Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium

Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 A X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.

Functional, structural and molecular plasticity of mammalian skeletal muscle in response to exercise stimuli

Biological systems have acquired effective adaptive strategies to cope with physiological challenges and to maximize biochemical processes under imposed constraints. Striated muscle tissue demonstrates a remarkable malleability and can adjust its metabolic and contractile makeup in response to alterations in functional demands. Activity-dependent muscle plasticity therefore represents a unique model to investigate the regulatory machinery underlying phenotypic adaptations in a fully differentiated tissue. Adjustments in form and function of mammalian muscle have so far been characterized at a descriptive level, and several major themes have evolved. These imply that mechanical, metabolic and neuronal perturbations in recruited muscle groups relay to the specific processes being activated by the complex physiological stimulus of exercise. The important relationship between the phenotypic stimuli and consequent muscular modifications is reflected by coordinated differences at the transcript level that match structural and functional adjustments in the new training steady state. Permanent alterations of gene expression thus represent a major strategy for the integration of phenotypic stimuli into remodeling of muscle makeup. A unifying theory on the molecular mechanism that connects the single exercise stimulus to the multi-faceted adjustments made after the repeated impact of the muscular stress remains elusive. Recently, master switches have been recognized that sense and transduce the individual physical and chemical perturbations induced by physiological challenges via signaling cascades to downstream gene expression events. Molecular observations on signaling systems also extend the long-known evidence for desensitization of the muscle response to endurance exercise after the repeated impact of the stimulus that occurs with training. Integrative approaches involving the manipulation of single factors and the systematic monitoring of downstream effects at multiple levels would appear to be the ultimate method for pinpointing the mechanism of muscle remodeling. The identification of the basic relationships underlying the malleability of muscle tissue is likely to be of relevance for our understanding of compensatory processes in other tissues, species and organisms.

The impact of structural conditions in communes on sports behaviour of adolescents and young adults in Switzerland

Young peoples’ sport activity in Switzerland differs considerably depending on the linguistic region (Lamprecht, Fischer, & Stamm, 2008). This appears to be based on cultural as well as on structural differences. The question then arises how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland cause variation in sport behaviour. Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio-cultural factors in which a person is socially embedded. In two case studies, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 25 year old inhabitants (N = 205) living in a German and French speaking commune were questioned about their sports participation in and outside of their commune, as well as their perception of sport-related structural characteristics in their commune. To collect information about communes’ sport facilities, the sport providers (N = 23) were interviewed. Sport-related characteristics of the communes were also collected through two interviews with representatives of the municipal administration. As expected, sport participation is significantly lower in the French speaking commune (Chi2 (1, N = 205) = 3.84, p < .05). Adolescents and young adults living in the French speaking commune are less satisfied with the sport infrastructure (F(1,135) = 9.65, p < .01) and evaluate the opportunities to be physically active in their commune significantly worse (F(1,144) = 15.33, p < .01) than their German-speaking counterparts. These first findings show the impact of structural conditions in communes on sport participation of adolescents and young people. However, it must be noted that this study is explorative and further communes would need to be examined in order to generalize the results. References Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Belknap. Lamprecht, M., Fischer, A. & Stamm, H. (2008). Sport Schweiz 2008. Das Sportverhalten der Schweizer Bevölkerung. Magglingen: BASPO.

The impact of structural conditions in communes on physical activity and sports behaviour of adolescents and young adults in Switzerland

Introduction The physical activity of the Swiss population differs considerably depending on the linguistic region. German speakers are more often physically active than people living in the French- or Italian-speaking part of Switzerland (Stamm & Lamprecht, 2008). This study analyses how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland correlate with physical activity and sports participation for adolescents and young adults. Methodological approach Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio-cultural factors in which a person is socially embedded. In two case studies, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 25 year old inhabitants (N = 205) living in a German- and French-speaking commune were questioned about their sports participation in and outside of their commune, as well as their perception of sport-related structural characteristics in their commune. To collect information about communes’ sport facilities, the sport providers (N = 23) were interviewed. Sport-related characteristics of the communes were also collected through two interviews with representatives of the municipal administration. Results and discussion Physical activity is significantly higher (Chi2 (1, N = 183) = 4.78, p < .05) and sport participation is significantly lower in the French speaking commune (Chi2 (1, N = 205) = 3.84, p < .05). Adolescents and young adults in the French speaking commune (M = 3.15, SD = 1.23) are less satisfied with the opportunities to be physically active in the environment than their counterparts living in the German speaking commune (p < .001, Mann-Whitney U – test). These first findings show the impact of structural conditions in communes on physical activity and sport participation of adolescents and young people. However, it must be noted that this study is explorative and further communes would need to be examined in order to generalize the results. References Coleman J S (1990). Foundations of social theory. Belknap, Cambridge, MA. Stamm H, Lamprecht M (2008). EJSS, 8(1+2), 15-29.

The impact of structural conditions in communes on sports behaviour of adolescents and young adults in Switzerland

Young peoples’ sport activity differs considerably depending on the linguistic region in Switzerland (Lamprecht, Fischer, & Stamm, 2014). This appears to be based on cultural as well as on structural differences. The question then arises how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland cause variation in sport behaviour. Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio - cultural factors in which a person is socially embedded . In 33 municipalities of the German and French speaking region of Switzerland, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 30 year old inhabitants (N=3677) were questi oned about their sports participation, as well as their perception of sport - related structural characteristics in their commune. To collect information about communes’ sport facilities, sport providers as well as representatives of the municipal administra tion were interviewed and document analyses were conducted. Representatives of the municipal administration attach more importance to sport promotion in the German speaking than in French - speaking municipalities. Young people living in the French speaking commune are less satisfied with the sport facilities (F(1,3266)=31.31, p<.01) and they are less physically active than their German - speaking counterparts (Chi2(1,N=3537)=22.51, p<.05). These first findings show the impact of structural conditions in commun es on sport participation of adolescents and young people. However, further multilevel analyses will be conducted for a better understanding of correlations between structural conditions and different sports behaviour of young people. References Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Belknap. Lamprecht, M., Fischer, A. & Stamm, H. (2014). Sport Schweiz 2014. Sportaktivität und Sportinteresse der Schweizer Bevölkerung. Magglingen: BASPO.