Exploring unfrequent events with accelerated molecular dynamics simulations: from photochemistry to drug design

La meva incorporació al grup de recerca del Prof. McCammon (University of California San Diego) en qualitat d’investigador post doctoral amb una beca Beatriu de Pinós, va tenir lloc el passat 1 de desembre de 2010; on vaig dur a terme les meves tasques de recerca fins al darrer 1 d’abril de 2012. El Prof. McCammon és un referent mundial en l’aplicació de simulacions de dinàmica molecular (MD) en sistemes biològics d’interès humà. La contribució més important del Prof. McCammon en la simulació de sistemes biològics és el desenvolupament del mètode de dinàmiques moleculars accelerades (AMD). Les simulacions MD convencionals, les quals estan limitades a l’escala de temps del nanosegon (~10-9s), no son adients per l’estudi de sistemes biològics rellevants a escales de temps mes llargues (μs, ms...). AMD permet explorar fenòmens moleculars poc freqüents però que son clau per l’enteniment de molts sistemes biològics; fenòmens que no podrien ser observats d’un altre manera. Durant la meva estada a la “University of California San Diego”, vaig treballar en diferent aplicacions de les simulacions AMD, incloent fotoquímica i disseny de fàrmacs per ordinador. Concretament, primer vaig desenvolupar amb èxit una combinació dels mètodes AMD i simulacions Car-Parrinello per millorar l’exploració de camins de desactivació (interseccions còniques) en reaccions químiques fotoactivades. En segon lloc, vaig aplicar tècniques estadístiques (Replica Exchange) amb AMD en la descripció d’interaccions proteïna-lligand. Finalment, vaig dur a terme un estudi de disseny de fàrmacs per ordinador en la proteïna-G Rho (involucrada en el desenvolupament de càncer humà) combinant anàlisis estructurals i simulacions AMD. Els projectes en els quals he participat han estat publicats (o estan encara en procés de revisió) en diferents revistes científiques, i han estat presentats en diferents congressos internacionals. La memòria inclosa a continuació conté més detalls de cada projecte esmentat.

Drug Utilization Studies and Data Registries in Primary Care.

This article reviews the methodology of the studies on drug utilization with particular emphasis on primary care. Population based studies of drug inappropriateness can be done with microdata from Health Electronic Records and e-prescriptions. Multilevel models estimate the influence of factors affecting the appropriateness of drug prescription at different hierarchical levels: patient, doctor, health care organization and regulatory environment. Work by the GIUMAP suggest that patient characteristics are the most important factor in the appropriateness of prescriptions with significant effects at the general practicioner level.

Predictability of drug expenditures: An application using morbidity data

The growth of pharmaceutical expenditure and its prediction is a major concern for policy makers and health care managers. This paper explores different predictive models to estimate future drug expenses, using demographic and morbidity individual information from an integrated healthcare delivery organization in Catalonia for years 2002 and 2003. The morbidity information consists of codified health encounters grouped through the Clinical Risk Groups (CRGs). We estimate pharmaceutical costs using several model specifications, and CRGs as risk adjusters, providing an alternative way of obtaining high predictive power comparable to other estimations of drug expenditures in the literature. These results have clear implications for the use of risk adjustment and CRGs in setting the premiums for pharmaceutical benefits.

Drug utilization studies and data registries in primary care

This article reviews the methodology of the studies on drug utilization with particular emphasis on primary care. Population based studies of drug inappropriateness can be done with microdata from Health Electronic Records and e-prescriptions. Multilevel models estimate the influence of factors affecting the appropriateness of drug prescription at different hierarchical levels: patient, doctor, health care organization and regulatory environment.Work by the GIUMAP suggest that patient characteristics are the most important factor in the appropriateness of prescriptions with significant effects at the general practicioner level.

Drug innovation, prices and health

This article tries to reconcile economic-industrial policy with health policy when dealing with biomedical innovation and welfare state sustainability. Better health accounts for an increasingly large proportion of welfare improvements. Explanation is given to the welfare losses coming from the fact than industrial and health policy tend to ignore each other. Drug s prices reflecting their relative relative effectiveness send the right signal to the industry rewarding innovation with impact on quantity and quality of life- and to the buyers of health care services.The level of drug s public reimbursement indicates the social willingness to pay of the different national health systems, not only by means of inclusion, or rejection, in the basket of services covered, but especially establishing the proportion of the price that is going to be financed publicly.Reference pricing for therapeutic equivalents as the upper limit of the social willingness to pay- and two-tiered co-payments for users (avoidable and inversely related with the incremental effectiveness of de drug) are deemed appropriate for those countries concerned at the same time with increasing their productivity and maintaining its welfare state. Profits drive R&D but not its location. There is no intrinsic contradiction between high productivity and a consolidated National Health Service (welfare state) as the European Nordic Countries are telling us every day.

Effectiveness of a drug dosing service provided by community pharmacists in polymedicated elderly patients with renal impairment a comparative study

Background: Drug dosing errors are common in renal-impaired patients. Appropriate dosing adjustment and drug selection is important to ensure patients" safety and to avoid adverse drug effects and poor outcomes. There are few studies on this issue in community pharmacies. The aims of this study were, firstly, to determine the prevalence of dosing inadequacy as a consequence of renal impairment in patients over 65 taking 3 or more drug products who were being attended in community pharmacies and, secondly, to evaluate the effectiveness of the community pharmacist"s intervention in improving dosing inadequacy in these patients when compared with usual care. Methods: The study was carried out in 40 Spanish community pharmacies. The study had two phases: the first, with an observational, multicentre, cross sectional design, served to determine the dosing inadequacy, the drug-related problems per patient and to obtain the control group. The second phase, with a controlled study with historical control group, was the intervention phase. When dosing adjustments were needed, the pharmacists made recommendations to the physicians. A comparison was made between the control and the intervention group regarding the prevalence of drug dosing inadequacy and the mean number of drug-related problems per patient. Results: The mean of the prevalence of drug dosing inadequacy was 17.5% [95% CI 14.6-21.5] in phase 1 and 15.5% [95% CI 14.5-16.6] in phase 2. The mean number of drug-related problems per patient was 0.7 [95% CI 0.5-0.8] in phase 1 and 0.50 [95% CI 0.4-0.6] in phase 2. The difference in the prevalence of dosing inadequacy between the control and intervention group before the pharmacists" intervention was 0.73% [95% CI (−6.0) - 7.5] and after the pharmacists" intervention it was 13.5% [95% CI 8.0 - 19.5] (p < 0.001) while the difference in the mean of drug-related problems per patient before the pharmacists" intervention was 0.05 [95% CI( -0.2) - 0.3] and following the intervention it was 0.5 [95% CI 0.3 - 0.7] (p < 0.001). Conclusion: A drug dosing adjustment service for elderly patients with renal impairment in community pharmacies can increase the proportion of adequate drug dosing, and improve the drug-related problems per patient. Collaborative practice with physicians can improve these results.

Drug price differentials caused by de-listing and price cap policies

This paper analyses the behaviour of pharmaceutical companies that face the threat of having their drugs excluded from reimbursement and the markets characterised also by price caps. We conclude that price elasticity of demand and cost differentials cause the price discounts which drug firms offer to health care organisations. Additionally, we conclude that price cap regulations affect the time path of prices, resulting in higher prices for new products and lower prices for old products.

Drug price differentials caused by de-listing and price cap policies

This paper analyses the behaviour of pharmaceutical companies that face the threat of having their drugs excluded from reimbursement and the markets characterised also by price caps. We conclude that price elasticity of demand and cost differentials cause the price discounts which drug firms offer to health care organisations. Additionally, we conclude that price cap regulations affect the time path of prices, resulting in higher prices for new products and lower prices for old products.

Automatic filtering and substantiation of drug safety signals

Drug safety issues pose serious health threats to the population and constitute a major cause of mortality worldwide. Due to the prominent implications to both public health and the pharmaceutical industry, it is of great importance to unravel the molecular mechanisms by which an adverse drug reaction can be potentially elicited. These mechanisms can be investigated by placing the pharmaco-epidemiologically detected adverse drug reaction in an information-rich context and by exploiting all currently available biomedical knowledge to substantiate it. We present a computational framework for the biological annotation of potential adverse drug reactions. First, the proposed framework investigates previous evidences on the drug-event association in the context of biomedical literature (signal filtering). Then, it seeks to provide a biological explanation (signal substantiation) by exploring mechanistic connections that might explain why a drug produces a specific adverse reaction. The mechanistic connections include the activity of the drug, related compounds and drug metabolites on protein targets, the association of protein targets to clinical events, and the annotation of proteins (both protein targets and proteins associated with clinical events) to biological pathways. Hence, the workflows for signal filtering and substantiation integrate modules for literature and database mining, in silico drug-target profiling, and analyses based on gene-disease networks and biological pathways. Application examples of these workflows carried out on selected cases of drug safety signals are discussed. The methodology and workflows presented offer a novel approach to explore the molecular mechanisms underlying adverse drug reactions

Use of antimicrobial biodegradable packaging to control Listeria monocytogenes during storage of cooked ham

The antimicrobial effect against L. monocytogenes of biodegradable films (alginate, zein and polyvinyl alcohol) containing enterocins was investigated. Survival of the pathogen was studied by means of challenge tests performed at 6 °C during 8 and 29 days, for air-packed and vacuum-packed sliced cooked ham, respectively. Air packaging was tested with two concentrations of enterocins (200 and 2000 AU/cm2). Control air-packed cooked ham showed an increase of L. monocytogenes from 104 to 107 CFU/g after 8 days. By contrast, packaging with antimicrobial films effectively slowed down the pathogen's growth, leading to final counts lower than in control lots. Air-packaging with alginate films containing 2000 AU/cm2 of enterocins effectively controlled L. monocytogenes for 8 days. An increase of only 1 log unit was observed in zein and polyvinyl alcohol lots at the same enterocin concentration. Vacuum packaging with films containing enterocins (2000 AU/cm2) also delayed the growth of the pathogen. No increase from inoculated levels was observed during 15 days in antimicrobial alginate films. After 29 days of storage, the lowest counts were obtained in samples packed with zein and alginate films containing enterocins, as well as with zein control films. The most effective treatment for controlling L. monocytogenes during 6 °C storage was vacuum-packaging of sliced cooked ham with alginate films containing 2000 AU/cm2 of enterocins. From the results obtained it can concluded that antimicrobial packaging can improve the safety of sliced cooked ham by delaying and reducing the growth of L. monocytogenes.

High-pressure processing and antimicrobial biodegradable packaging to control Listeria monocytogenes during storage of cooked ham

The efficiency of combining high-pressure processing (HPP) and active packaging technologies to control Listeria monocytogenes growth during the shelf life of artificially inoculated cooked ham was assessed. Three lots of cooked ham were prepared: control, packaging with alginate films, and packaging with antimicrobial alginate films containing enterocins. After packaging, half of the samples were pressurized. Sliced cooked ham stored at 6 °C experienced a quick growth of L. monocytogenes. Both antimicrobial packaging and pressurization delayed the growth of the pathogen. However, at 6 °C the combination of antimicrobial packaging and HPP was necessary to achieve a reduction of inoculated levels without recovery during 60 days of storage. Further storage at 6 °C of pressurized antimicrobial packed cooked ham resulted in L. monocytogenes levels below the detection limit (day 90). On the other hand, storage at 1 °C controlled the growth of the pathogen until day 39 in non-pressurized ham, while antimicrobial packaging and storage at 1 °C exerted a bacteriostatic effect for 60 days. All HPP lots stored at 1 °C led to counts <100 CFU/g at day 60. Similar results were observed when combining both technologies. After a cold chain break no growth of L. monocytogenes was observed in pressurized ham packed with antimicrobial films, showing the efficiency of combining both technologies.

Active packaging containing nisin and high pressure processing as post-processing listericidal treatments for convenience fermented sausages

Listeria monocytogenes was inoculated on the surface of sliced fermented sausages with no added sodium salt. The pathogen was progressively inactivated during the product shelf life (90 days). Antimicrobial packaging of fermented sausages with PVOH films containing nisin induced a more pronounced reduction of L. monocytogenes counts during refrigerated storage. HPP alone (600 MPa, 5 min, 12 °C) had no antimicrobial effect against L. monocytogenes at the studied conditions. Combination of HPP with antimicrobial packaging did not produce any extra protection against L. monocytogenes compared to antimicrobial packaging alone. The lack of effect of HPP on L. monocytogenes was attributed to a protective effect exerted by the low water activity of the product and its lactate content. These results reflect that antimicrobial packaging with the inclusion of nisin as a natural antimicrobial could be considered as an effective method to reduce the levels of L. monocytogenes in sliced fermented sausages with no added sodium salt

Physical performance of biodegradable films intended for antimicrobial food packaging

Antimicrobial films were prepared by including enterocins to alginate, polyvinyl alcohol (PVOH), and zein films. The physical performance of the films was assessed by measuring color, microstructure (SEM), water vapor permeability (WVP), and tensile properties. All studied biopolymers showed poor WVP and limited tensile properties. PVOH showed the best performance exhibiting the lowest WVP values, higher tensile properties, and flexibility among studied biopolymers. SEM of antimicrobial films showed increased presence of voids and pores as a consequence of enterocin addition. However, changes in microstructure did not disturb WVP of films. Moreover, enterocin-containing films showed slight improvement compared to control films. Addition of enterocins to PVOH films had a plasticizing effect, by reducing its tensile strength and increasing the strain at break. The presence of enterocins had an important effect on tensile properties of zein films by significantly reducing its brittleness. Addition of enterocins, thus, proved not to disturb the physical performance of studied biopolymers. Development of new antimicrobial biodegradable packaging materials may contribute to improving food safety while reducing environmental impact derived from packaging waste.