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12 pages, 848 KB  
Article
Targeting carA Using Optimized Antisense Peptide Nucleic Acid–Cell-Penetrating Peptide Conjugates in Acinetobacter baumannii: A Novel Antibacterial Approach
by Ju-Hui Seo, Yoo-Jeong Kim, Wook-Jong Jeon, Jung-Sik Yoo and Dong-Chan Moon
Int. J. Mol. Sci. 2025, 26(19), 9526; https://doi.org/10.3390/ijms26199526 - 29 Sep 2025
Abstract
Acinetobacter baumannii is an opportunistic pathogen associated with severe bloodstream infections. It exhibits a high level of multidrug resistance, posing major clinical challenges. Antisense peptide nucleic acids (PNAs) represent a promising alternative to conventional antibiotics; however, their therapeutic efficacy depends on optimal delivery [...] Read more.
Acinetobacter baumannii is an opportunistic pathogen associated with severe bloodstream infections. It exhibits a high level of multidrug resistance, posing major clinical challenges. Antisense peptide nucleic acids (PNAs) represent a promising alternative to conventional antibiotics; however, their therapeutic efficacy depends on optimal delivery and molecular design. In this study, we aimed to enhance the antibacterial activity of PNAs against A. baumannii by systematically optimizing cell-penetrating peptides (CPPs), PNA length, target region, and chemical modifications. The efficacy and safety of CPP–PNA constructs were evaluated using a comprehensive set of approaches, including determination of minimum bactericidal and minimum inhibitory concentrations, quantitative reverse transcription polymerase chain reaction, Western blotting, and cytotoxicity assays. Three CPP–PNA constructs targeting carA were synthesized. Among these, the KFFK (FFK)2–PNA conjugate showed the strongest bacterial growth-inhibitory effect, while the addition of extra lysine residues reduced its efficacy. Further analyses showed that a 10-mer alpha (α)-PNA modification targeting the ribosomal binding site of carA had the greatest inhibitory effect. These results underscore the importance of rational CPP design and PNA optimization in developing effective antisense antimicrobials against A. baumannii. Full article
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23 pages, 1852 KB  
Review
Contemporary and Emerging Therapeutics in Cardiovascular-Kidney-Metabolic (CKM) Syndrome: In Memory of Professor Akira Endo
by Inderjeet Singh Bharaj, Ajit Brar, Aayushi Kacheria, Karen Purewal, Austin Simister, Umabalan Thirupathy, Palak Gupta, Jasraj Kahlon, Juzer Munaim, Ei Ei Thwe, Samer Ibrahim, Valerie Martinez Vargas and Krishnaswami Vijayaraghavan
Biomedicines 2025, 13(9), 2192; https://doi.org/10.3390/biomedicines13092192 - 8 Sep 2025
Viewed by 882
Abstract
Cardiovascular-kidney-metabolic (CKM) syndrome is a multifaceted, systemic disorder characterized by the interplay of cardiovascular disease (CVD), chronic kidney disease (CKD), type 2 diabetes mellitus (T2DM), and obesity. This review synthesizes current and emerging therapeutic strategies aimed at addressing the shared pathophysiologic mechanisms driving [...] Read more.
Cardiovascular-kidney-metabolic (CKM) syndrome is a multifaceted, systemic disorder characterized by the interplay of cardiovascular disease (CVD), chronic kidney disease (CKD), type 2 diabetes mellitus (T2DM), and obesity. This review synthesizes current and emerging therapeutic strategies aimed at addressing the shared pathophysiologic mechanisms driving CKM progression, such as insulin resistance, inflammation, oxidative stress, and neurohormonal activation. Established pharmacotherapies that include sodium-glucose cotransporter 2 (SGLT2) inhibitors, glucagon-like peptide-1 receptor agonists (GLP-1 RAs), and nonsteroidal mineralocorticoid receptor antagonists like finerenone have demonstrated robust efficacy in reducing cardiovascular events, slowing renal decline, and improving metabolic outcomes. Additionally, novel agents targeting lipoprotein(a), interleukin-6, and hepatic fat accumulation are expanding the therapeutic landscape. RNA-based therapies, including antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs), are designed to modulate lipoprotein(a) and PCSK9 expression. Artificial intelligence (AI) is also emerging as a transformative tool for personalized CKM management, enhancing risk prediction and clinical decision-making. The review highlights the relevance of metabolic dysfunction-associated steatotic liver disease (MASLD) as a CKM modifier and discusses the approval of resmetirom, a selective thyroid hormone receptor β agonist, for noncirrhotic MASH. By integrating evidence from clinical trials, mechanistic studies, and emerging technologies, this review provides a comprehensive resource for clinicians and researchers navigating the evolving field of CKM syndrome. Full article
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40 pages, 470 KB  
Review
Biologics as Therapeutical Agents Under Perspective Clinical Studies for Alzheimer’s Disease
by Huan Li, Xinai Shen, Beiyu Zhang and Zheying Zhu
Molecules 2025, 30(17), 3479; https://doi.org/10.3390/molecules30173479 - 24 Aug 2025
Viewed by 1271
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterised by cognitive decline, synaptic loss, and multifaceted pathology involving amyloid-β (Aβ) aggregation, tau hyperphosphorylation, neuroinflammation, and impaired proteostasis. In recent years, biologic therapies, such as monoclonal antibodies, vaccines, antisense oligonucleotides (ASOs), and gene therapies, [...] Read more.
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterised by cognitive decline, synaptic loss, and multifaceted pathology involving amyloid-β (Aβ) aggregation, tau hyperphosphorylation, neuroinflammation, and impaired proteostasis. In recent years, biologic therapies, such as monoclonal antibodies, vaccines, antisense oligonucleotides (ASOs), and gene therapies, have gained prominence as promising disease-modifying strategies. In this review, we provide a comprehensive synthesis of current biologic approaches under clinical evaluation for AD. Drawing on data curated from ClinicalTrials.gov (as of 2025), we systematically summarise the molecular targets, therapeutic modalities, mechanisms of action, trial phases, and sponsors of over 60 biologic agents. These include Aβ-directed antibodies targeting distinct conformers such as protofibrils, pyroglutamate-modified species, and soluble oligomers; tau-targeted immunotherapies and RNA-based interventions; and emerging platforms focused on neuroimmune modulation, peptide hormones, and microbiota-based strategies. Gene and RNA therapeutics, particularly ASOs and small interfering RNAs (siRNAs) delivered intrathecally or via lipid nanoparticles, are also reviewed for their potential to modulate intracellular targets with high specificity. We also analyse the historical landscape of biologic candidates that failed to reach approval, discussing key reasons for trial discontinuation, including lack of clinical efficacy, safety concerns (e.g., amyloid-related imaging abnormalities), or inadequate biomarker responses. These cases offer crucial insights for refining future drug design. Looking ahead, we highlight major challenges and evolving perspectives in AD biologic therapy: expanding therapeutic targets beyond Aβ and tau, overcoming delivery barriers to the brain, designing prevention-oriented and genetically stratified trials, and navigating regulatory and ethical considerations. Together, these efforts signal a paradigm shift in AD drug development, from symptomatic treatment to mechanism-based precision biologics. By integrating real-time clinical trial data with mechanistic insight, this review aims to inform both translational research and therapeutic innovation in AD. Full article
(This article belongs to the Special Issue Therapeutic Agents for Neurodegenerative Disorders—2nd Edition)
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15 pages, 1438 KB  
Article
Broad Host Range Peptide Nucleic Acids Prevent Gram-Negative Biofilms Implicated in Catheter-Associated Urinary Tract Infections
by Hannah Q. Karp, Elizabeth S. Nowak, Gillian A. Kropp, Nihan A. Col, Michael D. Schulz, Nammalwar Sriranganathan and Jayasimha Rao
Microorganisms 2025, 13(8), 1948; https://doi.org/10.3390/microorganisms13081948 - 20 Aug 2025
Cited by 1 | Viewed by 576
Abstract
Biofilms develop in sequential steps resulting in the formation of three-dimensional communities of microorganisms that are encased in self-produced extracellular polymeric substances. Biofilms play a key role in device-associated infections, such as catheter-associated urinary tract infections (CAUTIs), because they protect microorganisms from standard [...] Read more.
Biofilms develop in sequential steps resulting in the formation of three-dimensional communities of microorganisms that are encased in self-produced extracellular polymeric substances. Biofilms play a key role in device-associated infections, such as catheter-associated urinary tract infections (CAUTIs), because they protect microorganisms from standard antimicrobial therapies. Current strategies to prevent biofilm formation in catheter-related infections, including prophylactic antibiotics and antibiotic-coated catheters, have been unsuccessful. This finding highlights a need for novel approaches to address this clinical problem. In this study, biofilm-forming phenotypes of common Gram-negative bacteria associated with CAUTIs were treated with antisense peptide nucleic acids (PNAs), and biofilm biomass and bacterial viability were quantified after 24 h of treatment. A cocktail of PNAs targeting the global regulator genes rsmA, amrZ, and rpoS in Pseudomonas aeruginosa significantly reduced viability and thus appropriately eliminated biofilm biomass. Antisense-PNAs against these same gene targets and the motility regulator gene motA inhibited biofilm formation among isolates of Klebsiella pneumoniae, Enterobacter cloacae, and Escherichia coli but did not reduce bacterial viability. These results suggest that antisense-PNAs are a promising new technology in preventing biofilm formation in urinary catheters, especially as a potential complement to conventional antimicrobials. Full article
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13 pages, 1649 KB  
Article
Targeted Peptide-Mediated Delivery of Antisense Oligonucleotides to SMA Cells for SMN2 Gene Splicing Correction
by Marianna Maretina, Anna Egorova, Arina Il’ina, Nadezhda Krylova, Maxim Donnikov, Oleg Glotov and Anton Kiselev
Sci. Pharm. 2025, 93(3), 38; https://doi.org/10.3390/scipharm93030038 - 14 Aug 2025
Viewed by 1594
Abstract
Spinal muscular atrophy (SMA) is a severe neurodegenerative disorder that has an approved treatment that can still be improved. Antisense oligonucleotides (AONs) are currently delivered intrathecally for SMA therapy based on SMN2 gene splicing correction, and high concentrations are required to achieve an [...] Read more.
Spinal muscular atrophy (SMA) is a severe neurodegenerative disorder that has an approved treatment that can still be improved. Antisense oligonucleotides (AONs) are currently delivered intrathecally for SMA therapy based on SMN2 gene splicing correction, and high concentrations are required to achieve an improvement of the disease symptoms. In this study, AONs were introduced into SMA fibroblast cell cultures by means of an arginine–histidine-rich peptide carrier that had been decorated with iRGD ligands. Due to the protected and receptor-mediated nature of AON delivery within these complexes, low concentrations can be used. We assessed the RNA-binding characteristics, cytotoxicity, size, and zeta potential of AON/carrier complexes as well as the efficiency of SMN2 gene splicing correction following transfections. After testing a variety of AON/carrier formulations, we selected those that produced the best outcomes. The AON/carrier complexes that were found to be the most effective significantly increased the proportion of full-length SMN transcripts and the quantity of nuclear gems. Thus, we demonstrated the potential of delivering therapeutic AONs into SMA cells using a ligand-modified peptide carrier. Full article
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22 pages, 2630 KB  
Review
Transfection Technologies for Next-Generation Therapies
by Dinesh Simkhada, Su Hui Catherine Teo, Nandu Deorkar and Mohan C. Vemuri
J. Clin. Med. 2025, 14(15), 5515; https://doi.org/10.3390/jcm14155515 - 5 Aug 2025
Viewed by 2102
Abstract
Background: Transfection is vital for gene therapy, mRNA treatments, CAR-T cell therapy, and regenerative medicine. While viral vectors are effective, non-viral systems like lipid nanoparticles (LNPs) offer safer, more flexible alternatives. This work explores emerging non-viral transfection technologies to improve delivery efficiency [...] Read more.
Background: Transfection is vital for gene therapy, mRNA treatments, CAR-T cell therapy, and regenerative medicine. While viral vectors are effective, non-viral systems like lipid nanoparticles (LNPs) offer safer, more flexible alternatives. This work explores emerging non-viral transfection technologies to improve delivery efficiency and therapeutic outcomes. Methods: This review synthesizes the current literature and recent advancements in non-viral transfection technologies. It focuses on the mechanisms, advantages, and limitations of various delivery systems, including lipid nanoparticles, biodegradable polymers, electroporation, peptide-based carriers, and microfluidic platforms. Comparative analysis was conducted to evaluate their performance in terms of transfection efficiency, cellular uptake, biocompatibility, and potential for clinical translation. Several academic search engines and online resources were utilized for data collection, including Science Direct, PubMed, Google Scholar Scopus, the National Cancer Institute’s online portal, and other reputable online databases. Results: Non-viral systems demonstrated superior performance in delivering mRNA, siRNA, and antisense oligonucleotides, particularly in clinical applications. Biodegradable polymers and peptide-based systems showed promise in enhancing biocompatibility and targeted delivery. Electroporation and microfluidic systems offered precise control over transfection parameters, improving reproducibility and scalability. Collectively, these innovations address key challenges in gene delivery, such as stability, immune response, and cell-type specificity. Conclusions: The continuous evolution of transfection technologies is pivotal for advancing gene and cell-based therapies. Non-viral delivery systems, particularly LNPs and emerging platforms like microfluidics and biodegradable polymers, offer safer and more adaptable alternatives to viral vectors. These innovations are critical for optimizing therapeutic efficacy and enabling personalized medicine, immunotherapy, and regenerative treatments. Future research should focus on integrating these technologies to develop next-generation transfection platforms with enhanced precision and clinical applicability. Full article
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40 pages, 2483 KB  
Review
Biological and Biosimilar Medicines in Contemporary Pharmacotherapy for Metabolic Syndrome
by Wiktoria Górecka, Daria Berezovska, Monika Mrozińska, Grażyna Nowicka and Monika E. Czerwińska
Pharmaceutics 2025, 17(6), 768; https://doi.org/10.3390/pharmaceutics17060768 - 11 Jun 2025
Viewed by 1840
Abstract
The discovery of new drugs offers valuable alternatives, particularly for treating diseases that are resistant to existing therapies or involving complex, multi-organ conditions such as metabolic syndrome. Although treatment algorithms are generally well established and primarily based on synthetic pharmaceuticals, they are increasingly [...] Read more.
The discovery of new drugs offers valuable alternatives, particularly for treating diseases that are resistant to existing therapies or involving complex, multi-organ conditions such as metabolic syndrome. Although treatment algorithms are generally well established and primarily based on synthetic pharmaceuticals, they are increasingly being supplemented by biological and biosimilar agents. This trend is particularly evident in the development and advancement of anti-diabetic and hypolipemic therapies. This review explores advances in the treatment of hypercholesterolemia and hypertriglyceridemia, elevated lipoprotein(a) [Lp(a)], diabetes, and obesity associated with metabolic syndrome. It focuses mainly on biopharmaceuticals such as proteins and nucleotide-based drugs (antisense oligonucleotides, small interfering RNA), but also on dipeptidyl peptidase-4 (DPP-4) inhibitors classified as incretin drugs along with glucagon-like peptide-1 (GLP-1) analogues. Due to the substantial role of SGLT-2 (sodium/glucose cotransporter 2) inhibitors in novel diabetes therapies, especially for managing cardiovascular risk, this group of compounds was also included in this review. Many clinical data in the field of effectiveness of biopharmaceuticals in metabolic disorders are provided. Therefore, in this review, we mainly include a brief history of drug development and approval, first synthesis and structure modifications, which relevantly influence pharmacokinetics, and safety. We provide only brief comparison of biological drugs with metformin and sulphonylureas derivatives. Databases such as PubMed, Scopus, and Google Scholar are searched for the period between 2000 and 2024. Full article
(This article belongs to the Section Biologics and Biosimilars)
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14 pages, 1523 KB  
Article
Regulatory T Cell Function Is Not Affected by Antisense Peptide-Conjugated Phosphorodiamidate Morpholino Oligomer (PPMO)-Mediated TMPRSS2 Truncation
by Sandra Gunne, Fiona K. Sailer, Lucas Keutmann, Marie Schwerdtner, Hong M. Moulton, Eva Böttcher-Friebertshäuser and Susanne Schiffmann
Drugs Drug Candidates 2025, 4(2), 25; https://doi.org/10.3390/ddc4020025 - 27 May 2025
Viewed by 808
Abstract
Background: TMPRSS2 plays an important role in the viral entry mechanisms of influenza viruses and coronaviruses. Therefore, TMPRSS2 seems to be a suitable antiviral drug target. To exclude possible side effects of TMPRSS2 truncation in an early stage of drug in-vitro testing, this [...] Read more.
Background: TMPRSS2 plays an important role in the viral entry mechanisms of influenza viruses and coronaviruses. Therefore, TMPRSS2 seems to be a suitable antiviral drug target. To exclude possible side effects of TMPRSS2 truncation in an early stage of drug in-vitro testing, this study aims to analyze the impact of TMPRSS2 truncation via antisense peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) targeting immune cells, using the example of regulatory T cells (Treg). Methods: TMPRSS2 was truncated in human Tregs using a splice-modulating PPMO. Effects on Treg function were analyzed by evaluation of surface marker and transcription factor expression, cytokine secretion, and effector cell suppression capability. Results: PPMO treatment led to a slight concentration-dependent toxicity in Tregs. Tregs with truncated TMPRSS2 behave similarly to untreated and control PPMO-treated cells in the analyzed assays. Conclusions: Treg function is not altered after TMPRSS2 truncation and therefore, no unwanted side effects in regard of Tregs are expected when using TMPRSS2-truncating PPMO as an anti-viral drug. Full article
(This article belongs to the Special Issue Fighting SARS-CoV-2 and Related Viruses)
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16 pages, 6714 KB  
Article
Construction of Graphene Oxide Probes Loaded with Antisense Peptide Nucleic Acid and Doxorubicin for Regulating Telomerase Activity and Inducing Apoptosis of Cancer Cells
by Yanyan Zhu, Qinghong Ji and Min Hong
Biosensors 2025, 15(6), 337; https://doi.org/10.3390/bios15060337 - 26 May 2025
Viewed by 830
Abstract
In this study, we developed a multifunctional graphene oxide (GO)-based nanoprobe co-loaded with antisense peptide nucleic acid (PNA) and the chemotherapeutic agent doxorubicin (DOX). The nanoplatform was strategically functionalized with folic acid ligands to enable folate receptor-mediated tumor targeting. Upon cellular internalization, the [...] Read more.
In this study, we developed a multifunctional graphene oxide (GO)-based nanoprobe co-loaded with antisense peptide nucleic acid (PNA) and the chemotherapeutic agent doxorubicin (DOX). The nanoplatform was strategically functionalized with folic acid ligands to enable folate receptor-mediated tumor targeting. Upon cellular internalization, the antisense PNA component selectively hybridized with human telomerase reverse transcriptase (hTERT) mRNA through sequence-specific recognition, inducing structural detachment from the GO surface. This displacement restored the fluorescence signal of previously quenched fluorophores conjugated to the PNA strand, thereby enabling the real-time in situ detection and quantitative fluorescence imaging of intracellular hTERT mRNA dynamics. The antisense PNA component effectively reduced the hTERT mRNA level and downregulated telomerase activity via an antisense gene regulation pathway, while the pH-responsive release of DOX induced potent cancer cell apoptosis through chemotherapeutic action. This combinatorial therapeutic strategy demonstrated enhanced anticancer efficacy compared to single-modality treatments, achieving a 60% apoptosis induction in HeLa cells through coordinated gene silencing and chemotherapy. This study establishes GO as a promising dual-drug nanocarrier platform for developing next-generation theranostic systems that integrate molecular diagnostics with multimodal cancer therapy. Full article
(This article belongs to the Special Issue Fluorescent Probes for Bioimaging and Biosensors)
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136 pages, 24434 KB  
Perspective
Alzheimer’s Is a Multiform Disease of Sustained Neuronal Integrated Stress Response Driven by the C99 Fragment Generated Independently of AβPP; Proteolytic Production of Aβ Is Suppressed in AD-Affected Neurons: Evolution of a Theory
by Vladimir Volloch and Sophia Rits-Volloch
Int. J. Mol. Sci. 2025, 26(9), 4252; https://doi.org/10.3390/ijms26094252 - 29 Apr 2025
Viewed by 1695
Abstract
The present Perspective analyzes the remarkable evolution of the Amyloid Cascade Hypothesis 2.0 (ACH2.0) theory of Alzheimer’s disease (AD) since its inception a few years ago, as reflected in the diminishing role of amyloid-beta (Aβ) in the disease. In the initial iteration of [...] Read more.
The present Perspective analyzes the remarkable evolution of the Amyloid Cascade Hypothesis 2.0 (ACH2.0) theory of Alzheimer’s disease (AD) since its inception a few years ago, as reflected in the diminishing role of amyloid-beta (Aβ) in the disease. In the initial iteration of the ACH2.0, Aβ-protein-precursor (AβPP)-derived intraneuronal Aβ (iAβ), accumulated to neuronal integrated stress response (ISR)-eliciting levels, triggers AD. The neuronal ISR, in turn, activates the AβPP-independent production of its C99 fragment that is processed into iAβ, which drives the disease. The second iteration of the ACH2.0 stemmed from the realization that AD is, in fact, a disease of the sustained neuronal ISR. It introduced two categories of AD—conventional and unconventional—differing mainly in the manner of their causation. The former is caused by the neuronal ISR triggered by AβPP-derived iAβ, whereas in the latter, the neuronal ISR is elicited by stressors distinct from AβPP-derived iAβ and arising from brain trauma, viral and bacterial infections, and various types of inflammation. Moreover, conventional AD always contains an unconventional component, and in both forms, the disease is driven by iAβ generated independently of AβPP. In its third, the current, iteration, the ACH2.0 posits that proteolytic production of Aβ is suppressed in AD-affected neurons and that the disease is driven by C99 generated independently of AβPP. Suppression of Aβ production in AD seems an oxymoron: Aβ is equated with AD, and the later is inconceivable without the former in an ingrained Amyloid Cascade Hypothesis (ACH)-based notion. But suppression of Aβ production in AD-affected neurons is where the logic leads, and to follow it we only need to overcome the inertia of the preexisting assumptions. Moreover, not only is the generation of Aβ suppressed, so is the production of all components of the AβPP proteolytic pathway. This assertion is not a quantum leap (unless overcoming the inertia counts as such): the global cellular protein synthesis is severely suppressed under the neuronal ISR conditions, and there is no reason for constituents of the AβPP proteolytic pathway to be exempted, and they, apparently, are not, as indicated by the empirical data. In contrast, tau protein translation persists in AD-affected neurons under ISR conditions because the human tau mRNA contains an internal ribosomal entry site in its 5′UTR. In current mouse models, iAβ derived from AβPP expressed exogenously from human transgenes elicits the neuronal ISR and thus suppresses its own production. Its levels cannot principally reach AD pathology-causing levels regardless of the number of transgenes or the types of FAD mutations that they (or additional transgenes) carry. Since the AβPP-independent C99 production pathway is inoperative in mice, the current transgenic models have no potential for developing the full spectrum of AD pathology. What they display are only effects of the AβPP-derived iAβ-elicited neuronal ISR. The paper describes strategies to construct adequate transgenic AD models. It also details the utilization of human neuronal cells as the only adequate model system currently available for conventional and unconventional AD. The final alteration of the ACH2.0, introduced in the present Perspective, is that AβPP, which supports neuronal functionality and viability, is, after all, potentially produced in AD-affected neurons, albeit not conventionally but in an ISR-driven and -compatible process. Thus, the present narrative begins with the “omnipotent” Aβ capable of both triggering and driving the disease and ends up with this peptide largely dislodged from its pedestal and retaining its central role in triggering the disease in only one, although prevalent (conventional), category of AD (and driving it in none). Among interesting inferences of the present Perspective is the determination that “sporadic AD” is not sporadic at all (“non-familial” would be a much better designation). The term has fatalistic connotations, implying that the disease can strike at random. This is patently not the case: The conventional disease affects a distinct subpopulation, and the basis for unconventional AD is well understood. Another conclusion is that, unless prevented, the occurrence of conventional AD is inevitable given a sufficiently long lifespan. This Perspective also defines therapeutic directions not to be taken as well as auspicious ways forward. The former category includes ACH-based drugs (those interfering with the proteolytic production of Aβ and/or depleting extracellular Aβ). They are legitimate (albeit inefficient) preventive agents for conventional AD. There is, however, a proverbial snowball’s chance in hell of them being effective in symptomatic AD, lecanemab, donanemab, and any other “…mab” or “…stat” notwithstanding. They comprise Aβ-specific antibodies, inhibitors of beta- and gamma-secretase, and modulators of the latter. In the latter category, among ways to go are the following: (1) Depletion of iAβ, which, if sufficiently “deep”, opens up a tantalizing possibility of once-in-a-lifetime preventive transient treatment for conventional AD and aging-associated cognitive decline, AACD. (2) Composite therapy comprising the degradation of C99/iAβ and concurrent inhibition of the neuronal ISR. A single transient treatment could be sufficient to arrest the progression of conventional AD and prevent its recurrence for life. Multiple recurrent treatments would achieve the same outcome in unconventional AD. Alternatively, the sustained reduction/removal of unconventional neuronal ISR-eliciting stressors through the elimination of their source would convert unconventional AD into conventional one, preventable/treatable by a single transient administration of the composite C99/iAβ depletion/ISR suppression therapy. Efficient and suitable ISR inhibitors are available, and it is explicitly clear where to look for C99/iAβ-specific targeted degradation agents—activators of BACE1 and, especially, BACE2. Directly acting C99/iAβ-specific degradation agents such as proteolysis-targeting chimeras (PROTACs) and molecular-glue degraders (MGDs) are also viable options. (3) A circumscribed shift (either upstream or downstream) of the position of transcription start site (TSS) of the human AβPP gene, or, alternatively, a gene editing-mediated excision or replacement of a small, defined segment of its portion encoding 5′-untranslated region of AβPP mRNA; targeting AβPP RNA with anti-antisense oligonucleotides is another possibility. If properly executed, these RNA-based strategies would not interfere with the protein-coding potential of AβPP mRNA, and each would be capable of both preventing and stopping the AβPP-independent generation of C99 and thus of either preventing AD or arresting the progression of the disease in its conventional and unconventional forms. The paper is interspersed with “validation” sections: every conceptually significant notion is either validated by the existing data or an experimental procedure validating it is proposed. Full article
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23 pages, 2924 KB  
Article
Design and Binding Affinity of Antisense Peptides for Snake Venom Neutralization
by Ivan Biruš, Tino Šeba, Marin Marić, Mario Gabričević and Tin Weitner
Molecules 2025, 30(4), 903; https://doi.org/10.3390/molecules30040903 - 15 Feb 2025
Viewed by 959
Abstract
Snakebites are a significant public health problem in many tropical and subtropical regions, causing extensive morbidity and mortality. Traditional snake antivenoms face multiple challenges, including allergenicity, high production costs, and logistical difficulties, highlighting the urgent need for new therapeutic approaches. This pilot study [...] Read more.
Snakebites are a significant public health problem in many tropical and subtropical regions, causing extensive morbidity and mortality. Traditional snake antivenoms face multiple challenges, including allergenicity, high production costs, and logistical difficulties, highlighting the urgent need for new therapeutic approaches. This pilot study explores the potential of oligopeptides as therapeutic inhibitors targeting the neurotoxic sites of ammodytoxin A (AtxA; PDB: 3G8G) from Vipera ammodytes. We selected two sense oligopeptides to represent critical neurotoxic regions of AtxA as targets for inhibition by complementary antisense peptides. Utilizing a heuristic antisense peptide design based on the molecular recognition theory, we modeled two antisense oligopeptides as complementary counterparts for each sense oligopeptide. The modeled sense and antisense peptides were commercially synthesized, and their binding affinities were evaluated using spectrofluorometric titrations. The determined dissociation constants (KD) were in the range of 1–10 μM for all sense–antisense pairs, revealing relatively strong binding affinities. Confirmation of sense–antisense peptide binding prompted further investigation into their potential binding to the native target protein through global docking simulations using the HPEPDOCK web server. The results highlight the applicability of molecular recognition theory in the development of antisense peptides that could change therapeutic strategies in various biomedical fields. Further studies are needed to investigate the therapeutic efficacy and broader applications of these peptides. Full article
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25 pages, 867 KB  
Review
From Genetics to Neuroinflammation: The Impact of ApoE4 on Microglial Function in Alzheimer’s Disease
by Daniela Dias, Camila Cabral Portugal, João Relvas and Renato Socodato
Cells 2025, 14(4), 243; https://doi.org/10.3390/cells14040243 - 7 Feb 2025
Cited by 10 | Viewed by 5302
Abstract
Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder marked by progressive cognitive decline and memory loss, impacting millions of people around the world. The apolipoprotein E4 (ApoE4) allele is the most prominent genetic risk factor for late-onset AD, dramatically increasing disease susceptibility and [...] Read more.
Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder marked by progressive cognitive decline and memory loss, impacting millions of people around the world. The apolipoprotein E4 (ApoE4) allele is the most prominent genetic risk factor for late-onset AD, dramatically increasing disease susceptibility and accelerating onset compared to its isoforms ApoE2 and ApoE3. ApoE4’s unique structure, which arises from single-amino-acid changes, profoundly alters its function. This review examines the critical interplay between ApoE4 and microglia—the brain’s resident immune cells—and how this relationship contributes to AD pathology. We explore the molecular mechanisms by which ApoE4 modulates microglial activity, promoting a pro-inflammatory state, impairing phagocytic function, and disrupting lipid metabolism. These changes diminish microglia’s ability to clear amyloid-beta peptides, exacerbating neuroinflammation and leading to neuronal damage and synaptic dysfunction. Additionally, ApoE4 adversely affects other glial cells, such as astrocytes and oligodendrocytes, further compromising neuronal support and myelination. Understanding the ApoE4–microglia axis provides valuable insights into AD progression and reveals potential therapeutic targets. We discuss current strategies to modulate ApoE4 function using small molecules, antisense oligonucleotides, and gene editing technologies. Immunotherapies targeting amyloid-beta and ApoE4, along with neuroprotective approaches to enhance neuronal survival, are also examined. Future directions highlight the importance of personalized medicine based on individual ApoE genotypes, early biomarker identification for risk assessment, and investigating ApoE4’s role in other neurodegenerative diseases. This review emphasizes the intricate connection between ApoE4 and microglial dysfunction, highlighting the necessity of targeting this pathway to develop effective interventions. Advancing our understanding in this area holds promise for mitigating AD progression and improving outcomes for those affected by this relentless disease. Full article
(This article belongs to the Special Issue Glial Cells in Aging Neuroscience)
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23 pages, 7855 KB  
Article
Cell-Penetrating Peptide-Mediated Delivery of Gene-Silencing Nucleic Acids to the Invasive Common Reed Phragmites australis via Foliar Application
by Qing Ji, Kurt P. Kowalski, Edward M. Golenberg, Seung Ho Chung, Natalie D. Barker, Wesley A. Bickford and Ping Gong
Plants 2025, 14(3), 458; https://doi.org/10.3390/plants14030458 - 5 Feb 2025
Cited by 2 | Viewed by 1938
Abstract
As a popular tool for gene function characterization and gene therapy, RNA interference (RNAi)-based gene silencing has been increasingly explored for potential applications to control invasive species. At least two major hurdles exist when applying this approach to invasive plants: (1) the design [...] Read more.
As a popular tool for gene function characterization and gene therapy, RNA interference (RNAi)-based gene silencing has been increasingly explored for potential applications to control invasive species. At least two major hurdles exist when applying this approach to invasive plants: (1) the design and screening of species- and gene-specific biomacromolecules (i.e., gene-silencing agents or GSAs) made of DNA, RNA, or peptides that can suppress the expression of target genes efficiently, and (2) the delivery vehicle needed to penetrate plant cell walls and other physical barriers (e.g., leaf cuticles). In this study, we investigated the cell-penetrating peptide (CPP)-mediated delivery of multiple types of GSAs (e.g., double-stranded RNA (dsRNA), artificial microRNA (amiRNA), and antisense oligonucleotide (ASO)) to knock down a putative phytoene desaturase (PDS) gene in the invasive common reed (Phragmites australis spp. australis). Both microscopic and quantitative gene expression evidence demonstrated the CPP-mediated internalization of GSA cargos and transient suppression of PDS expression in both treated and systemic leaves up to 7 days post foliar application. Although various GSA combinations and application rates and frequencies were tested, we observed limitations, including low gene-silencing efficiency and a lack of physiological trait alteration, likely owing to low CPP payload capacity and the incomplete characterization of the PDS-coding genes (e.g., the recent discovery of two PDS paralogs) in P. australis. Our work lays a foundation to support further research toward the development of convenient, cost-effective, field-deployable, and environmentally benign gene-silencing technologies for invasive P. australis management. Full article
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22 pages, 1150 KB  
Review
Endosomal Escape and Nuclear Localization: Critical Barriers for Therapeutic Nucleic Acids
by Randall Allen and Toshifumi Yokota
Molecules 2024, 29(24), 5997; https://doi.org/10.3390/molecules29245997 - 19 Dec 2024
Cited by 10 | Viewed by 5801
Abstract
Therapeutic nucleic acids (TNAs) including antisense oligonucleotides (ASOs) and small interfering RNA (siRNA) have emerged as promising treatment strategies for a wide variety of diseases, offering the potential to modulate gene expression with a high degree of specificity. These small, synthetic nucleic acid-like [...] Read more.
Therapeutic nucleic acids (TNAs) including antisense oligonucleotides (ASOs) and small interfering RNA (siRNA) have emerged as promising treatment strategies for a wide variety of diseases, offering the potential to modulate gene expression with a high degree of specificity. These small, synthetic nucleic acid-like molecules provide unique advantages over traditional pharmacological agents, including the ability to target previously “undruggable” genes. Despite this promise, several biological barriers severely limit their clinical efficacy. Upon administration, TNAs primarily enter cells through endocytosis, becoming trapped inside membrane-bound vesicles known as endosomes. Studies estimate that only 1–2% of TNAs successfully escape endosomal compartments to reach the cytosol, and in some cases the nucleus, where they bind target mRNA and exert their therapeutic effect. Endosomal entrapment and inefficient nuclear localization are therefore critical bottlenecks in the therapeutic application of TNAs. This review explores the current understanding of TNA endosomal escape and nuclear transport along with strategies aimed at overcoming these challenges, including the use of endosomal escape agents, peptide-TNA conjugates, non-viral delivery vehicles, and nuclear localization signals. By improving both endosomal escape and nuclear localization, significant advances in TNA-based therapeutics can be realized, ultimately expanding their clinical utility. Full article
(This article belongs to the Section Chemical Biology)
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24 pages, 725 KB  
Review
Antibiofilm Effects of Novel Compounds in Otitis Media Treatment: Systematic Review
by Ana Jotic, Katarina Savic Vujovic, Andja Cirkovic, Dragana D. Božić, Snezana Brkic, Nikola Subotic, Bojana Bukurov, Aleksa Korugic and Ivana Cirkovic
Int. J. Mol. Sci. 2024, 25(23), 12841; https://doi.org/10.3390/ijms252312841 - 29 Nov 2024
Cited by 1 | Viewed by 3111
Abstract
Otitis media (OM) is a frequent disease with incidence rate of 5300 cases per 100,000 people. Recent studies showed that polymicrobial biofilm formation represents a significant pathogenic mechanism in recurrent and chronic forms of OM. Biofilm enables bacteria to resist antibiotics that would [...] Read more.
Otitis media (OM) is a frequent disease with incidence rate of 5300 cases per 100,000 people. Recent studies showed that polymicrobial biofilm formation represents a significant pathogenic mechanism in recurrent and chronic forms of OM. Biofilm enables bacteria to resist antibiotics that would typically be recommended in guidelines, contributing to the ineffectiveness of current antimicrobial strategies. Given the challenges of successfully treating bacterial biofilms, there is an growing interest in identifying novel and effective compounds to overcome antibacterial resistance. The objective of this review was to provide an overview of the novel compounds with antibiofilm effects on bacterial biofilm formed by clinical isolates of OM. The systematic review included studies that evaluated antibiofilm effect of novel natural or synthetic compounds on bacterial biofilm formed from clinical isolates obtained from patients with OM. The eligibility criteria were defined using the PICOS system: (P) Population: all human patients with bacterial OM; (I) Intervention: novel natural or synthetic compound with biofilm effect; (C) Control standard therapeutic antimicrobial agents or untreated biofilms, (O) Outcome: antibiofilm effect (biofilm inhibition, biofilm eradication), (S) Study design. The PRISMA protocol for systematic reviews and meta-analysis was followed. From 3564 potentially eligible studies, 1817 duplicates were removed, and 1705 were excluded according to defined exclusion criteria. A total of 41 studies with available full texts were retrieved by two independent authors. Fifteen articles were selected for inclusion in the systematic review which included 125 patients with OM. A total of 17 different novel compounds were examined, including N-acetyl-L-cysteine (NAC), tea tree oil, xylitol, eugenol, Aloe barbadensis, Zingiber officinale, Curcuma longa, Acacia arabica, antisense peptide nucleic acids, probiotics Streptococcus salivarius and Streptococcus oralis, Sodium 2-mercaptoethanesulfonate (MESNA), bioactive glass, green synthesized copper oxide nanoparticles, radish, silver nanoparticles and acetic acid. Staphylococcus aureus was the most commonly studied pathogen, followed by Pseudomonas aeruginosa and Haemophilus influenzae. Biofilm inhibition only by an examined compound was assessed in six studies; biofilm eradication in four studies, and both biofilm inhibition and biofilm eradication were examined in five studies. This systematic review indicates that some compounds like NAC, prebiotics, nanoparticles and MESNA that have significant effects on biofilm are safe and could be researched more extensively for further clinical use. However, a lack of data about reliable and efficient compounds used in therapy of different types of otitis media still remains in the literature. Full article
(This article belongs to the Special Issue Biofilm Antimicrobial Strategies: Outlook and Future Perspectives)
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