Most online mobile services make use of location data to improve customer experience. Mobile users can locate points of interest near them, or can receive recommendations tailored to their whereabouts. However, serious privacy concerns arise when location data is revealed in clear to service providers. Several solutions employ Searchable Encryption (SE) to evaluate spatial predicates directly on location ciphertexts. While doing so preserves privacy, the performance overhead incurred is high. We focus on a prominent SE technique in the public-key setting – Hidden Vector Encryption (HVE), and propose a graph embedding technique to encode location data in a way that significantly boosts the performance of processing on ciphertexts. We show that finding the optimal encoding is NP-hard, and provide several heuristics that are fast and obtain significant performance gains. Our extensive experimental evaluation shows that our solutions can improve computational overhead by a factor of two compared to the baseline.