Citations

Abstract Blood–Brain Barrier (BBB) is a specialized vascular structure that protects the brain by controlling what can pass from the bloodstream into the central nervous system. BBB’s highly selective nature prevents neurotoxins and foreign substances, including drugs, from entering the brain. Understanding and predicting whether a drug can cross the BBB is hence crucial in brain-related diseases. Over the past two decades, deep learning in drug discovery has witnessed an upward trend to reduce the cost, labor, and time for finding potential drugs. Majority of recent deep learning-based studies use molecular-level physiochemical properties of known drugs, which are limited and may not be sufficient to capture patterns. Here, we propose a parameter efficient Graph Convolution-based model, graphB3, which uses detailed information about the atoms in a molecule to predict the BBB permeability of drug candidates, outperforming existing methods. In addition to high predictive performance, graphB3 also offers an explanation of which parts of the molecule are most important for crossing the BBB. graphB3 can be employed to discover new BBB-permeable compounds and potential drugs. A free and easy-to-use graphB3 web server is available at https://dhanjal-lab.iiitd.edu.in/graphb3.html, and a standalone tool available at https://github.com/dhanjal-lab/graphB3.

Cervicofacial actinomycosis is a well-recognized infectious disease caused by Actinomyces, a Gram-positive filamentous bacterium. In contrast, Nocardia, a morphologically similar, hyphae-forming organism, is an exceedingly rare cause of cervicofacial abscesses, and even more uncommon associated osteomyelitis of mandible. We present such a case involving a kidney transplant recipient who presented with opioid-induced constipation, along with left jaw pain and swelling. CT scan of the soft tissue in the neck revealed a complex cervicofacial abscess with enhancement of underlying mandible. Culture growth and RNA sequencing of USG-guided aspirate identified a Nocardia species closely related to N. beijingensis/exalbida. The patient initially received broad-spectrum antibiotics, including ceftriaxone, imipenem, and trimethoprim-sulfamethoxazole (TMP-SMX). Imipenem was later discontinued in view of new-onset unexplained encephalopathy and replaced with linezolid, which was subsequently switched to minocycline following thrombocytopenia development. Minocycline therapy was intended for a total of 12 months. TMP-SMX was avoided long-term due to avoid nephrotoxicity risk in kidney transplant patients. On six-month follow-up, the patient showed clinical and radiological improvement; minocycline was discontinued after additional six months. This case highlights the importance of considering Nocardia as a differential diagnosis in immunosuppressed patients presenting with cervicofacial symptoms, especially following orofacial surgery or trauma. Early recognition, prompt diagnosis, and appropriate antibiotic therapy with adequate bone penetration seem crucial for optimal management and may help avoid the need for surgical intervention.

Spinal sarcomas are rare, aggressive tumors requiring wide resection that creates large, challenging defects. Conventional reconstruction using allografts or metallic implants is prone to failure in compromised settings like irradiated or infected tissue. This narrative review synthesizes the literature on biologic reconstruction strategies, focusing on vascularized bone grafts (VBGs) and the ‘spinoplastic’ reconstruction approach, to provide a clinical framework for their application. We performed a narrative literature review using PubMed and Scopus to synthesize clinical studies describing biologic spinal reconstruction in compromised host beds. The main findings show that pedicled VBGs (e.g., rib, iliac crest) and free VBGs (e.g., fibula) function as living structural components. ‘Spinoplastic’ reconstruction leverages these grafts to promote biologic fusion, with clinical series reporting high union rates, even in irradiated or revision settings, offering a durable alternative to avascular constructs. Biologic reconstruction using VBGs is a critical strategy for achieving durable spinal stability in these challenging scenarios, and future directions point toward hybrid strategies combining 3D-printed implants with the biologic power of VBGs.

Background/Objectives: Overall survival in patients with amyotrophic lateral sclerosis (ALS) is linked to the rate of predicted respiratory vital capacity (PVC) loss. The objective of this study was to test whether changes in quantitative PVC measures over time linked to survival would define an immunopathogenic subset of ALS responsive to NP001, a regulator of innate immunity. Methods: In a retrospective study, data from intent-to-treat (ITT) population of two phase 2 trials of NP001 were evaluated for over time changes in PVC, time-to-event (TTE) loss of 15% PVC and PVC change from baseline, as linked to survival outcomes in patients treated with NP001 vs placebo. Results: Treatment with NP001 was associated with a significantly lower risk compared to placebo in the loss of 15% PVC over six months (p = 0.01; HR = 0.60, 95% CI: 0.39, 0.90). Data from the two trials were subsequently divided by a disease progression rate (DPR) value of 0.50 units of ALSFRS-R score lost per month for analysis of slow vs. rapid disease. In ALS patients with slowly progressive disease (DPR < 0.50), TTE PVC changes from baseline were slowed (p < 0.0005) and overall survival extended significantly (18.5 months) in NP001-treated vs. placebo groups. The rapidly progressive ALS patients (DPR ≥ 0.50) treated with NP001 showed no significant difference in PVC change or survival from the placebo group. Conclusions: These hypothesis-generating observations suggest that inflammation might play a significant role in the loss of respiratory function in a major subset of ALS patients.

Abstract Cryo-electron microscopy (cryoEM) is a powerful tool for atomic- and molecular-resolution structure determination, while molecular dynamics (MD) simulations are similarly powerful tools for predicting molecular trajectories. Given the challenges in estimating biomolecule dynamics with cryoEM alone, MD simulations are employed to forecast molecular motions and to interpret cryoEM reconstructions. Few methods, however, can evaluate MD predictions directly. Here, we use multislice wave propagation to project sampled snapshots of MD trajectories, either coarse-grained (CG) or all-atom (AA), into simulated cryoEM 3D reconstructions. We compared simulated and experimental images of low- and high-curvature membranes to show that MD simulations qualitatively reflect the fluidity and thus the contrast of biological membranes observed by cryoEM. MD simulations also correctly predicted bilayer dimensions for single component flat bilayers observed in cryoEM images. However, Martini3 CG-MD simulations failed to predict changes in membrane thickness induced by high curvature and with heterogeneous lipid compositions. We pinpointed the misbehavior of polyunsaturated lipid tails and cholesterol in Martini3 simulations as the main error sources contributing to inaccurate bilayer thicknesses. Our comparisons also explain membrane structure discrepancies between cryoEM and small angle X-ray scattering (SAXS). Further testing of MD predictions by direct comparisons between simulated and experimental cryoEM images should lead to the development of more accurate MD force fields. Statement of Significance Molecular dynamics (MD) simulations are frequently employed to predict the dynamics of biological macromolecules and assemblies, but these predictions remain difficult to validate experimentally. Cryo-electron microscopy (cryoEM) can be used to directly image the conformational ensemble of macromolecules, but images of Coulombic potential cannot be easily compared to snapshots of atoms from MD simulations. Here, we show that a physics-based multislice image projection algorithm accurately converts MD trajectories to simulated cryoEM 2D images and 3D reconstructions. Using this approach, we identify consistencies and discrepancies between MD simulations and cryoEM experiments. Notably, coarse-grained MD performs poorly compared to all-atom MD when simulating membranes composed of mixtures of lipids that include cholesterol and polyunsaturated lipids, providing observables for MD force field improvement.