Tuning Potential Functions to Host-Guest Binding Data.

Software to more rapidly and accurately predict protein-ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of these methods depends critically on the accuracy of the potential functions that they use. Potential functions are typically trained against a combination of quantum chemical and experimental data. However, although binding affinities are among the most important quantities to predict, experimental binding affinities have not to date been integrated into the experimental data set used to train potential functions. In recent years, the use of host-guest complexes as simple and tractable models of binding thermodynamics has gained popularity due to their small size and simplicity, relative to protein-ligand systems. Host-guest complexes can also avoid ambiguities that arise in protein-ligand systems such as uncertain protonation states. Thus, experimental host-guest binding data are an appealing additional data type to integrate into the experimental data set used to optimize potential functions. Here, we report the extension of the Open Force Field Evaluator framework to enable the systematic calculation of host-guest binding free energies and their gradients with respect to force field parameters, coupled with the curation of 126 host-guest complexes with available experimental binding free energies. As an initial application of this novel infrastructure, we optimized generalized Born (GB) cavity radii for the OBC2 GB implicit solvent model against experimental data for 36 host-guest systems. This refitting led to a dramatic improvement in accuracy for both the training set and a separate test set with 90 additional host-guest systems. The optimized radii also showed encouraging transferability from host-guest systems to 59 protein-ligand systems. However, the new radii are significantly smaller than the baseline radii and lead to excessively favorable hydration free energies (HFEs). Thus, users of the OBC2 GB model currently may choose between GB cavity radii that yield more accurate binding affinities and GB cavity radii that yield more accurate HFEs. We suspect that achieving good accuracy on both will require more far-reaching adjustments to the GB model. We note that binding free-energy calculations using the OBC2 model in OpenMM gain about a 10× speedup relative to corresponding explicit solvent calculations, suggesting a future role for implicit solvent absolute binding free-energy (ABFE) calculations in virtual compound screening. This study proves the principle of using host-guest systems to train potential functions that are transferrable to protein-ligand systems and provides an infrastructure that enables a range of applications.

Spine, hip, and femoral neck bone mineral density in relation to vegetarian type and status among Taiwanese adults.

We determined the association of vegetarian type and status with bone mineral density (BMD) Z-scores at the spine, hip, and femoral neck. Compared to non-vegetarians, current vegetarians, especially vegans, lacto-vegetarians, and lacto-ovo-vegetarians had lower Z-scores at multiple sites. Sole reliance on a vegetarian diet might be detrimental to the bone. PURPOSE: The impact of vegetarian diets on BMD is contentious. We determined the association of vegetarian type and status with the spine, hip, and femoral neck BMD Z-scores. METHODS: We analyzed data from 20,110 Taiwan Biobank volunteers. BMD was measured using dual-energy X-ray absorptiometry (DXA). The vegetarian status (non-, former, and current vegetarians) and type (non-vegetarians, ovo-vegetarians, lacto-vegetarians, lacto-ovo-vegetarians, and vegans) were determined using questionnaires. RESULTS: The participants consisted of 12,910 women and 7200 men, with a mean age of 55.5 years. Based on vegetarian status (reference: non-vegetarians), current vegetarians had significantly lower BMD Z-scores at the spine (unstandardized regression coefficient, B = - 0.195, p = 0.006), left hip (B = - 0.125, p = 0.008), and right hip (B = - 0.100, p = 0.027), respectively. Based on vegetarian status and type (reference: non-vegetarians), current vegans and non-vegans had notably lower BMD Z-scores at specific skeletal sites. For non-vegans, the BMD Z-scores were significant at the spine (B = -0.184, p = 0.010), left hip (B = - 0.124, p = 0.010), and left femoral neck (B = - 0.125, p = 0.012). For current vegans, however, the BMD Z-scores were significant only at the right hip (B = - 0.232; p = 0.028). Nonetheless, after stratifying vegetarian diet into more subgroups, current vegans exhibited a significant reduction in BMD Z-scores at the spine and right hip, with B-coefficients of - 0.326 and - 0.238, respectively. Current lacto-vegetarians also had significantly lower Z-scores (p < 0.05) at the spine (B = - 0.459), left hip (B = - 0.313), and right hip (B = - 0.214). Moreover, current lacto-ovo-vegetarians had significantly lower Z-scores at the spine (B = - 0.175) and left hip (B = - 0.115). CONCLUSION: Current vegetarians, particularly vegans, lacto-vegetarians, and lacto-ovo-vegetarians, demonstrated significantly lower BMD Z-scores at various skeletal sites compared to non-vegetarians. Sole reliance on a vegetarian diet might be detrimental to the bone.

Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A.

Objectives: Transcript sequencing of patient-derived samples has been shown to improve the diagnostic yield for solving cases of suspected Mendelian conditions, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods: We applied short-read and full-length transcript sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results: We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts the branch point critical for intron 6 splicing. Full-length long-read isoform complementary DNA (cDNA) sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates 5 distinct altered splicing transcripts. All 5 altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion: This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.

Copper(II) Affects the Biochemical Behavior of Proinsulin C-peptide by Forming Ternary Complexes with Serum Albumin.

Peptide hormones are essential signaling molecules with therapeutic importance. Identifying regulatory factors that drive their activity gives important insight into their mode of action and clinical development. In this work, we demonstrate the combined impact of Cu(II) and the serum protein albumin on the activity of C-peptide, a 31-mer peptide derived from the same prohormone as insulin. C-peptide exhibits beneficial effects, particularly in diabetic patients, but its clinical use has been hampered by a lack of mechanistic understanding. We show that Cu(II) mediates the formation of ternary complexes between albumin and C-peptide and that the resulting species depend on the order of addition. These ternary complexes notably alter peptide activity, showing differences from the peptide or Cu(II)/peptide complexes alone in redox protection as well as in cellular internalization of the peptide. In standard clinical immunoassays for measuring C-peptide levels, the complexes inflate the quantitation of the peptide, suggesting that such adducts may affect biomarker quantitation. Altogether, our work points to the potential relevance of Cu(II)-linked C-peptide/albumin complexes in the peptide's mechanism of action and application as a biomarker.

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.

We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein-ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔHmix, ρ(x), ΔGsolv, and ΔGtrans. Additionally, we benchmarked against protein-ligand binding free energies (ΔGbind), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage.

De novo variants in MRTFB have gain-of-function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features.

PURPOSE: Myocardin-related transcription factor B (MRTFB) is an important transcriptional regulator, which promotes the activity of an estimated 300 genes but is not known to underlie a Mendelian disorder. METHODS: Probands were identified through the efforts of the Undiagnosed Disease Network. Because the MRTFB protein is highly conserved between vertebrate and invertebrate model organisms, we generated a humanized Drosophila model expressing the human MRTFB protein in the same spatial and temporal pattern as the fly gene. Actin binding assays were used to validate the effect of the variants on MRTFB. RESULTS: Here, we report 2 pediatric probands with de novo variants in MRTFB (p.R104G and p.A91P) and mild dysmorphic features, intellectual disability, global developmental delays, speech apraxia, and impulse control issues. Expression of the variants within wing tissues of a fruit fly model resulted in changes in wing morphology. The MRTFBR104G and MRTFBA91P variants also display a decreased level of actin binding within critical RPEL domains, resulting in increased transcriptional activity and changes in the organization of the actin cytoskeleton. CONCLUSION: The MRTFBR104G and MRTFBA91P variants affect the regulation of the protein and underlie a novel neurodevelopmental disorder. Overall, our data suggest that these variants act as a gain of function.

Loss of MBNL1-mediated retrograde BDNF signaling in the myotonic dystrophy brain.

Reduced brain volume including atrophy in grey and white matter is commonly seen in myotonic dystrophy type 1 (DM1). DM1 is caused by an expansion of CTG trinucleotide repeats in the 3' untranslated region (UTR) of the Dystrophia Myotonica Protein Kinase (DMPK) gene. Mutant DMPK mRNA containing expanded CUG RNA (DMPK-CUGexp) sequesters cytoplasmic MBNL1, resulting in morphological impairment. How DMPK-CUGexp and loss of MBNL1 cause histopathological phenotypes in the DM1 brain remains elusive. Here, we show that BDNF-TrkB retrograde transport is impaired in neurons expressing DMPK-CUGexp due to loss of cytoplasmic MBNL1 function. We reveal that mature BDNF protein levels are reduced in the brain of the DM1 mouse model EpA960/CaMKII-Cre. Exogenous BDNF treatment did not rescue impaired neurite outgrowth in neurons expressing DMPK-CUGexp, whereas overexpression of the cytoplasmic MBNL1 isoform in DMPK-CUGexp-expressing neurons improved their responsiveness to exogenous BDNF. We identify dynein light chain LC8-type 2, DYNLL2, as an MBNL1-interacting protein and demonstrate that their interaction is RNA-independent. Using time-lapse imaging, we show that overexpressed MBNL1 and DYNLL2 move along axonal processes together and that MBNL1-knockdown impairs the motility of mCherry-tagged DYNLL2, resulting in a reduced percentage of retrograde DYNLL2 movement. Examination of the distribution of DYNLL2 and activated phospho-TrkB (pTrkB) receptor in EpA960/CaMKII-Cre brains revealed an increase in the postsynaptic membrane fraction (LP1), indicating impaired retrograde transport. Finally, our neuropathological analysis of postmortem DM1 tissue reveals that reduced cytoplasmic MBNL1 expression is associated with an increase in DYNLL2 and activated pTrkB receptor levels in the synaptosomal fraction. Together, our results support that impaired MBNL1-mediated retrograde BDNF-TrkB signaling may contribute to the histopathological phenotypes of DM1.

Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A.

Objectives: Transcript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods: We applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results: We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion: This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.

The impact of conformational sampling on first-principles calculations of vicinal COCH J-couplings in carbohydrates.

Dihedral angles in organic molecules and biomolecules are vital structural parameters that can be indirectly probed by nuclear magnetic resonance (NMR) measurements of vicinal J-couplings. The empirical relations that map the measured couplings to dihedral angles are typically determined by fitting using static structural models, but this neglects the effects of thermal fluctuations at the finite temperature conditions under which NMR measurements are often taken. In this study, we calculate ensemble-averaged J-couplings for several structurally rigid carbohydrate derivatives using first-principles molecular dynamics simulations to sample the thermally accessible conformations around the minimum energy structure. Our results show that including thermal fluctuation effects significantly shifts the predicted couplings relative to single-point calculations at the energy minima, leading to improved agreement with experiments. This provides evidence that accounting for conformational sampling in first-principles calculations can improve the accuracy of NMR-based structure determination for structurally complex carbohydrates.

The diagnostic performance in clinically significant prostate cancer with PI-RADS version 2.1: simplified bpMRI versus standard mpMRI.

OBJECTIVES: To compare the diagnostic performance for the detection of clinically significant prostate cancer (csPCa) between bpMRI with only axial T2WI (simplified bpMRI) and standard-multiparametric MRI (mpMRI). METHODS: A total of 569 patients who underwent mpMRI followed by biopsy or prostatectomy were enrolled in this retrospective study. According to PI-RADS v2.1, three radiologists (A, B, C) from three centers blinded to clinical variables were assigned scores on lesions with simplified bpMRI and then with mpMRI 2 weeks later. Diagnostic performance of simplified bpMRI was compared with mpMRI using histopathology as reference standard. RESULTS: For all the three radiologists, the diagnostic sensitivity was significantly higher with mpMRI than with simplified bpMRI (P < 0.001 to P = 0.035); and although specificity was also higher with mpMRI than with simplified bpMRI for radiologist B and radiologist C, it was statistically significant only for radiologist B (P = 0.011, P = 0.359, respectively). On the contrary, for radiologist A, specificity was higher with simplified bpMRI than with mpMRI (P = 0.001). The area under the receiver operating characteristic curve (AUC) was significantly higher for mpMRI than for simplified bpMRI except for radiologist A (radiologist A: 0.903 vs 0.913, P = 0.1542; radiologist B: 0.861 vs 0.834 P = 0.0013; and radiologist C: 0.884 vs 0.848, P = 0.0003). Interobserver reliability of PI-RADS v2.1 showed good agreement for both simplified bpMRI (kappa = 0.665) and mpMRI (kappa = 0.739). CONCLUSION: Although the detection of csPCa with simplified bpMRI was comparatively lower than that with mpMRI, the diagnostic performance was still high in simplified bpMRI. Our data justify using mpMRI outperforms simplified bpMRI for prostate cancer screening and imply simplified bpMRI as a potential screening tool.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides.

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions (H-). When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations with different combinations of density functionals, basis sets, and solvent models for a set of organic molecules with known experimental hydricity values. The data are analyzed by comparing the R2 and root-mean-squared error (RMSE) of linear fits with a fixed slope of 1 and using the Akaike Information Criterion to determine statistical significance of the RMSE rank ordering. Based on these results, we quantified the accuracy of theoretical predictions of hydricity and found that the best compromise between accuracy and computational cost was obtained by using the B3LYP-D3 density functional for the geometry optimization and free-energy corrections, either ωB97X-D3 or M06-2X-D3 for single-point energy corrections, combined with a basis set no larger than def-TZVP and the C-PCM ISWIG solvation model. At this level of theory, the RMSEs of hydricity calculations for organic molecules in acetonitrile and dimethyl sulfoxide were found to be <4 and <10 kcal/mol, respectively, for an experimental data set with a dynamic range of 20-150 kcal/mol.

O-Acetyl Migration within the Sialic Acid Side Chain: A Mechanistic Study Using the Ab Initio Nanoreactor.

Many disease-causing viruses target sialic acids on the surface of host cells. Some viruses bind preferentially to sialic acids with O-acetyl modification at the hydroxyl group of C7, C8, or C9 on the glycerol-like side chain. Studies of proteins binding to sialosides containing O-acetylated sialic acids are crucial in understanding the related diseases but experimentally difficult due to the lability of the ester group. We recently showed that O-acetyl migration among hydroxyl groups of C7, C8, and C9 in sialic acids occurs in all directions in a pH-dependent manner. In the current study, we elucidate a full mechanistic pathway for the migration of O-acetyl among C7, C8, and C9. We used an ab initio nanoreactor to explore potential reaction pathways and density functional theory, pKa calculations, and umbrella sampling to investigate elementary steps of interest. We found that when a base is present, migration is easy in any direction and involves three key steps: deprotonation of the hydroxyl group, cyclization between the two carbons, and the migration of the O-acetyl group. This dynamic equilibrium may play a defensive role against pathogens that evolve to gain entry to the cell by binding selectively to one acetylation state.

SARS-CoV-2 and MERS-CoV Spike Protein Binding Studies Support Stable Mimic of Bound 9-O-Acetylated Sialic Acids.

Many disease-causing viruses target sialic acids (Sias), a class of nine-carbon sugars known to coat the surface of many cells, including those in the lungs. Human beta coronaviridae, known for causing respiratory tract diseases, often bind Sias, and some preferentially bind to those with 9-O-Ac-modification. Currently, co-binding of SARS-CoV-2, a beta coronavirus responsible for the COVID-19 pandemic, to human Sias has been reported and its preference towards α2-3-linked Neu5Ac has been shown. Nevertheless, O-acetylated Sias-protein binding studies are difficult to perform, due to the ester lability. We studied the binding free energy differences between Neu5,9Ac2α2-3GalßpNP and its more stable 9-NAc mimic binding to SARS-CoV-2 spike protein using molecular dynamics and alchemical free energy simulations. We identified multiple Sia-binding pockets, including two novel sites, with similar binding affinities to those of MERS-CoV, a known co-binder of sialic acid. In our binding poses, 9-NAc and 9-OAc Sias bind similarly, suggesting an experimentally reasonable mimic to probe viral mechanisms.

Tubulinopathy Presenting as Developmental and Epileptic Encephalopathy.

Tubulin proteins play a role in the cortical development. Mutations in the tubulin genes affect patients with brain malformations. The present report describes two cases of developmental and epileptic encephalopathy (DEE) due to tubulinopathy. Case 1, a 23-year-old boy, was found to have a brain malformation with moderate ventriculomegaly prenatally. Hypotonia was noted at birth. Seizures were noted on the 1st day with multifocal discharges on the EEGs, which became intractable to many anticonvulsants. Brain MRI showed marked dilated ventricles and pachy/polymicrogyri. He became a victim of DEE. A de novo mutation in TUBB2B was proven through next-generation sequencing (NGS). Case 2, a mature male baby, began to have myoclonic jerks of his limbs 4 h after birth. EEG showed focal sharp waves from central and temporal regions. Brain MRI showed lissencephaly, type I. The seizures were refractory initially. A de novo mutation in TUBA1A was proven at the 6th week through NGS. He showed the picture of DEE at 1 year and 2 months of age. The clinical features of the tubulinopathies include motor delay, intellectual disabilities, epilepsy, and other deficits. Our cases demonstrated the severe form of tubulinopathy due to major tubulin gene mutations. NGS makes the early identification of genetic etiology possible for clinical evaluation.

Multireference configuration interaction study of the predissociation of C2 via its F1Πu state.

Photodissociation is one of the main destruction pathways for dicarbon (C2) in astronomical environments, such as diffuse interstellar clouds, yet the accuracy of modern astrochemical models is limited by a lack of accurate photodissociation cross sections in the vacuum ultraviolet range. C2 features a strong predissociative F1Πu-X1Σg + electronic transition near 130 nm originally measured in 1969; however, no experimental studies of this transition have been carried out since, and theoretical studies of the F1Πu state are limited. In this work, potential energy curves of excited electronic states of C2 are calculated with the aim of describing the predissociative nature of the F1Πu state and providing new ab initio photodissociation cross sections for astrochemical applications. Accurate electronic calculations of 56 singlet, triplet, and quintet states are carried out at the DW-SA-CASSCF/MRCI+Q level of theory with a CAS(8,12) active space and the aug-cc-pV5Z basis set augmented with additional diffuse functions. Photodissociation cross sections arising from the vibronic ground state to the F1Πu state are calculated by a coupled-channel model. The total integrated cross section through the F1Πu v = 0 and v = 1 bands is 1.198 × 10-13 cm2 cm-1, giving rise to a photodissociation rate of 5.02 × 10-10 s-1 under the standard interstellar radiation field, much larger than the rate in the Leiden photodissociation database. In addition, we report a new 21Σu + state that should be detectable via a strong 21Σu +-X1Σg + band around 116 nm.

Exploration and validation of force field design protocols through QM-to-MM mapping.

The scale of the parameter optimisation problem in traditional molecular mechanics force field construction means that design of a new force field is a long process, and sub-optimal choices made in the early stages can persist for many generations. We hypothesise that careful use of quantum mechanics to inform molecular mechanics parameter derivation (QM-to-MM mapping) should be used to significantly reduce the number of parameters that require fitting to experiment and increase the pace of force field development. Here, we design and train a collection of 15 new protocols for small, organic molecule force field derivation, and test their accuracy against experimental liquid properties. Our best performing model has only seven fitting parameters, yet achieves mean unsigned errors of just 0.031 g cm-3 and 0.69 kcal mol-1 in liquid densities and heats of vaporisation, compared to experiment. The software required to derive the designed force fields is freely available at https://github.com/qubekit/QUBEKit.

Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages.

The results of quantum chemical and molecular dynamics calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols as a result of substrate cage interactions, preferential binding of reactive conformations of substrate/H3O+ pairs, and increased substrate basicity. However, the increase in basicity dominates. Experimental structure-activity relationship studies in which the metal vertices and overall charge of the cage are varied confirm the model derived via calculations.