Physics-Based Solubility Prediction for Organic Molecules.

Accurate prediction of aqueous solubility for organic molecules is of great importance across a range of fields, from the design and manufacturing of energy materials, to assessing the environmental impact of potential pollutants. It is of particular significance to the pharmaceutical industry, in which problems with low aqueous solubility frequently hamper the development of new drugs. Experimental measurements of solubility are used extensively, but are often time-consuming, resource intensive and only applicable to already synthesized molecules.

Benchmarking 3D Structure-Based Molecule Generators.

To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set with a hold-out blind set, the sequential graph neural network generators, Pocket2Mol and PocketFlow, diffusion models, DiffSBDD and MolSnapper, and combinatorial genetic algorithms, AutoGrow4 and LigBuilderV3, were evaluated. It was discovered that deep learning methods fail to generate structurally valid molecules and 3D conformations, whereas combinatorial methods are slow and generate molecules that are prone to failing 2D MOSES filters.

Managing functional neurological disorder: treatment recommendations for health professionals in Australia.

Functional Neurological Disorder (FND) can present significant management challenges due to its sometimes-complex presentation and the historical stigma attached to this diagnosis. Recent advances have improved understanding and management of FND, emphasising the benefit of a multidisciplinary approach to management. The prognosis of FND varies but evidence-based treatments offer the potential of remission to many people for whom FND might otherwise cause long-term disability, and meaningful symptomatic and functional improvement for many more.

Videographic and Microbiologic Evaluation of Eye Drop Bottle Contamination in Clinics: A Pilot Study.

Background: Many multidose eyedrops in the clinic and operating room are discarded after single use due to cross-contamination concerns. This practice contributes to significant hospital costs, drug shortages, and unnecessary greenhouse gas emissions.

Methods: 9-week, prospective, observational study of 97 patients.

Magnetic Resonance Imaging as a Readout of CLN5 Gene Therapy Efficacy in Sheep.

Purpose: Neuronal ceroid lipofuscinoses (NCL; Batten disease) are a group of rare inherited neurodegenerative disorders caused by mutations in one of 13 ceroid lipofuscinosis neuronal (CLN) genes. The diseases share a common set of symptoms, including motor and cognitive dysfunction, progressive loss of vision, and seizure activity. A naturally occurring model of CLN5 NCL exists in New Zealand Borderdale sheep, which exhibit similar clinical disease and post-mortem pathology to the human disease.

Caffeine and Nicotine with N-Substituted Diazirine Photoaffinity Labels Form Adducts at Tyrosine-39 of α-Synuclein.

Aggregates of the protein α-synuclein are found in Lewy bodies in the brains of Parkinson's disease (PD) patients. Small molecules that can attenuate or halt α-synuclein aggregation have been studied as potential therapeutics for PD. However, we have a limited understanding of how these molecules bind to α-synuclein.

Lived experience of driving in individuals with functional neurological disorder.

Background: Functional neurological disorder (FND) is a common neurological diagnosis that encapsulates a range of incapacitating clinical presentations. These include functional seizures, movement disorders, and sensory disturbances. Safe driving requires both cognitive skills and physical abilities, which may be impacted by FND symptoms.

Enhanced analysis of equine plasma for the presence of recombinant human erythropoietin - Implementation of an improved workflow.

An improved screening workflow and a robust capillary flow LC-MS confirmatory method for the detection of recombinant human erythropoietin (rHuEPO) has been implemented to increase the sensitivity of rHuEPO detection and to reduce the number of suspect samples committed to confirmatory testing. The influence of repeated dosing of epoetin-β on the detection window of rHuEPO in equine plasma was assessed using the optimised method. Samples were initially assessed using an economical R&D Human EPO Duo-Set ELISA Development System.

Bioprocess monitoring applications of an innovative ATR-FTIR spectroscopy platform.

Pharmaceutical manufacturing is reliant upon bioprocessing approaches to generate the range of therapeutic products that are available today. The high cost of production, susceptibility to process failure, and requirement to achieve consistent, high-quality product means that process monitoring is paramount during manufacturing. Process analytic technologies (PAT) are key to ensuring high quality product is produced at all stages of development.

bbSelect - An Open-Source Tool for Performing a 3D Pharmacophore-Driven Diverse Selection of R-Groups.

The design of compounds during hit-to-lead often seeks to explore a vector from a core scaffold to form additional interactions with the target protein. A rational approach to this is to probe the region of a protein accessed by a vector with a systematic placement of pharmacophore features in 3D, particularly when bound structures are not available. Herein, we present bbSelect, an open-source tool built to map the placements of pharmacophore features in 3D Euclidean space from a library of R-groups, employing partitioning to drive a diverse and systematic selection to a user-defined size.

Toward a Behavioral Interpretation of English Grammar.

Behavior analysis is virtually alone among disciplines in assuming that the orderly arrangement of words in sentences, or grammar, arises from exposure to contingencies of reinforcement. In the face of the novelty, subtlety, complexity, and speed of acquisition of verbal behavior, this position will remain difficult to defend until the field can show that a representative range of grammatical phenomena is within reach of its interpretive tools. Using modern English as a case in point, this article points to the important role of automatic reinforcement in language acquisition and suggests that Skinner's concept of autoclitic frames (e.

Structure-Guided Design of a Domain-Selective Bromodomain and Extra Terminal N-Terminal Bromodomain Chemical Probe.

Small-molecule-mediated disruption of the protein-protein interactions between acetylated histone tails and the tandem bromodomains of the bromodomain and extra-terminal (BET) family of proteins is an important mechanism of action for the potential modulation of immuno-inflammatory and oncology disease. High-quality chemical probes have proven invaluable in elucidating profound BET bromodomain biology, with seminal publications of both pan- and domain-selective BET family bromodomain inhibitors enabling academic and industrial research. To enrich the toolbox of structurally differentiated N-terminal bromodomain (BD1) BET family chemical probes, this work describes an analysis of the GSK BRD4 bromodomain data set through a lipophilic efficiency lens, which enabled identification of a BD1 domain-biased benzimidazole series.

Efficacy of dual intracerebroventricular and intravitreal gene therapy in sheep prompts the first clinical trial to treat CLN5 Batten disease.

Mutations in the gene cause the fatal, pediatric, neurodegenerative disease CLN5 neuronal ceroid lipofuscinosis. Affected children suffer progressive neuronal loss, visual failure and premature death. Presently there is no treatment.

A spectroscopic liquid biopsy for the earlier detection of multiple cancer types.

Background: A rapid, low-cost blood test that can be applied to reliably detect multiple different cancer types would be transformational.

Methods: In this large-scale discovery study (n = 2092 patients) we applied the Dxcover® Cancer Liquid Biopsy to examine eight different cancers. The test uses Fourier transform infrared (FTIR) spectroscopy and machine-learning algorithms to detect cancer.

Long-term safety and dose escalation of intracerebroventricular CLN5 gene therapy in sheep supports clinical translation for CLN5 Batten disease.

CLN5 neuronal ceroid lipofuscinosis (NCL, Batten disease) is a rare, inherited fatal neurodegenerative disorder caused by mutations in the gene. The disease is characterised by progressive neuronal loss, blindness, and premature death. There is no cure.

Global serum profiling: an opportunity for earlier cancer detection.

The advances in cancer research achieved in the last 50 years have been remarkable and have provided a deeper knowledge of this disease in many of its conceptual and biochemical aspects. From viewing a tumor as a 'simple' aggregate of mutant cells and focusing on detecting key cell changes leading to the tumorigenesis, the understanding of cancer has broadened to consider it as a complex organ interacting with its close and far surroundings through tumor and non-tumor cells, metabolic mechanisms, and immune processes. Metabolism and the immune system have been linked to tumorigenesis and malignancy progression along with cancer-specific genetic mutations.

Intraparenchymal convection enhanced delivery of AAV in sheep to treat Mucopolysaccharidosis IIIC.

Background: Mucopolysaccharidosis IIIC (MPSIIIC) is one of four Sanfilippo diseases sharing clinical symptoms of severe cognitive decline and shortened lifespan. The missing enzyme, heparan sulfate acetyl-CoA: α-glucosaminide-N-acetyltransferase (HGSNAT), is bound to the lysosomal membrane, therefore cannot cross the blood-brain barrier or diffuse between cells. We previously demonstrated disease correction in MPSIIIC mice using an Adeno-Associated Vector (AAV) delivering HGSNAT via intraparenchymal brain injections using an AAV2 derived AAV-truetype (AAV-TT) serotype with improved distribution over AAV9.

Outcomes of an Integrated Multidisciplinary Clinic for People with Functional Neurological Disorder.

Background: Functional neurological disorder (FND) is a disabling condition which has poor prognosis without treatment. This study aimed to evaluate the effectiveness of an outpatient integrated multidisciplinary intervention for the condition.

Objectives: This study aimed to assess the outcomes of a pilot integrated multidisciplinary treatment clinic for FND with motor symptoms.

Characterization of neuropathology in ovine CLN5 and CLN6 neuronal ceroid lipofuscinoses (Batten disease).

Sheep with naturally occurring CLN5 and CLN6 forms of neuronal ceroid lipofuscinoses (Batten disease) share the key clinical features of the human disease and represent an ideal model system in which the clinical efficacy of gene therapies is developed and test. However, it was first important to characterize the neuropathological changes that occur with disease progression in affected sheep. This study compared neurodegeneration, neuroinflammation, and lysosomal storage accumulation in CLN5 affected Borderdale, CLN6 affected South Hampshire, and Merino sheep brains from birth to end-stage disease at ≤24 months of age.

Phosphonate and α-fluorophosphonate analogs of d-glucose 6-phosphate as active-site probes of 1l-myo-inositol 1-phosphate synthase.

Phosphate ester analogs in which the bridging oxygen is replaced with a methylene or fluoromethylene group are well known non-hydrolyzable mimics of use as inhibitors and substrate analogs for reactions involving phosphate esters. Properties of the replaced oxygen are often best mimicked by a mono-fluoromethylene group, but such groups are challenging to synthesize and can exist as two stereoisomers. Here, we describe the protocol for our method of synthesizing the α-fluoromethylene analogs of d-glucose 6-phosphate (G6P), as well as the methylene and difluoromethylene analogs, and their application in the study of 1l-myo-inositol-1-phosphate synthase (mIPS).

Solvation entropy, enthalpy and free energy prediction using a multi-task deep learning functional in 1D-RISM.

Simultaneous calculation of entropies, enthalpies and free energies has been a long-standing challenge in computational chemistry, partly because of the difficulty in obtaining estimates of all three properties from a single consistent simulation methodology. This has been particularly true for methods from the Integral Equation Theory of Molecular Liquids such as the Reference Interaction Site Model which have traditionally given large errors in solvation thermodynamics. Recently, we presented pyRISM-CNN, a combination of the 1 Dimensional Reference Interaction Site Model (1D-RISM) solver, pyRISM, with a deep learning based free energy functional, as a method of predicting solvation free energy (SFE).

Liquid biopsies: the future of cancer early detection.

Cancer is a worldwide pandemic. The burden it imposes grows steadily on a global scale causing emotional, physical, and financial strains on individuals, families, and health care systems. Despite being the second leading cause of death worldwide, many cancers do not have screening programs and many people with a high risk of developing cancer fail to follow the advised medical screening regime due to the nature of the available screening tests and other challenges with compliance.

Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models.

Accurate methods to predict solubility from molecular structure are highly sought after in the chemical sciences. To assess the state of the art, the American Chemical Society organized a "Second Solubility Challenge" in 2019, in which competitors were invited to submit blinded predictions of the solubilities of 132 drug-like molecules. In the first part of this article, we describe the development of two models that were submitted to the Blind Challenge in 2019 but which have not previously been reported.