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Keywords = proteolysis inhibitors

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20 pages, 1953 KiB  
Review
Limited Proteolysis as a Regulator of Lymphatic Vessel Function and Architecture
by Takuro Miyazaki
Int. J. Mol. Sci. 2025, 26(15), 7144; https://doi.org/10.3390/ijms26157144 - 24 Jul 2025
Viewed by 174
Abstract
Recent advances have highlighted the multifaceted roles of the lymphatic vasculature in immune cell trafficking, immunomodulation, nutrient transport, and fluid homeostasis. Beyond these physiological functions, lymphatic vessels are critically involved in pathologies such as cancer metastasis and lymphedema, rendering their structural and functional [...] Read more.
Recent advances have highlighted the multifaceted roles of the lymphatic vasculature in immune cell trafficking, immunomodulation, nutrient transport, and fluid homeostasis. Beyond these physiological functions, lymphatic vessels are critically involved in pathologies such as cancer metastasis and lymphedema, rendering their structural and functional regulation of major interest. Emerging evidence suggests that limited proteolysis is a key regulatory mechanism for lymphatic vascular function. In dyslipidemic conditions, dysregulated calpain activity impairs lymphatic trafficking and destabilizes regulatory T cells, partly via the limited proteolysis of mitogen-activated kinase kinase kinase 1 and inhibitor of κBα. In addition, a disintegrin and metalloprotease with thrombospondin motifs-3-mediated proteolytic activation of vascular endothelial growth factor-C has been implicated in both developmental and tumor-associated lymphangiogenesis. Proteolytic shedding of lymphatic vessel endothelial hyaluronan receptor-1 by a disintegrin and metalloprotease 17 promotes lymphangiogenesis, whereas cleavage by membrane-type 1 matrix metalloproteinase inhibits it. This review is structured around two core aspects—lymphatic inflammation and lymphangiogenesis—and highlights recent findings on how limited proteolysis regulates each of these processes. It also discusses the therapeutic potential of targeting these proteolytic machineries and currently unexplored research questions, such as how intercellular junctions of lymphatic endothelial cells are controlled. Full article
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63 pages, 3732 KiB  
Review
TrypPROTACs Unlocking New Therapeutic Strategies for Chagas Disease
by Ana Luísa Rodriguez Gini, Pamela Souza Tada da Cunha, Emílio Emílio João, Chung Man Chin, Jean Leandro dos Santos, Esteban Carlos Serra and Cauê Benito Scarim
Pharmaceuticals 2025, 18(6), 919; https://doi.org/10.3390/ph18060919 - 19 Jun 2025
Viewed by 1396
Abstract
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi), continues to pose significant public health challenges due to the toxicity, poor tolerability, and limited efficacy of current treatments. Targeted protein degradation (TPD) using proteolysis-targeting chimeras (PROTACs) represents a novel [...] Read more.
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi), continues to pose significant public health challenges due to the toxicity, poor tolerability, and limited efficacy of current treatments. Targeted protein degradation (TPD) using proteolysis-targeting chimeras (PROTACs) represents a novel therapeutic avenue by leveraging the ubiquitin–proteasome system to selectively degrade essential parasite proteins. This review introduces the conceptual framework of “TrypPROTACs” as a prospective strategy for T. cruzi, integrating a comprehensive analysis of druggable targets across critical biological pathways, including ergosterol biosynthesis, redox metabolism, glycolysis, nucleotide synthesis, protein kinases, molecular chaperones such as heat shock protein 90 (Hsp90), and epigenetic regulators such as T. cruzi bromodomain factor 3 (TcBDF3). It is important to note that no TrypPROTAC compound has yet been synthesized or experimentally validated in T. cruzi; the approach discussed herein remains theoretical and forward-looking. Representative inhibitors for each target class are compiled, highlighting potency, selectivity, and structural features relevant to ligand design. We also examine the parasite’s ubiquitination machinery and compare it to the human system to identify putative E3 ubiquitin ligases. Key aspects of linker engineering and ternary complex stabilization are discussed, alongside potential validation techniques such as the cellular thermal shift assay (CETSA) and bioluminescence resonance energy transfer (NanoBRET). Collectively, these insights outline a roadmap for the rational design of TrypPROTACs and support the feasibility of expanding targeted protein degradation strategies to neglected tropical diseases. Full article
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20 pages, 2505 KiB  
Review
Emerging Concepts of Targeted Protein Degrader Technologies via Lysosomal Pathways
by Mohammad Maqusood Alam, Sobia Wasim and Sang-Yoon Lee
Int. J. Mol. Sci. 2025, 26(12), 5582; https://doi.org/10.3390/ijms26125582 - 11 Jun 2025
Viewed by 1055
Abstract
Targeted protein degradation (TPD) has emerged as a revolutionary strategy for modulating protein function, offering a promising alternative to traditional small-molecule inhibitors. The distinctive mechanism of action in TPD has previously allowed researchers to target undruggable proteins, broadening the scope of “druggable” properties [...] Read more.
Targeted protein degradation (TPD) has emerged as a revolutionary strategy for modulating protein function, offering a promising alternative to traditional small-molecule inhibitors. The distinctive mechanism of action in TPD has previously allowed researchers to target undruggable proteins, broadening the scope of “druggable” properties and expanding the scope of therapeutic possibilities. As the field of TPD advances, several alternative strategies to proteolysis-targeting chimeras (PROTACs) have emerged, which do not rely on the E3 ubiquitin ligase recruitment mechanism, expending the scope of TPD. Recently, several new technologies have emerged for TPD of extracellular and membrane proteins. While encouraging progress has been made in this field, the application of these technologies remains in its early stages. In this review, we explore the therapeutic potential of current key emerging lysosome-mediated TPD approaches by summarizing key discoveries and address the challenges associated with degrading extracellular and membrane protein targets. We also outline the chemical structure, activity, and pharmaceutical properties of each degrader, as well as the development of chemical probes for perturbing autophagy pathways. Full article
(This article belongs to the Section Molecular Pharmacology)
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17 pages, 1965 KiB  
Article
The Role of Long-Range Non-Specific Electrostatic Interactions in Inhibiting the Pre-Fusion Proteolytic Processing of the SARS-CoV-2 S Glycoprotein by Heparin
by Yi Du, Yang Yang, Son N. Nguyen and Igor A. Kaltashov
Biomolecules 2025, 15(6), 778; https://doi.org/10.3390/biom15060778 - 28 May 2025
Viewed by 501
Abstract
The proteolytic processing of the SARS-CoV-2 spike glycoprotein by host cell membrane-associated proteases is a key step in both the entry of the invading virus into the cell and the release of the newly generated viral particles from the infected cell. Because of [...] Read more.
The proteolytic processing of the SARS-CoV-2 spike glycoprotein by host cell membrane-associated proteases is a key step in both the entry of the invading virus into the cell and the release of the newly generated viral particles from the infected cell. Because of the critical importance of this step for the viral infectivity cycle, it has been a target of extensive efforts aimed at identifying highly specific protease inhibitors as potential antiviral agents. An alternative strategy to disrupt the pre-fusioviden processing of the SARS-CoV-2 S glycoprotein aims to protect the substrate rather than directly inhibit the proteases. In this work, we focused on furin, a serine protease located primarily in the Golgi apparatus, but also present on the cell membrane. Its cleavage site within the S glycoprotein is located within the stalk region of the latter and comprises an arginine-rich segment (SPRRARS), which fits the definition of the Cardin–Weintraub glycosaminoglycan recognition motif. Native mass spectrometry (MS) measurements confirmed the binding of a hexadecameric peptide representing the loop region at the S1/S2 interface and incorporating the furin cleavage site (FCS) to heparin fragments of various lengths, as well as unfractionated heparin (UFH), although at the physiological ionic strength, only UFH remains tightly bound to the FCS. The direct LC/MS monitoring of FCS digestion with furin revealed a significant impact of both heparin fragments and UFH on the proteolysis kinetics, although only the latter had IC50 values that could be considered physiologically relevant (0.6 ± 0.1 mg/mL). The results of this work highlight the importance of the long-range and relatively non-specific electrostatic interactions in modulating physiological and pathological processes and emphasize the multi-faceted role played by heparin in managing coronavirus infections. Full article
(This article belongs to the Special Issue Molecular Mechanism and Detection of SARS-CoV-2)
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136 pages, 24434 KiB  
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 1349
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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13 pages, 2709 KiB  
Article
Development of Peptidomimetic PROTACs as Potential Degraders of 3-Chymotrypsin-like Protease of SARS-CoV-2
by Chao Wei, Yuhua Li, Lina Guo, Zhiyu Shao and Hua Diao
Int. J. Mol. Sci. 2025, 26(8), 3903; https://doi.org/10.3390/ijms26083903 - 21 Apr 2025
Viewed by 726
Abstract
3CL protease (3CLpro), a key enzyme of SARS-CoV-2 replication, is one of the most selective targets of antivirals, as no homologous protease has been recognized in the human body. As proteolysis-targeting chimeras (PROTACs) are superior to traditional inhibitors, based on the [...] Read more.
3CL protease (3CLpro), a key enzyme of SARS-CoV-2 replication, is one of the most selective targets of antivirals, as no homologous protease has been recognized in the human body. As proteolysis-targeting chimeras (PROTACs) are superior to traditional inhibitors, based on the reported cereblon (CRBN) ligands thalidomide and lenalidomide, 3CLpro ligands of peptidomimetic inhibitors, and suitable linkers, we aimed to develop novel PROTACs that may trigger efficient intracellular 3CLpro degradation through a balance of hydrophilicity and lipophilicity. In brief, we designed and synthesized 5 PROTAC molecules. The 3CLpro degradation efficiency of the PROTACs was assayed in stable SARS-CoV-2 3CLpro expression HEK293 cell models and evaluated by Western blot. All compounds showed prominent 3CLpro degradation activity with tolerable HEK293 cytotoxicity. The most prominent PROTAC compounds, 15 and 16, have DC50 values of approximately 1 µM, and Dmax of 89.3% and 75% respectively, indicating good potential for further application. Full article
(This article belongs to the Section Molecular Microbiology)
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27 pages, 6986 KiB  
Article
Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, Rhynchophorus ferrugineus
by Nazmi Harith-Fadzilah, Mohammad Nihad, Mohammed Ali AlSaleh, Abdulqader Yaslam Bazeyad, Subash-Babu Pandurangan, Kashif Munawar, Arya Vidyawan, Hattan A. Alharbi, Jernej Jakše, Arnab Pain and Binu Antony
Insects 2025, 16(4), 421; https://doi.org/10.3390/insects16040421 - 17 Apr 2025
Viewed by 796
Abstract
The red palm weevil, Rhynchophorus ferrugineus, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening [...] Read more.
The red palm weevil, Rhynchophorus ferrugineus, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target R. ferrugineus proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes, annotated DE-related genes from the R. ferrugineus gut and abdomen, manually annotated the DE gene family from the recently available genome and our transcriptome data, and reported 34 glycosidases, 85 lipases, and 201 proteases. We identified several tandem duplicates and allelic variants from the lipase and protease families, notably, 10 RferLip and 21 RferPro alleles, which emerged primarily through indels and single-site substitution. These alleles may confer enhanced digestive lipolysis and proteolysis. Phylogenetic analyses identified and classified different subfamilies of DEs and revealed close evolutionary relationships with other coleopterans. We assessed select candidate DEs’ activity and the potential for inhibition in silico to better understand the herbivory arsenal. In silico analysis revealed that the selected enzymes exhibited similar ligand-binding affinity to their corresponding substrate, except for protease aminopeptidase N, RferPro40, which exhibited poorer affinity to the inhibitor bestatin. Overall, our study serves as a foundation for further functional analysis and offers a novel target for the development of a novel bio-rational insecticide for R. ferrugineus. Full article
(This article belongs to the Special Issue Natural Metabolites as Biocontrol Agents of Insect Pests)
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21 pages, 1089 KiB  
Review
Modulation of Lonp1 Activity by Small Compounds
by Giada Zanini, Giulia Micheloni, Giorgia Sinigaglia, Valentina Selleri, Anna Vittoria Mattioli, Milena Nasi, Ciro Leonardo Pierri and Marcello Pinti
Biomolecules 2025, 15(4), 553; https://doi.org/10.3390/biom15040553 - 9 Apr 2025
Viewed by 1380
Abstract
The Lon protease homolog 1 (LONP1) is an ATP-dependent mitochondrial protease essential for maintaining proteostasis, bioenergetics, and cellular homeostasis. LONP1 plays a pivotal role in protein quality control, mitochondrial DNA maintenance, and oxidative phosphorylation system (OXPHOS) regulation, particularly under stress conditions. Dysregulation of [...] Read more.
The Lon protease homolog 1 (LONP1) is an ATP-dependent mitochondrial protease essential for maintaining proteostasis, bioenergetics, and cellular homeostasis. LONP1 plays a pivotal role in protein quality control, mitochondrial DNA maintenance, and oxidative phosphorylation system (OXPHOS) regulation, particularly under stress conditions. Dysregulation of LONP1 has been implicated in various pathologies, including cancer, metabolic disorders, and reproductive diseases, positioning it as a promising pharmacological target. This review examines compounds that modulate LONP1 activity, categorizing them into inhibitors and activators. Inhibitors such as CDDO and its derivatives selectively target LONP1, impairing mitochondrial proteolysis, inducing protein aggregation, and promoting apoptosis, particularly in cancer cells. Compounds like Obtusilactone A and proteasome inhibitors (e.g., MG262) demonstrate potent cytotoxicity, further expanding the therapeutic landscape. Conversely, LONP1 activators, including Artemisinin derivatives and 84-B10, restore mitochondrial function and protect against conditions such as polycystic ovary syndrome (PCOS) and acute kidney injury (AKI). Future research should focus on improving the specificity, bioavailability, and pharmacokinetics of these modulators. Advances in structural biology and drug discovery will enable the development of novel LONP1-targeted therapies, addressing diseases driven by mitochondrial dysfunction and proteostasis imbalance. Full article
(This article belongs to the Section Molecular Medicine)
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24 pages, 4745 KiB  
Article
“Villains” Turning Good: Antimycin A and Rotenone, Mitochondrial Respiratory Chain Inhibitors, Protect H9c2 Cardiac Cells Against Insults Triggering the Intrinsic Apoptotic Pathway
by Kyriaki Zikaki, Eleni Kiachaki, Catherine Gaitanaki and Ioanna-Katerina Aggeli
Int. J. Mol. Sci. 2025, 26(6), 2435; https://doi.org/10.3390/ijms26062435 - 8 Mar 2025
Viewed by 1464
Abstract
Mitochondria are the powerhouses of cells, also involved in ROS (reactive oxygen species) generation and cellular death regulation. Thus, several diseases are associated with mitochondrial impairment, including cardiovascular disorders (CVDs). Since CVDs are currently the leading cause of death worldwide, it is very [...] Read more.
Mitochondria are the powerhouses of cells, also involved in ROS (reactive oxygen species) generation and cellular death regulation. Thus, several diseases are associated with mitochondrial impairment, including cardiovascular disorders (CVDs). Since CVDs are currently the leading cause of death worldwide, it is very important to evaluate targeting mitochondrial effectors in clinical treatment protocols. Hence, in the present study, antimycin A and rotenone, established inhibitors of the mitochondrial electron transfer chain, were shown to halt apoptotic death induced by curcumin (50 μM) and sorbitol (0.5 M), in H9c2 cardiac cells. In particular, immunoblotting analysis revealed that they totally abolished PARP [poly(ADP-ribose) polymerase] proteolysis, under these conditions. This finding was accompanied by an enhancement of cell viability, recovery of mitochondria networks’ integrity, suppression of cytochrome c release into the cytoplasm, and reversal of chromatin condensation. Chelating extracellular calcium (with EGTA) further enhanced the beneficial impact of antimycin A and rotenone on curcumin- or sorbitol-treated H9c2 cells viability. Of interest, the phosphorylation of eIF2α, indicative of the onset of the pro-survival Integrated Stress Response (IRS), was sustained under these conditions. Overall, our data highlight the anti-apoptotic effect of these compounds, unmasking their potential as mediators in novel therapeutic interventions against mitochondria-associated cardiac dysfunction. Full article
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14 pages, 2648 KiB  
Review
CSN-CRL Complexes: New Regulators of Adipogenesis
by Dawadschargal Dubiel, Michael Naumann and Wolfgang Dubiel
Biomolecules 2025, 15(3), 372; https://doi.org/10.3390/biom15030372 - 5 Mar 2025
Viewed by 957
Abstract
Recent discoveries revealed mechanistic insights into the control of adipogenesis by the Constitutive Photomorphogenesis 9 Signalosome (CSN) and its variants, CSNCSN7A and CSNCSN7B, which differ in the paralog subunits, CSN7A and CSN7B. CSNCSN7A and CSNCSN7B variants form permanent [...] Read more.
Recent discoveries revealed mechanistic insights into the control of adipogenesis by the Constitutive Photomorphogenesis 9 Signalosome (CSN) and its variants, CSNCSN7A and CSNCSN7B, which differ in the paralog subunits, CSN7A and CSN7B. CSNCSN7A and CSNCSN7B variants form permanent complexes with cullin-RING-ubiquitin ligases 3 and 4A (CRL3 and CRL4A), respectively. These complexes can be found in most eukaryotic cells and represent a critical reservoir for cellular functions. In an early stage of adipogenesis, mitotic clonal expansion (MCE), CSN-CRL1, and CSNCSN7B-CRL4A are blocked to ubiquitinate the cell cycle inhibitor p27KIP, leading to cell cycle arrest. In addition, in MCE CSN-CRL complexes rearrange the cytoskeleton for adipogenic differentiation and CRL3KEAP1 ubiquitylates the inhibitor of adipogenesis C/EBP homologous protein (CHOP) for degradation by the 26S proteasome, an adipogenesis-specific proteolysis. During terminal adipocyte differentiation, the CSNCSN7A-CRL3 complex is recruited to a lipid droplet (LD) membrane by RAB18. Currently, the configuration of the substrate receptors of CSNCSN7A-CRL3 on LDs is unclear. CSNCSN7A-CRL3 is activated by neddylation on the LD membrane, an essential adipogenic step. Damage to CSN/CUL3/CUL4A genes is associated with diverse diseases, including obesity. Due to the tremendous impact of CSN-CRLs on adipogenesis, we need strategies for adequate treatment in the event of malfunctions. Full article
(This article belongs to the Section Molecular Biology)
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30 pages, 400 KiB  
Review
Novel Therapeutics in Soft Tissue Sarcoma
by Leonidas Mavroeidis, Andrea Napolitano, Paul Huang and Robin L. Jones
Cancers 2025, 17(1), 10; https://doi.org/10.3390/cancers17010010 - 24 Dec 2024
Cited by 4 | Viewed by 2702
Abstract
There has been noteworthy progress in molecular characterisation and therapeutics in soft tissue sarcomas. Novel agents have gained regulatory approval by the FDA. Examples are the tyrosine kinase inhibitors avapritinib and ripretinib in gastrointestinal stromal tumours (GIST), the immune check point inhibitor atezolizumab [...] Read more.
There has been noteworthy progress in molecular characterisation and therapeutics in soft tissue sarcomas. Novel agents have gained regulatory approval by the FDA. Examples are the tyrosine kinase inhibitors avapritinib and ripretinib in gastrointestinal stromal tumours (GIST), the immune check point inhibitor atezolizumab in alveolar soft part tissue sarcoma, the γ-secretase inhibitor nirogacestat in desmoid tumours, the NTRK inhibitors larotrectinib and entrectinib in tumours with NTRK fusions, the mTOR inhibitor nab-sirolimus in PEComa, and the EZH-2 inhibitor tazemetostat in epithelioid sarcoma. The FDA has also recently granted accelerated approval for autologous T-cell therapy with afami-cel in patients with HLA-A*02 and MAGE-A4-expressing synovial sarcoma. There are other promising treatments that are still investigational, such as MDM2 and CDK4/6 inhibitors in well-/dedifferentiated liposarcoma, immune checkpoint inhibitors in the head and neck angiosarcoma and a subset of patients with undifferentiated pleomorphic sarcoma, and PARP inhibitors in leiomyosarcoma. The challenges in drug development in soft tissue sarcoma are due to the rarity and the molecular heterogeneity of the disease and the fact that many subtypes are associated with complex karyotypes or non-targetable molecular alterations. We believe that progress maybe possible with a better understanding of the complex biology, the development of novel compounds for difficult targets such as proteolysis targeting chimeras (Protacs), the utilisation of modern clinical trial designs, and enhanced collaboration of academia with industry to develop treatments with a strong biologic rationale. Full article
(This article belongs to the Special Issue Advances in Cancer Therapeutics)
14 pages, 1694 KiB  
Article
Effects of Suwari Suppression and Enzyme Inhibitors on Water Holding Capacity of Alaska Pollock (Theragra chalcogramma) Surimi Gel and Its Improvement by Modified Grinding Method
by Yusa Nakamura and Kigen Takahashi
Fishes 2024, 9(12), 504; https://doi.org/10.3390/fishes9120504 - 10 Dec 2024
Cited by 1 | Viewed by 1122
Abstract
The processes before heating in surimi gel production, such as grinding and molding, are performed below 10 °C to prevent unintentional protein gelation (suwari or setting) catalyzed by endogenous transglutaminase. Adding transglutaminase and protease inhibitors contributes to obtaining surimi gel with superior breaking [...] Read more.
The processes before heating in surimi gel production, such as grinding and molding, are performed below 10 °C to prevent unintentional protein gelation (suwari or setting) catalyzed by endogenous transglutaminase. Adding transglutaminase and protease inhibitors contributes to obtaining surimi gel with superior breaking properties after suwari suppression. However, the impact of suwari suppression and enzyme inhibitors on the water holding capacity (WHC) of surimi gel remains unclear. This study investigated changes in the WHC of surimi gel during long-term suwari suppression by adding enzyme inhibitors at 25 °C and clarified its mechanism. The expressible drip of samples with EGTA, a transglutaminase inhibitor, increased with heating time at 25 °C to 12.3% owing to proteolysis. The use of N-ethylmaleimide and E-64, cysteine protease inhibitors, further increased the expressible drip of samples (18.9–19.4%) because of protein conformational changes which were observed by DSC analysis and salt solubility measurement. However, this increase was inhibited by a modified grinding method where NaCl was mixed with surimi before adding enzyme inhibitors. This modified method prevented the reduction in protein salt solubility due to protein conformational changes, thereby maintaining WHC in surimi gel with suwari suppression. Full article
(This article belongs to the Section Processing and Comprehensive Utilization of Fishery Products)
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22 pages, 19618 KiB  
Article
Advanced PROTAC and Quantitative Proteomics Strategy Reveals Bax Inhibitor-1 as a Critical Target of Icaritin in Burkitt Lymphoma
by Peixi Zhang, Ziqing Zhang, Jie Li, Meng Xu, Weiming Lu, Ming Chen, Jiaqi Shi, Qiaolai Wang, Hengyuan Zhang, Shi Huang, Chenlei Lian, Jia Liu, Junjie Ma and Jieqing Liu
Int. J. Mol. Sci. 2024, 25(23), 12944; https://doi.org/10.3390/ijms252312944 - 2 Dec 2024
Viewed by 1536
Abstract
Understanding the molecular targets of natural products is crucial for elucidating their mechanisms of action, mitigating toxicity, and uncovering potential therapeutic pathways. Icaritin (ICT), a bioactive flavonoid, demonstrates significant anti-tumor activity but lacks defined molecular targets. This study employs an advanced strategy integrating [...] Read more.
Understanding the molecular targets of natural products is crucial for elucidating their mechanisms of action, mitigating toxicity, and uncovering potential therapeutic pathways. Icaritin (ICT), a bioactive flavonoid, demonstrates significant anti-tumor activity but lacks defined molecular targets. This study employs an advanced strategy integrating proteolysis targeting chimera (PROTAC) technology with quantitative proteomics to identify ICT’s key targets. A library of 22 ICT-based PROTAC derivatives were synthesized, among which LJ-41 exhibited a superior IC50 of 5.52 μM against Burkitt lymphoma (CA-46) cells. Then, differential proteomic analysis identified Bax inhibitor-1 (BI-1) as a potential target. Target validation techniques, including cellular thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) assay, surface plasmon resonance (SPR) assay, and molecular docking, confirmed LJ-41’s high specificity for BI-1. Mechanistic investigations revealed that LJ-41 induces apoptosis through BI-1 degradation, triggering endoplasmic reticulum stress and activating inositol-requiring enzyme 1 α (IRE1α), activating transcription factor 6 (ATF6), and nuclear factor erythroid 2-related factor transcription factor heme oxygenase 1 (NRF2-HO-1) signaling pathways. This study establishes a refined methodological framework for natural product target discovery and highlights ICT-PROTAC derivatives’ potential for clinical application in Burkitt lymphoma treatment. Full article
(This article belongs to the Section Molecular Oncology)
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15 pages, 492 KiB  
Review
Recent Advances in Peptide Drug Discovery: Novel Strategies and Targeted Protein Degradation
by Katarina Vrbnjak and Raj Nayan Sewduth
Pharmaceutics 2024, 16(11), 1486; https://doi.org/10.3390/pharmaceutics16111486 - 20 Nov 2024
Cited by 2 | Viewed by 3695
Abstract
Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significantly improved the [...] Read more.
Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significantly improved the efficiency of peptide drug discovery when compared with traditional in vitro and in vivo methods, cutting costs and improving their reliability. An added benefit of peptide-based drugs is the ability to precisely target protein–protein interactions, which are normally a particularly challenging aspect of drug discovery. Another recent breakthrough in this field is targeted protein degradation through proteolysis-targeting chimeras. These revolutionary compounds represent a noteworthy advancement over traditional small-molecule inhibitors due to their unique mechanism of action, which allows for the degradation of specific proteins with unprecedented specificity. The inclusion of a peptide as a protein-of-interest-targeting moiety allows for improved versatility and the possibility of targeting otherwise undruggable proteins. In this review, we discuss various novel wet-lab and computational multi-omic methods for peptide drug discovery, provide an overview of therapeutic agents discovered through these cutting-edge techniques, and discuss the potential for the therapeutic delivery of peptide-based drugs. Full article
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16 pages, 5977 KiB  
Article
Novel Deep Sea Isoindole Alkaloid FGFC1 Exhibits Its Fibrinolytic Effects by Inhibiting Thrombin-Activatable Fibrinolysis Inhibitor
by Haixing Zhang, Xiaozhen Diao, Tingting Jiang, Mingjun Wei, Yue Su, Jingjing Shen, Chunlin Bao and Wenhui Wu
Pharmaceuticals 2024, 17(10), 1401; https://doi.org/10.3390/ph17101401 - 20 Oct 2024
Viewed by 1301
Abstract
Background: The thrombin-activatable fibrinolysis inhibitor (TAFI) is an important regulator in the balance between blood clot formation (coagulation) and dissolution (fibrinolysis), which is mainly activated by thrombin bonded with thrombomodulin (TM). Methods: In this study, the investigation focused on the unique target TAFI [...] Read more.
Background: The thrombin-activatable fibrinolysis inhibitor (TAFI) is an important regulator in the balance between blood clot formation (coagulation) and dissolution (fibrinolysis), which is mainly activated by thrombin bonded with thrombomodulin (TM). Methods: In this study, the investigation focused on the unique target TAFI of fungi fibrinolytic compound 1 (FGFC1), a novel fibrinolytic compound sourced from the deep sea. In this sense, the regulation of TAFI by FGFC1, in comparison to established TAFI inhibitors such as DS-1040 and PCTI in hPPP, was investigated, which was validated through the molecular docking of FGFC1 to TAFI. The inhibitory effect of FGFC1 on TAFI-mediating coagulation (ex vivo and in vitro) and its fibrinolytic effect (ex vivo) were investigated in hPPP and hCMEC/D3 cells, respectively, followed by SEM. Results: FGFC1 solutions ranging from 0.023 to 0.736 mM effectively inhibited TAFI activation. Notably, the 0.023 mM concentration demonstrated significant suppression, comparable to DS-1040 and PCTI. These inhibitory effects of FGFC1 (0.023–0.368 mM) were further validated through the enhancement in TAFI (TAFIa) activation by fibrins in the coagulum prior to proteolysis, resulting in the cleavage of TAFIa from 33 kDa to 28 kDa. Furthermore, these regulatory effects of FGFC1 on TAFI were demonstrated to have minimal association with TM-mediated control, as confirmed through a molecular docking analysis. FGFC1 (0.023–0.092 mM) was suggested to have obstructive effects on TAFI-mediated coagulation in the hPPP, which was demonstrated by the inhibition of clot aggregation, protein crystallization, and platelet anchoring, as observed through SEM. Simultaneously, FGFC1 (0.023 to 0.368 mM) significantly enhanced TAFI-mediated fibrinolysis, which was also supported by increased levels of t-PA, u-PA, and plasmin. Conclusions: From the above findings, FGFC1 is identified as a novel dual-target bioactive compound participating in blood formation/dissolution that demonstrates anti-coagulation and fibrinolytic effects by regulating TAFI activation, inhibiting TAFIa–fibrin combination, and initiating proteolysis. It also provided convincing evidence that TAFI plays a critical role in thrombolysis as a molecular link between coagulation and fibrinolysis. Furthermore, the application of FGFC1 was indicated as a potential therapeutic strategy in thromboembolic and hemorrhagic diseases. Full article
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