A search for specificity in DNA-drug interactions.

The GRID force field and a principal component analysis have been used in order to predict the interactions of small chemical groups with all 64 different triplet sequences of B-DNA. Factors that favor binding to guanine-cytosine base pairs have been identified, and a dictionary of ligand groups and their locations is presented as a guide to the design of specific DNA ligands.

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds.

The specificity of interactions between biological macromolecules and their ligands may be partially attributed to the directional properties of hydrogen bonds. We have now extended the GRID method (Goodford, P. J.

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds.

The directional properties of hydrogen bonds play a major role in determining the specificity of intermolecular interactions. An energy function which takes explicit account of these properties has been developed for use in the determination of energetically favorable ligand binding sites on molecules of known structure by the GRID method (Goodford, P.J.

Identifying targets for bioreductive agents: using GRID to predict selective binding regions of proteins.

A computational procedure is described for investigating potential binding sites of a target macromolecule for their ability to bind both a reduced probe molecule and an oxidized probe molecule. The interaction energies are obtained using a molecular mechanics method and can be displayed as three-dimensional (3D) energy contours, indicating regions of the target molecule that may have favorable interactions with the probe molecule. Differences in the interaction energies of the oxidized and reduced probe with the target can also be plotted as contours, indicating regions that are selective for the reduced probe.

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term.

The role of hydrogen-bonds in drug binding.

Hydrogen-bonds play a crucial role in determining the specificity of ligand binding. Their important contribution is explicitly incorporated into a computational method, called GRID, which has been designed to detect energetically favourable ligand binding sites on a chosen target molecule of known structure. An empirical energy function consisting of a Lennard-Jones, an electrostatic and a hydrogen-bonding term is employed.

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.

The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values. The probes include water, the methyl group, amine nitrogen, carboxy oxygen, and hydroxyl. Contour surfaces at appropriate energy levels are calculated for each probe and displayed by computer graphics together with the protein structure.

Substituted benzaldehydes designed to increase the oxygen affinity of human haemoglobin and inhibit the sickling of sickle erythrocytes.

Substituted benzaldehydes have been designed to bind preferentially to the oxy conformation of human haemoglobin at a site between the amino terminal residues of the alpha-subunits. Such compounds should stabilize the oxygenated form of haemoglobin and thereby increase its oxygen affinity. The compounds produce the expected effect, left-shifting the oxygen saturation curve of dilute haemoglobin solutions and of whole blood, although the binding pattern to haemoglobin is more complex than envisaged by the design hypothesis.

The interaction of human haemoglobin with allosteric effectors as a model for drug-receptor interactions.

1 The release of bound oxygen from oxyhaemoglobin by allosteric effectors is considered as a model for those drug-receptor interactions where the primary response to agonist binding is the release of a second messenger species. 2 A theory of haemoglobin oxygenation, based on the two-state model of Monod, Wyman & Changeux (1965) is used to predict the relationship between 'pharmacological' response and dose of agonist. This relationship is the same as that derived from classical pharmacological occupancy theory.

Species differences in the binding of compounds designed to fit a site of known structure in adult human haemoglobin.

1. Oxygen dissociation curves are reported for human haemoglobins A1, FII, FI, A1c and Raleigh (beta1 valine leads to acetylalanine) and for horse haemoglobin in the absence and presence of 2,3-diphosphoglycerate (DPG), or 4,4'-diformyl-2-bibenzyl oxyacetic acid, or the bisulphite addition compound of the latter. 2.

A quantitative analysis of the effects of 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate on the oxygen dissociation curve of human haemoglobin.

1. Oxygen dissociation curves have been measured for human haemoglobin solutions with different concentrations of the allosteric effectors 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate. 2.

The effect of 2,3-diphosphoglycerate on the oxygen dissociation curve of human haemoglobin.

1. Oxygen dissociation curves for concentrated human haemoglobin solutions (1.6 mmol dm-3 in haem) have been measured by mixing known quantities of oxy- and deoxyhaemoglobin solutions and measuring the resulting partial pressure of oxygen with an oxygen electrode.

The interaction of some bis-arylhydroxysulphonic acids with a site of known structure in human haemoglobin.

1 Two bis-arylhydroxysulphonic acids were previously designed to interact with the known molecular configuration of the 2,3-diphosphoglycerate (DPG) receptor-site of human haemoglobin. These compounds liberate oxygen from the haemoglobin similarly to DPG. 2 Solutions of haemoglobin have now been observed under physiological conditions by nuclear magnetic resonance (n.

Symmetry in prostaglandins.

Observations of the agonist activity of prostaglandins on the guinea-pig ileum are analysed. The structure-activity relationships are interpreted in relation to the approximate diad axis of symmetry in the molecules. It is suggested that some receptors for prostaglandins may have a perfect diad axis of symmetry between identical protein subunits.

Symmetrical features in polypeptide hormone-receptor interactions.

Symmetrical features were observed in the amino acid sequences of some biologically active peptides. It is suggested that this approximate symmetry is reflected in the conformations of the peptides at their respective biological receptors, and has arisen by natural selection as both peptides and receptors evolved to optimise their mutual fit. It follows that the binding site for each peptide at its receptor would share the same symmetry element.

Physicochemical-activity relationships in asymmetrical analogues of methoxychlor.

Compounds of the general formula 2-aryl-2-(p-methoxyphenyl)-1,1,1-trichloroethane have been prepared and tested for toxicity toward houseflies, pretreated for 1 h with 2mug of piperonyl butoxide. The majority of the compounds synthesized were chosen with the aid of computer programs designed to ensurewell-spread sets of minimally correlated physicochemical parameter values. A nonlinear two-dimensional representation was used to map the active region of physiochemical parameter space and a regression equation was obtained relating the observed toxicity to a combination of these physicochemical parameters.

Compounds designed to fit a site of known structure in human haemoglobin.

1 The three-dimensional coordinates of the atoms in human haemoglobin are known, and there is a specific site in the deoxygenated form of the protein at which 2,3-diphosphoglycerate (DPG) interacts. 2 Molecular models of this site have been constructed and used to design compounds which should bind to the deoxy conformation and stabilize it. These compounds should therby promote oxygen liberation, as does DPG.

The ratio of smooth muscle cell volume to cell surface area measured by electron microscopy with corrections for shrinkage.

The ratio of cell volume to cell surface area (V/A) has been measured by electron microscopy, for smooth muscle cells of the guinea-pig taenia coli. The extent of shrinkage which occurs during processing for electron microscopy has been estimated using Archimedes' principle. The corrected ratio of V/A is 0.