ABSTRACT
Four new ligands that bind to the minor groove of DNA have been designed, synthesized, and evaluated by DNA footprinting. Two of the ligands are polyamides containing central regions with five or six N-methylpyrrole units, conferring hydrophobicity and good binding affinity but without retaining the correct spacing for hydrogen bonding in the base of the minor groove. The two remaining ligands have central regions which are head-to-head-linked polyamides, in which the linker is designed to improve the phasing of hydrogen bonding of the ligand with the floor of the minor groove. The highest affinity was obtained with the two polypyrroles without headgroup spacers, indicating that H-bond phasing is secondary in determining affinity compared to the major hydrophobic driving force. With a dimethylaminoalkyl group, representing a moiety with modest base strength, at both ends, water solubility is good and pH-partition theory predicts that penetration through lipid membranes will be enhanced, compared to strongly basic amidine analogues of the alkaloid precursors. All four compounds bind to DNA, with strong selectivity for AT sequences but some tolerance of GC base pairs and subtle individual preferences. The data show that very high affinities can be anticipated for future compounds in this series, but drug design must take account of overall physicochemical properties as well as the details of hydrogen bonding between ligands and the floor of the minor groove.
Subject(s)
DNA/chemistry , Netropsin/analogs & derivatives , Pyrroles/chemistry , DNA/chemical synthesis , DNA Footprinting , Electrophoresis, Polyacrylamide Gel , Hydrogen Bonding , Hydrogen-Ion Concentration , Ligands , Netropsin/chemical synthesis , Netropsin/chemistry , Pyrroles/chemical synthesis , SolubilityABSTRACT
Prediction of protein structure is an open-ended problem. Since an approach from first principles cannot be taken in reasonable computer time, short-cuts using further data are necessary. Such data include information about the specific protein in question, and information in databases which are about proteins in general. Is it possible to write a general, flexible 'superalgorithm' which would suit most circumstances? If so, it would seem likely to overcome one of the most understated but nonetheless greatest difficulties associated with molecular modelling and computer-aided drug design--reproducibility. To this end, a 'polymorphic programming environment' has been developed which represents both an expert system and a high-level language for theoretical chemists and molecular biologists. This language is GLOBAL (Ball et al., 1990). In a series of earlier studies, and more recently by means of GLOBAL itself, the nature of reproducibility and its rather surprising limits have been explored, and in general the current status and future potential of protein modelling have been examined.
Subject(s)
Expert Systems , Proteins/chemistry , Molecular Structure , Protein Conformation , SoftwareABSTRACT
An analogue of LHRH containing an extension of Gly-Cys at the carboxyl-terminus has been designed to permit reproducible coupling to a suitably modified carrier via a thioether bond. Potential energy calculations indicated that this analogue adopted a conformation in solution virtually identical to the type II' turn around Gly-6-Leu-7 predicted for native LHRH. Intradermal administration of a conjugate of this analogue with purified protein derivative of tuberculin to male rats previously primed with BCG vaccine rapidly led to complete testicular regression. This adjuvant-free immunisation protocol may represent an alternative to castration for the veterinary control of reproductive function.
Subject(s)
Autoantibodies/biosynthesis , Gonadotropin-Releasing Hormone/analogs & derivatives , Gonadotropin-Releasing Hormone/immunology , Testis/immunology , Animals , Computer Simulation , Immunization , Male , Models, Chemical , Molecular Conformation , Rats , TuberculinABSTRACT
The molecular modelling of larger proteins benefits from a preliminary analysis of the sequence to identify regions of potential structural and functional importance. In this study the sequence of the epidermal growth factor receptor has been analysed using a variety of established methods and novel procedures developed for the study of weak internal and external homologies and for the use of homologous sequences in the prediction of secondary and super-secondary structures. The procedures explored here are potentially suitable for incorporation into an expert system for the initial investigation of protein sequence data.
