BioChem

The elderly population is growing worldwide. Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed, but their adverse events can pose significant risks. Different NSAID molecules can exhibit varying risk profiles. This study aims to evaluate the cardiovascular, gastrointestinal, and renal safety profiles of ibuprofen, naproxen, acemetacin, diclofenac, celecoxib, and etoricoxib in elderly patients. A comprehensive literature search was conducted in PubMed and Cochrane Library. For the selection of articles, we used Medical Subject Headings (MeSH) terms “aged” sequentially and together with “ibuprofen”, “diclofenac”, “naproxen”, “acemetacin”, “celecoxib”, and “etoricoxib”. To assess the quality and interest of the articles, four independent reviewers screened titles and abstracts to identify potentially eligible studies. Strength of Recommendation Taxonomy (SORT) was used to rate the quality of individual studies and to establish recommendation strengths (RS). From 2086 articles identified, 39 studies met the inclusion criteria. Twenty studies analyzed cardiovascular safety, fourteen gastrointestinal safety, and four renal safety. When CV risk is the main concern celecoxib or naproxen are a good first choice (RS B). In high GI risk addition of PPI to naproxen or celecoxib use should be recommended (RS A). When renal function is on focus, celecoxib remains as first line of therapy (RS A). Diclofenac in the geriatric population should be avoided (RS B). Celecoxib is a good choice for elderly patients for whom it is difficult to direct pain treatment based on a single known risk factor (RS B). Full article

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor. Full article

Background: Levels of chronic inflammation, oxidative stress, and neurotransmitter availability are altered in depressed patients and can be used as biological markers. This study aimed to analyze these markers in female Wistar rats under chronic inflammation induced by E. coli lipopolysaccharide (LPS), treated with aqueous extract of A. gratissima and rutin, the major flavonoid of its extract. Methods: Thirty female Wistar rats under a chronic inflammatory regimen induced by 1 mg/kg i.p. of LPS were divided into six experimental groups: control (1), treated with fluoxetine 5 mg/kg (2), rutin at 50 mg/kg (3) or 100 mg/kg (4), aqueous extract of A. gratissima 100 mg/kg (5), and co-treatment with 50 mg/kg of extract and 10 mg/kg of rutin (6). Treatments were administered by gavage for 15 days. Results: Oxidative damage to proteins and lipids was lower in group 6 compared to group 2. Pro- and anti-inflammatory cytokines increased in group 1 but not in group 2, indicating a relationship with depression. Similar effects were observed in the treated groups, showing no significant differences from group 2. Neurotransmitter levels of dopamine and serotonin were low in group 1, and all treatments effectively increased them. Additionally, A. gratissima extract at 100 ppm increased locomotor activity in planarians. Conclusions: This study demonstrates the effectiveness of the LPS induction model in subacute experimental designs and the potential antidepressant effect of the treatments due to their antioxidant and anti-inflammatory properties, and ability to increase neurotransmitter levels. Full article

Pulmonary arterial hypertension (PAH) is a progressive disorder caused by the narrowing of small blood vessels in the lungs, which, in the absence of therapies, leads to right heart failure and premature death. No cure for this devastating disorder is known. Current management therapies aim to improve symptoms, and hence, there is a need to identify novel therapeutic interventions. The major objectives of this review are to critically evaluate current treatment strategies and highlight the challenges and prospects of established drugs and natural products for the resolution of PAH. Full article

Colorectal cancer (CRC) is a prevalent and deadly tumor worldwide. Understanding the molecular mechanisms underlying CRC development will improve treatment outcomes and patient survival. Natural molecules and metabolites from plants, such as Tillandsia usneoides, reduce tumor growth by modulating glucose metabolism and increasing reactive oxygen species (ROS). To shed light on the mechanism involved in the anti-tumor effects of T. usneoides, we evaluated the cytotoxic effect of the ethanolic extract of this plant on the colon cancer cell line SW480 through the activation of the peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor that plays a role on lipid metabolism and inflammation in cancer cells. To this end, we assessed the activation of PPARγ by T. usneoides extract in transactivation luciferase assays, as well as the cytotoxic effect of this extract on the SW480 cell line after knocking down PPARγ using shRNA. Our findings indicate that the T. usneoides extract exhibits cytotoxic effects on the SW480 cell line, potentially in the same way as PPARγ activator, pioglitazone, i.e., by increasing reactive oxygen species (ROS). In addition, both T. usneoides extract and pioglitazone exert lipogenic properties in the SW480 cells. Taken together, these results demonstrate that the T. usneoides extract decreases the viability of the colon cancer cell line SW480, at least in part, through the activation of PPARγ. This suggests the potential for further use of this plant in the treatment of other chronic diseases. Full article

Gastrointestinal diseases have been among the main concerns of medical and scientific societies for a long time. Several studies have emphasized the critical role of oxidative stress in the pathogenesis of the most common gastrointestinal diseases. To provide a comprehensive overview of gastrointestinal diseases caused by oxidative stress, their biological aspects, molecular mechanisms and specific pathways, the results of the most recent published articles from the online databases were studied considering both the upper and lower parts of the digestive tract. The results revealed that although the oxidative stress in each part of the digestive system manifests itself in a specific way, all these diseases arise from the imbalance between the generation of the reactive intermediates (especially reactive oxygen species) and the antioxidant defense system. Annual incidence and mortality statistics of gastrointestinal diseases worldwide emphasize the urgent need to find an effective and non-invasive treatment method to overcome these life-threatening problems. Therefore, in the next step, a variety of nanomedicurfines developed to treat these diseases and their effect mechanisms were investigated precisely. Furthermore, the most important nanomedicines responsive to endogenous and exogenous stimuli were evaluated in detail. This review could pave the way to open a new horizon in effectively treating gastrointestinal diseases. Full article

In the present work, methanolic extracts from thyme and dittany plants were prepared and characterized in terms of their polyphenolic content through analytical and spectrophotometric techniques. Rosmarinic acid, thymol and carvacrol were found to be the main components of the extracts, which were further biologically assessed for their antioxidant, anti-tyrosinase, anti-lipase and antibacterial activity against Gram-negative and Gram-positive bacteria. As found, thyme extracts exhibited superior antioxidant activity (SC₅₀ at 33.9 μg mL⁻¹), while dittany extracts inhibited the microbial growth to a great extent against Bacillus subtilis strain (MIC at 0.5 mg mL⁻¹) and E. coli strain (MIC at 2 mg mL⁻¹). Furthermore, the thyme extract was proven to strongly inhibit the activity of lipase from Candida rugosa (IC₅₀ at 63.9 μg mL⁻¹), comparable to the standard inhibitor orlistat, while its inhibitory effect against mushroom tyrosinase was weak. On the other hand, the dittany extract presented an inhibitory effect against the tested lipase (IC₅₀ over 500 μg mL⁻¹) and an activation effect against tyrosinase (at concentrations > 500 μg mL⁻¹). Additionally, molecular docking studies of the main compounds of the extracts showed that rosmarinic acid plays a crucial role on the inhibitory activity of the extracts against lipase, while thymol has a stronger effect on inhibiting tyrosinase. Furthermore, both extracts were employed in the preparation of gelatin-deep eutectic solvent (DES) hydrogels that were further studied for their antioxidant and antibacterial activity. The results showed that the incorporation of the extracts offered antibacterial properties to the biopolymer-based hydrogels and enhanced the antioxidant activity of gelatin up to 85%. Full article

Otoliths of the fish’s inner ear serve as a natural chronological recorder because of their continuous formation marked by daily, monthly, and annual increments. Despite their importance, the comprehensive protein content of otoliths remains not fully identified. Using the label-free shotgun proteomics method with one-dimensional liquid chromatography coupled to electrospray ionization-orbitrap tandem mass spectrometry, we quantified a broad range of proteins, with individual otoliths containing between 1341 and 1839 proteins. The identified proteins could potentially serve as a blueprint for fish growth from embryo to adult. We quantified eleven heat-shock proteins (HSPs) in both sexes and several proteins impacted by endocrine disruptors, indicating the otolith’s capacity to reflect environmental stress, potentially linked to climate change effects and altering of hormonal and neuroendocrine functions. Our bioinformatic ontology analysis confirmed the presence of proteins critical for various biological processes, including structural and enzymatic proteins. Protein–protein interaction (PPI) mapping also identified key interactions between the identified proteins. These findings significantly advance our understanding of otolith proteomics, offering a solid foundation for future work. Most of the identified proteins deposited daily and influenced by the environment were not implicated in the biomineralization of otolith, raising the potential for the otolith proteome to recreate details of fish life history at previously unrealized levels. Full article

Glioblastoma is the most common and aggressive type of malignant brain tumor with a poor prognosis due to the lack of effective treatment options. Therefore, new treatment options are required. Sphingolipids are essential components of the cell membrane, while complement components are integral to innate immunity, and both play a critical role in regulating glioblastoma survival signaling. This review focuses on recent studies investigating the functional roles of sphingolipid metabolism and complement activation signaling in glioblastoma. It also discusses how targeting these two systems together may emerge as a novel therapeutic approach. Full article

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a human pathogenic virus that encodes for a helicase (SC2Hel) that is essential for viral replication. SC2Hel has the ability to unravel dsRNA or dsDNA in an NTP-dependent manner from the 5′ to 3′ directionality. The standard helicase assay from studies involving SARS-CoV and SARS-CoV-2 have relied on the concept of fluorescence resonance energy transfer. Adding to the collection of helicase assays, herein, we have developed a novel tetrazolium-based colorimetric assay system for the detection of ADP that is produced via SC2Hel activity. This SC2Hel assay combines three enzyme-coupled steps involving the ADP-dependent Thermococcus litoralis glucokinase (TlGlcK), Leuconostoc mesenteroides glucose-6-phosphate dehydrogenase (LmG6PDH), and Clostridium kluyveri diaphorase (CkDIA). Iodonitrotetrazolium chloride (INT), a colorimetric tetrazolium reagent, was used in the final step of the assay that converted into INT-formazan during reduction. INT-formazan in the assay’s buffered solution at pH 7.6 exhibited an intense colorimetric response at a wavelength maximum of 505 nm. The assay exhibited excellent performance characteristics as it revealed a Z’ factor of 0.87 and it has the potential to be further adopted into high-throughput screening studies for therapeutic drug discovery research. Full article

Metabolites are at the end of the gene–transcript–protein–metabolism cascade. As such, metabolomics is the omics approach that offers the most direct correlation with phenotype. This allows, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics to possibly provide an answer. Complex phenotypes, which are determined by the influence of multiple small-effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased exponentially in recent years. As a newer discipline, metabolomic bioinformatic analysis pipelines are not as standardized as in the other omics approaches. In this review, we synthesized the different steps that need to be carried out to obtain biological insight from annotated metabolite abundance raw data. These steps were grouped into three different modules: preprocessing, statistical analysis, and metabolic pathway enrichment. We included within each one of them the different state-of-the-art procedures and tools that can be used depending on the characteristics of the study, providing details about each method’s characteristics and the issues the reader might encounter. Finally, we introduce genome-scale metabolic modeling as a tool for obtaining pseudo-metabolomic data in situations where their acquisition is difficult, enabling the analysis of the resulting data with the modules of the described workflow. Full article

Heat Shock Protein 90 (Hsp90) acts as a crucial molecular chaperone, playing an essential role in activating numerous signaling proteins. The intricate mechanism of Hsp90 involving ATPase-coupled conformational changes and interactions with cochaperone proteins has been elucidated through biochemical and structural analyses, revealing its activation mechanism and its diverse set of “client” proteins. Despite recent advancements, certain aspects of Hsp90’s ATPase-coupled mechanism remain contentious, and the specific nature of the alterations induced by Hsp90 in client proteins remains largely undiscovered. In this review, we explore the current understanding of Hsp90’s structure and function, drawing insights from single-particle cryoEM studies. Structural studies on Hsp90 using cryoEM have provided valuable insights into the structural dynamics and interactions of this molecular chaperone. CryoEM structures have been instrumental in understanding the ATPase-coupled conformational changes that Hsp90 undergoes during its chaperone cycle. We also highlight recent progress in elucidating the structure of the ATP-bound state of the complete dimeric chaperone. Furthermore, we delve into the roles played by the multitude of cochaperones that collaborate with Hsp90, providing a glimpse into their biochemical mechanisms through the newly obtained cryoEM structures of Hsp90 cochaperone complexes. Full article

Arthritis, a global health burden comprising osteoarthritis and rheumatoid arthritis, demands advanced therapeutic approaches. In this context, flavonoids, a diverse group of naturally occurring compounds abundant in fruits, vegetables, and medicinal plants, have emerged as promising candidates for mitigating the inflammatory processes associated with arthritic conditions. This review aims, first, to provide a comprehensive exploration of the potential of flavonoids, focusing on specific compounds such as quercetin, epigallocatechin-3-gallate (EGCG), apigenin, luteolin, fisetin, silibinin, kaempferol, naringenin, and myricetin. The second section of this review delves into the anti-arthritic activities of these flavonoids, drawing insights from clinical trials and scientific studies. Each flavonoid is scrutinized individually to elucidate its mechanisms of action and therapeutic efficacy in the context of both osteoarthritis and rheumatoid arthritis. The third section of this review highlights the challenges associated with harnessing flavonoids for anti-inflammatory purposes. Bioavailability limitations pose a significant hurdle, prompting the exploration of innovative strategies such as the use of nanoparticles as delivery vehicles. In response to these challenges, the fourth section focuses on the emerging field of flavonoid-based nanoparticles. This includes detailed discussions on quercetin, EGCG, fisetin, and naringenin-based nanoparticles, highlighting formulation strategies and preclinical evidence supporting their potential in arthritis management. The targeted delivery to inflammatory sites and the exploration of synergistic combinations with other compounds are also discussed as promising avenues to enhance the therapeutic impact of flavonoids. This review consolidates current knowledge on flavonoids and their nanoformulations as potential therapeutic interventions for osteoarthritis and rheumatoid arthritis. By addressing challenges and presenting future research directions, this review aims to contribute to the advancement of innovative and effective strategies for alleviating the global burden of arthritis. Full article

Muscle lactate dehydrogenase (LDH-A) catalyzes the reduction of pyruvate to lactate, the end product of anaerobic glycolysis. LDH-A is overexpressed in many cancers prior to and even when tumors receive adequate oxygen, and lactate has multiple cellular roles. We assessed the effect of singlet oxygen and hypochlorous acid (HOCl) on mammalian LDH-A. Oxidants induced distinct patterns of protein crosslinks observed by SDS-PAGE under reducing conditions. LDH-A cysteines were detected using fluorescein-modified maleimide to assess their oxidation and accessibility. Singlet oxygen initially increased cysteine exposure, but higher doses resulted in their oxidation in addition to non-reducible covalent crosslinks. LDH-A cysteines were oxidized by micromolar HOCl (1–10 equivalents over enzyme) but were resistant to millimolar H₂O₂, chloramines and Angeli’s salt. HOCl oxidation inhibited LDH-A activity and yielded inter-chain disulfides observed by nonreducing SDS-PAGE. Disulfide reduction did not restore LDH-A activity that was lost due to HOCl oxidation. An irreversible conformational change induced by HOCl was detected by native gel electrophoresis and tryptophan fluorescence. In the absence of pyruvate, LDH-A enhanced NADH oxidation resulting in H₂O₂ formation. Singlet oxygen, but not HOCl, initiated this superoxide-dependent chain reaction. Once damaged by both singlet oxygen or HOCl, LDH-A had decreased NADH oxidation activity. Full article

The current standard technique for vascular grafting in cerebral revascularization surgery employs the interposition of an autologous blood vessel. Technical complications have necessitated the development of a synthetic alternative, but classical biomaterials are not suited for small caliber vascular grafting due to the resulting neointimal hyperplasia and thrombosis. The electrospinning of polymers is a promising technique for the development of small vascular grafts. The in vivo performance and efficacy of electrospun polyurethane (ePU) grafts with an internal diameter of <1.5 mm have thus far not been evaluated. We developed a novel ePU graft, with a diameter of 1.25 mm, for implantation into the infrarenal aorta of rats. The patency rates of grafts after a 4-month period were equal to those reported in other studies using larger ePU graft diameters and equal or higher than in studies employing other biomaterials. We observed some loss in flow velocity throughout the grafts, which suggests a decreased elasticity of the graft compared to that of the native rat aorta. However, the grafts demonstrated good neo-endothelialization and minimal neointimal hyperplasia. Their porosity promoted cellular infiltration, as observed under tissue slide examination. Our results show that ePU vascular grafts with an internal diameter of <1.5 mm are promising candidates for vascular grafting in cerebral revascularization surgery. Full article

Signaling pathways that integrate a large set of inputs (both extra- and intracellular) to control cell proliferation are essential during both development and adult stages to guarantee organism homeostasis. Mobs are small adaptor proteins that participate in several of these signaling pathways. Here, we review recent advances unravelling Mob4 cellular functions, a highly conserved non-catalytic protein, that plays a diversity of roles in cell proliferation, sperm cell differentiation and is simultaneously involved in synapse formation and neural development. In addition, the gene is often overexpressed in a large diversity of tumors and is linked to poor clinical outcomes. Nevertheless, Mob4 molecular functions remain poorly defined, although it integrates the core structure of STRIPAK, a kinase/phosphatase protein complex, that can act upstream of the Hippo pathway. In this review we focus on the recent findings of Mob4 functions, that have begun to clarify its critical role on cell proliferation and the development of tissues and individuals. Full article

Diapause-like features can be extended to naïve mouse embryonic stem cells (mESCs) to induce paused pluripotency by using INK128 (mTi), a mammalian target of rapamycin (mTOR) inhibitor. As a core integrative pathway, mTOR senses diverse stimuli and translates these cues to coordinate several processes. We have previously shown that the withdrawal of leucine and arginine from the culture medium of naïve mESCs can induce features of a paused-pluripotent state, including reduced cell proliferation, cell cycle arrest, and reductions in glycolytic and oxidative metabolism. However, surprisingly, although mTi did indeed provoke a paused-like state, this was distinct from and less pronounced than what resulted from leucine and arginine removal, and, according to our results, these features did not seem to necessarily be mTOR-driven. Therefore, this possibility should be considered in further experiments, and mTOR inhibition when using INK128 should always be confirmed and not merely assumed when INK128 is present in the culture medium. Full article

A betel quid (BQ) chewing habit has been strongly associated with the development of several oral mucosal diseases. In order to investigate whether individual components of BQ mixtures have distinct physio-pathological effects on oral mucosal cells, we examined the impact of areca nut (AN), Piper betle leaf (Leaf), Piper betle stem inflorescence (SI), areca husk (Husk) and the complete BQ mixture on the growth of oral keratinocytes (OKF-6) and primary oral fibroblasts (MMF-1). Based on their known chemical properties, we selected BQ samples from Banda Aceh (BA) and West Papua (WP) regions for our in vitro study. We used a fluorescein diacetate assay (FDA) to assess the cell viability of BQ components on OKF-6 and MMF-1 cells. The cytotoxic effect of WP-AN on the OKF-6 cell line was observed at a concentration of 100 μg/mL, resulting in a 50% reduction in cell viability (IC50) after a 2-day incubation. Similarly, BA-AN exhibited cytotoxic effect, although at a higher concentration (500 μg/mL). WP-SI also displayed cytotoxic effects at a concentration of 500 μg/mL following 2 days of incubation. In contrast, Leaf, BQ mixture and husk extracts did not show any cytotoxic effects even after 3 days of incubation. No cytotoxic effects were observed at any concentration of BQ components when exposed to MMF-1 cells. Regarding cell proliferation, MMF-1 cells exposed to BA-AN and WP-AN showed increased growth on day 1, followed by decreased growth on day 2, in a dose- and time-dependent manner. Overall, our study indicates that BQ components induce distinctive cytotoxic effects on stromal and epithelial cells from the oral cavity. Full article

The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or the assay method must be as rapid as possible. We have developed a new method of isothermal amplification based on the formation of hairpins at the ends of DNA fragments containing palindromic sequences and increased by the hydrolysis of one or both DNA strands by restriction endonuclease, known as hairpin-assisted isothermal reaction (HAIR). The key steps in HAIR are the formation of a self-complementary hairpin and the DNA breakage introduced by nickase. The end hairpins facilitate primer-free amplification, the amplicon strand cleavage by nickase produces additional 3′ ends that serve as new amplification points, and the amount of DNA can increase exponentially. The rate of amplification in HAIR is more than five times the rate of loop-mediated isothermal amplification (LAMP), and the total amount of DNA product of HAIR is more than double the amount of the LAMP product. Full article