Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers

One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a second problem arises, namely the eventual development of resistance. We wish to suggest a scheme for the design of non--conventional drugs which do not face any of these problems and apply it to the case of HIV--1 protease. It is based on the knowledge that the folding of single--domain proteins, like e.g. each of the monomers forming the HIV--1--PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting and highly conserved amino acids which play a central role in the folding process. Because LES have evolved over myriads of generations to recognize and strongly interact with each other so as to make the protein fold fast as well as to avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding--inhibitor drugs suggest themselves: short peptides (or eventually their mimetic molecules), displaying the same amino acid sequence of that of LES (p--LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance: in fact, mutations which successfully avoid their action imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations within the framework of a simple although not oversimplified model, which is able to reproduce the main thermodynamic as well as dynamic properties of monoglobular proteins, we first identify the LES of the HIV--1--PR and then show that the corresponding p--LES peptides act as effective inhibitors of the folding of the protease which do not create resistance

Influence of pH on the kinetics of hydrolysis reactions: the case of epichlorohydrin and glycidol

Glycidol (GL) and epichlorohydrin (EPI) are two widely used molecules in chemical, pharmaceutical and food industry applications. However, their use in aqueous environments causes the formation of compounds, like monochloropropanediol (MCPD) and dichloropropanol (DCP), reported as dangerous for human health and therefore regulated by severe law restrictions. To identify the conditions leading to such species and design the corresponding processes in order to prevent their formation, hydrolysis and chlorination of EPI and GL, together with dehydrohalogenation of DCP and MCPD, have been systematically analysed. Different reaction conditions in terms of temperature, pH and chloride ion concentration have been experimentally investigated and the concentration of the involved species was tracked over time by gas chromatography and high-performance liquid chromatography. These experimental data were fitted through a kinetic model, which allowed a general expression of the observed rate constant of each reaction as a function of temperature and pH to be quantified. In particular, the reaction rates are conveniently expressed as combinations of three contributions: alkaline, neutral and acid. The corresponding rate laws explicitly account for the critical role of pH. The developed mechanistic model exhibits good prediction ability and may represent the basis for optimising processes employing EPI and GL

‘Everybody knows’, but the rest of the world: the case of a caterpillar-borne reproductive loss syndrome in dromedary camels observed by Sahrawi pastoralists of Western Sahara

Abstract Background The traditional knowledge of local communities throughout the world is a valuable source of novel ideas and information to science. In this study, the ethnoveterinary knowledge of Sahrawi pastoralists of Western Sahara has been used in order to put forward a scientific hypothesis regarding the competitive interactions between camels and caterpillars in the Sahara ecosystem. Methods Between 2005 and 2009, 44 semi-structured interviews were conducted with Sahrawi pastoralists in the territories administered by the Sahrawi Arab Democratic Republic, Western Sahara, using a snow-ball sampling design. Results Sahrawi pastoralists reported the existence of a caterpillar-borne reproductive loss syndrome, known locally as duda, affecting their camels. On the basis of Sahrawi knowledge about duda and of a thorough literature review, we built the hypothesis that: 1) caterpillars of the family Lasiocampidae (genera Lasiocampa, Psilogaster, or Streblote) have sudden and rare outbreaks on Acacia treetops in the Western Sahara ecosystem after heavy rainfall; 2) during these outbreaks, camels ingest the caterpillars while browsing; 3) as a consequence of this ingestion, pregnant camels have sudden abortions or give birth to weaklings. This hypothesis was supported by inductive reasoning built on circumstantiated evidence and analogical reasoning with similar syndromes reported in mares in the United States and Australia. Conclusions The possible existence of a caterpillar-borne reproductive loss syndrome among camels has been reported for the first time, suggesting that such syndromes might be more widespread than what is currently known. Further research is warranted to validate the reported hypothesis. Finally, the importance of studying folk livestock diseases is reinforced in light of its usefulness in revealing as yet unknown biological phenomena that would deserve further investigation. Resumen ‘Todos lo saben’, menos el resto del mundo: el caso de un síndrome de pérdida reproductiva en dromedarios transmitido por orugas y observado por pastores nómadas saharauis del Sáhara Occidental. Antecedentes Los conocimientos tradicionales de las comunidades locales de todo el mundo son una valiosa fuente de nuevas ideas e información para la ciencia. En este estudio, se utilizaron los conocimientos de etnoveterinaria de pastores saharauis del Sáhara Occidental con el fin de proponer una hipótesis científica sobre las interacciones competitivas entre los camellos y las orugas en el ecosistema del Sáhara. Métodos Entre los años 2005 y 2009, se realizaron 44 entrevistas semi-estructuradas a los pastores saharauis en los territorios administrados por la República Árabe Saharaui Democrática, Sáhara Occidental, mediante un diseño de muestreo por bola de nieve. Resultados Los pastores nómadas saharauis describieron un síndrome reproductivo transmitido por orugas, llamado duda, entre sus camellas. Sobre la base de los conocimientos saharauis sobre el duda y una revisión literaria exhaustiva, se propuso la siguiente hipótesis: 1) brotes esporádico de orugas de la familia Lasiocampidae (géneros Lasiocampa, Psilogaster o Streblote) en árboles de Acacia se pueden presentar después de fuertes lluvias en el ecosistema del Sáhara Occidental; 2) durante estos brotes, los camellos ingieren las orugas durante el pastoreo; 3) como consecuencia de esta ingestión, se producen abortos repentinos o partos de crías debilitadas. Apoyamos esta hipótesis mediante razonamiento inductivo basado en evidencia circunstancial y razonamiento analógico con síndromes similares en yeguas de los Estados Unidos y Australia. Conclusiones Este es el primer reporte de la posible existencia de un síndrome de pérdida reproductiva en camellos, transmitido por orugas. Se insinúa que estos síndromes son más comunes que lo que actualmente se conoce. Se sugieren investigaciones adicionales para poner a prueba nuestra hipótesis. Finalmente, se destaca la importancia de estudios de las enfermedades del ganado en pueblos de pastores nómadas porque pueden revelar fenómenos biológicos aún desconocidos y merecen ser investigados.</p

A preliminary microbiological assessment of process hygiene of traditional outdoor camel slaughter in Sahrawi refugee camps.

The aim of this study was to investigate the hygiene performance of a camel (Camelus dromedarius) slaughtering process as carried out with the traditional method in the Sahrawi refugee camps located in southwestern Algeria. The camel slaughtering process in this region differs significantly from that carried out in commercial abattoirs. Slaughtering is performed outdoors in desert areas, and dehiding of the carcass is approached via the dorsoventral route rather than the classic ventrodorsal route. Samples were taken from 10 camel carcasses from three different areas: the hide, the carcass meat immediately after dehiding, and the meat after final cutting. Enterobacteriaceae counts (EC) were enumerated employing conventional laboratory techniques. Carcass meat samples resulted in EC below the detection limit more frequently if the hide samples from the same carcass had also EC counts below the detection limit. Because of the low number of trials, the calculation of statistical significance of the results was not possible. Further experimental research is needed in order to validate the results presented in this study. The comparison of the microbiological hygiene performance between dorsal dehiding and traditional ventral dehiding of slaughtered animals could serve to validate the hypothesis of the potential positive impact of the dorsal dehiding method in carcass meat hygiene

The Recovery Orientation of a Farm Community for Severe Autism — Data from the DREEM-IT (Developing Recovery Enhancing Environment Measures — Italian Version)

Recent years have witnessed an increasing interest in the concept of ‘recovery’ in the field of mental health and psychiatry. Autism is a neurodevelopmental disorder characterized by qualitative impairments in social interaction and communication skill, along with a restricted, repetitive, and stereotyped pattern of behavior and interests. The diagnosis is lifelong and can be a major impediment to independent living. It has been previously demonstrated that organized and structured forms of intervention, starting from early childhood and developing during all the different life stages, may improve outcome and quality of life in patients with autism. It is therefore conceivable that diverse forms of recovery (e.g. optimal level of motivation, skills, social involvement) may be possible in autism. There are no fully developed tools with which to evaluate the recovery orientation of a service, but the National Institute for Mental Health in England (NIMHE) has identified the Developing Recovery Enhancing Environments Measure (DREEM) as the most promising of an emerging group of recovery sensitive measures. This study explores the use of DREEM, as a tool to evaluate the effectiveness of recovery-based care in an Italian farm community center specifically designed for adult patients with autism and intellectual disability

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.Comment: to be submitted to Computer Physics Communication

Systematic versus on-demand early palliative care: results from a multicentre, randomised clinical trial

Background Early palliative care (EPC) in oncology has been shown to have a positive impact on clinical outcome, quality-of-care outcomes, and costs. However, the optimal way for activating EPC has yet to be defined. Methods This prospective, multicentre, randomised study was conducted on 207 outpatients with metastatic or locally advanced inoperable pancreatic cancer. Patients were randomised to receive ‘standard cancer care plus on-demand EPC’ (n&nbsp;=&nbsp;100) or ‘standard cancer care plus systematic EPC’ (n&nbsp;=&nbsp;107). Primary outcome was change in quality of life (QoL) evaluated through the Functional Assessment of Cancer Therapy – Hepatobiliary questionnaire between baseline (T0) and after 12 weeks (T1), in particular the integration of physical, functional, and Hepatic Cancer Subscale (HCS) combined in the Trial Outcome Index (TOI). Patient mood, survival, relatives' satisfaction with care, and indicators of aggressiveness of care were also evaluated. Findings The mean changes in TOI score and HCS score between T0 and T1 were −4.47 and −0.63, with a difference between groups of 3.83 (95% confidence interval [CI] 0.10–7.57) (p&nbsp;=&nbsp;0.041), and −2.23 and 0.28 (difference between groups of 2.51, 95% CI 0.40–4.61, p&nbsp;=&nbsp;0.013), in favour of interventional group. QoL scores at T1 of TOI scale and HCS were 84.4 versus 78.1 (p&nbsp;=&nbsp;0.022) and 52.0 versus 48.2 (p&nbsp;=&nbsp;0.008), respectively, for interventional and standard arm. Until February 2016, 143 (76.9%) of the 186 evaluable patients had died. There was no difference in overall survival between treatment arms. Interpretations Systematic EPC in advanced pancreatic cancer patients significantly improved QoL with respect to on-demand EPC

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

The physics of protein folding and of non-conventional drug design : attacking AIDS with its own weapons

General physical principles have taught us that, good folders are those sequences of amino acids which have a particularly low energy in the native state. Furthermore, it has become clear during the last few years that most of the stabilization energy in this state is associated with few, strongly interacting, highly conserved, as a rule hydrophobic (hot) amino acids, amino acids which in the very early stages of the folding process stabilize local elementary structures (LES). The docking of these LES gives rise to the (post-critical) folding nucleus (FN), that is the minimum set of native contacts needed to bring the system over the highest free-energy barrier of the whole folding process. This physical scenario of the folding of proteins contains the clue for designing protein-folding inhibitors. A particularly attractive example of the workings of such non-conventional drugs is provided by the folding inhibitors of the HIV-1 Protease. Because HIV-1-PR is an essential enzyme in the viral life cycle, inhibition of the protease can control AIDS. In this paper we will review the theoretical and experimental evidence which testifies to the second-order phase transition undergone by the evolution of chains of amino acids from a random sequence to a good folder, and to the hierarchical physical mechanism which is at the basis of the first-order phase transition undergone by the enzyme (good folder): from the unfolded to the native, biologically active state of the protein. Special emphasis of this review will be set on the identification of hot, warm and cold sites as well as of the LES, and of (post-critical) folding nucleus (FN) of the enzyme. This identification will then be used to individuate the best candidates of folding inhibitors, that is peptides (p-LES) which, displaying the same sequence of LES, attach to the complementary LES, and denaturate the enzyme. Because LES have been designed by evolution over myriad of generations, p-LES are expected to be efficient inhibitors unlike to create resistance