Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host–guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more than 90% loss of activity of the wild-type G6PD. The crystal structure of G6PD reveals these mutations are located away from the active site, concentrating around the noncatalytic NADP+-binding site and the dimer interface. However, the molecular mechanisms of class I mutant dysfunction have remained elusive, hindering the development of efficient therapies. To resolve this, we performed integral structural characterization of five G6PD mutants, including four class I mutants, associated with the noncatalytic NADP+ and dimerization, using crystallography, small-angle X-ray scattering (SAXS), cryogenic electron microscopy (cryo-EM), and biophysical analyses. Comparisons with the structure and properties of the wild-type enzyme, together with molecular dynamics simulations, bring forward a universal mechanism for this severe G6PD deficiency due to the class I mutations. We highlight the role of the noncatalytic NADP+-binding site that is crucial for stabilization and ordering two β-strands in the dimer interface, which together communicate these distant structural aberrations to the active site through a network of additional interactions. This understanding elucidates potential paths for drug development targeting G6PD deficiency.

Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with aromatic or adamantane core and the CB7 host using molecular electron density derived non-bonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the minimal basis iterative stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound state. The resulting non-bonded force field parameters improve binding affinity prediction, especially for guests with adamantane core in which repulsive exchange and dispersion interactions to the host dominate.

Oxidative stress caused by infection, medication, food, and imbalance of metabolic cycles damages DNA and organelles, which may lead to cancer, blood disorders, and other serious diseases. Glucose‐6‐phosphate dehydrogenase (G6PD) is the rate‐limiting enzyme in the pentose phosphate pathway, which is essential for nucleotide, fatty acid, cholesterol, and hormone synthesis. In addition to those roles, G6PD reduces NADP+ to NADPH, which is crucial for reducing reactive oxygen species. Dysfunction of G6PD increases susceptibility to oxidative stress, especially in erythrocyte due to the lack of mitochondria, which is another source of NADPH. Interestingly, 400 million people worldwide have mutations on the g6pd gene, and the World Health Organization (WHO) has classified more than 160 missense mutations into five classes. The Class I G6PD deficiency is the most severe form; patients have less than 10% enzymatic activity of wild‐type G6PD and suffer from chronic non‐spherocytic hemolytic anemia. Here, we provide a new insight into the loss of activity in G6PD deficiency, based on the structure of the Class I pathogenic mutants of G6PD. We will discuss the structural basis of the Class I mutants of G6PD and its implications to various symptoms in G6PD deficiency. Support or Funding Information National Institutes of Health, R01 grant, HD084422; Japan Society for the Promotion of Science KAKENHI, Grant‐in Aid for Research Activity Start‐up, JP19K23713; University of Tsukuba; Stanford University; SLAC National Accelerator Laboratory