A “quasi‐flexible” automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

The main purpose of this work is the development and validation of a general scheme based on a systematic and automatic “quasi‐flexible” docking approach for studying stereoselective recognition mechanisms. To achieve our goals we explore the conformational and configurational space for small‐ or medium‐size flexible molecules in a systematic way, seeking a method that is both reasonably accurate and relatively fast from the computational point of view. In particular, we have developed a general computational protocol for the global molecular interaction evaluation (“Glob‐MolInE”) to efficiently explore the orientational and conformational space of flexible selectors and selectands used in modern chiral high‐performance liquid chromatography (HPLC); the enantioselective binding of the selector (S)‐N‐(3,5‐dinitrobenzoyl)‐leucine‐ n‐propylamide (S)‐1 towards the selectand N‐(2‐naphthyl)‐alanine methyl ester 2 has been studied; the global minimum obtained for the homochiral associate [S(1)/S(2)] (Pop. >99%) is very close (RMS≃0.20) to the crystallographically determined structure. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 515–530, 2000

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