Multi-functional small molecules attached to an electrode surface can bind non-covalently to the redox enzyme fructose dehydrogenase (FDH) to ensure efficient electrochemical electron transfer (ET) and electrocatalysis of the enzyme in both mediated (MET) and direct (DET) ET modes. The present work investigates the potential of exploiting secondary, electrostatic and hydrophobic interactions between substituents on a small molecular bridge and the local FDH surfaces. Such interactions ensure alignment of the enzyme in an orientation favourable for both MET and DET. We have used a group of novel synthesized anthraquinones as the small molecule bridge, functionalised with electrostatically neutral, anionic, or cationic substituents. Particularly, we investigated the immobilisation of FDH on a nanoporous gold (NPG) electrode decorated with the novel synthesised anthraquinones using electrochemical methods. The best DET-capable fraction out of four anthraquinone derivatives tested is achieved for an anthraquinone functionalised with an anionic sulphonate group. Our study demonstrates, how the combination of chemical design and bioelectrochemistry can be brought to control alignment of enzymes in productive orientations on electrodes, a paradigm for thiol modified surfaces in biosensors and bioelectronics.