A. I. Scott

Conformation in solution and dynamics of a structurally constrained linear insect kinin pentapeptide analogue.

The preferred conformations of the active diuretic insect kinin pentapeptide analogue Phe-Phe-Aib-Trp-Gly-NH2 were studied using nmr spectroscopy and molecular modeling. Structure sets consistent with rotating frame nuclear Overhauser effect spectroscopy distance constraints obtained by restrained simulated annealing in vacuo indicate a predominant population of a type II beta-turn involving the Phe1-Trp4 region. An equilibrium between this type II and a type I beta-turn formed by residues Phe2 and Gly5 was observed in a 5 ns restrained molecular dynamics simulation using the implicit generalized Born solvent accessible surface area (GB/SA) solvation model. When subjected to 500 ps dynamics with explicit water both beta-turn folds were conserved throughout the simulations. The results obtained with implicit and explicit solvation models are compared, and their consistency with the nmr observations is discussed. The behavior of the linear pentapeptide in this study is in agreement with an earlier report on the consensus conformation of the insect kinin active core derived from analysis of cyclic active analogues.

Synthesis, biological activity, and conformational studies of insect allatostatin neuropeptide analogues incorporating turn-promoting moieties

Allatostatins are 6-18 amino acid peptides synthezed by insects to control production of juvenile hormones, which in turn regulate functions including metamorphosis and egg production. Four insect allatostatin neuropeptide analogues incorporating turn-promoting pseudopeptide moieties in the region responsible for biological activity were prepared by solid phase peptide synthetic methods. Bioassay indicated that activities approached those of the natural neuropeptides, and molecular models based on NMR data showed similar conformations and the presence of a beta-turn in the active core region for the four analogues. Differences in activity are believed to be due to differences in bulk and relative position of atoms in the unnatural portion of the analogues, and their differing degrees of conformational freedom. The studies support the feasibility of development of neuropeptide-based insect control agents resistant to peptidase deactivation.

COMPARISON OF RING CURRENT METHODS FOR USE IN MOLECULAR MODELING REFINEMENT OF NMR DERIVED THREE-DIMENSIONAL STRUCTURES

A comparison between three different methods commonly used to estimate ring current effects on chemical shifts is presented. Haigh-Mallion, Johnson-Bovey, and classical point-dipole approximations were used to estimate the ring current contribution to chemical shifts for protons in several proteins for which both detailed X-ray crystal structures and chemical shift assignments were available. For the classical point-dipole model, new proportionality constants were calculated by fitting to ring current estimations from both the quantum-mechanical Haigh-Mallion and semiclassical Johnson-Bovey methods and compared with the previously used point-dipole constant of Perkins and Dwek. Statistical analysis of the predictions obtained by all methods indicates that the point-dipole approximation parametrized against quantum-mechanical data is superior to the previously used classical model, comparable to Johnson-Bovey calculations, and slightly poorer than predictions from the Haigh-Mallion theory. The implementation of a pseudoenergy penalty term for use in structure refinement from chemical shift data based on the classical point-dipole model is described, and its usefulness in cases where other NMR information is limited is discussed with a specific example.

Synthesis of L-α-Aminoadipic Acid from L-Lysine

Abstract L-α-Aminoadipic acid (1), a constituent amino acid of the Arnstein tripeptide,1 δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine, a putative acyclic precursor2 of the penicillins and cephalo-sporins, has previously been prepared by resolution of the racemate3 and by homologation of L-glutamic acid.4 We report herein an alternative procedure based on the conversion of the terminal methylene group of L-lysine to the corresponding acid.

Preparation of aminated taxol side chain precursors. A Simple Approach to 2,3-Diamond Acids Using the β-Lactam Synthon Method.

Abstract Coupling-ready aminated side chain analog precursors of the anticancer drug taxol were prepared through the β-lactam synthon method. The procedure described represents an easy connection between β-lactams and 2,3-diamino acids, is highly stereospecific, and causes no racemization due to vicinal group participation.

An Improved Procedure for the Epoxidation of Methyl Cinnamate Derivatives and Production of Acid Sensitive Epoxides

Abstract By using a biphasic epoxidation system, unreactive methyl cinnamate derivatives were epoxidized at higher rates, and epoxides that decomposed in the presence of m-chlorobenzoic acid (mCBA) to diol ester opening products under standard conditions were obtained in fair to excellent yields.

A simple algorithm for superimposing sets of NMR derived structures: its application to the conformational study of cephalomannine in lipophobic and lipophilic solution.

A simple iterative method for superimposing sets of NMR derived structures and calculation of the root mean square deviation (RMSD) of the sets is described. It was compared to the commonly used algorithm involving pairwise best fitting in the conformational study of the taxoid anticancer drug cephalomannine in lipophobic and lipophilic solvents. Lower RMSD values were obtained, indicating a better superposition of the structures in the sets. The conformations of cephalomannine in the two solvent systems reported are in good agreement with earlier conformational studies on other active taxoids.

Development of Weiner et al. Force Field Parameters Suitable for Conformational Studies of [1,4]-Benzodiazepines and Related Compounds

A set of force field parameters capable of reproducing the preferred conformations of the biologically important [1,4]-benzodiazepines was developed for AMBER and other molecular modeling programs that utilize the Weiner et al. force field. Equilibrium parameters were obtained from representative model compounds found in the Cambridge Structural Database, and bond stretching and torsion potential force constants were estimated using AM1 and PM3 semiempirical Hamiltonians. Parameters obtained with the two semiempirical methods and the existing linear interpolation method are compared. Molecular mechanics and dynamic simulations showed that AM1 derived parameters, together with MNDO ESP fitted atomic charges, predicted the X-ray structure of a number of representative [1,4]-benzodiazepines within 0.01 A, 0.8 degree, and 5 degrees, from observed bond lengths, bond angles, and bond torsions, respectively.