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Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in  E.   coli  to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value ( S )-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure to predict product chirality.    Results  Six enzymes originating from  Sulfolobus   sulfotaricus, Zygosaccharomyces   rouxii ,  Hansenula   polymorpha ,  Corynebacterium  sp. ST-10,  Synechococcus  sp. PCC 7942 and  Bacillus  sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole–cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using  E.   coli  over-expressing these enzymes yielded ( S )-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e.,  Z.   rouxii  ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565 (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of ( S ) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95% ( S )-specific alcohol with a chemical yield of 23–79% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85–99%.    Conclusions  Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials,  Zygosaccharomyces   rouxii  ketoreductase was identified as a proficient enzyme to obtain ( S )-specific alcohols from their respective ketones. The whole–cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield.    Electronic supplementary material  The online version of this article (10.1186/s12934-018-1036-2) contains supplementary material, which is available to authorized users.

A strategy to identify a ketoreductase that preferentially synthesizes pharmaceutically relevant (S)-alcohols using whole-cell biotransformation