Accurate structure prediction of biomolecular interactions with AlphaFold 3.

The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Total Synthesis of Aflastatin A.

The total syntheses of aflastatin A and its C3-C48 degradation fragment (6a, R = H) have been accomplished. The syntheses feature several complex diastereoselective fragment couplings, including a Felkin-selective trityl-catalyzed Mukaiyama aldol reaction, a chelate-controlled aldol reaction involving soft enolization with magnesium, and an anti-Felkin-selective boron-mediated oxygenated aldol reaction. Careful comparison of the spectroscopic data for the synthetic C3-C48 degradation fragment to that reported by the isolation group revealed a structural misassignment in the lactol region of the naturally derived degradation product. Ultimately, the data reported for the naturally derived aflastatin A C3-C48 degradation lactol (6a, R = H) were attributed to its derivative lactol trideuteriomethyl ether (6c, R = CD3). Additionally, the revised absolute configurations of six stereogenic centers (C8, C9, and C28-C31) were confirmed.

Crystal structures of the M1 and M4 muscarinic acetylcholine receptors.

Muscarinic M1-M5 acetylcholine receptors are G-protein-coupled receptors that regulate many vital functions of the central and peripheral nervous systems. In particular, the M1 and M4 receptor subtypes have emerged as attractive drug targets for treatments of neurological disorders, such as Alzheimer's disease and schizophrenia, but the high conservation of the acetylcholine-binding pocket has spurred current research into targeting allosteric sites on these receptors. Here we report the crystal structures of the M1 and M4 muscarinic receptors bound to the inverse agonist, tiotropium. Comparison of these structures with each other, as well as with the previously reported M2 and M3 receptor structures, reveals differences in the orthosteric and allosteric binding sites that contribute to a role in drug selectivity at this important receptor family. We also report identification of a cluster of residues that form a network linking the orthosteric and allosteric sites of the M4 receptor, which provides new insight into how allosteric modulation may be transmitted between the two spatially distinct domains.

Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis.

Optimization in medicinal chemistry often involves designing replacements for a section of a molecule which aim to retain potency while improving other properties of the compound. In this study, we perform a retrospective analysis using a number of computational methods to identify active side chains amongst a pool of random decoy side chains, mimicking a similar procedure that might be undertaken in a real medicinal chemistry project. We constructed a dataset derived from public ChEMBL and PDB data by identifying all ChEMBL assays where at least one of the compounds tested has also been co-crystallized in the PDB. Additionally, we required that there be at least ten active compounds tested in the same ChEMBL assay that are matched molecular pairs to the crystallized ligand. Using the compiled dataset consisting of sets of compounds from 402 assays, we have tested a number of methods for scoring side chains including Spark, a bioisostere replacement tool from Cresset, molecular docking using Glide from Schrodinger, docking with Smina, as well as other methods. In this work, we present a comparison of the performance of these methods in discriminating active side chains from decoys as well as recommendations for circumstances when different methods should be used.

α-Synuclein-Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation.

α-Synuclein fibrils are considered a hallmark of Parkinson's disease and other synucleinopathies. However, small oligomers that formed during the early stages of α-synuclein aggregation are thought to be the main toxic species causing disease. The formation of α-synuclein oligomers has proven difficult to follow, because of the heterogeneity and transient nature of the species formed. Here, a novel bead-based aggregation assay for monitoring the earliest stages of α-synuclein oligomerization, α-Synuclein-Confocal Nanoscanning (ASYN-CONA), is presented. The α-synuclein A91C single cysteine mutant is modified with a trifunctional chemical tag, which allows simultaneous fluorescent labeling with a green dye (tetramethylrhodamine, TMR) and attachment to microbeads. Beads with bound TMR-labeled α-synuclein are then incubated with a red dye (Cy5)-labeled variant of α-synuclein A91C, and EtOH (20%) to induce aggregation. Aggregation is detected by confocal scanning imaging, below the equatorial plane of the beads, which is known as the CONA technique. On-bead TMR-labeled α-synuclein and aggregated Cy5-labeled α-synuclein from the solution are quantitatively monitored in parallel by detection of fluorescent halos or "rings". α-Synuclein on-bead oligomerization results in a linear increase of red bead ring fluorescence intensity over a period of 5 h. Total internal reflection fluorescence microscopy was performed on oligomers cleaved from the beads, and it revealed that (i) oligomers are sufficiently stable in solution to investigate their composition, consisting of 6 ± 1 monomer units, and (ii) oligomers containing a mean of 15 monomers bind Thioflavin-T. Various known inhibitors of α-synuclein aggregation were used to validate the ASYN-CONA assay for drug screening. Baicalein, curcumin, and rifampicin showed concentration-dependent inhibition of the α-synuclein aggregation and the IC50 (the concentration of the compound at which the maxiumum intensity was reduced by one-half) were calculated.

Atomic Layer Deposition of Metal Oxide on Nanocellulose for Enabling Microscopic Characterization of Polymer Nanocomposites.

Analysis of cellulose nanocrystals (CNCs) at low volume fractions in polymer nanocomposites through conventional electron microscopy still remains a challenge due to insufficient contrast between CNCs and organic polymer matrices. Herein, a methodology for enhancing the contrast of CNC, through atomic layer deposition (ALD) of alumina (Al2 O3 ) on CNCs is demonstrated. The metal oxide coated CNC allows clear visualization by transmission electron microscopy, when they are dispersed in water and polyol. A coating of about 6 ± 1 nm thick alumina layer on the CNC is achieved after 50 ALD cycles. This also enables the characterization of CNC dispersion/orientation (at 0.2 wt% loading) in an amorphous cellular system rigid polyurethane foam (RPUF), using backscattered electron microscopy with energy-dispersive X-ray spectroscopy. Microscopic analysis of the RPUF with alumina-coated CNC confirms that the predominant alignment of CNC occurs in a direction parallel to the foam rise.

Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.

Two of the major ongoing challenges in computational drug discovery are predicting the binding pose and affinity of a compound to a protein. The Drug Design Data Resource Grand Challenge 2 was developed to address these problems and to drive development of new methods. The challenge provided the 2D structures of compounds for which the organizers help blinded data in the form of 35 X-ray crystal structures and 102 binding affinity measurements and challenged participants to predict the binding pose and affinity of the compounds. We tested a number of pose prediction methods as part of the challenge; we found that docking methods that incorporate protein flexibility (Induced Fit Docking) outperformed methods that treated the protein as rigid. We also found that using binding pose metadynamics, a molecular dynamics based method, to score docked poses provided the best predictions of our methods with an average RMSD of 2.01 Å. We tested both structure-based (e.g. docking) and ligand-based methods (e.g. QSAR) in the affinity prediction portion of the competition. We found that our structure-based methods based on docking with Smina (Spearman ρ = 0.614), performed slightly better than our ligand-based methods (ρ = 0.543), and had equivalent performance with the other top methods in the competition. Despite the overall good performance of our methods in comparison to other participants in the challenge, there exists significant room for improvement especially in cases such as these where protein flexibility plays such a large role.

Supercontinent cycles and the calculation of absolute palaeolongitude in deep time.

Traditional models of the supercontinent cycle predict that the next supercontinent--'Amasia'--will form either where Pangaea rifted (the 'introversion' model) or on the opposite side of the world (the 'extroversion' models). Here, by contrast, we develop an 'orthoversion' model whereby a succeeding supercontinent forms 90° away, within the great circle of subduction encircling its relict predecessor. A supercontinent aggregates over a mantle downwelling but then influences global-scale mantle convection to create an upwelling under the landmass. We calculate the minimum moment of inertia about which oscillatory true polar wander occurs owing to the prolate shape of the non-hydrostatic Earth. By fitting great circles to each supercontinent's true polar wander legacy, we determine that the arc distances between successive supercontinent centres (the axes of the respective minimum moments of inertia) are 88° for Nuna to Rodinia and 87° for Rodinia to Pangaea--as predicted by the orthoversion model. Supercontinent centres can be located back into Precambrian time, providing fixed points for the calculation of absolute palaeolongitude over billion-year timescales. Palaeogeographic reconstructions additionally constrained in palaeolongitude will provide increasingly accurate estimates of ancient plate motions and palaeobiogeographic affinities.

Discovery of selective RIO2 kinase small molecule ligand.

We report the discovery and initial optimization of diphenpyramide and several of its analogs as hRIO2 kinase ligands. One of these analogs is the most selective hRIO2 ligand reported to date. Diphenpyramide is a Cyclooxygenase 1 and 2 inhibitor that was used as an anti-inflammatory agent. The RIO2 kinase affinity of diphenpyramide was discovered by serendipity while profiling of 13 marketed drugs on a large 456 kinase assay panel. The inhibition values also suggested a relative selectivity of diphenpyramide for RIO2 against the other kinases in the panel. Subsequently three available and eight newly synthesized analogs were assayed, one of which showed a 10 fold increased hRIO2 binding affinity. Additionally, this compound shows significantly better selectivity over assayed kinases, when compared to currently known RIO2 inhibitors. As RIO2 is involved in the biosynthesis of the ribosome and cell cycle regulation, our selective ligand may be useful for the delineation of the biological role of this kinase. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.

Policy Analysis: Valuation of Ecosystem Services in the Southern Appalachian Mountains.

This study estimates the economic value of an increase in ecosystem services attributable to the reduced acidification expected from more stringent air pollution policy. By integrating a detailed biogeochemical model that projects future ecological recovery with economic methods that measure preferences for specific ecological improvements, we estimate the economic value of ecological benefits from new air pollution policies in the Southern Appalachian ecosystem. Our results indicate that these policies generate aggregate benefits of about $3.7 billion, or about $16 per year per household in the region. The study provides currently missing information about the ecological benefits from air pollution policies that is needed to evaluate such policies comprehensively. More broadly, the study also illustrates how integrated biogeochemical and economic assessments of multidimensional ecosystems can evaluate the relative benefits of different policy options that vary by scale and across ecosystem attributes.

Recombination can lead to spurious results in retroviral transduction with dually fluorescent reporter genes.

Fluorescent proteins are routinely employed as reporters in retroviral vectors. Here, we demonstrate that transduction with retroviral vectors carrying a tandem-dimer Tomato (TdTom) reporter produces two distinct fluorescent cell populations following template jumping due to a single nucleotide polymorphism between the first and second Tomato genes. Template jumping also occurs between repeated sequences in the Tomato and green fluorescent protein (GFP) genes. Thus, proper interpretation of the fluorescence intensity of transduced cells requires caution.

Prescription Drug Prices: An AAN Position Statement.

This position statement serves to establish the AAN's stance on the methods to address the cost of prescription drugs being considered by state and federal policymakers so that the AAN can continue to advocate effectively for its members. Neurologists seek to provide high-value care for patients with neurologic diseases at the lowest cost possible. However, many therapies for neurologic diseases are among the most expensive in the United States. The 3 major cost challenges include (1) unjustified increases in the pricing for drugs used to treat neurologic disorders, (2) the high cost of medications used to treat rare diseases where there are limited or no therapeutic options available, and (3) the high cost of noninnovative (already FDA-approved) therapies that used accelerated FDA approval pathways or Orphan Drug Act designated to expedite approvals in neurologic disorders. In each of these cases, AAN is concerned that the high cost does not deliver sufficient value to patients or society. The AAN's position is that action must be taken to ensure that effective prescription medications are accessible for patients with complex, chronic neurologic conditions. Potential solutions should be affordable, simple, and transparent. Cost-containment efforts must also address the burden on the entire healthcare system because high prescription drug prices may be shifted and absorbed in ways that negatively affect patient and prescriber access to important medications. AAN supports price negotiations, the cost saving potential of generics and biosimilars, development of novel therapeutics, price transparency, and importation.

Total synthesis of (-)-nakadomarin A.

The convergent synthesis of the polycyclic alkaloid (-)-nakadomarin A (1) is reported. The synthesis plan identified macrocyclic lactam 4 as one of the important synthons (eight steps). The other synthon (five steps) was bicyclo[6.3.0] lactam 5 containing a single stereocenter that controlled all of the subsequent stereochemistry during the assembly process. A silyl triflate-promoted cascade of 4 and 5 was used to assemble the bulk of the alkaloid skeleton with the exception of the C5-C6 bond. The nakadomarin synthesis was then completed in one additional step.

The stereochemical course of intramolecular Michael reactions.

We present a general model for understanding the stereochemical course of intramolecular Michael reactions. We show that the addition of ß-ketoester enolates to α,ß-unsaturated esters and imides bearing adjacent stereocenters (X, Y = H, Me, OR) leads to high levels of asymmetric induction. Reinforcing and nonreinforcing stereochemical relationships are evaluated from the syn and anti reactant diastereomers. On the basis of synthetic, spectroscopic, and computational studies, we propose that the outcomes of these reactions can be rationalized by a dipole-minimized chair transition-state model.

The Brain Health Imperative in the 21st Century-A Call to Action: The AAN Brain Health Platform and Position Statement.

Brain health is crucial to optimizing both the function and well-being of every person at each stage of life and is key to both individual and social progress. As a concept, brain health is complex and requires a multidisciplinary collaborative approach between many professional and public organizations to bring into effect meaningful change. Neurologists are uniquely positioned to serve as specialists in brain health and to advance the newly evolving field of preventive neurology, which aims to identify individuals at high risk of brain disorders and other neurologic conditions and offer strategies to mitigate disease emergence or progression. For decades, the American Academy of Neurology (AAN) has demonstrated a commitment to brain health through its public outreach and advocacy. The AAN's Brain Health Initiative launched in 2022 with a strategic plan prioritizing brain health as a key aspect of public engagement and positioning the AAN and neurologists as champions of brain health in collaboration with a broad range of other brain health providers. In this study, we present (1) the new definition of brain health developed by the AAN for neurologists, patients, partners in health care, and the public; (2) the strategic objectives of the AAN Brain Health Initiative; and (3) the AAN Brain Health Platform and Action Plan framework, including key positions on brain health, its 3 ambitious goals, and a national brain health vision. The top-line priorities of the AAN Brain Health Action Plan highlight the need for research, education, public policy, and direct-to-public messaging across the individual's life span and will serve as a catalyst for future cross-disciplinary collaborations within each epoch and longitudinally. The AAN Brain Health Platform is designed to communicate the AAN's vision for brain health and provide a blueprint toward achieving the future of optimal brain health across the life span for all. Through this position statement, we call upon neurologists and other stakeholders in brain health to join our collective efforts to accomplish the ultimate goal of transforming the current trajectory of public health of an increasing burden of neurologic disorders-from both illness and injury-to achieving optimal brain health for all.

Progress toward the syntheses of (+)-GB 13, (+)-himgaline, and himandridine. new insights into intramolecular imine/enamine aldol cyclizations.

A full account of our total synthesis of the galbulimima alkaloids GB 13 and himgaline is provided. Using a strategy adapted from the proposed biosynthesis of the GB alkaloid family, a linear precursor underwent successive intramolecular Diels-Alder, Michael, and imine aldol cyclizations to form the polycyclic alkaloid core. We now show that modification of this strategy can also deliver an advanced intermediate en route to the related alkaloid himandridine. The success of the key imine aldol cyclization is acutely sensitive to substrate structure and solvent, including a case in which cyclization was spontaneous in protic solvents. A detailed computational investigation of the course of the reaction closely correlates with, and suggests a rationale for, the observed patterns of imine aldol reactivity.

Using ecosystem services to inform decisions on U.S. air quality standards.

The ecosystem services (ES) framework provides a link between changes in a natural system's structure and function and public welfare. This systematic integration of ecology and economics allows for more consistency and transparency in environmental decision making by enabling valuation of nature's goods and services in a manner that is understood by the public. This policy analysis (1) assesses the utility of the ES conceptual framework in the context of setting a secondary National Ambient Air Quality Standard (NAAQS), (2) describes how economic valuation was used to summarize changes in ES affected by NOx and SOx in the review, and (3) uses the secondary NOxSOx NAAQS review as a case study to highlight the advantages and challenges of quantifying air pollutant effects on ES in a decision making context. Using an ES framework can benefit the decision making process by accounting for environmental, ecological, and social elements in a holistic manner. As formal quantitative linkages are developed between ecosystem structure and function and ES, this framework will increasingly allow for a clearer, more transparent link between changes in air quality and public welfare.

Proterozoic low orbital obliquity and axial-dipolar geomagnetic field from evaporite palaeolatitudes.

Palaeomagnetism of climatically sensitive sedimentary rock types, such as glacial deposits and evaporites, can test the uniformitarianism of ancient geomagnetic fields and palaeoclimate zones. Proterozoic glacial deposits laid down in near-equatorial palaeomagnetic latitudes can be explained by 'snowball Earth' episodes, high orbital obliquity or markedly non-uniformitarian geomagnetic fields. Here I present a global palaeomagnetic compilation of the Earth's entire basin-scale evaporite record. Magnetic inclinations are consistent with low orbital obliquity and a geocentric-axial-dipole magnetic field for most of the past two billion years, and the snowball Earth hypothesis accordingly remains the most viable model for low-latitude Proterozoic ice ages. Efforts to reconstruct Proterozoic supercontinents are strengthened by this demonstration of a consistently axial and dipolar geomagnetic reference frame, which itself implies stability of geodynamo processes on billion-year timescales.

Gender Discrepancies in Neurologist Compensation.

BACKGROUND AND OBJECTIVES: Previous studies have shown gender disparities in physician pay in various specialties. This retrospective, cross-sectional study evaluated data from the American Academy of Neurology (AAN) Compensation and Productivity Survey for differences in neurologist compensation by gender. METHODS: Of the 3,268 completed surveys submitted, 2,719 were from neurologists and 1,466 had sufficient data for analysis (551 women, 951 men respondents). We calculated an hourly wage from full-time equivalent (FTE) status and weeks worked per year. We evaluated differences in men and women neurologist compensation with multivariable generalized linear models adjusting for race, ethnicity, geographic region, practice setting, years in practice, call status, leadership role, straight salary, and subspecialty. RESULTS: Baseline characteristics for men and women neurologists were similar with the exception of subspecialty distribution. More men were practicing in higher-wage subspecialties compared to women (p < 0.05). Mean FTE annual salary for all neurologists was $280,315, and mean standardized hourly compensation was $131. Estimated annual salary for women was 10.7% less (p ≤ 0.001, 95% confidence interval -4% to -16%) after controlling for race, region, years of practice, practice setting, call status, leadership role, and subspecialty-wage category. FTE annual salary for women neurologists in high-compensation specialties ($281,838) was lower than the mean annual salary for men neurologists in both high-compensation ($365,751) and low-compensation subspecialties ($282,813). When broken down by years of practice, the highest earning women neurologists' mean hourly wage (11-20 years of practice, $128/h) was less than that of all men neurologists except those with 0 to 5 years of practice ($125/h). DISCUSSION: This study, using convenience sample data, adds to the existing body of evidence demonstrating that, despite adjustment for multiple confounding variables, ongoing disparities exist in physician compensation. Despite efforts by professional societies such as the AAN, ongoing systemic issues and barriers exist. Further research into underlying causes and mitigation strategies is recommended; use of probability sampling methods in future research will be important to decrease potential bias and to increase generalizability.