Prions, prionoids and pathogenic proteins in Alzheimer disease

Like patients with prion disease, Alzheimer patients suffer from a fatal, progressive form of dementia. There is growing evidence that amyloid-β (Aβ) aggregates may be transmissible similar to prions, at least under extreme experimental conditions. However, unlike mice infected with prion protein (PrP) prions, those inoculated with Aβ do not die. The transmission of Aβ and PrP thus differs conspicuously in the neurological effects they induce in their hosts, the difference being no less than a matter of life and death. Far from being a mere academic nuance, this distinction between Aβ and PrP begs the crucial questions of what, exactly, controls prion toxicity and how prion toxicity relates to prion infectivity.

Targeted protein degradation at the host-pathogen interface

Infectious diseases remain a major burden to global health. Despite the implementation of successful vaccination campaigns and efficient drugs, the increasing emergence of pathogenic vaccine or treatment resistance demands novel therapeutic strategies. The development of traditional therapies using small-molecule drugs is based on modulating protein function and activity through the occupation of active sites such as enzyme inhibition or ligand-receptor binding. These prerequisites result in the majority of host and pathogenic disease-relevant, nonenzymatic and structural proteins being labeled "undruggable." Targeted protein degradation (TPD) emerged as a powerful strategy to eliminate proteins of interest including those of the undruggable variety. Proteolysis-targeting chimeras (PROTACs) are rationally designed heterobifunctional small molecules that exploit the cellular ubiquitin-proteasome system to specifically mediate the highly selective and effective degradation of target proteins. PROTACs have shown remarkable results in the degradation of various cancer-associated proteins, and several candidates are already in clinical development. Significantly, PROTAC-mediated TPD holds great potential for targeting and modulating pathogenic proteins, especially in the face of increasing drug resistance to the best-in-class treatments. In this review, we discuss advances in the development of TPD in the context of targeting the host-pathogen interface and speculate on their potential use to combat viral, bacterial, and parasitic infection.

Gut microbiota, pathogenic proteins and neurodegenerative diseases

As the world's population ages, neurodegenerative diseases (NDs) have brought a great burden to the world. However, effective treatment measures have not been found to alleviate the occurrence and development of NDs. Abnormal accumulation of pathogenic proteins is an important cause of NDs. Therefore, effective inhibition of the accumulation of pathogenic proteins has become a priority. As the second brain of human, the gut plays an important role in regulate emotion and cognition functions. Recent studies have reported that the disturbance of gut microbiota (GM) is closely related to accumulation of pathogenic proteins in NDs. On the one hand, pathogenic proteins directly produced by GM are transmitted from the gut to the central center via vagus nerve. On the other hand, The harmful substances produced by GM enter the peripheral circulation through intestinal barrier and cause inflammation, or cross the blood-brain barrier into the central center to cause inflammation, and cytokines produced by the central center cause the production of pathogenic proteins. These pathogenic proteins can produced by the above two aspects can cause the activation of central microglia and further lead to NDs development. In addition, certain GM and metabolites have been shown to have neuroprotective effects. Therefore, modulating GM may be a potential clinical therapeutic approach for NDs. In this review, we summarized the possible mechanism of NDs caused by abnormal accumulation of pathogenic proteins mediated by GM to induce the activation of central microglia, cause central inflammation and explore the therapeutic potential of dietary therapy and fecal microbiota transplantation (FMT) in NDs.

In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri

Naegleria fowleri (N. fowleri) is a free-living thermophilic amoeba of fresh water and soil. The amoeba primarily feeds on bacteria but can be transmitted to humans upon contact with freshwater sources. Furthermore, this brain-eating amoeba enters the human body through the nose and travels to the brain to cause primary amebic meningoencephalitis (PAM). N. fowleri has been reported globally since its discovery in 1961. Recently a new strain of N. fowleri named Karachi-NF001 was found in a patient who had traveled from Riyadh, Saudi Arabia to Karachi in 2019. There were 15 unique genes identified in the genome of the Karachi-NF001 strain compared to all the previously reported strains of N. fowleri worldwide. Six of these genes encode well-known proteins. In this study, we performed in-silico analysis on 5 of these 6 proteins, namely, Rab family small GTPase, NADH dehydrogenase subunit 11, two Glutamine-rich protein 2 proteins (locus tags: 12086 and 12110), and Tigger transposable element-derived protein 1. We conducted homology modeling of these 5 proteins followed by their active site identification. These proteins were subjected to molecular docking against 105 anti-bacterial ligand compounds as potential drugs. Subsequently, the 10 best-docked compounds were determined for each protein and ranked according to the number of interactions and their binding energies. The highest binding energy was recorded for the two Glutamine-rich protein 2 proteins with different locus tags, and results have shown that the protein-inhibitor complex was stable throughout the simulation run. Moreover, future in-vitro studies could validate the findings of our in-silico analysis and identify potential therapeutic drugs against N. fowleri infections.

Time-Frequency Approach Applied to Finding Interaction Regions in Pathogenic Proteins

Protein-protein interactions govern all molecular processes for living organisms, even those involved in pathogen infection. Pathogens such as virus, bacteria, and parasites contain proteins that help the pathogen to attach, penetrate, and settle inside the target cell. Thus, it is necessary to know the regions in pathogenic proteins that interact with host cell receptors. Currently, powerful pathogen databases are available and many pathogenic proteins have been recognized, but many pathogenic proteins have not been characterized. This work developed a program in MATLAB environment based on the time-frequency analysis to recognize important sites in proteins. Our program highlights the highest energy patches in proteins from their time-frequency distribution and matches the corresponding frequency. We sought to know if this approach is able to recognize stretches residues related to interaction. Our approach was applied to five study cases from pathogenic co-crystallized structures that have been well characterized. We searched the frequencies that characterize interaction regions in pathogenic proteins and with this information tried to identify new interaction patches in either paralogs or orthologs. We found that our program generates a well-interpretable graphic under several descriptors that can show important regions in proteins even those related to interaction. We propose that this MATLAB program could be used as a tool to explore outstanding regions in uncharacterized proteins.

RNA-Based Therapies for Neurodegenerative Diseases Targeting Pathogenic Proteins

Neurodegeneration is featured by the gradual stagnation of neuronal function and structure, leading to significant motor and cognitive impairments. The primary histopathological features underlying these conditions include the cumulation of pathological protein aggregates, chronic inflammation, and neuronal cell death. Alzheimer's disease (AD) and Parkinson's disease (PD) are prominent examples of neurodegenerative diseases (NDDs). As of 2023, over 65 million people worldwide are affected by AD and PD, with the prevalence of these conditions steadily increasing over time. Interestingly, there are no effective therapies available to halt or slow NDD progression. Most approved treatments are focused on symptom management and are often associated with substantial side effects. Given these limitations, the development of novel therapeutic approaches targeting the molecular mechanisms underlying these disorders is essential. Notably, RNA-based therapeutics have recently emerged as a potential therapeutic approach for managing various neurological diseases, offering the potential for innovative molecular interventions in NDD. In this review, we have discussed the pathogenic role of various protein aggregates in NDD and highlighted emerging RNA-based strategies aimed at targeting these pathological proteins.

Multianalyte Nanopore Detection of Alzheimer's Biomarkers: A Label-Free Platform with Improved Sensitivity and Range

Due to matrix interference, detection methods for protein biomarkers in body fluids are limited. Commonly used methods often require antibody modification or fluorescent labeling. Furthermore, subtle differences in protein sequences make it more challenging to detect and differentiate multiple biomarkers. This study introduces a novel nanopore-based method for simultaneous, label-free detection of key Alzheimer's disease (AD) biomarkers in biological samples. The technique enables distinguishable and ultrasensitive detection of amyloid-beta peptides (Aβ42,Aβ40) amyloid precursor protein (APP669-711), and tubulin associated unit (Tau) proteins in cerebrospinal fluid and serum. The method successfully identifies AD biomarkers by directly detecting Aβ42 in cerebrospinal fluid and can detect age-dependent changes in Aβ levels in AD mice models, demonstrating reliability comparable to established enzyme linked immunosorbent assay (ELISA) assays and brain plaque-staining confocal imaging. Notably, this method achieves significant advancements in detecting 2.1 pm Aβ42 and 1.5 pm APP(669-711), as well as 627 fm Aβ40 in serum. This improvement in nanopore technology addresses the challenges of detecting Aβ and Tau alterations in complex biological samples and differentiating between similar protein sequences. The study marks a significant advancement in the analysis of pathogenic proteins in physiological samples, also offering a powerful tool for AD research and diagnostics.