↗
The bacteriorhodopsin model membrane system as a prototype molecular computing element.
The quest for more sophisticated integrated circuits to overcome the limitation of currently available silicon integrated circuits has led to the proposal of using biological molecules as computational elements by computer scientists and engineers. While the theoretical aspect of this possibility has been pursued by computer scientists, the research and development of experimental prototypes have not been pursued with an equal intensity. In this survey, we make an attempt to examine model membrane systems that incorporate the protein pigment bacteriorhodopsin which is found in Halobacterium halobium. This system was chosen for several reasons. The pigment/membrane system is sufficiently simple and stable for rigorous quantitative study, yet at the same time sufficiently complex in molecular structure to permit alteration of this structure in an attempt to manipulate the photosignal. Several methods of forming the pigment/membrane assembly are described and the potential application to biochip design is discussed. Experimental data using these membranes and measured by a tunable voltage clamp method are presented along with a theoretical analysis based on the Gouy-Chapman diffuse double layer theory to illustrate the usefulness of this approach. It is shown that detailed layouts of the pigment/membrane assembly as well as external loading conditions can modify the time course of the photosignal in a predictable manner. Some problems that may arise in the actual implementation and manufacturing, as well as the use of existing technology in protein chemistry, immunology, and recombinant DNA technology are discussed.
Bacteriorhodopsins↗
Molecular computer.
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Anti-Bacterial Agents↗
Gene expression profiling diagnosis through DNA molecular computation.
Gene expression profiling is the characterization of cells based on the level of gene activity represented by concentrations of complementary DNA reverse transcribed from messenger RNA. The spectrum of cDNA concentrations, the expression profile, is determined using a DNA microarray. Although this approach is valuable for research, a simpler scheme that would give answers on a shorter time-scale for clinical applications is needed. An Adleman DNA self-assembly computer that would use cDNA as input might be ideal for clinical cell discrimination and a neural network architecture would be appropriate for making the necessary classifications. Preliminary experimental results suggest that expression profiling should be feasible using a DNA neural network that acts directly on cDNA.
Algorithms↗
Novel lavendamycin analogues as antitumor agents: synthesis, in vitro cytotoxicity, structure-metabolism, and computational molecular modeling studies with NAD(P)H:quinone oxidoreductase 1.
Novel lavendamycin analogues with various substituents were synthesized and evaluated as potential NAD(P)H:quinone oxidoreductase (NQO1)-directed antitumor agents. Pictet-Spengler condensation of quinoline- or quninoline-5,8-dione aldehydes with tryptamine or tryptophans yielded the lavendamycins. Metabolism studies with recombinant human NQO1 revealed that addition of NH2 and CH2OH groups at the quinolinedione-7-position and indolopyridine-2'-position had the greatest positive impact on substrate specificity. The best and poorest substrates were 37 (2'-CH2OH-7-NH2 derivative) and 31 (2'-CONH2-7-NHCOC3H7-n derivative) with reduction rates of 263 +/- 30 and 0.1 +/- 0.1 micromol/min/mg NQO1, respectively. Cytotoxicity toward human colon adenocarcinoma cells was determined for the lavendamycins. The best substrates for NQO1 were also the most selectively toxic to the NQO1-rich BE-NQ cells compared to NQO1-deficient BE-WT cells with 37 as the most selective. Molecular docking supported a model in which the best substrates were capable of efficient hydrogen-bonding interactions with key residues of the active site along with hydride ion reception.
Antineoplastic Agents↗