The results reported here demonstrate that the joint sMD/MSM protocol can be used to discriminate allosteric inhibitors from non-functional binders. They provide an inverse view of how this workflow could be applied in a computer-aided drug design (CADD) project. The most potent allosteric PTP1B inhibitor reported in the literature (1) was analysed and subsequently deconstructed into a less potent variant 2 . The MSM model for 1 suggest potent inhibition in agreement with literature data. Reliable analysis of compound 2 requires the use of restraints to prevent spontaneous unbinding during MD simulations. The judicious use of distance restraints provides information on what interactions are important in the activity of compounds 1 and suggests which vectors could be grown or changed to achieve the desired functional results. Similarly, compound 3 is deconstructed into 3u by replacing a covalent link with an in silico distance restraint, causing a decrease in inhibition. These different strategies to enforce proximity with PTP1B have a significant effect on the conformation of the ligand, and the interactions that are formed with the protein. Compound 4 behaves similarly to 3u, demonstrating how the protocol may be used to profile compounds with unknown allosteric potential. Further developing 3u or 4 to behave more like covalently linked 3 (such as moving the compound 4 acetyl group around the benzene ring) could lead to increased efficacy as allosteric inhibitors. Through modelling active state probabilities via MSMs, these binding pose changes can be related to protein activity.