On the Simulation of Thermal Isomerization of Molecular Photoswitches in Biological Systems

Molecular photoswitches offer precise, reversible photocontrolover biomolecular functions and are promising light-regulated drugcandidates with minimal side effects. Quantifying thermal isomerizationrates of photoswitches in their target biomolecules is essential forfine-tuning their light-controlled drug activity. However, the effectsof protein binding on isomerization kinetics remain poorly understood,and simulations are crucial for filling this gap. Challenges in thesimulation include describing multireference electronic structuresnear transition states, disentangling competing reaction pathways,and sampling protein-ligand interactions. To overcome thesechallenges, we used multiscale simulations to characterize the thermalisomerization of photostatins (PSTs), which are light-regulated microtubuleinhibitors for potential cancer phototherapy. We employed a new abinitio multireference electronic structure method in a quantum mechanics/molecularmechanics setting and combined it with enhanced sampling techniquesto characterize the cis to trans free-energy profiles of three PSTs in a vacuum, aqueous solution,and tubulin dimer. The significant advantage of our novel approachis the efficient treatment of the multireference character in PSTs'electronic wavefunction throughout the conformational sampling ofprotein-ligand interactions along their isomerization pathways.We also benchmarked our calculations using high-level ab initio multireferenceelectronic structure methods and explored the competing isomerizationpathways. Notably, calculations in a vacuum and implicit solvent modelscannot predict the order of the PSTs' thermal half-lives inthe aqueous solution observed in the experiment. Only by explicitlytreating the solvent molecules can the correct order of isomerizationkinetics be reproduced. Protein binding perturbs free-energy barriersdue to hydrogen bonding between PSTs and nearby polar residues. Ourwork generates comprehensive, high-quality benchmark data and offersguidance for selecting computational methods to study the thermalisomerization of photoswitches. Ab initio multireference free-energycalculations in explicit molecular environments are crucial for predictingthe effects of substituents on the thermal half-lives of photoswitchesin biological systems.