Characterization of the conformational ensemble from bioactive N-acylhydrazone derivatives Laercio Pol-Fachin a , Carlos Alberto Massour Fraga c,d , Eliezer J. Barreiro c,d , Hugo Verli a,b, * a Programa de Po ´s-Graduac ¸a ˜o em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonc ¸alves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil b Faculdade de Farma ´cia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre 90610-000, Rio Grande do Sul, RS, Brazil c Laborato ´rio de Avaliac ¸a ˜o e Sı´ntese de Substaˆncias Bioativas (LASSBio), Faculdade de Farma ´cia, Universidade Federal do Rio de Janeiro, PO Box 68023, Rio de Janeiro 21941-902, RJ, Brazil d Programa Po ´s-Graduac ¸a ˜o em Quı´mica, Instituto de Quı´mica, Universidade Federal do Rio de Janeiro, RJ, Brazil 1. Introduction An important strategy in medicinal chemistry efforts to develop new bioactive compounds is the identification of the pharmaco- phore, a structural framework that comprises stereoelectronic properties and three-dimensional characteristics necessary to the complexation of ligands to a specific target receptor [1] and, consequently, to initiate a set of activities. An example of such group may be found in the N-acylhydrazone (NAH) moiety, already shown to be related to a series of biological activities such as analgesic, anti-inflammatory, and platelet aggregation inhibition activities [2–10], as well as protozoa proteases inhibition [11], HIV- 1 reverse transcriptase dimmer destabilization [12], antibiotic and antifungal activities [13], and cardiovascular actions [14–18]. The prototype of this class of compounds, LASSBio-294, was first synthesized from natural safrole and identified as a potential alternative therapeutic for congestive heart failure due to a positive cardioinotropic effect through an interaction with the Ca 2+ uptake/release process of the sarcoplasmic reticulum [14,15,17]. More recently, a vasodilatory action was also observed [16]. These diverse biological activities appear to be related to the same pharmacophoric group (in each case, added by specific substituents), rendering to the NAH moiety the status of privileged structure [7]. However, its conformational characterization as a function of biological solutions and specific or non-specific target receptors is highly difficult to be obtained under experimental techniques, as NMR and X-ray crystallography, due to few inter- proton distances and potential crystal packing effects [19,20]. One strategy usually employed attempting to circumvent such limitations in the conformational description of bioactive com- pounds consists in performing a conformational analysis. While Journal of Molecular Graphics and Modelling 28 (2010) 446–454 ARTICLE INFO Article history: Received 9 June 2009 Received in revised form 15 October 2009 Accepted 21 October 2009 Available online 30 October 2009 Keywords: Conformational analysis GROMACS LASSBio-294 Molecular dynamics N-Acylhydrazone ABSTRACT The search for bioactive conformations from prototypes is mostly referenced on crystallographic ligand– receptor complexes, in which the molecule conformation is already caged inside its binding site. However, the complexation process is a thermodynamic event depending on both complexed and uncomplexed states. As ligand affinity originates from such equilibrium, the development of novel computational models capable of supplying data on ligand dynamics in biological solutions is potentially applicable in more efficient methods for prediction of compounds binding and affinity. In this context, the current work employs a series of molecular dynamics simulations on three N-acylhydrazone derivatives, already shown to present promising cardioinotropic and vasodilatory activities, in order to obtain a precise characterization of each compound conformational ensemble in aqueous solutions, instead of a single minimum energy conformation. Consequently, we were able to observe the influence of each functional group of the studied molecules on the conformation of the entire compounds and thus on the exposure of functional groups that might potentially bind to target receptors. Additionally, the differences between the molecules conformational behavior were characterized, supporting a spatial and temporal image of each ligand, which may be potentially correlated to their biological activities. So in the context of conformational selection, such strategy may represent a useful methodology to contribute in the choice of ligands conformations for both 3D-QSAR and docking calculations. ß 2009 Elsevier Inc. All rights reserved. * Corresponding author at: Faculdade de Farma ´ cia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre 90610-000, Rio Grande do Sul, RS, Brazil. Tel.: +55 51 3308 7770; fax: +55 51 3308 7309. E-mail address: hverli@cbiot.ufrgs.br (H. Verli). URL: http://www.cbiot.ufrgs.br/bioinfo Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journal homepage: www.elsevier.com/locate/JMGM 1093-3263/$ – see front matter ß 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2009.10.004