Binding affinities of cofactor and ligands to the active site of two different isoforms of lactate dehydrogenase (LDH), heart and skeletal muscles (H4 and M4, respectively), can be used for medical and biological applications. Herein, a hybrid QM/MM computational approach based on free energy perturbation methods has been carried out to estimate binding affinities and binding isotope effects (BIEs) for NADH/NAD(+) and oxamate, pyruvate, L-lactate, and D-lactate ligands to the M4 and H4 isoforms of L-LDH. Here, we show that determining how cofactor and ligands interact with the active site of LDH isoforms advanced the still open discussion on the intracellular lactate shuttle hypothesis. In our discussion we deny the key concept of this hypothesis showing, based on interaction energy values, that there is no evidence that the M4 type of LDH in the skeletal muscles cells served as a catalyst of the conversion of lactate to pyruvate. Additionally, theoretical determination of BIEs for H4 and M4 types of LDH shows that there is a way of using the BIEs as a tool capable to distinguish these isoforms, and for this purpose D-lactate labeled with deuterium in positions 11 or 7, 8, 9 ([11-2H]-BIE and [7,8,9-2H3]-BIE) or L-lactate labeled only in position 11 ([11-2H]-BIE) could be used. We propose the BIEs as a useful tool which can be applied in order to experimentally determine the types of LDH.