Three-dimensional quantitative structure activity relationship (3D QSAR) analysis was carried out on set of 56 N,N\u27-diarylsquaramides, N,N\u27-diarylureas and diaminocyclobutenediones in order to understand their antagonistic activities against CXCR2. The studies include comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Models with good predictive abilities were generated with CoMFA q2 = 0.709, r2 (non-cross-validated square of correlation coefficient) = 0.951, F value = 139.903, r2 bs = 0.978 with five components, standard error of estimate = 0.144 and the CoMSIA q2 = 0.592, r2 = 0.955, F value = 122.399, r2 bs = 0.973 with six components, standard error of estimate = 0.141. In addition, a homology model of CXCR2 was used for docking based alignment of the compounds. The most active compound then served as a template for the alignment of the remaining structures. Further, mapping of contours onto the active site validated each other in terms of residues involved with reference to the respected contours. This integrated molecular docking based alignment followed by 3D QSAR studies provided a further insight to support the structure-based design of CXCR2 antagonistic agents with improved activity profiles. Furthermore, in silico screening was adapted to the QSAR model in order to predict structures of new, potentially active compounds.
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