Redesign of a thioflavin-T-binding protein with a flat ß-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity.

Amyloids, proteinous aggregates with ß-sheet-rich fibrils, are involved in several neurodegenerative diseases such as Alzheimer's disease; thus, their detection is critically important. The most common fluorescent dye for amyloid detection is thioflavin-T (ThT), which shows on/off fluorescence upon amyloid binding. We previously reported that an engineered globular protein with a flat ß-sheet, peptide self-assembly mimic (PSAM), can be used as an amyloid binding model. In this study, we further explored the residue-specific properties of ThT-binding to the flat ß-sheet by introducing systematic mutations. We found that site-specific mutations at the ThT-binding channel enhanced affinity. We also evaluated the binding of a ThT-based photocatalyst, which showed the photooxygenation activity on the amyloid fibril upon light radiation. Upon binding of the photocatalyst to the PSAM variant, singlet oxygen-generating activity was observed. The results of this study expand our understanding of the detailed binding mechanism of amyloid-specific molecules.

RISMiCal: A software package to perform fast RISM/3D-RISM calculations.

Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.

Solvent Distribution Effects on Quantum Chemical Calculations with Quantum Computers.

We present a combination of three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) theory and the variational quantum eigensolver (VQE) to consider the solvent distribution effects within the framework of quantum-classical hybrid computing. The present method, 3D-RISM-VQE, does not include any statistical errors from the solvent configuration sampling owing to the analytical treatment of the statistical solvent distribution. We apply 3D-RISM-VQE to compute the spatial distribution functions of solvent water around a water molecule, the potential and Helmholtz energy curves of NaCl, and to analyze the Helmholtz energy component and related properties of H2O and NH4+. Moreover, we utilize 3D-RISM-VQE to analyze the extent to which solvent effects alter the efficiency of quantum calculations compared with calculations in the gas phase using the L1-norms of molecular electronic Hamiltonians. Our results demonstrate that the efficiency of quantum chemical calculations on a quantum computer in solution is virtually the same as that in the gas phase.

Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory.

Mixing Gibbs energy and phase equilibria of aqueous solutions of polyglycine were studied theoretically by means of polymer reference interaction site model integral equation theory combined with the Gibbs-Duhem method. In addition to the ordinary liquid-liquid phase separation between dilute and concentrated solutions, the theoretical calculation predicted the coexistence of two coacervate phases, namely, the lower- and higher-density coacervates. The relative thermodynamic stabilities of these two phases change with the polymerization degree of polyglycine. The higher-density coacervate phase was rapidly stabilized by increasing the polymer length, and the lower-density phase became metastable at large polymers. The hydrogen bonds between the peptide chains were strengthened, and water was thermodynamically destabilized in the higher-density coacervate. A possible relation with the formation of amyloid fibril within a liquid droplet is also discussed.

Effects of intramolecular chain conformation on the hydration and miscibility of polyethylene glycol in water studied by means of polymer reference interaction site model theory.

To examine the conventional idea that the gauche conformation of the OCCO dihedral angle promotes the dissolution of polyethylene glycol (PEG) in water through strong hydration, the thermodynamic properties of liquid mixtures of PEG and water were studied by means of polymer reference interaction site model (PRISM) theory. The intramolecular correlation functions required as input for PRISM theory were calculated by the generator matrix method, accompanied by changes in the distribution of dihedral angles. In the infinite dilution limit, the increased probability of gauche conformation of the OCCO dihedral angles stabilizes the hydration of PEG through enhanced hydrogen bonding between the ether oxygen of PEG and water. The mixing Gibbs energies of the liquid mixtures were also calculated in the whole concentration range based on the Gibbs-Duhem equation, as per our recent proposal. A liquid-liquid phase separation was observed when all the dihedral angles of PEG were in the trans conformation; for the liquid mixture to be miscible in the whole concentration range, the introduction of the OCCO gauche conformation was found to be indispensable. The above theoretical results support the conventional idea that the OCCO gauche conformation is important for the high miscibility of PEG and water.

Tuning the ATP-ATP and ATP-disordered protein interactions in high ATP concentration by altering water models.

The adenosine triphosphate (ATP)-protein interactions have been of great interest since the recent experimental finding of ATP's role as a hydrotrope. The interaction between ATP and disordered proteins is fundamental to the dissolution of protein aggregates and the regulation of liquid-liquid phase separation by ATP. Molecular dynamics simulation is a powerful tool for analyzing these interactions in molecular detail but often suffers from inaccuracies in describing disordered proteins and ATPs in high concentrations. Recently, several water models have been proposed to improve the description of the protein-disordered states, yet how these models work with ATP has not been explored. To this end, here, we study how water models affect ATP and alter the ATP-ATP and ATP-protein interactions for the intrinsically disordered protein, α-Synuclein. Three water models, TIP4P-D, OPC, and TIP3P, are compared, while the protein force field is fixed to ff99SBildn. The results show that ATP over-aggregates into a single cluster in TIP3P water, but monomers and smaller clusters are found in TIP4P-D and OPC waters. ATP-protein interaction is also over-stabilized in TIP3P, whereas repeated binding/unbinding of ATP to α-Synuclein is observed in OPC and TIP4P-D waters, which is in line with the recent nuclear magnetic resonance experiment. The adenine ring-mediated interaction is found to play a major role in ATP-ATP and ATP-protein contacts. Interestingly, changing Mg2+ into Na+ strengthened the electrostatic interaction and promoted ATP oligomerization and ATP-α-Synuclein binding. Overall, this study shows that changing the water model can be an effective approach to improve the properties of ATP in high concentration.

Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes.

The role of water in host-ligand binding was investigated using a combination of molecular dynamics simulation and three-dimensional reference interaction site model theory. Three different hosts were selected (CB6, CB7, and CB8). Six organic molecules were used as representative ligands: dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetone, 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), cyclopentanone (CPN), and pyrrole. From the binding free energy and its components, we divided the ligands into two groups: those with relatively small molecular size (DMSO, DMF, acetone, and pyrrole) and those with relatively large molecular size (DBO and CPN). We established that the solvent water in the CB6 cavity can be completely displaced by small ligands, resulting in a greater binding affinity compared with larger CBs, except in the case of the small pyrrole ligand, due to outstanding intrinsic properties such as the relatively high hydrophobicity and low dipole moment. In the case of the large ligands, the solvent water can be displaced by DBO and CPN in both CB6 and CB7; there were similar tendencies in their binding affinities, with the greatest affinity in the CB7 complexes. However, the tendencies of the binding affinity components are completely different due to the difference between the complex structure and the solvation structure when a ligand binds with a CB structure. The binding affinities suggest that the size fit between the ligand and CB cannot guarantee the greatest binding affinity gain because the binding structure and intrinsic properties of CB and ligand equally play a crucial role.

Phase equilibrium of three-component liquid systems composed of water, alcohol, and sodium chloride studied by the reference interaction-site model integral equation theory.

A theoretical method for calculating the thermodynamic properties and phase equilibria of a binary liquid mixture using the reference interaction-site model (RISM) integral equation theory, which we had proposed recently, was extended to ternary liquid systems containing salt. A novel dielectric correction of the RISM theory for a mixture of solvents was also proposed. The theory was applied to mixtures composed of water, alcohol, and NaCl, where the alcohol was either methanol or ethanol. The decrease in NaCl solubility with increasing alcohol molar fractions in the solvent was calculated. In the ethanol system, the theory yielded salt-induced liquid-liquid phase separation, which was observed experimentally in a ternary mixture of water, 1-propanol, and NaCl. The phase diagram of the ternary system was determined theoretically.

Fulminant Type 1 Diabetes Mellitus Caused by Long-Term Nivolumab Administration Followed by Nivolumab plus Cabozantinib Combination.

Nivolumab, an immune checkpoint inhibitor (ICI), is now used to treat many advanced cancers, including non-small cell lung cancer (NSCLC) and renal cancer. Immune-related adverse events are characteristic side effects of ICIs. Among them, fulminant type 1 diabetes mellitus is an infrequent but potentially life-threatening and clinically significant concern. Cabozantinib is known as a multikinase inhibitor. In recent years, combination therapy with nivolumab and cabozantinib has begun to be used to treat renal cell carcinoma. A 74-year-old man with no history of diabetes was treated with nivolumab for 5 years for NSCLC, followed by the combination of nivolumab and cabozantinib for clear cell renal cell carcinoma. He was diagnosed with fulminant type 1 diabetes 5 weeks after starting combination therapy, with symptoms of nausea and dry mouth. He was admitted to the intensive care unit and improved clinically with continuous insulin infusion and saline. The involvement of cabozantinib in the development of fulminant type 1 diabetes with long-term nivolumab use, which has not been reported previously, is unknown, but caution may be necessary in terms of glycemic control in combination therapy with nivolumab and cabozantinib.

Solvent effects in four-component relativistic electronic structure theory based on the reference interaction-site model.

A combined method of the Dirac-Hartree-Fock (DHF) method and the reference interaction-site model (RISM) theory is reported; this is the initial implementation of the coupling of the four-component relativistic electronic structure theory and an integral equation theory of molecular liquids. In the method, the DHF and RISM equations are solved self-consistently, and therefore the electronic structure of the solute, including relativistic effects, and the solvation structure are determined simultaneously. The formulation is constructed based on the variational principle with respect to the Helmholtz energy, and analytic free energy gradients are also derived using the variational property. The method is applied to the iodine ion (I- ), methyl iodide (CH3 I), and hydrogen chalcogenide (H2 X, where X = O-Po) in aqueous solutions, and the electronic structures of the solutes, as well as the solvation free energies and their component analysis, solvent distributions, and solute-solvent interactions, are discussed.

Study of phase equilibria and thermodynamic properties of liquid mixtures using the integral equation theory: Application to water and alcohol mixtures.

A theoretical method for calculating the thermodynamic properties and phase equilibria of liquid-liquid mixtures using the integral equation theory is proposed. The solvation chemical potentials of the two components are evaluated by the integral equation theory and the isothermal-isobaric variation of the total density with composition is determined to satisfy the Gibbs-Duhem relation. Given the density of a pure component, the method can calculate the densities of the mixture at any composition. Furthermore, it can treat the phase equilibrium without thermodynamic inconsistency with respect to the Gibbs-Duhem relation. This method was combined with the reference interaction-site model integral equation theory and applied to mixtures of water + 1-alcohol by changing the alcohol from methanol to 1-butanol. The destabilization of the mixing Gibbs energy by increasing the hydrophobicity of the alcohol and demixing of the water-butanol mixture were reproduced. However, quantitative agreement with experiments is not satisfactory, and further improvements of the integral equation theory and the molecular models are required.

Clinical efficacy of osimertinib in EGFR-mutant non-small cell lung cancer with distant metastasis.

BACKGROUND: Osimertinib-the third-generation epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI)-has been widely used as a first-line treatment for patients with metastatic EGFR-mutant non-small cell lung cancer (NSCLC). Osimertinib demonstrated central nervous system activity in patients with brain metastasis; however, its efficacy against other distant metastatic organs, including bone and liver, remains unclear. Therefore, we retrospectively analyzed the clinical efficacy of osimertinib in these patients in comparison to other EGFR-TKIs. METHODS: Clinical data of patients with advanced NSCLC receiving gefitinib/erlotinib (n = 183), afatinib (n = 55), or osimertinib (n = 150) at five medical institutions were retrospectively assessed for progression-free survival (PFS), overall survival (OS), and best overall response rate (ORR). RESULTS: In univariate and multivariate analyses, most distant metastases, including the brain and bone, were unrelated to the therapeutic efficacy of osimertinib, although liver metastasis and L858R mutation were independently associated with shorter PFS. PFS and OS in patients with liver metastases were significantly shorter than those in patients without liver metastases (PFS: 7.4 vs. 19.7 months, OS: 12.1 months vs. not reached, respectively). Osimertinib provided significantly longer PFS in patients with brain or bone metastasis and exon 19 deletion than the other EGFR-TKIs. The PFS of patients with liver metastases was not significantly different among the three EGFR-TKI groups. Furthermore, the ORR of osimertinib in patients with liver metastases was significantly attenuated, and the effectiveness was similar to 1st- or 2nd -generation EGFR-TKIs. CONCLUSION: Osimertinib provided better clinical benefits than 1st- and 2nd-generation EGFR-TKIs for patients with EGFR-mutant NSCLC, particularly those with brain or bone metastases and exon 19 deletion; however, its efficacy against liver metastasis was remarkably attenuated. New therapeutic developments for patients with EGFR-mutant NSCLC with liver metastases are needed.

Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory.

The binding process of angiotensin-converting enzyme 2 (ACE2) to the receptor-binding domain (RBD) of the severe acute respiratory syndrome-like coronavirus 2 spike protein was investigated using molecular dynamics simulation and the three-dimensional reference interaction-site model theory. The results suggested that the protein-binding process consists of a protein-protein approaching step, followed by a local structural rearrangement step. In the approaching step, the interprotein interaction energy decreased as the proteins approached each other, whereas the solvation free energy increased. As the proteins approached, the glycan of ACE2 first established a hydrogen bond with the RBD. Thereafter, the number of interprotein hydrogen bonds increased rapidly. The solvation free energy increased because of the desolvation of the protein as it approached its partner. The spatial distribution function of the solvent revealed the presence of hydrogen bonds bridged by water molecules on the RBD-ACE2 interface. Finally, principal component analysis revealed that ACE2 showed a pronounced conformational change, whereas there was no significant change in RBD.

＜Editors' Choice＞ Effects of high-flow nasal cannula oxygen therapy on oral intake of do-not-intubate patients with respiratory diseases.

High-flow nasal cannula (HFNC) oxygen therapy is used widely for hypoxemic respiratory failure. However, it is unknown whether the use of HFNC is compatible with retaining the ability to eat and drink of patients with end-stage respiratory diseases as a part of palliative care. A retrospective study was conducted on subjects with hypoxic respiratory failure due to end-stage respiratory diseases, including interstitial pneumonia and malignant respiratory diseases, who were treated with HFNC or reservoir mask oxygen therapy and died with do-not-resuscitate (DNR) and do-not-intubate (DNI) status. We compared the duration of eating solids and drinking liquids and clinical variables in the HFNC group with those in the reservoir mask group. The data from a total 43 subjects including 20 with HFNC and 23 with a reservoir mask were analyzed. Fitting HFNC to subjects temporarily improved oxygenation. Durations of survival, eating solids, and drinking liquids in the HFNC group were significantly longer than those in the reservoir mask group. No significant adverse effects were observed in either group. In conclusion, the use of HFNC led to prolonged survival while preserving the ability of oral intake in patients with DNR and DNI status.

Temperature-responsive morphology formation of a PS-b-PI copolymer: a dissipative particle dynamics simulation study.

Self-assembly responsiveness to stimuli of polystyrene-block-polyisoprene (PS-b-PI) diblock copolymer materials is explored by means of classical molecular dynamics (MD) and dissipative particle dynamics (DPD) simulations. A concerted relationship between the parameters achieved from atomistic and DPD simulations is obtained for this molecular recognition as clearly pronounced in a phase transition. Effects of temperature, model size and composition on the morphological formation were systematically investigated for the diblock copolymeric system. Structural changes resulting in the evolution of rheology as well as an equilibrium ordered structure were analyzed in terms of order parameters and radial distribution functions. From our models, various morphologies were observed including discrete clusters (sphere-liked morphology), connected clusters (gyroid-liked morphology), hexagonally packed cylinders (HEX), connected cylinders, irregular cylinders, perfect lamellae, perforated lamellae and defected lamellae. Based on this finding, a bottom-up multi-scale simulation of the PS-b-PI diblock copolymer provides a link between equilibrium copolymeric morphologies and the crucial parameters.

Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory.

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

A computational method to simulate global conformational changes of proteins induced by cosolvent.

A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three-dimensional reference interaction site model (3D-RISM) theory, which is referred to as the LRPF/3D-RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D-RISM. The proposed method is applied to the urea-induced denaturation of ubiquitin. The LRPF/3D-RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 µs standard MD simulation. The obtained LRPF/3D-RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.

Solvation dynamics in electronically polarizable solvents: Theoretical treatment using solvent-polarizable three-dimensional reference interaction-site model theory combined with time-dependent density functional theory.

The theory of solvation structure in an electronically polarizable solvent recently proposed by us, referred to as the "solvent-polarizable three-dimensional reference interaction-site model theory," is extended to dynamics in this study through the combination with time-dependent density functional theory. Test calculations are performed on model charge-transfer systems in water, and the effects of electronic polarizability on solvation dynamics are examined. The electronic polarizability slightly retards the solvation dynamics. This is ascribed to the decrease in the curvature of the nonequilibrium free energy profile along the solvation coordinate. The solvent relaxation is bimodal, and the faster and the slower modes are assigned to the reorientational and the translational modes, respectively, as was already reported by the surrogate theory combined with the site-site Smoluchowski-Vlasov equation. The relaxation path along the solvation coordinate is a little higher than the minimum free energy path because the translational mode is fixed in the time scale of the reorientational relaxation.

Nonequilibrium free-energy profile of charge-transfer reaction in polarizable solvent studied using solvent-polarizable three-dimensional reference interaction-site model theory.

The effects of the electronic polarization of solvent on the nonequilibrium free-energy profiles of charge-transfer reactions were studied using integral equation theory. Employing the solvent-polarizable three-dimensional reference interaction-site model theory, recently proposed by us, we first present a theoretical formalism that gives the free-energy profile in polarizable solvents. We then perform numerical calculations on three model systems. We demonstrate that electronic polarization of the solvent alters the solvent reorganization energy in two different ways. The first is the reorganization of the equilibrium solvation structure through the modification of the solute-solvent interaction, and the second is the stabilization of the nonequilibrium solvent fluctuation through the electronic polarization. The former increases, whereas the latter decreases the reorganization energy. In our model calculations, the solvent reorganization energy is reduced because the latter makes a larger contribution than does the former.

Residue-Specific Binding Mechanisms of Thioflavin T to a Surface of Flat ß-Sheets within a Peptide Self-Assembly Mimic.

Thioflavin T (ThT) is a popular fluorescent dye for detecting amyloid, a protein aggregate with a ß-sheet-rich structure that causes many neurodegenerative diseases. Despite the dye's popularity, a detailed understanding of its molecular binding mechanism remains elusive. We previously reported a protein model that can bind ThT on a single-layer ß-sheet and revealed that a channel formed by aromatic rings with a confined length enhanced ThT binding. One of the mutants of the model system, 5-YY/LL, showed the highest affinity with a low micromolar dissociation constant. Here, we investigate the residue-specific mechanism of binding of ThT to 5-YY/LL. We introduced tyrosine to phenylalanine and tyrosine to histidine mutations into the channel. The mutants revealed that the fifth position of tyrosine (Y5) is important for binding of ThT. Positive charges introduced by histidine under a low-pH condition at the channel repel the binding of cationic ThT. Furthermore, we found a positive to negative conversion in the vicinity of the binding channel increases ThT fluorescence 4-fold. A detailed understanding of the ThT binding mechanism will enhance our ability to develop amyloid-specific small molecules.