To assess a tumor biomarker like the cyclooxygenase-2 enzyme (COX-2), non-invasive imaging techniques are powerful tools. The (non-) linear optical properties of activatable fluorescent probes which are selectively bound to the biomarker can therefore be exploited. The here presented molecular modelling results based on multi-scale modelling techniques highlight the importance of the conformational versatility and of changes in the electronic interactions of such probes when they are embedded in water or in the COX-2 homodimer enzyme. The ANQIMC-6 probe, which combines the binding domain/scaffold of indomethacin (IMC) on COX-2 with the optical properties of acenaphtho[1,2-b]quinoxaline (ANQ), is found to be folded in the solvent and unfolded in the enzyme. A concerted movement of the probe and the protein is seen, while the rotational autocorrelation function exhibits also the intrinsic properties of the probe. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations are used to simulate the one-photon and two-photon absorption spectra along with the first hyperpolarizability. The transition has a local character in vacuum, but changes to a charge transfer one in the presence of the microenvironment of the enzyme. This is also visible through a change of the shape of the absorption spectrum, while at the same time the simulated signals of second harmonic generation experiments are strongly enhanced. The results of this work prove that an environment sensitive probe with an anchoring group and an optical active part can be constructed for use in absorption spectroscopy, without the need to revert to fluorescence experiments.