Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi (wBm) offers an unprecedented opportunity to identify new wolbachia drug targets. Genome analysis of the glycolytic/gluconeogenic pathway has revealed that wBm lacks pyruvate kinase (PK) and may instead utilize the enzyme pyruvate phosphate dikinase (PPDK; ATP: pyruvate, orthophosphate phosphotransferase, EC 2.7.9.1). PPDK catalyses the reversible conversion of AMP, PPi and phosphoenolpyruvate into ATP, Pi and pyruvate. Most organisms including mammals exclusively possess PK. Therefore the absence of PPDK in mammals makes this enzyme as attractive wolbachia drug target. In the present study we have modeled the three dimensional structure of wBm PPDK. The template with 50% identity and 67% similarity in amino acid sequence was employed for homology-modeling approach. The putative active site consists of His476, Arg360, Glu358, Asp344, Arg112, Lys43 and Glu346 was selected as site of interest for designing suitable inhibitor molecules. Docking studies were carried out using induced fit algorithms with OPLS force field of Schrödinger's Glide. The lead molecules which inhibit the PPDK activity are taken from the small molecule library (Pubchem database) and the interaction analysis showed that these compounds may inhibit the function of PPDK in wBm.