Lee Banting

An investigation of the ionophoric characteristics of destruxin A

Destruxin A, a cyclohexadepsipeptide related to the enniatins and beauvericin, exhibits ionophoric properties. Calcium ion mobilization across liposomal membrane barriers, for example, has been demonstrated using the calcium ion-sensitive dyes Arsenazo III and Fura-2. Initial molecular mechanics/molecular dynamics calculations indicate the potential for destruxin A to form a coordination complex with calcium in which the divalent cation is bound at the center of a sandwich formed by two molecules of destruxin A. This novel calcium ion binding may help explain the diverse biological effects exhibited by the destruxins.

QSAR studies of the pyrethroid insecticides. Part 3. A putative pharmacophore derived using methodology based on molecular dynamics and hierarchical cluster analysis.

Previous studies of the conformational behaviour of a group of synthetic pyrethroid insecticides have been extended to a more structurally diverse set. This includes compounds with different backbones and differing stereochemistry, with both Types I and II biological activity. These compounds also encompass a large range of biological activities. A parameterisation of the CHARMM force field for these compounds has been performed and the extra parameters are reported. Conformational sampling, using molecular dynamics (MD), has been performed for each of the 41 active structures. The accessible conformations of each have been characterised by the values of the common torsion angles using hierarchichal cluster analysis (HCA). A further CA, based on the centroids derived from the conformational sampling, identified a conformation common to at least 39 of the 41 structures. The critical torsion angles of this conformation lie at the centre of the molecule about the ester linkage and are defining an extended conformation, which differs from the minimum energy conformation of deltamethrin used previously. This may represent a putative pharmacophore for kill. The methods used here improve significantly on those used previously. The CHARMM force field was parameterised for the compounds and an improved method of conformational sampling, based on centroid clustering, has also been used.

Aromatase: the enzyme and its inhibition

The genetic control, mechanism of action and inhibition of aromatase for potential therapeutic benefits in the arena of hormone dependent illness continues to be of considerable interest. The work presented here concentrates on recent advances in the mechanistic aspects of the aromatase enzyme and the nature of the chemical entities that lead to its inhibition.

Conformation and dynamics of human urotensin II and urotensin related peptide in aqueous solution

Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. UII and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, open and folded, with rapidly interchanging subtypes. The open states are characterized by turns of various types centered at K8Y9 or F6W7 predominantly with no or only sparsely populated transannular hydrogen bonds. The folded conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers F6W7K8 or W7K8Y9. Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% open:28% folded conformations in aqueous solution. URP shows very similar ring conformations as UII but differs in an open:folded equilibrium shifted further toward open conformations (86:14) possibly arising from the absence of folded N-terminal tail-ring interaction. The results suggest that the different biological effects of UII and URP are not caused by differences in ring conformations but rather by different interactions with UTR.

Drug design strategies:computational techniques and applications

This book documents the latest research into the theory and application of force-fields, semi-empirical molecular orbital, density functional and ab initio calculations, Quantum Mechanical (QM) based modelling, Atoms in Molecules (AIM) approach, and biomolecular dynamics. It also covers theory and application of 2D cheminformatics, QSAR/QSPR, ADME properties of drugs, drug docking/scoring protocols and approaches, topological methodology, and modelling accurate inhibition constants of enzymes. Finally, the book gives the theory and applications of multiscale modelling of proteins and biomolecular systems. The information need for a book in this area is due to the continuing rapid advance of firstly theoretical approaches, secondly software/hardware and lastly the successful application of the technology and this book fills a gap in the literature. The co-editors have extensive experience of teaching and researching in the field and the book includes contributions from cutting-edge academic and industrial researchers in their respective fields. It is essential reading for medicinal chemists, computational chemists and those in the pharmaceutical industry.

Can Simulations and Modeling Decipher NMR Data for Conformational Equilibria? Arginine-Vasopressin.

Arginine vasopressin (AVP) has been suggested by molecular-dynamics (MD) simulations to exist as a mixture of conformations in solution. The (1)H and (13)C NMR chemical shifts of AVP in solution have been calculated for this conformational ensemble of ring conformations (identified from a 23 μs molecular-dynamics simulation). The relative free energies of these conformations were calculated using classical metadynamics simulations in explicit water. Chemical shifts for representative conformations were calculated using density-functional theory. Comparison with experiment and analysis of the results suggests that the (1)H chemical shifts are most useful for assigning equilibrium concentrations of the conformations in this case. (13)C chemical shifts distinguish less clearly between conformations, and the distances calculated from the nuclear Overhauser effect do not allow the conformations to be assigned clearly. The (1)H chemical shifts can be reproduced with a standard error of less than 0.24 ppm (<2.2 ppm for (13)C). The combined experimental and theoretical results suggest that AVP exists in an equilibrium of approximately 70% saddlelike and 30% clinched open conformations. Both newly introduced statistical metrics designed to judge the significance of the results and Smith and Goodmans DP4 probabilities are presented.

In Silico Adoption of an Orphan Nuclear Receptor NR4A1.

A 4.1μs molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the ‘traditional’ nuclear receptor ligand-binding site. A NR4A1/bis-indole ligand complex at this novel site has been found to be stable over 1 μs of simulation and to result in an interesting conformational transmission to a remote loop that has the capacity to communicate with a NBRE within a RXR-α/NR4A1 heterodimer. Several features of the simulations undertaken indicate how NR4A1 can be affected by alternate-site modulators.

Synthesis and Ring Cyclization–Expansion–Contraction Reactions of Some New 2,2-Disubstituted Indan-1,3-diones and Related Compounds

We have found that the hydrochloride of 2-phenyl-2-[2-(2-piperidyl)ethyl]-4,5,6,7-tetrahydroindan-1,3-dione 1 possesses marked analgesic activity (100% inhibition referenced to codeine) and report, as part of an extensive synthetic program, the synthesis of 38 new and structurally related compounds. Selective catalytic hydrogenation of the pyridine ring of 2-phenyl-2-[2-(2-pyridyl)ethyl]-indan-1,3-dione 2 yields the nine-membered nitrogen-containing heterocycle 6 by a novel ring cyclization–expansion reaction. The structural and functional group parameters required for this novel ring-expansion reaction have been extensively and thoroughly investigated through the synthesis of a series of structurally related compounds; principally by modification, substitution, and replacement of the various functionality contained within 2. In addition, we report the synthesis of a series of new 2-methyl-2-(ω-N-phthalimidoalkyl)-indan-1,3-diones 41, 45, and 53, two of which, like the parent 2-phenyl substituted indan-1,3-dione 2, also undergo a novel ring cyclization–expansion reaction to yield eight- and nine-membered nitrogen-containing rings. However, in these cases, further transannular reactions occur to produce the new 5,5- and 5,6-ring-fused nitrogen-containing heterocycles 44, 48 and 51, 52. Hydrazinolysis of the third, 2-methyl-2-(4-N-phthalimidobutyl)-indan-1,3-dione yields the new azepine-containing ring structure 56 by direct cyclization. Furthermore, some interesting and unexpected chemical properties of the final compounds, which include selective and non-selective pyridine-ring hydrogenations and a few unexpected side reactions, are described.