This paper introduces the use of complex Fermi orbital descriptors (FODs) in the Fermi-Löwdin self-interaction-corrected density functional theory (FLOSIC). With complex FODs, the Fermi-Löwdin orbitals (FLOs) that are used to evaluate the SIC correction to the total energy become complex. Complex FLO-SIC (cFLOSIC) calculations based on the local spin density approximation produce total energies that are generally lower than the corresponding energies found with FLOSIC restricted to real orbitals (rFLOSIC). The cFLOSIC results are qualitatively similar to earlier Perdew-Zunger SIC (PZ-SIC) calculations using complex orbitals [J. Chem. Phys. 80, 1972 (1984); Phys. Rev. A 84, 050501(R) (2011); and J. Chem. Phys. 137, 124102 (2012)]. The energy lowering stems from the exchange-correlation part of the self-interaction correction. The Hartree part of the correction is more negative in rFLOSIC. The energy difference between real and complex solutions is greater for more strongly hybridized FLOs in atoms and for FLOs corresponding to double and triple bonds in molecules. The case of N is examined in detail to show the differences between the real and complex FLOs. We show that the complex triple-bond orbitals are simple, and physically appealing combinations of π and σ orbitals that have not been discussed before. Consideration of complex FODs, and resulting unitary transformations, underscores the fact that FLO centroids are not necessarily good guesses for FOD positions in a FLOSIC calculation.
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http://dx.doi.org/10.1063/5.0091212 | DOI Listing |
Background: The therapeutic management of dementia with Lewy bodies (LBD) is a challenge given the high sensitivity to drugs in this disease. This is particularly sensitive with regard to the management of parkinsonism. In particular, treatment of motor symptoms with levodopa or dopaminergic agonists poses a risk of worsening cognitive and behavioral symptoms.
View Article and Find Full Text PDFBackground: Alzheimer's disease (AD) is the most common cause of dementia worldwide. It is characterized by dysfunction in the U1 small nuclear ribonucleoproteins (snRNPs) complex, which may precede TAU aggregation, enhancing premature polyadenylation, spliceosome dysfunction, and causing cell cycle reentry and death. Thus, we evaluated the effects of a synthetic single-stranded cDNA, called APT20TTMG, in induced pluripotent stem cells (iPSC) derived neurons from healthy and AD donors and in the Senescence Accelerated Mouse-Prone 8 (SAMP8) model.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
The University of Texas Health Science Center at Houston, Houston, TX, USA.
Background: Developing drugs for treating Alzheimer's disease (AD) has been extremely challenging and costly due to limited knowledge on underlying biological mechanisms and therapeutic targets. Repurposing drugs or their combination has shown potential in accelerating drug development due to the reduced drug toxicity while targeting multiple pathologies.
Method: To address the challenge in AD drug development, we developed a multi-task machine learning pipeline to integrate a comprehensive knowledge graph on biological/pharmacological interactions and multi-level evidence on drug efficacy, to identify repurposable drugs and their combination candidates RESULT: Using the drug embedding from the heterogeneous graph representation model, we ranked drug candidates based on evidence from post-treatment transcriptomic patterns, mechanistic efficacy in preclinical models, population-based treatment effect, and Phase 2/3 clinical trials.
Background: Convergent evidence indicates that deficits in the endosomal recycling pathway underlies pathogenesis of Alzheimer's disease (AD). SORL1 encodes the retromer-associated receptor SORLA that plays an essential role in recycling of AD-associated cargos such as the amyloid precursor protein and the glutamatergic AMPA receptor. Importantly, loss of function pathogenic SORL1 variants are associated with AD.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
MRC Protein Phosphorylation and Ubiquitylation Unit, Dundee, Scotland, United Kingdom.
Background: Accumulation of misfolded a-synuclein protein in intracellular inclusion bodies of dopaminergic neurons underlies the pathogenesis of synucleinopathies, which include Parkinson's Disease (PD), Dementia with Lewy Bodies (DLB) and Multiple System Atrophy (MSA). Therefore, clearance of misfolded α-synuclein from dopaminergic neurons could in principle offer a an approach for modifying synucleinopathies, which currently remain untreatable.
Method: In this study, we employ the Affinity-directed PROtein Missile (AdPROM) system consisting of the substrate receptor of the CUL2-E3 ligase complex VHL and a nanobody selectively recognising the human α-synuclein protein RESULT: We demonstrate targeted degradation of endogenous α-synuclein from human cell lines with exquisite selectivity.
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