Molecular-Level Structural Analysis of siRNA-Loaded Lipid Nanoparticles by 1H NMR Relaxometry: Impact of Lipid Composition on Their Structural Properties.

1H NMR relaxometry was applied for molecular-level structural analysis of siRNA-loaded lipid nanoparticles (LNPs) to clarify the impact of the neutral lipids, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol, on the physicochemical properties of LNP. Incorporating DSPC and cholesterol in ionizable lipid-based LNP decreased the molecular mobility of ionizable lipids. DSPC reduced the overall molecular mobility of ionizable lipids, while cholesterol specifically decreased the mobility of the hydrophobic tails of ionizable lipids, suggesting that cholesterol filled the gap between the hydrophobic tails of ionizable lipids. The decrease in molecular mobility and change in orientation of lipid mixtures contributed to the maintenance of the stacked bilayer structure of siRNA and ionizable lipids, thereby increasing the siRNA encapsulation efficiency. Furthermore, NMR relaxometry revealed that incorporating those neutral lipids enhanced PEG chain flexibility at the LNP interface. Notably, a small amount of DSPC effectively increased PEG chain flexibility, possibly contributing to the improved dispersion stability and narrower size distribution of LNPs. However, cryogenic transmission electron microscopy represented that adding excess amounts of DSPC and cholesterol into LNP resulted in the formation of deformed particles and demixing cholesterol within the LNP, respectively. The optimal lipid composition of ionizable lipid-based LNPs in terms of siRNA encapsulation efficiency and PEG chain flexibility was rationalized based on the molecular-level characterization of LNPs. Moreover, the NMR relaxation rate of tertiary amine protons of ionizable lipids, which are the interaction site with siRNA, can be a valuable indicator of the encapsulated amount of siRNA within LNPs. Thus, NMR-based analysis can be a powerful tool for efficiently designing LNP formulations and their quality control based on the molecular-level elucidation of the physicochemical properties of LNPs.

Proton Hyperpolarization Relay from Nanocrystals to Liquid Water.

Dynamic nuclear polarization (DNP) using transient electron spin polarization generated by photoexcitation can improve nuclear magnetic resonance (NMR) sensitivity far beyond the thermal equilibrium limit for analysis in life science and drug discovery. However, DNP of liquid water at room temperature remains an important challenge. Here, we propose a new method called hyperpolarization relay, in which the nonequilibrium polarization of electron spins is transferred to proton spins in the nanocrystals and then to proton spins in bulk water. Molecular nanocrystals doped with a polarizing agent that generates a highly polarized photoexcited triplet are synthesized by a reprecipitation method while controlling the size of the nanocrystals. The triplet-DNP sequence of repeated laser and microwave irradiation enhances the NMR signal of bulk water as well as nanocrystals. The smaller size of the nanocrystals increases the efficiency of polarization transfer from the nanocrystals to water due to the increased surface area. A series of control experiments and simulations based on Solomon equations confirmed the hyperpolarization relay mechanism.

Triplet Dynamic Nuclear Polarization of Guest Molecules through Induced Fit in a Flexible Metal-Organic Framework.

Dynamic nuclear polarization utilizing photoexcited triplet electrons (triplet-DNP) has great potential for room-temperature hyperpolarization of nuclear spins. However, the polarization transfer to molecules of interest remains a challenge due to the fast spin relaxation and weak interaction with target molecules at room temperature in conventional host materials. Here, we demonstrate the first example of DNP of guest molecules in a porous material at around room temperature by utilizing the induced-fit-type structural transformation of a crystalline yet flexible metal-organic framework (MOF). In contrast to the usual hosts, 1 H spin-lattice relaxation time becomes longer by accommodating a pharmaceutical model target 5-fluorouracil as the flexible MOF changes its structure upon guest accommodation to maximize the host-guest interactions. Combined with triplet-DNP and cross-polarization (CP), this system realizes an enhanced 19 F NMR signal of guest target molecules.

Design Guidelines to Elongate Spin-Lattice Relaxation Times of Porphyrins with Large Triplet Electron Polarization.

The spin-polarized triplet state generated by light irradiation has potential for applications such as triplet dynamic nuclear polarization (triplet-DNP). Recently, we have reported free-base porphyrins as versatile and biocompatible polarizing agents for triplet-DNP. However, the electron polarization of free-base porphyrins is not very high, and the dilemma is that the high polarization of metalloporphyrins is accompanied by a too short spin-lattice relaxation time to be used for triplet-DNP. We report here that the introduction of electron-withdrawing fluorine groups into Zn porphyrins enables a long enough spin-lattice relaxation time (>1 µs) while maintaining a high polarization (Px:Py:Pz = 0:0:1.0) at room temperature. Interestingly, the spin-lattice relaxation time of Zn porphyrin becomes much longer by introducing fluorine substituents, whereas the spin-lattice relaxation time of free-base porphyrin becomes shorter by the fluorine substitution. Theoretical calculations suggest that this is because the introduction of the electron-withdrawing fluorine substituents reduces the spin density on Zn atoms and weakens the spin-orbit interaction.

Fgf- and Bmp-signaling regulate gill regeneration in Ambystoma mexicanum.

Gill regeneration has not been well studied compared to regeneration of other appendages, such as limb and tail regeneration. Here, we focused on axolotl gill regeneration and found that Fgf- and Bmp-signaling are involved in their gill regeneration mechanism. Axolotls have three pairs of gill rami, and each gill ramus has multiple gill filaments. The gills consist of mesenchyme rich in extracellular matrix and epidermis. The gill nerves are supplied from the trigeminal ganglia located in the head. Denervation resulted in no gill regeneration responses. Nerves and gills express Bmp and Fgf genes, and treating animals with Fgf- and Bmp-signaling inhibitors results in phenotypes similar to those seen in denervated gills. Inducing an accessory appendage is a standard assay in amphibian regeneration research. In our study, an accessory gill could be induced by lateral wounding, suggesting that thin axon fibers and mesenchymal Fgfs and Bmps contributed to the induction of the accessory structure. Such accessory gill induction was inhibited by the denervation. Exogenous Fgf2+Fgf8+Bmp7, which have been determined to function as a regeneration inducer in urodele amphibians, could compensate for the effects denervation has on accessory blastema formation. Our findings suggest that regeneration of appendages in axolotls is regulated by common Fgf- and Bmp-signaling cascades.

Triplet dynamic nuclear polarization of nanocrystals dispersed in water at room temperature.

While dynamic nuclear polarization using photo-excited triplet electrons (triplet-DNP) can improve the sensitivity of nuclear magnetic resonance at room temperature, it has not been carried out in water. Here, we report the first example of triplet-DNP in water by downsizing the conventional bulk crystals to nanocrystals.

Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path.

The formulation of active pharmaceutical ingredients involves discovering stable crystal packing arrangements or polymorphs, each of which has distinct pharmaceutically relevant properties. Traditional experimental screening techniques utilizing various conditions are commonly supplemented with in silico crystal structure prediction (CSP) to inform the crystallization process and mitigate risk. Predictions are often based on advanced classical force fields or quantum mechanical calculations that model the crystal potential energy landscape but do not fully incorporate temperature, pressure, or solution conditions during the search procedure. This study proposes an innovative alchemical path that utilizes an advanced polarizable atomic multipole force field to predict crystal structures based on direct sampling of the NPT ensemble. The use of alchemical (i.e., nonphysical) intermediates, a novel Monte Carlo barostat, and an orthogonal space tempering bias combine to enhance the sampling efficiency of the deposition/sublimation phase transition. The proposed algorithm was applied to 2-((4-(2-(3,4-dichlorophenyl)ethyl)phenyl)amino)benzoic acid (Cambridge Crystallography Database Centre ID: XAFPAY) as a case study to showcase the algorithm. Each experimentally determined polymorph with one molecule in the asymmetric unit was successfully reproduced via approximately 1000 short 1 ns simulations per space group where each simulation was initiated from random rigid body coordinates and unit cell parameters. Utilizing two threads of a recent Intel CPU (a Xeon Gold 6330 CPU at 2.00 GHz), 1 ns of sampling using the polarizable AMOEBA force field can be acquired in 4 h (equating to more than 300 ns/day using all 112 threads/56 cores of a dual CPU node) within the Force Field X software (https://ffx.biochem.uiowa.edu). These results demonstrate a step forward in the rigorous use of the NPT ensemble during the CSP search process and open the door to future algorithms that incorporate solution conditions using continuum solvation methods.

Generation and Transfer of Triplet Electron Spin Polarization at the Solid-Liquid Interface.

The photoexcited triplet state of dyes can generate highly polarized electron spins for sensing and dynamic nuclear polarization. However, while triplets exhibit long spin-lattice relaxation times (T1) on the microsecond scale in solids, the polarization quickly relaxes on the nanosecond scale in solution due to the rotational motion of chromophores. Here, we report that the immobilization of dye molecules on a solid surface allows molecular contact with a liquid while maintaining high polarization and long T1 as in a solid. By adsorbing anionic porphyrins on cationic mesoporous silica gel, porphyrin triplets exhibit high polarization and long T1 at the solid-liquid interface of silica and toluene. Furthermore, porphyrin triplets on the solid surface can exchange spin polarization with TEMPO radicals in solution. This simple and versatile method using the solid-liquid interface will open the door for utilizing the photoinduced triplet spin polarization in solution, which has been mainly limited to the solid-state.

Dynamic Electron Polarization Lasting More Than 10 µs by Hybridizing Porphyrin and TEMPO with Flexible Linkers.

Dynamic electron polarization (DEP), induced by quenching of photoexcited species by stable radicals, can hyperpolarize electron spins in solution at room temperature. Recently, development of technologies based on electron spin polarization such as dynamic nuclear polarization (DNP) has been progressing, where it is important to design molecules that achieve long-lasting DEP in addition to high DEP. Hybridization by linking dyes and radicals is a promising approach for efficient DEP, but strong interactions between neighboring dyes and radicals often result in the rapid decay of DEP. In this study, we introduce a flexible linker into the hybrid system of porphyrin and TEMPO to achieve both efficient DEP and long-lasting DEP. The structural flexibility of the linker switches the interaction between the radical and the triplet, which promotes the DEP process by bringing the radical and the triplet into close proximity, while avoiding abrupt relaxation due to strong interactions. As a result, the new hybridized system exhibits a larger DEP than the unlinked system, while at the same time achieving a DEP lasting more than 10 µs.

The mechanism of thrombocytopenia caused by cholesterol-conjugated antisense oligonucleotides.

In this study, we investigated thrombocytopenia caused by cholesterol-conjugated antisense oligonucleotides (Chol-ASO). First, we evaluated platelet activation induced by Chol-ASO in mice by flow cytometry after administration of platelet-rich plasma (PRP). An increase in the number of large particle-size events with platelet activation was detected in the Chol-ASO-treated group. In a smear study, numerous platelets were observed to attach to nucleic acid-containing aggregates. A competition binding assay showed that the conjugation of cholesterol to ASOs increased their affinity for glycoprotein VI. Platelet-free plasma was then mixed with Chol-ASO to form aggregates. The assembly of Chol-ASO was confirmed by dynamic light scattering measurements in the concentration range in which the formation of aggregates with plasma components was observed. In conclusion, the mechanism by which Chol-ASOs causes thrombocytopenia is proposed to be as follows: (1) Chol-ASOs form polymers, (2) the nucleic acid portion of the polymers interacts with plasma proteins and platelets, which cross-links them to form aggregates, and (3) platelets bound to aggregates become activated, resulting in platelet aggregation, leading to a decrease in platelet count in vivo. The details of the mechanism revealed in this study could contribute to creating safer oligonucleotide therapies without the risk of thrombocytopenia.

Triplet dynamic nuclear polarization of pyruvate via supramolecular chemistry.

Dynamic nuclear polarization (DNP) significantly improves the sensitivity of magnetic resonance imaging, and its most important medical application is cancer diagnosis via hyperpolarized 13C-labeled pyruvate. Unlike cryogenic DNP, triplet-DNP uses photoexcited triplet electrons under mild conditions. However, triplet-DNP of pyruvate has not been observed because of incompatibility of the hydrophobic polarizing agent with hydrophilic pyruvate. This work demonstrates that supramolecular complexation with ß-cyclodextrin can disperse 4,4'-(pentacene-6,13-diyl)dibenzoate (NaPDBA), a pentacene derivative with hydrophilic substituents, even in the presence of high sodium pyruvate concentrations. The polarization of photoexcited triplet electron spins in NaPDBA was transferred to the 13C spins of sodium pyruvate via triplet-DNP of 1H spins in water and 1H-to-13C cross-polarization. This provides an important step toward the widespread use of ultra-sensitive MRI for cancer diagnosis.

Singlet fission as a polarized spin generator for dynamic nuclear polarization.

Singlet fission (SF), converting a singlet excited state into a spin-correlated triplet-pair state, is an effective way to generate a spin quintet state in organic materials. Although its application to photovoltaics as an exciton multiplier has been extensively studied, the use of its unique spin degree of freedom has been largely unexplored. Here, we demonstrate that the spin polarization of the quintet multiexcitons generated by SF improves the sensitivity of magnetic resonance of water molecules through dynamic nuclear polarization (DNP). We form supramolecular assemblies of a few pentacene chromophores and use SF-born quintet spins to achieve DNP of water-glycerol, the most basic biological matrix, as evidenced by the dependence of nuclear polarization enhancement on magnetic field and microwave power. Our demonstration opens a use of SF as a polarized spin generator in bio-quantum technology.

Anti-inflammatory effects of siponimod on astrocytes.

Siponimod, which is approved to treat active secondary progressive multiple sclerosis, acts as a functional antagonist of sphingosine-1-phosphate (S1P) receptor 1 (S1P1) and an agonist of S1P5. S1P1 antagonization, which inhibits lymphocyte egress from lymphoid tissues and subsequent infiltration into the central nervous system (CNS), is considered the main therapeutic mechanism of siponimod. In addition, siponimod's direct effects on CNS glial cells are another potential neuroprotective mechanism because siponimod can penetrate the blood-brain barrier and CNS glial cells express S1P receptors. However, it remains uncertain whether siponimod directly affects CNS glial cells. In this study, we investigated siponimod's effects on astrocytes using mouse primary cultures. Siponimod suppressed nuclear factor kappa B activation and pro-inflammatory cytokine production. Using antagonists for S1P1 and S1P5, we found that siponimod partially exerts its anti-inflammatory effects via S1P1, but not via S1P5. Moreover, siponimod also inhibited histone deacetylase, suggesting that siponimod exerts broad anti-inflammatory effects via S1P1 antagonization and histone deacetylase inhibition. Siponimod might suppress disease progression in multiple sclerosis in part via direct inhibition of astroglial CNS neuroinflammation.

Porphyrins as Versatile, Aggregation-Tolerant, and Biocompatible Polarizing Agents for Triplet Dynamic Nuclear Polarization of Biomolecules.

Triplet dynamic nuclear polarization (triplet-DNP) achieves nuclear spin polarization at moderate temperatures by using spin polarization of photoexcited triplet electrons. The applications of triplet-DNP for biomolecules have been hampered because acenes, the only polarizing agents used so far, tend to aggregate and lose their polarization in biomolecular matrices. Here, we report for the first time use of porphyrins as polarizing agents of triplet-DNP and propose a new concept of aggregation-tolerant polarizing agents. Sodium salts of tetrakis(4-carboxyphenyl)porphyrin (TCPPNa) can be dispersed in amorphous as well as crystalline biomolecular matrices, and importantly, it can generate polarized triplet electrons even in a slightly aggregated state. Triplet-DNP of crystalline erythritol containing slightly aggregated TCPPNa can achieve more than 120-fold signal enhancement. Because TCPPNa is also the first biocompatible triplet-DNP polarizing agent, this work provides a crucial step forward for the biological and medical applications of triplet-DNP.

Neural regulation in tooth regeneration of Ambystoma mexicanum.

The presence of nerves is an important factor in successful organ regeneration in amphibians. The Mexican salamander, Ambystoma mexicanum, is able to regenerate limbs, tail, and gills when nerves are present. However, the nerve-dependency of tooth regeneration has not been evaluated. Here, we reevaluated tooth regeneration processes in axolotls using a three-dimensional reconstitution method called CoMBI and found that tooth regeneration is nerve-dependent although the dentary bone is independent of nerve presence. The induction and invagination of the dental lamina were delayed by denervation. Exogenous Fgf2, Fgf8, and Bmp7 expression could induce tooth placodes even in the denervated mandible. Our results suggest that the role of nerves is conserved and that Fgf+Bmp signals play key roles in axolotl organ-level regeneration. The presence of nerves is an important factor in successful organ regeneration in amphibians. The Mexican salamander, Ambystoma mexicanum, is able to regenerate limbs, tail, and gills when nerves are present. However, the nervedependency of tooth regeneration has not been evaluated. Here, we reevaluated tooth regeneration processes in axolotls using a three-dimensional reconstitution method called CoMBI and found that tooth regeneration is nerve-dependent although the dentary bone is independent of nerve presence. The induction and invagination of the dental lamina were delayed by denervation. Exogenous Fgf2, Fgf8, and Bmp7 expression could induce tooth placodes even in the denervated mandible. Our results suggest that the role of nerves is conserved and that Fgf+Bmp signals play key roles in axolotl organ-level regeneration.

Triplet dynamic nuclear polarization of crystalline ice using water-soluble polarizing agents.

Triplet dynamic nuclear polarization (triplet-DNP) allows hyperpolarization at a moderate temperature. While the triplet-DNP of water is strongly desired, water-soluble triplet polarizing agents have not yet been reported. Herein, the first example of triplet-DNP of crystalline ice is demonstrated by molecularly dispersing a novel water-soluble polarizing agent into ice.

Materials chemistry of triplet dynamic nuclear polarization.

Dynamic nuclear polarization with photo-excited triplet electrons (triplet-DNP) has the potential to enhance the sensitivity of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) at a moderate temperature. While many efforts have been devoted to achieving a large nuclear polarization based on triplet-DNP, the application of triplet-DNP has been limited to nuclear physics experiments. The recent introduction of materials chemistry into the field of triplet-DNP has achieved air-stable and water-soluble polarizing agents as well as the hyperpolarization of nanomaterials with a large surface area such as nanoporous metal-organic frameworks (MOFs) and nanocrystal dispersion in water. This Feature Article overviews the recently-emerged materials chemistry of triplet-DNP that paves new paths towards unprecedented biological and medical applications.

Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations.

UNLABELLED: BRAF mutations occur in approximately 10% of colorectal cancers. Although RAF inhibitor monotherapy is highly effective in BRAF-mutant melanoma, response rates in BRAF-mutant colorectal cancer are poor. Recent clinical trials of combined RAF/EGFR or RAF/MEK inhibition have produced improved efficacy, but patients ultimately develop resistance. To identify molecular alterations driving clinical acquired resistance, we performed whole-exome sequencing on paired pretreatment and postprogression tumor biopsies from patients with BRAF-mutant colorectal cancer treated with RAF inhibitor combinations. We identified alterations in MAPK pathway genes in resistant tumors not present in matched pretreatment tumors, including KRAS amplification, BRAF amplification, and a MEK1 mutation. These alterations conferred resistance to RAF/EGFR or RAF/MEK combinations through sustained MAPK pathway activity, but an ERK inhibitor could suppress MAPK activity and overcome resistance. Identification of MAPK pathway reactivating alterations upon clinical acquired resistance underscores the MAPK pathway as a critical target in BRAF-mutant colorectal cancer and suggests therapeutic options to overcome resistance. SIGNIFICANCE: RAF inhibitor combinations represent promising approaches in clinical development for BRAF-mutant colorectal cancer. Initial characterization of clinical acquired resistance mechanisms to these regimens identified several MAPK pathway alterations driving resistance by reactivating MAPK signaling, highlighting the critical dependence of BRAF-mutant colorectal cancers on MAPK signaling and offering potential strategies to overcome resistance.