Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems

End-point free-energy methods as an indispensable component in virtual screening are commonly recognized as a tool with a certain level of screening power in pharmaceutical research. While a huge number of records could be found for end-point applications in protein-ligand, protein-protein, and protein-DNA complexes from academic and industrial reports, up to now, there is no large-scale benchmark in host-guest complexes supporting the screening power of end-point free-energy techniques. A good benchmark requires a data set of sufficient coverage of pharmaceutically relevant chemical space, a long-time sampling length supporting the trajectory approximation of the ensemble average, and a sufficient sample size of receptor-acceptor pairs to stabilize the performance statistics. In this work, selecting a popular family of macrocyclic hosts named cucurbiturils, we construct a large data set containing 154 host-guest pairs, perform extensive end-point sampling of several hundred nanosecond lengths for each system, and extract the free-energy estimates with a variety of end-point free-energy techniques, including the advanced three-trajectory dielectric-constant-variable regime proposed in our recent work. The best-performing end-point protocol employs GAFF2 for solute descriptions, the three-trajectory end-point sampling regime, and the MM/GBSA Hamiltonian in free-energy extraction, achieving a high ranking metrics of Kendall τ > 0.6, a Pearlman predictive index of ∼0.8, and a high scoring power of Pearson r > 0.8. The current project as the first large-scale systematic benchmark of end-point methods in host-guest complexes in academic publications provides solid evidence of the applicability of end-point techniques and direct guidance of computational setups in practical host-guest systems.

A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions

Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.

Standard Redox Potentials of Fe(III) Aqua Complexes Included into the Cavities of Cucurbit[ n]urils ( n = 6-8): A DFT Forecast

An approach for estimating at the DFT level of the standard redox potentials of the inclusion compounds based on Fe(III) and Fe(II) aqua complexes inside the cavities of cucurbit[ n]urils ( n = 6-8) has been proposed. These inclusion compounds were established to have compositions which can be described by the formulas [Fe(H₂O)₆]^3+/2+@CB[6] and [Fe(H₂O)₆·4H₂O]^3+/2+@CB[7,8]. Redox potentials E⁰ relative to the standard hydrogen electrode for the half-reaction Fe(III)/Fe(II) in the CB[ n] cavities calculated at the PBE/TZVP level within the molecular-continuum solvation model are 1.607, 0.949, and 0.847 V for n = 6, 7, and 8, respectively. The obtained values indicate a relative increase of the oxidative ability of Fe(III) aqua-ions in the cavities of the examined CB[ n], especially in CB[6], compared to the calculated value ( E⁰ = 0.786 V) for the same half-reaction in the bulk of aqueous solution. Possible causes of the detected trend are discussed. The calculations also showed that the Fe(III) aqua complex inside the CB[6] changes its magnetic properties, transforming into a low-spin state with a total spin S = 1/2, whereas for all other systems high-spin states in accord with the classical ligand field theory are realized.