Identification and characterization of folding inhibitors of hen egg lysozyme: an example of a new paradigm of drug design.

Studies of protein folding indicate the presence of native contacts in the denatured state, giving rise to folding elements which contribute to the accomplishment of the native state. The possibility of finding molecules which can interact with specific folding elements of a target protein preventing it from reaching its native state, and hence from becoming biologically active, is particularly attractive. The notion that folding elements not only provide molecular recognition directing the folding process, but also have conserved sequence, implies that targeting such elements will make protein folding inhibitors less susceptible to mutations which, in many cases, abrogate drug effects. The folding-inhibition strategy can lead to a truly novel and rational approach to drug design, aside from providing new insight into folding. This is illustrated in the case of hen egg lysozyme.

Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm.

Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical.

Low-throughput model design of protein folding inhibitors.

The stabilization energy of proteins in their native conformation is not distributed uniformly among all the amino acids, but is concentrated in few (short) fragments, fragments which play a key role in the folding process and in the stability of the protein. Peptides displaying the same sequence as these key fragments can compete with the formation of the most important native contacts, destabilizing the protein and thus inhibiting its biological activity. We present an essentially automatic method to individuate such peptidic inhibitors based on a low-throughput screening of the fragments which build the target protein. The efficiency and generality of the method is tested on proteins Src-SH3, G, CI2, and HIV-1-PR with the help of a simplified computational model. In each of the cases studied, we find few peptides displaying strong inhibitory properties, properties which are quite robust with respect to point mutations. The possibility of implementing the method through low-throughput experimental screening of the target protein is discussed.

A folding inhibitor of the HIV-1 protease.

Because the human immunodeficiency virus type 1 protease (HIV-1-PR) is an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single-domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids, which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV-1-PR monomers found among these peptides are demonstrated with the help of spectrophotometric assays and circular dichroism spectroscopy.

Designability of lattice model heteropolymers.

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20-letter lattice model of proteins which, relying only on the central limit theorem, has a generality which goes beyond the simple model used in its derivation. This expression displays an exponential dependence on the energy of the optimal sequence folding on the given conformation measured with respect to the lowest energy of the conformational dissimilar structures, an energy difference which constitutes the only parameter controlling designability. Accordingly, the designability of a native conformation is intimately connected to the stability of the sequences folding to them.

Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins.

Some dimeric proteins first fold and then dimerize (three-state dimers) while others first dimerize and then fold (two-state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences following one or the other mechanism on the basis of the distribution of the ground state energy between bulk and interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up of a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both, in the folding and in the evolutionary history of the protein. Three-state dimers, where a large fraction of energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchical pathway controlled by local elementary structures, as also happens in the folding of single-domain monomeric proteins. On the other hand, two-state dimers display a relative contact energy of interface contacts, which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and leads the two chains to fold. The specific properties of three-state dimers acquired through evolution are expected to be more robust than those of two-state dimers; a fact that has consequences on proteins connected with viral diseases.

Progress in elucidating the structural and dynamic character of G Protein-Coupled Receptor oligomers for use in drug discovery.

G Protein-Coupled Receptors (GPCRs) are the most targeted group of proteins for the development of therapeutic drugs. Until the last decade, structural information about this family of membrane proteins was relatively scarce, and their mechanisms of ligand binding and signal transduction were modeled on the assumption that GPCRs existed and functioned as monomeric entities. New crystal structures of native and engineered GPCRs, together with important biochemical and biophysical data that reveal structural details of the activation mechanism(s) of this receptor family, provide a valuable framework to improve dynamic molecular models of GPCRs with the ultimate goal of elucidating their allostery and functional selectivity. Since the dynamic movements of single GPCR protomers are likely to be affected by the presence of neighboring interacting subunits, oligomeric arrangements should be taken into account to improve the predictive ability of computer-assisted structural models of GPCRs for effective use in drug design.

Off-label use of drugs in Italy: a prospective, observational and multicentre study.

UNLABELLED: The aims of the study were to measure the paediatric, off-label use of drugs in the Italian hospital setting and to reveal areas for priority intervention by investigating the therapeutic indications most involved. Prescriptions given to all children admitted to nine general paediatric hospital wards from December 1998 to February 1999 were analysed. In total, 4265 prescriptions were given to 1461 children, 10 of which were unlicensed and excluded from further analysis. Sixty percent of prescriptions (range between centres: 44-71%) were off-label and concerned 89% of children receiving medications (80-96%). The main drug classes were antibacterials, antiasthmatics and analgesics, and represented 56% of off-label prescriptions. Paracetamol (385 prescriptions) and beclomethasone (339) were the generic substances most often used off-label. The most common off-label categories were dosage/frequency (50% of prescriptions), indication and lack of paediatric licence (7% each). Fifty-four per cent of all indications that led to off-label prescribing involved only respiratory problems, fever, respiratory tract infections and bronchospasm. CONCLUSIONS: Despite prescription profile differences among centres, off-label use was high everywhere. Immediate action for more rational drug use is necessary and requires not only regulatory intervention but also a more evidence-based, therapeutic approach.

Incidence of adverse drug reactions in paediatric in/out-patients: a systematic review and meta-analysis of prospective studies.

AIMS: To explore the usefulness of data derived from observational studies on adverse drug reactions (ADRs) in defining and preventing the risk of pharmacological interventions in children in different health care settings. METHODS: A systematic review of studies on ADRs in hospitalized children, in outpatient children, and on ADRs causing paediatric hospital admissions was performed. Studies were identified through a search of the MEDLINE and EMBASE databases. The inclusion criteria required that the population was not selected for particular conditions or drug exposure and prospective monitoring was used for identifying ADRs. Data were analysed by a random-effects model. RESULTS: Seventeen prospective studies were included. In hospitalized children, the overall incidence of ADRs was 9.53% (95% confidence interval [CI], 6.81, 12.26); severe reactions accounted for 12.29% (95%CI, 8.43,16.17) of the total. The overall rate of paediatric hospital admissions due to ADRs was 2.09% (95%CI, 1.02, 3.77); 39.3% (95%CI, 30.7,47.9) of the ADRs causing hospital admissions were life threatening reactions. For outpatient children the overall incidence of ADRs was 1.46% (95%CI, 0.7, 3.03). CONCLUSIONS: The results show that ADRs in children are a significant public health issue. The completeness and accuracy of prescription reporting as well as clinical information from studies was a rarity, making it difficult for health practitioners to implement evidence based preventive strategies. Further, methodologically sound drug surveillance studies are necessary for an effective promotion of a safer use of drugs in children.