Skin Sensitisation (Q)SARs/Expert Systems: from Past, Present to Future

This review describes the state of the art of available (Q)SARs/expert systems for skin sensitisation and evaluates their utility for potential regulatory use. There is a strong mechanistic understanding with respect to skin sensitisation which has facilitated the development of different models. Most existing models fall into one of two main categories either they are local in nature, usually specific to a chemical class or reaction chemical mechanism or else they are global in form, derived empirically using statistical methods. Some of the published global QSARs available have been recently characterised and evaluated elsewhere in accordance with the OECD principles. An overview of expert systems capable of predicting skin sensitisation is also provided. Recently, a new perspective regarding the development of mechanistic skin sensitisation QSARs so-called Quantitative Mechanistic Modelling (QMM) has been proposed, where reactivity and hydrophobicity, are used as the key parameters in mathematically modelling skin sensitisation. Whilst hydrophobicity can be conveniently modelled using log P, the octanol-water partition coefficient; reactivity is less readily determined from chemical structure. Initiatives are in progress to generate reactivity data for reactions relevant to skin sensitisation but more resources are required to realise a comprehensive set of reactivity data. This is a fundamental and necessary requirement for the future assessment of skin sensitisation.JRC.I.3-Toxicology and chemical substance

Review of Data Sources, QSARs and Integrated Testing Strategies for Skin Sensitisation

This review collects information on sources of skin sensitisation data and computational tools for the estimation of skin sensitisation potential, such as expert systems and (quantitative) structure-activity relationship (QSAR) models. The review also captures current thinking of what constitutes an integrated testing strategy (ITS) for this endpoint. The emphasis of the review is on the usefulness of the models for the regulatory assessment of chemicals, particularly for the purposes of the new European legislation for the Registration, Evaluation, Authorisation and Restriction of CHemicals (REACH), which entered into force on 1 June 2007. Since there are no specific databases for skin sensitisation currently available, a description of experimental data found in various literature sources is provided. General (global) models, models for specific chemical classes and mechanisms of action and expert systems are summarised. This review was prepared as a contribution to the EU funded Integrated Project, OSIRIS.JRC.I.3-Consumer products safety and qualit

Virtual Design of Chemical Penetration Enhancers

This study focused on identifying new potential chemical penetration enhancers (CPEs) for transdermal drug delivery. A computer-aided molecular design (CAMD) algorithm was developed by integrating a new genetic algorithm and non-linear QSPR models to develop a reliable virtual screening algorithm for generation of potential CPEs. Structure-based predictive models for prediction of skin sensitization and skin irritation were developed using reliable experimental data for a wide range of molecular species to estimate the toxic potential of the generated chemical compounds. Non-linear neural network algorithms with superior capabilities were used for model development.School of Chemical Engineerin

Chemical Similarity and Threshold of Toxicological Concern (TTC) Approaches: Report of an ECB Workshop held in Ispra, November 2005

There are many national, regional and international programmes – either regulatory or voluntary – to assess the hazards or risks of chemical substances to humans and the environment. The first step in making a hazard assessment of a chemical is to ensure that there is adequate information on each of the endpoints. If adequate information is not available then additional data is needed to complete the dataset for this substance. For reasons of resources and animal welfare, it is important to limit the number of tests that have to be conducted, where this is scientifically justifiable. One approach is to consider closely related chemicals as a group, or chemical category, rather than as individual chemicals. In a category approach, data for chemicals and endpoints that have been already tested are used to estimate the hazard for untested chemicals and endpoints. Categories of chemicals are selected on the basis of similarities in biological activity which is associated with a common underlying mechanism of action. A homologous series of chemicals exhibiting a coherent trend in biological activity can be rationalised on the basis of a constant change in structure. This type of grouping is relatively straightforward. The challenge lies in identifying the relevant chemical structural and physicochemical characteristics that enable more sophisticated groupings to be made on the basis of similarity in biological activity and hence purported mechanism of action. Linking two chemicals together and rationalising their similarity with reference to one or more endpoints has been very much carried out on an ad hoc basis. Even with larger groups, the process and approach is ad hoc and based on expert judgement. There still appears to be very little guidance about the tools and approaches for grouping chemicals systematically. In November 2005, the ECB Workshop on Chemical Similarity and Thresholds of Toxicological Concern (TTC) Approaches was convened to identify the available approaches that currently exist to encode similarity and how these can be used to facilitate the grouping of chemicals. This report aims to capture the main themes that were discussed. In particular, it outlines a number of different approaches that can facilitate the formation of chemical groupings in terms of the context under consideration and the likely information that would be required. Grouping methods were divided into one of four classes – knowledge-based, analogue-based, unsupervised, and supervised. A flowchart was constructed to attempt to capture a possible work flow to highlight where and how these approaches might be best applied.JRC.I.3-Toxicology and chemical substance

Modeling skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol compounds with quantum mechanistic properties

Background: Advanced structure-activity relationship (SAR) modeling can be used as an alternative tool for identification of skin sensitizers and in improvement of the medical diagnosis and more effective practical measures to reduce the causative chemical exposures. It can also circumvent ethical concern of using animals in toxicological tests, and reduce time and cost. Compounds with aniline or phenol moieties represent two large classes of frequently skin sensitizing chemicals but exhibiting very variable, and difficult to predict, potency. The mechanisms of action are not well-understood. Methods: A group of mechanistically hard-to-be-classified aniline and phenol chemicals were collected. An in silico model was established by statistical analysis of quantum descriptors for the determination of the relationship between their chemical structures and skin sensitization potential. The sensitization mechanisms were investigated based on the features of the established model. Then the model was utilized to analyze a subset of FDA approved drugs containing aniline and/or phenol groups for prediction of their skin sensitization potential. Results and discussion: A linear discriminant model using the energy of the highest occupied molecular orbital (εHOMO) as the descriptor yielded high prediction accuracy. The contribution of εHOMO as a major determinant may suggest that autoxidation or free radical binding could be involved. The model was further applied to predict allergic potential of a subset of FDA approved drugs containing aniline and/or phenol moiety. The predictions imply that similar mechanisms (autoxidation or free radical binding) may also play a role in the skin sensitization caused by these drugs. Conclusions: An accurate and simple quantum mechanistic model has been developed to predict the skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol chemicals. The model could be useful for the skin sensitization potential predictions of a subset of FDA approved drugs

A Strategy for assigning new NIOSH skin notations

"NIOSH skin notations are hazard warnings used worldwide to alert workers and employers to the health risks of skin exposures to chemicals in the workplace. This Current Intelligence Bulletin (CIB) provides the rationale for assigning new NIOSH skin notations. The new system reflects the current state of scientific knowledge and involves critical evaluation of scientific data so that scientists can assign multiple skin notations that distinguish between the systemic, direct, and sensitizing effects of skin exposures to chemicals. This new strategy is a form of hazard identification that advances our understanding of the hazards posed by skin exposures to chemicals. Such improved understanding will enable us to implement better risk management practices and controls for the prevention of workplace skin diseases and other occupational diseases where skin exposure may contribute to disease development." -- NIOSHTIC-21. Introduction. -- 2. Assigning Skin Notations -- Appendix A: Protocols Used in Studies of Health Effects from Skin Exposure and the Determination of Criteria Derived for Assigning Skin Notations -- Appendix B: Algorithm for estimating skin absorption and systemic toxicity and suggested application for assigning SYS notations -- Appendix C: Identifying skin corrosives and sensitizers using physicochemical properties and structure activity relationship-based analysis. -- Appendix D: Selecting and Prioritizing Candidate Chemicals. -- Appendix E: Guidelines and Criteria for the Search Strategy, Evaluation, and Selection of Supporting Data Used for the Assignment of Skin Notations -- Appendix F: Example of Assigning New NIOSH Skin Notations and Format of the Skin Notation Profile -- Appendix G: Supplemental informationDepartment of Health and Human Services, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health."This document was prepared by the Education and Information Division (EID), Paul Schulte, Ph.D., Director. Heinz W. Alhers, J.D., Chen-Peng Chen, Ph.D., Eugene Demchuk, Ph.D., and G. Scott Dotson, Ph.D. were the principle authors." - p. xvi"July, 2009."Includes bibliographical references (p. 12-14).Also available via the World Wide Web as Acrobat .pdf file (3.6 MB, 80 p.)

In sillico μελέτες αναστολέων της μεταλλαγμένης ογκοπρωτεΐνης BRAFV600E

Το σηματοδοτικό μονοπάτι MAPK το οποίο επηρεάζει τον κυτταρικό πολλαπλασιασμό, την απόπτωση, την διαφοροποίηση και την επιβίωση έχει προκαλέσει το ενδιαφέρον στον τομέα της έρευνας κατά του καρκίνου αφού μεταλλάξεις σε κομβικές πρωτεΐνες του διαταράσσουν την κανονική λειτουργία του με αποτέλεσμα τη δημιουργία νεοπλασιών. Η BRAF είναι μία πρωτεϊνική κινάση σερίνης θρεονίνης και ανήκει στην οικογένεια των RAF πρωτεϊνών που αποτελούν ρυθμιστές στο μονοπάτιMAPK. Μεταλλάξεις που οδηγούν σε συνεχή ενεργοποίηση του BRAF εντοπίζονται σε διαφόρους τύπους καρκίνου όπως το μελάνωμα (50%), ο καρκίνος του θυρεοειδούς (35-70%), ο καρκίνος του παχέoς εντέρου (5-20%), ο καρκίνος του ήπατος (~14%) και ο καρκίνος των ωοθηκών (~30%). Η μετάλλαξη BRAFV600E είναι η πιο συχνή μετάλλαξη οδηγώντας σε υπερενεργοποίηση του μονοπατιού και σε καρκινογένεση. Το Vemurafenib (Zelboraf) και το Dabrafenib (Tafinlar) αποτελούν τα δύο εγκεκριμένα φάρμακα, εκλεκτικοί αναστολείς της BRAFV600E που χορηγούνται για τη θεραπεία μεταστατικού ή μη χειρουργήσιμου μελανώματος που φέρει τη συγκεκριμένη μετάλλαξη. Η αποτελεσματικότητά τους όμως είναι περιορισμένη λόγω εμφάνισης αντίστασης αλλά και της επαγωγής νέων καρκίνων μέσω της παράδοξης ενεργοποίησης του MAPK μονοπατιού σε wt-BRAF κύτταρα που φέρουν ογκογενή μετάλλαξη σε πρωτεΐνες που προηγούνται της BRAF στο μονοπάτι (RAS, υποδοχείς κινάσες τυροσίνης). Αν και η χρήση συνδυαστικών θεραπειών έχει δώσει ορισμένα καλά αποτελέσματα, πρόσφατα αναπτύχθηκε μια νέα γενιά εκλεκτικών αναστολέων της BRAFV600E (PLX7904 και PLX8394) που φαίνεται να διαφεύγουν της παράδοξης ενεργοποίησης του MAPK (paradox breakers). Επιπλέον, οι αναστολείς αυτοί παρουσιάζουν αποτελεσματικότητα έναντι αρκετών μηχανισμών που εμφανίζουν ανθεκτικότητα και επί του παρόντος είναι σε στάδιο κλινικών μελετών. Στην συγκεκριμένη διπλωματική εργασία διενεργήθηκε εικονική σάρωση με την χρήση φαρμακοφόρων μοντέλων και τεχνικές μοριακής πρόσδεσης (molecular docking) στοχεύοντας στην εύρεση νέων αναστολέων της BRAFV600E με βελτιωμένο βιολογικό προφίλ. Η δημιουργία των φαρμακοφόρων μοντέλων στόχευσε στην διατήρηση των ισχυρότερων στοιχείων (features) των φαρμακοφόρων μοντέλων που δημιουργήθηκαν με βάση τo φάρμακο Dabrafenib και το paradox breaker plx7904. Τα φαρμακοφόρα μοντέλα επικυρώθηκαν μέσω μιας βιβλιοθήκη ενεργών και ανενεργών μορίων από την βάση δεδομένων ChEMBL και στη συνέχεια εφαρμόστηκαν στην εικονική σάρωση της βιβλιοθήκη μορίων ZINC (~12 εκατ. μόρια). Οι ενώσεις που επιλέχθηκαν με βάση τη βέλτιστη προσαρμογή τους στα φαρμακοφόρα μοντέλα ελέχθησαν ως προς την insilico πρόσδεσή τους στο ενεργό κέντρο της BRAFV600E με χρήση μιας σειράς αλγορίθμων μοριακής πρόσδεσης (Glide HTVS και SP και πρωτόκολλο IFD) ενώ στα φίλτρα που εφαρμόστηκαν συμπεριελήφθηκαι η μελέτη των ADME ιδιοτήτων τους. Η διαδικασία προέκρινε μια τελική ομάδα ενώσεων με δυνατότητα ανάπτυξης ισχυρών αλληλεπιδράσεων με τα κρίσιμα αμινοξέα του ενεργού κέντρου της πρωτεΐνης και ικανοποιητικές ADME ιδιότητες. Η προμήθεια των ενώσεων θα επιτρέψει την in vitro αξιολόγηση της ανασταλτικής τους δράσης και εκλεκτικότητας έναντι της BRAFV600E ενώ τα πλέον υποσχόμενα μόρια θα δοκιμαστούν σε κυτταρικές σειρές για την αποτελεσματικότητά τους.The mitogen-activated protein kinase (MAPK) signaling pathway which affects cell proliferation, apoptosis, migration and differentiation has attracted the attention of anticancer research since abnormal activation of the pathway components is often identified in human cancers. BRAF belongs to the RAF family of serine/threonine protein kinases which are key regulators of the MAPK cascade. Activating BRAF mutations are harbored in certain cancers as in melanoma (50%), thyroid cancer (35-70%), colorectal cancer (5-20%), liver cancer (~14%) and ovarian cancer (~30%). BRAF-V600E is the most frequent mutation leading to multiple and uncontrolled amplification of downstream signal with tumorigenesis as a result. Two selective BRAFV600E inhibitors, Vemurafenib (Zelboraf) and Dabrafenib (Tafinlar), have been already approved for the treatment of unresectable and metastatic BRAF mutated melanoma. However, their efficacy is limited due to intrinsic resistance or the development of acquired resistance. Besides, in the context of wild-type BRAF cells bearing upstream activation (RAS, receptor tyrosine kinase), treatment with BRAF-V600E inhibitors leads to the paradoxical enhancement of MAPK signaling, resulting in enhancement of wt-tumour growth and adverse effects. For that reason combined treatments are being tested with very good clinical outcomes. A new generation of BRAF V600E inhibitors (PLX7904 and PLX8394), being capable of overcoming the MAPK paradoxical activation, has been discovered recently and are currently in clinical investigations. In this thesis, we have conducted a virtual screening approach ,utilizing structure based pharmacophore modeling and in silico docking, towards the identification of novel, selective BRAFV600E inhibitors which potentially could be less prone to resistance and avoid the paradox enhancement of MAPK pathway in wt-BRAF cells. Pharmacophore model generation was based on the top-ranked features extracted from the respective models originated from the crystal complexes of BRAFV600E with the paradox breaker PLX7904 (pdb: 4xv1) and Dabrafenib (pdb: 4xv2). We validated our models by utilizing a library of actives and inactives recovered by ChEMBL database. ZINC database (12M compounds) was queried against the generated pharmacophore models and the selected compounds based on the pharmacophore fit score we refiltered according to a defined set of physicochemical properties. . The filtered compounds were evaluated for their in silico binding at the BRAFV600E active site using Glide HTVS and SP and Induced Fit Docking protocol.The best ranked molecules were further analysed for their drug-likeness properties. The process qualified a final dataset of molecules capable of developing strong interactions with the crucial amino acids of the binding site,and predicted to bear a satisfactory ADME profile. Our future plans include the purchase of the qualified molecules and the in vitro assessment of their inhibitory activity and selectivity against BRAFV600E