Search Results (408)

Arginine kinase is a key phosphagen kinase in invertebrates that facilitates rapid ATP regeneration by reversibly transferring phosphate groups between phosphoarginine and ADP. Structural studies have shown that the enzyme adopts distinct conformations in its ligand-free and ligand-bound states, known as the “open” and “closed” forms, respectively. These conformational changes are crucial for catalytic activity, enabling precise positioning of active-site residues and loop closure during phosphoryl transfer. Transition-state analog complexes have provided additional insights by mimicking intermediate states of catalysis, supporting the functional relevance of the open/closed structural model. Furthermore, studies across multiple species reveal how monomeric and dimeric forms of arginine kinase contribute to its allosteric regulation and substrate specificity. Beyond its metabolic role, arginine kinase is also recognized as a major allergen in crustaceans. Its structural uniqueness and absence in vertebrates make it a promising candidate for selective drug targeting. By integrating crystallographic data with functional context, this review highlights conserved features and species-specific variations of arginine kinase that may inform the design of inhibitors. Such molecules have the potential to serve both as antiparasitic agents and as novel therapeutics to manage crustacean-related allergic responses in humans. Full article

Resistance of various bacterial pathogens to the activity of clinically approved drugs currently leads to serious infections, rapid spread of difficult-to-treat diseases, and even death. Taking the threats for human health in mind, researchers are focused on the isolation and characterization of novel natural products, including plant secondary metabolites. These molecules serve as inspiration and a suitable structural platform in the design and development of novel semi-synthetic and synthetic derivatives. All considered compounds have to be adequately evaluated in silico, in vitro, and in vivo using relevant approaches. The current review paper briefly focuses on the chemical and metabolic properties of resveratrol (1), as well as its oligomeric structures, viniferins, and viniferin-based molecules. The core scaffolds of these compounds contain so-called privileged structures, which are also present in many clinically approved drugs, indicating that those natural, properly substituted semi-synthetic, and synthetic molecules can provide a notably broad spectrum of beneficial pharmacological activities, including very impressive antimicrobial efficiency. Except for spectral verification of their structures, these compounds suffer from the determination or prediction of other structural and physicochemical characteristics. Therefore, the structure–activity relationships for specific dihydrodimeric and dimeric viniferins, their bioisosteres, and derivatives with notable efficacy in vitro, especially against chosen Gram-positive bacterial strains, are summarized. In addition, a set of descriptors related to their structural, physicochemical, pharmacokinetic, and toxicological properties is generated using various computational tools. The obtained values are compared to those of clinically approved drugs. The particular relationships between these in silico parameters are also explored. Full article

Background/Objectives: Tegoprazan (TPZ) is a potassium-competitive acid blocker (P-CAB) used to treat conditions such as gastroesophageal reflux disease, peptic ulcer, and Helicobacter pylori infection. It exists in three solid forms: amorphous, Polymorph A, and Polymorph B. This study investigates the molecular basis of polymorph selection, focusing on conformational bias and solvent-mediated phase transformations (SMPTs). Methods: The conformational energy landscapes of two TPZ tautomers were constructed using relaxed torsion scans with the OPLS4 force field and validated by nuclear Overhauser effect (NOE)-based nuclear magnetic resonance (NMR). Hydrogen-bonded dimers were analyzed using DFT-D. Powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), solubility, and slurry tests were conducted using methanol, acetone, and water. Kinetic profiles were modeled with the Kolmogorov–Johnson–Mehl–Avrami (KJMA) equation. Results: Polymorph A was thermodynamically stable across all analyses. Both amorphous TPZ and Polymorph B converted to A in a solvent-dependent manner. Methanol induced direct A formation, while acetone showed a B → A transition. Crystallization was guided by solution conformers and hydrogen bonding. Conclusions: TPZ polymorph selection is governed by solution-phase conformational preferences, tautomerism, and solvent-mediated hydrogen bonding. DFT-D and NMR analyses showed that protic solvents favor the direct crystallization of stable Polymorph A, while aprotic solvents promote the transient formation of metastable Polymorph B. Elevated temperatures and humidity accelerate polymorphic transitions. This crystal structure prediction (CSP)-independent strategy offers a practical framework for rational polymorph control and the mitigation of disappearing polymorph risks in tautomeric drugs. Full article

The elderly population in Japan was 29.3% in 2024, the highest in the world, making medical care for elderly patients an urgent social issue. There are challenges in providing care for elderly patients with head injury, since the buffering effect of the expansion of the subdural space due to brain atrophy masks the neurological symptoms caused by a hematoma, making detection difficult. However, brain damage can be detected with high sensitivity and specificity using blood D-dimer as a biomarker without the need for head computed tomography (CT). Also, about 30% of elderly patients with traumatic brain injury (TBI) are taking antithrombotic drugs, and the effects of these drugs on TBI may include an increase in intracranial hematomas and an increased risk of deterioration. Reversal therapy is used as a countermeasure to prevent hematoma expansion, but this requires the administration of a reversal agent early after injury and before hematoma expansion. In decompression surgery, the use of a mini-craniotomy with neuroendoscopic assistance under local anesthesia can reduce invasiveness, and this method significantly reduces intraoperative bleeding and operation times compared to a major craniotomy. These innovations have improved mortality for TBI in elderly patients, but there is still a need for improvements in functional outcomes. Full article

Zoonotic viral diseases have continued to threaten global public health in recent decades, with rodent-borne viruses being significant contributors. Infection by rodent-carried hantaviruses (HV) can result in hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in humans, with varying degrees of morbidity and mortality. However, no Food and Drug Administration (FDA) vaccines or therapeutics have been approved for the treatment of these diseases. In an effort to identify antiviral bioactive molecules, we isolated four oligomeric phloroglucinols from Callistemon rigidus leaves, including two new phloroglucinol trimers, callistemontrimer A and B, along with two previously characterized phloroglucinol dimers, rhodomyrtosone B and rhodomyrtone. We evaluated the anti-Hantaan virus (HTNV) activity of these compounds. Notably, callistemontrimer A demonstrated higher anti-HTNV activity compared to ribavirin. Mechanistic studies revealed that callistemontrimer A exerted its antiviral effects by inhibiting viral replication, likely through interaction with RNA-dependent RNA polymerase (RdRp) of HTNV, as supported by molecular docking analysis. These results highlight oligomeric phloroglucinols as promising lead candidates for the development of anti-HV therapeutics. Full article

The purpose of this study was to investigate polymorphic variants of the genes FGB (rs1800790), NOS3 (rs2070744) and TMPRSS2 (rs12329760) in patients with SARS-CoV-2 and to determine their role in the COVID-19 severity course against the background of antiviral therapy. Real-time polymerase chain reaction (RT-PCR) was used to genotype the polymorphism of the selected genes. GS-5734 (remdesivir) was prescribed as the basic antiviral drug. Binary logistic regression confirmed a low probability of COVID-19 developing in carriers of the A-allele of the FGB gene. The highest probability of moderate and severe COVID-19 clinical forms developing was found in G-allele carriers (especially the GG genotype) of the FGB gene (rs1800790) and the T-allele of the TMPRSS2 gene (rs12329760). Antiviral drug GS-5734 (remdesivir) administration with anti-inflammatory therapy reduces the TMPRSS2 blood level in moderate COVID-19, IL-6 in severe COVID-19 course, and fibrinogen A- and D-dimers in both groups. The proposed treatment does not significantly affect the concentration of endothelin-1, but a decrease in procalcitonin associated with additional antibacterial use was observed, especially in severe COVID-19. Full article

Mn(III)– and Co(III)–salen complexes (Mn-1 and Co-2) have been synthesized by a simple one-pot procedure through oxidation of Mn(II) and Co(II) precursors in air. X-ray structural analysis reveals that both complexes adopt similar coordination modes, including a typical square planar metal/salen coordination sphere, which is further occupied by two axial ligands, i.e., an acetate anion and a water molecule. Despite their structural similarity, they are not isomorphous given their distinct cell parameters. In the solid-state structures, both complexes exist as hydrogen-bonded dimers through hydrogen bonding interactions between the axially coordinating water molecules and outer O₄ cavity from another molecule of the complex. The reductive activity of both complexes has been explored. While the reaction of Mn-1 with potassium triethylborohydride was unsuccessful, leading to a complicated mixture, the use of Co-2 furnished the formation of a novel product (CoK-3) that was isolated as red crystals in reasonable yield. CoK-3 was characterized as a heterometallic dimer involving the coordination of a K⁺ ion within the O₄ cavity of a semi-hydrogenated salen/cobalt complex while the cobalt center has been reduced from Co(III) to Co(II). In addition, an attempt at reducing Co-2 with pinacolborane resulted in the isolation of crystals of Co-4, whose structure was determined as a simple square planar Co^II–salen complex. Finally, three complexes (Mn-1, Co-2 and CoK-3) have been investigated for their cytotoxic activities against two human breast cancer cell lines (MCF-7 and MDA-MB 468) and a normal breast epitheliel cell line (MCF-10A), with cisplatin used as a reference in order to discover potential drug candidates that may compete with cisplatin. The results reveal that Co-2 can be a promising drug candidate, specifically for the MCF-7 cancer cells, with minimal damage to healthy cells. Full article

ADAM (A Disintegrin and Metalloproteinase) family members are multifunctional transmembrane proteases that govern tumorigenesis and metastasis by cleaving membrane-bound substrates such as growth factors, cytokines, and cell adhesion molecules. Several ADAMs, including ADAM8, ADAM9, ADAM10, ADAM12, and ADAM17, are overexpressed in malignancies and are linked with a poor prognosis. These proteases contribute to tumour growth by regulating cell proliferation, cell fate, invasion, angiogenesis, and immune evasion. ADAM10 and ADAM17, especially, facilitate the shedding of critical developmental and growth factors and their receptors, as well as immuno-regulatory molecules, hence promoting tumour progression, immune escape, and resistance to therapy. Recent work has unveiled multiple regulatory pathways that modulate ADAM functions, which include trafficking, dimerization, and conformational modifications that affect substrate accessibility. These observations have rekindled efforts to produce selective ADAM inhibitors, avoiding the off-target consequences reported with early small molecule inhibitors targeting the enzyme active site, which is conserved also in matrix metalloproteinases (MMPs). Promising approaches tested in preclinical models and, in some cases, clinical settings include more selective small-molecule inhibitors, monoclonal antibodies, and antibody–drug conjugates designed to specifically target ADAMs. In this review, we will discuss the emerging roles of ADAMs in cancer biology, as well as the molecular processes that control their function. We further discuss the therapeutic potential of targeting ADAMs, with a focus on recent advances and future directions in the development of ADAM-specific cancer therapies. Full article

Familial amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by the selective degeneration of motor neurons. Among the main genetic causes of ALS, over 200 mutations have been identified in the Cu/Zn superoxide dismutase (SOD1) protein, a dimeric metalloenzyme essential for converting superoxides from cellular respiration into less toxic products. Point mutations in SOD1 monomers can induce protein misfolding, which spreads to wild-type monomers through a prion-like mechanism, leading to dysfunctions that contribute to the development of the disease. Understanding the structural and functional differences between the wild-type protein and its mutated variants, as well as developing drugs capable of inhibiting the propagation of misfolding, is crucial for identifying new therapeutic strategies. In this work, seven SOD1 mutations (A4V, G41D, G41S, D76V, G85R, G93A, and I104F) were selected, and three-dimensional models of SOD1 dimers composed of one wild-type monomer and one mutated monomer were generated, along with a control dimer consisting solely of wild-type monomers. Molecular dynamics simulations were conducted to investigate conformational differences between the dimers. Additionally, molecular docking was performed using a library of ligands to identify compounds with high affinity for the mutated dimers. The study reveals some differences in the mutated dimers following molecular dynamics simulations and in the docking of the selected ligands with the various dimers. Full article

With the rise of antibiotic resistance, there is a need for innovative drugs with alternative mechanisms of action. Endolysins meet most of the requirements, but are limited for parenteral use due to their short blood circulation time. In this article, a number of modifications to the ML06-engineered, lysin-targeting Gram-negative bacteria are proposed to improve its pharmacokinetic parameters. Genetic modification with albumin-binding and dimerization domains ranging from 11–12 aa to 45 aa at both the C- and N-termini has resulted in six enzymes that do not exhibit critically reduced antibacterial properties in vitro, and in the case of the ABP1 modification, an improved antibacterial rate and spectra of enzymes. The ML06-ABP1, ML06-ABP2, and HDD-ML06 modifications also retained activity in blood serum and significantly increased serum stability. A pharmacokinetic study of the three modifications in mice showed that ML06-ABP2 and HDD-ML06 have a prolonged half-life compared to the ML06 half-life. In addition, the serum C_max concentration for HDD-ML06 (22.2 μg/mL) was significantly increased compared to ML06 (C_max < 5 μg/mL). Our results allow for a comparison of the different types of modifications that are useful in the development of parenteral antibacterials. Full article

Mesothelioma is a rare and aggressive cancer linked to asbestos exposure and characterized by rapid metastasis and poor prognosis. Inhibition of adenosine deaminase acting on dsRNA 2 (ADAR2) RNA binding but not ADAR2 editing has shown antitumor effects in mesothelioma. Natural compounds from the Traditional Chinese Medicine (TCM) database were docked to the RNA-binding interface of ADAR2’s second dsRNA binding domain (dsRBD2), and their drug-likeness and predicted safety were assessed. Eight ligands (ZINC000085597263, ZINC000085633079, ZINC000014649947, ZINC000034512861, ZINC000070454124, ZINC000085594944, ZINC000085633008, and ZINC000095909822) showed high binding affinity to dsRBD2 from molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculations. Protein–ligand interactions were analyzed to identify key residues contributing to these binding affinities. Molecular dynamics (MD) simulations of dsRBD–ligand–RNA complexes revealed that four compounds (ZINC000085597263, ZINC000085633079, ZINC000014649947, and ZINC000034512861) had negative binding affinities to dsRBD2 in the presence of the RNA substrate GluR-2. Key residues, including Val164, Met165, Lys209, and Lys212, were crucial for ligand binding, even with RNA present, suggesting these compounds could inhibit dsRBD2’s RNA-binding function. The predicted biological activities of these compounds indicate potential anticancer properties, particularly for the treatment of mesothelioma. These compounds are structurally similar to known anti-mesothelioma agents or anticancer drugs, highlighting their therapeutic potential. Current mesothelioma treatments are limited. Optimization of these compounds, alone or in combination with current therapeutics, has potential for mesothelioma treatment. Additionally, five high-quality full-length ADAR2 models were developed. These models provide insights into ADAR2 function, mutation impacts, and potential areas for protein engineering to enhance stability, RNA-binding specificity, or protein interactions, particularly concerning dimerization or complex formation with other proteins and RNAs. Full article

Breast cancer (BC) remains a significant global health challenge due to its complex biology, which complicates both diagnosis and treatment. Immunotherapy and cancer vaccines have emerged as promising alternatives, harnessing the body’s immune system to precisely target and eliminate cancer cells. However, several key factors influence the selection and effectiveness of these therapies, including BC subtype, tumor mutational burden (TMB), tumor-infiltrating lymphocytes (TILs), PD-L1 expression, HER2 resistance, and the tumor microenvironment (TME). BC subtypes play a critical role in shaping treatment responses. Triple-negative breast cancer (TNBC) exhibits the highest sensitivity to immunotherapy, while HER2-positive and hormone receptor-positive (HR+) subtypes often require combination strategies for optimal outcomes. High TMB enhances immune responses by generating neoantigens, making tumors more susceptible to immune checkpoint inhibitors (ICIs); whereas, low TMB may indicate resistance. Similarly, elevated TIL levels are associated with better immunotherapy efficacy, while PD-L1 expression serves as a key predictor of checkpoint inhibitor success. Meanwhile, HER2 resistance and an immunosuppressive TME contribute to immune evasion, highlighting the need for multi-faceted treatment approaches. Current breast cancer immunotherapies encompass a range of targeted treatments. HER2-directed therapies, such as trastuzumab and pertuzumab, block HER2 dimerization and enhance antibody-dependent cellular cytotoxicity (ADCC), while small-molecule inhibitors, like lapatinib and tucatinib, suppress HER2 signaling to curb tumor growth. Antibody–drug conjugates (ADCs) improve tumor targeting by coupling monoclonal antibodies with cytotoxic agents, minimizing off-target effects. Meanwhile, ICIs, including pembrolizumab, restore T-cell function, and CAR-macrophage (CAR-M) therapy leverages macrophages to reshape the TME and overcome immunotherapy resistance. While immunotherapy, particularly in TNBC, has demonstrated promise by eliciting durable immune responses, its efficacy varies across subtypes. Challenges such as immune-related adverse events, resistance mechanisms, high costs, and delayed responses remain barriers to widespread success. Breast cancer vaccines—including protein-based, whole-cell, mRNA, dendritic cell, and epitope-based vaccines—aim to stimulate tumor-specific immunity. Though clinical success has been limited, ongoing research is refining vaccine formulations, integrating combination therapies, and identifying biomarkers for improved patient stratification. Future advancements in BC treatment will depend on optimizing immunotherapy through biomarker-driven approaches, addressing tumor heterogeneity, and developing innovative combination therapies to overcome resistance. By leveraging these strategies, researchers aim to enhance treatment efficacy and ultimately improve patient outcomes. Full article

Background: Reynoutria japonica Houtt. has been used for inflammatory diseases, skin burns, and high cholesterol in traditional Chinese medicine, and the roots and rhizomes of the plant were registered in the Chinese Pharmacopoeia. This study evaluated the enzyme inhibitory activities of R. japonica extracts from Türkiye. Its major phytochemical content was elucidated, molecular interaction studies of the main compounds were conducted, and toxicokinetic predictions and absorption, distribution, metabolism, and elimination studies were performed with in silico methods. Methods: R. japonica extracts were tested for their enzyme inhibitory activities using an ELISA microplate reader. The phytochemical profile was elucidated by LC-MS QTOF. Docking and other in silico studies evaluated interactions of its main components with cholinesterase, collagenase, and elastase. Results: R. japonica exhibited significant cholinesterase inhibitory effectiveness, while the stem and root extracts showed moderate tyrosinase inhibition. R. japonica leaf (IC₅₀ = 117.20 ± 4.84 g/mL) and flower extracts (IC₅₀ = 111.40 ± 1.45 µg/mL) exhibited considerable elastase activity. R. japonica leaf (IC₅₀ = 171.00 ± 6.76 g/mL) and root (IC₅₀ = 160.00 ± 6.81 g/mL) extracts displayed similar and potent collagenase inhibition. In the LC-MS QTOF analysis, procyanidin dimer, catechin, piceid, torachrysone, and its glucoside isomers were identified as the major components and resveratrol as the minor component. Galloylglucose showed the strongest binding at cholinesterase via key hydrogen bonds, while emodin-6-glucoside and emodin formed stable interactions with elastase. Piceid displayed significant polar and water-mediated contacts with collagenase. These findings underscore the potential of these ligands as protein inhibitors. In silico predictions reveal that emodin possessed the most favorable drug-like properties but posed potential interaction risks. Conclusions: This research represents the first investigation of the bioactivity and phytochemistry of R. japonica grown and documented in 2020 in Türkiye. Our findings point out that R. japonica could be used for cosmetic purposes, and further studies on neurological disorders could be performed. Full article

Metronidazole is the preferred drug for treating amoebiasis caused by Entamoeba histolytica. Its antiamoebic activity is primarily attributed to activation by various reductases. This study reports an alternative activation pathway in E. histolytica mediated by the decarboxylating malic enzyme. Functional characterization of this NADPH-dependent enzyme reveals that it is secreted into the extracellular milieu and may play a role in E. histolytica adhesion to human enteric cells. Structural analysis of the E. histolytica malic enzyme (EhME) demonstrates that the protein forms a strict dimer, with the protomers interlocked by a unique knot structure formed by two polypeptide chains. This distinctive structural feature closely aligns EhME with its prokaryotic counterparts. In conclusion, our findings reveal that E. histolytica harbors a deeply entangled dimeric malic enzyme that contributes to metronidazole susceptibility, sharing structural similarities with bacterial malic enzymes. Full article

Background: Osteoporosis has become an inevitable health issue with global aging, and the current drug treatments often have adverse side effects, highlighting the need for safer and more effective therapies. Collagen-derived peptides are promising alternatives due to their favorable safety profile and biological activity. This study aimed to investigate the osteogenic and anti-apoptotic properties of collagen peptide UU1 (GASGPMGPR) in addition to its antioxidant activity. Methods: The effects of UU1 were evaluated in MC3T3-E1 cells by assessing osteogenic markers, including alkaline phosphatase (ALP), Cyclin D1, runt-related transcription factor 2 (Runx2), and Akt/β-catenin signaling. Western blot analysis quantified collagen I, osteocalcin, and phosphorylated Akt levels. Anti-apoptotic effects were measured via p-Akt levels and the Bax/Bcl-2 ratio. Computational molecular docking was performed to explore the molecular mechanism of UU1 via its interaction with epidermal growth factor receptor (EGFR) and collagen-binding integrin. Results: UU1 treatment promoted cell differentiation, with elevated ALP, Cyclin D1, Runx2, and Akt/β-catenin signaling. Notably, at 0.025 mg/mL, UU1 upregulated the levels of collagen I, osteocalcin, and phosphorylated Akt by 2.14, 3.37, and 1.95 times, respectively, compared to the control. Additionally, UU1 exhibited anti-apoptotic effects, indicated by increased p-Akt levels and a reduced Bax/Bcl-2 ratio. Molecular docking analysis suggested that UU1 could assist the dimerization of EGFR, facilitating downstream signaling transductions and activating collagen-binding integrin. Conclusions: These findings highlight UU1 as a multifunctional peptide with antioxidant, osteogenic, and anti-apoptotic properties, positioning it as a promising candidate for anti-osteoporosis applications in the food and pharmaceutical industries. Full article