Search Results (141)

Application of organic ligand 2-(3-ethyl-pyrazin-2-yl)quinoline-4-carboxylate with N/O donor atoms enabled solvothermal synthesis of a 2D Cu(II) coordination polymer, {Cu(L)BF₄}_n (L = deprotonated 2-(3-ethyl-pyrazin-2-yl)quinoline-4-carboxylate). Both the ligand and its coordination polymer have been characterized. The condensed ring system of the applied ligand promotes the formation of coordination polymers rather than mononuclear species. The obtained 2D coordination polymer is photoluminescent with bathochromic/hypsochromic shifts in ligand absorption bands leading to a single absorption band at 465 nm. Density Functional Theory was employed to provide a theoretical description of the possible conformational changes within the ligand, with emphasis on the difference between the ligand conformation in its hydrochloride salt and in the polymer. Two models of polymer fragments were constructed to describe the electronic structure and non-covalent interactions. The Quantum Theory of Atoms in Molecules (QTAIM) was applied for this purpose. Using the obtained results, we were able to develop potential energy profiles for various conformations of the ligand. For the set of the studied systems, we detected non-covalent interactions, which are responsible for the spatial conformation. Concerning the models of polymers, electron spin density distribution has been visualized and discussed. Full article

Carbon dots (CDs), a class of carbon-based fluorescent nanomaterials, have garnered significant attention due to their tunable optical properties and functional versatility. In this study, we developed a hybrid material by grafting pH- and temperature-responsive copolymers onto CDs via reversible addition-fragmentation chain-transfer (RAFT) polymerization. Triamino-tetraphenylethylene (ATPE) and N-isopropylacrylamide (NIPAM) were copolymerized at varying ratios and covalently linked to CDs, forming a dual-responsive system. Structural characterization using FTIR, ¹H NMR, and TEM confirmed the successful grafting of the copolymers onto CDs. The hybrid material exhibited pH-dependent fluorescence changes in acidic aqueous solutions, with emission shifting from 450 nm (attributed to CDs) to 500 nm (aggregation-induced emission, AIE, from ATPE) above a critical pH threshold. Solid films of the hybrid material demonstrated reversible fluorescence quenching under HCl vapor and recovery/enhancement under NH₃ vapor, showing excellent fatigue resistance over multiple cycles. Temperature responsiveness was attributed to the thermosensitive poly(NIPAM) segments, with fluorescence intensity increasing above 35 °C due to polymer chain collapse and ATPE aggregation. This work provides a strategy for designing multifunctional hybrid materials with potential applications in recyclable optical pH/temperature sensors. Full article

Background/Objectives: The physiological activation of cytotoxic CD8^pos T cells (CTLs) relies on the engagement of the TCR/CD3 complex with cognate peptide-HLA class I (pHLA-I) on target cells, triggering cell lysis with appropriate cytokine release and minimized off-target toxicity. In contrast, current immunotherapies for CD19-expressing hematological malignancies, such as chimeric antigen receptor (CAR) T cells and bispecific T cell engagers (BiTEs), bypass TCR/pHLA interactions, resulting in CTL hyperactivation and excessive cytokine release, which frequently cause severe immune-related adverse events (irAEs). Thus, there is a pressing need for T cell-based therapies that preserve physiological activation while maintaining antitumor efficacy. Methods: To address this, we developed CD19-ReTARG^TPR, a novel fusion protein consisting of the immunodominant cytomegalovirus (CMV) pp65-derived peptide TPRVTGGAM (TPR) covalently presented by a soluble HLA-B*07:02/β2-microglobulin complex fused to a high-affinity CD19-targeting Fab antibody fragment. The treatment of CD19-expressing cancer cells with CD19-ReTARG^TPR makes them recognizable for pre-existing anti-CMV_pp65 CTLs via physiological TCR-pHLA engagement. Results: Our preclinical data demonstrate that CD19-ReTARG^TPR efficiently redirects anti-CMV CTLs to eliminate CD19-expressing cancer cells, including both established cell lines and primary chronic lymphocytic leukemia (CLL) cells. Unlike CD19-directed CAR T cells or the CD19/CD3 BiTE blinatumomab, CD19-ReTARG^TPR mediated robust cytotoxic activity without triggering supraphysiological cytokine release. Importantly, this approach retained efficacy even against cancer cells with low CD19 expression. Conclusions: In summary, we provide a robust proof-of-concept study and show that CD19-ReTARG^TPR offers a promising alternative strategy for T cell redirection, enabling the selective and effective killing of CD19-expressing malignancies while minimizing cytokine-driven toxicities through physiological CTL activation pathways. Full article

Fungal cell walls, composed of polysaccharides and proteins, play critical roles in adaptation, cell division, and protection against environmental stress. Their polyglucan components are continuously remodeled by various types of glycosyl hydrolases (GHs) and transferases (GTs). In Saccharomyces cerevisiae and other ascomycetes, enzymes of the Dfg5 subfamily, which belong as GTs to the GH76 family, cleave an α1,4 linkage between glucosamine and mannose to facilitate covalent linkage of GPI-anchored proteins to the cell wall’s polyglucans. In contrast, the functions of other fungal GH76 subfamilies are not understood. We characterized CtGH76 from the sordariomycete Chaetomium thermophilum, a member of the Fungi/Bacteria-mixed GH76 subfamily, revealing conserved structural features and functional divergence within the GH76 family. Notably, our structural characterization by X-ray crystallography combined with glycan fragment screening indicated that CtGH76 can recognize GPI-anchors like members of the Dfg5 subfamily but shows a broader promiscuity toward other glycans with central α1,6-mannobiose motifs due to the presence of an elongated glycan-binding canyon. These findings provide new insights into GH76 enzyme diversity and fungal cell wall maturation. Full article

Quantum mechanics (QM) revolutionizes drug discovery by providing precise molecular insights unattainable with classical methods. This review explores QM’s role in computational drug design, detailing key methods like density functional theory (DFT), Hartree–Fock (HF), quantum mechanics/molecular mechanics (QM/MM), and fragment molecular orbital (FMO). These methods model electronic structures, binding affinities, and reaction mechanisms, enhancing structure-based and fragment-based drug design. This article highlights the applicability of QM to various drug classes, including small-molecule kinase inhibitors, metalloenzyme inhibitors, covalent inhibitors, and fragment-based leads. Quantum computing’s potential to accelerate quantum mechanical (QM) calculations is discussed alongside novel applications in biological drugs (e.g., gene therapies, monoclonal antibodies, biosimilars), protein–receptor dynamics, and new therapeutic indications. A molecular dynamics (MD) simulation exercise is included to teach QM/MM applications. Future projections for 2030–2035 emphasize QM’s transformative impact on personalized medicine and undruggable targets. The qualifications and tools required for researchers, including advanced degrees, programming skills, and software such as Gaussian and Qiskit, are outlined, along with sources for training and resources. Specific publications on quantum mechanics (QM) in drug discovery relevant to QM and molecular dynamics (MD) studies are incorporated. Challenges, such as computational cost and expertise requirements, are addressed, offering a roadmap for educators and researchers to leverage quantum mechanics (QM) and molecular dynamics (MD) in drug discovery. Full article

To overcome the negative effects of the biochemical application of nano-substances in medicine (toxicity problem), using the example of fullerene C₆₀’s first derivative (fullerenol, FD-C₆₀), we show that their biophysical effect is possible through non-covalent hydrogen bonds when around FD-C₆₀ water layers are formed. SD-C₆₀ (Zeta potential is −43.29 mV) is much more stable than fullerol (Zeta potential is −25.85 mV), so agglomeration/fragmentation of the fullerol structure, due to instability, can cause toxic effects. When fullerol in solution was exposed to an oscillatory magnetic field with Re (real) part [250/−92 mT, H(ωt) = Acos(ωt)], water layers around FD-C₆₀ (fullerenol) are formed according to the Penrose process of 3D tiling formation, and the second derivative, SD-C₆₀ (or 3HFWC), is self-organized. However, when Im (imaginary) part [250/−92 mT, H(ωt) = Bisin (ωt)] of the external magnetic field is applied in addition to SD-C₆₀, ordered water chains and bubbling of water (“micelle”) are formed as a third derivative (TD-C₆₀). Fullerol (FD-C₆₀) interacts with biological structures biochemically, while the second (SD-C₆₀) and third (TD-C₆₀) derivatives act biophysically via non-covalent hydrogen bond oscillation. SD-C₆₀ and TD-C₆₀ significantly increased water solubility and reduced toxicity. The paper explains the synthesis of SD-C60 and TD-C60 from FD-C60 (fullerol) as a precursor by the influence of an oscillatory magnetic field (“Yin-Yang” principle) on hydrogen bonds in order to create water layers around fullerol. Examples of biomedical applications (cancer and Alzheimer’s) of this synergetic complex are given. This study shows that the “Yin-Yang” machinery, based on the nanophysics of C₆₀ molecules and non-covalent hydrogen bonds, is possible. The first attempt has been composed to synthesize nanomaterial for biophysical vibrational nanomedicine. Full article

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease of 2019 (COVID-19) and has persistently caused infections since its emergence in late 2019. The main protease (Mpro) of SARS-CoV-2 plays a crucial role in its life-cycle; thus, it is an important target for drug development. One of the first virus-specific drugs that has been approved for the treatment of COVID-19 patients is Paxlovid, which contains nirmatrelvir, a covalent inhibitor of Mpro. Screening of inhibitor candidates and specificity studies also rely on efficient substrates and activity assays. Casein is one of the most commonly applied universal substrates that can be used to study a wide range of proteases, including SARS-CoV-2 Mpro. Casein is a known substrate for Mpro in vitro, but the specific casein isoform cleaved by Mpro remained unidentified, and the cleavage sites have yet to be determined. This work studied cleavage of α-, β- and κ-isoforms of bovine casein by SARS-CoV-2 Mpro, using in vitro and in silico approaches. The candidate cleavage sites were predicted in silico based on the protein sequences, and the cleavage positions were identified based on mass spectrometric analysis of cleavage fragments. Based on our results, only β-casein contains cleavage sites for Mpro and thus can be used as its substrate in vitro. The newly identified cleavage site sequences further widen the knowledge about the specificity of SARS-CoV-2 Mpro. Full article

The organic multi-chromophore system has been increasingly attractive due to the potential optoelectronic applications. The inter-chromophore electronic coupling (EC), i.e., J_Coul and J_CT, plays a critical role in determining the relaxation path of the excited state. However, the molecular designing strategy for effective tuning of inter-chromophore EC is still challenging. In this computational work, we designed a series of perylene diimides (PDI) covalent dimers with rigid linking cores containing thiophene (Th) or phenyl (Ph) fragments and performed corresponding theoretical investigation to analyze the inter-PDI electronic coupling. Vibrational analysis indicated that the minimized excited state structural relaxation (ES-SR) can ensure the rigid inter-PDI geometry pre-defined by the topological characteristic of linking cores, leading to comparable |J_Coul| on S₀ and S₁ states. The saddle-shaped linking cores allow collaborative tuning of inter-PDI dihedral (α) and slipping (θ) angles, leading to effective tuning of inter-PDI |J_Coul| = 0–1000 cm⁻¹. Our work provides a new molecular designing strategy for effective tuning of inter-chromophore EC for organic chromophores. By using a rigid inter-chromophore structure, the ignorable ES-SR allows simplified molecular designing without considering the plausible geometric difference between S₁ and S₀ states, which might be useful for future applications in organic optoelectronics. Full article

A series of novel fluorescent donor–acceptor–donor (D-A-D) dyes containing [1,2,5]oxadiazolo[3,4-d]pyridazine and its 1-oxide as electron-withdrawing groups has been synthesized and thoroughly investigated using X-ray diffraction and molecular spectroscopy methods. This study showed that the introduction of N-oxide into the 1,2,5-oxadiazole ring in the acceptor fragment leads to a significant decrease in the luminescence intensity and quantum yield of the dyes. A comprehensive comparison of the photophysical properties of the obtained compounds containing the 1,2,5-oxadiazole ring with the previously studied [1,2,5]thia- and 1,2,5-selenadiazolo[3,4-d]pyridazine analogs showed that the oxygen substitution in the acceptor fragment shifts the phosphorescence maximum from the NIR region of 980–1100 nm to the red region of 690–770 nm. In contrast, for oxygen- and sulfur-containing dyes, purely red fluorescence with a maximum in the spectral range of 620–900 nm is observed. The crystal structures of furoxan-containing 3d·½CHCl₃ and furazan-containing 4d exhibit a non-planar [1,2,5]oxadiazolo[3,4-d]pyridazine fragment. We have found that short non-covalent interactions of the furoxan system with a lattice chloroform molecule in 3d lead to luminescence quenching. Meanwhile, in the 4d dye, the intermolecular π-π interactions of pyridazine nitrogen atoms with the N-carbazolyl group of the adjacent molecule should facilitate intermolecular charge transfer (ICT) emission. Thus, the luminescence maxima for these dyes can be tuned across a broad range of 700–1100 nm by varying the number of chalcogen atoms, highlighting the potential for tailoring optical properties in optoelectronic applications. Full article

Allostery is a fundamental biological phenomenon that occurs when a molecule binds to a protein’s allosteric site, triggering conformational changes that regulate the protein’s activity. However, allostery in antibodies remains largely unexplored, and only a few reports have focused on allostery from antigen-binding fragments (Fab) to crystallizable fragments (Fc). But this study, using anti-phenobarbital antibodies—which are widely applied for detecting the potential health food adulterant phenobarbital—as a model and employing multiple computational methods, is the first to identify a cyclopeptide (cyclo[Link-M-WFRHY-K]) that induces allostery from Fc to Fab in antibody and elucidates the underlying antibody allostery mechanism. The combination of molecular docking and multiple allosteric site prediction algorithms in these methods identified that the cyclopeptide binds to the interface of heavy chain region-1 (CH₁) in antibody Fab and heavy chain region-2 (CH₂) in antibody Fc. Meanwhile, molecular dynamics simulations combined with other analytical methods demonstrated that cyclopeptide induces global conformational shifts in the antibody, which ultimately alter the Fab domain and enhance its antigen-binding activity from Fc to Fab. This result will enable cyclopeptides as a potential Fab-targeted allosteric modulator to provide a new strategy for the regulation of antigen-binding activity and contribute to the construction of novel immunoassays for food safety and other applications using allosteric antibodies as the core technology. Furthermore, graph theory analysis further revealed a common allosteric signaling pathway within the antibody, involving residues Q123, S207, S326, C455, A558, Q778, D838, R975, R1102, P1146, V1200, and K1286, which will be very important for the engineering design of the anti-phenobarbital antibodies and other highly homologous antibodies. Finally, the non-covalent interaction analysis showed that allostery from Fc to Fab primarily involves residue signal transduction driven by hydrogen bonds and hydrophobic interactions. Full article

The complexity of therapeutic proteins like antibody–drug conjugates (ADCs) holds a tremendous analytical challenge. Complementary mass spectrometry approaches such as peptide mapping and intact mass analysis are required for the in-depth characterization of these bioconjugates. Cysteine-linked ADCs have shown a unique challenge for characterization, mainly when the conjugation is carried out on interchain cysteines, because their intact analysis requires native mass spectrometry conditions to preserve non-covalent binding between antibody chains. In this work, two different approaches were proposed. Specifically, a full scan data-independent all ion fragmentation (FS-AIF) and a full scan data-dependent targeted MS2 (FS-ddtMS2) were applied to generate complementary datasets for a cysteine-linked ADC characterization with a highly reactive payload. These two methods were applied to in vitro plasma stability and in vivo PK samples to calculate and refine mean drug-to-antibody ratio over time. Using this approach, we successfully characterized an ADC containing a hydrolysis-sensitive payload and refined the “active” drug-to-antibody ratio on in vitro stability and in vivo samples. These two methods allowed the confirmation of the different ADC species and potential metabolites of conjugated payload attached to the antibody backbone in a single analysis without needing a dedicated method for the conjugated payload metabolite identification. Full article

To investigate the impact of tea polyphenols on the thermodynamic properties, gelatinization properties, rheological properties, and digestion characteristics of starch after ball milling, canna starch and tea polyphenols were mixed at a 10:1 ratio (w/w) in an experiment and processed with different ball milling times. After ball milling for 3 h, the tea polyphenols and starch fragments formed complexes. Compared with the unmilled mixture, the solubility increased by 199.4%; the shear stress decreased by 89.48%; and the storage modulus and loss modulus decreased. The content of resistant starch first decreased and then increased. Infrared results revealed that ball milling led to a non-covalent interaction between the tea polyphenols and starch. Molecular dynamics simulations were used to study the interaction between the starch and tea polyphenols. The binding free energy of the main component, epigallocatechin gallate (EGCG), in tea polyphenols with starch was reduced from −23.20 kcal/mol to −26.73 kcal/mol. This experiment can provide a reference for the development of functional starch with high resistant starch content. Full article

We have designed and produced 39 amino acid peptide mimics of the Torpedo and human acetylcholine receptors’ (AChRs) main immunogenic regions (MIRs). These conformationally sensitive regions consist of three non-contiguous segments of the AChR α-subunits and are the target of 50–70% of the anti-AChR autoantibodies (Abs) in human myasthenic serum and in the serum of rats with a model of that disease, experimental autoimmune myasthenia gravis (EAMG), induced by immunizing the rats with the Torpedo electric organ AChR. These MIR segments covalently joined together bind a significant fraction of the monoclonal antibodies (mAbs) raised in rats against electric organ AChR. Many of these mAbs cross react with the rat neuromuscular AChR MIR and induce myasthenic symptoms when injected into naïve rats. The human MIR mimic peptide (H39MIR) is evolutionarily related to that of the Torpedo electric organ MIR mimic peptide (T39MIR) with eight amino acid differences between the two MIR mimics. The mAbs raised to the electric organ AChR MIR cross react with the human and scores of other species’ neuromuscular AChRs. However, the mAbs do not cross react with the H39MIR mimic attached to the N-terminus of an intein–chitin-binding domain (H39MIR-IChBD) even though they do bind to the T39MIR-IChBD construct. To account for this difference in binding anti-MIR mAbs, each of the eight human amino acids was substituted individually into the T39MIR-IChBD, and four of them were found to weaken mAb recognition. Substituting the corresponding four Torpedo amino acids individually and in combination into the homologous positions in H39MIR-IChBD makes chimeric human MIR mimic peptides (T/H39MIR), some of which bind anti-MIR mAbs and anti-MIR Abs from rat EAMG and human MG sera. The best mAb binding chimeric peptide constructs may potentially serve as the basis of a diagnostic anti-MIR Ab titer assay that is both prognostic and predictive of disease severity. Furthermore, the best peptides may also serve as the targeting element of a non-steroidal antigen-specific treatment of MG to remove anti-AChR MIR Abs, either as fused to the N-terminals of the human immunoglobin F_c fragment or as the targeting component of a T cell chimeric autoantibody receptor (CAAR) directed to anti-MIR memory B cells for elimination. Full article

The MALDI-TOF mass-spectrometry was employed to analyze the structure of the reaction products of limonene, a natural terpene, and elemental sulfur, with the objective of identifying the occurrence of side processes, such as oxidative dehydrogenation, aromatization, and the Diels–Alder reaction cascade. The MALDI-TOF mass-spectrometry was demonstrated to be effective for the analysis of high-sulfur polymers obtained by the inverse vulcanization reaction, allowing for the unambiguous separation of sulfur-containing and hydrocarbon molecular fragments and the detailed characterization of macromolecular structures. By varying the ratio of sulfur (S₈) and limonene in the initial reaction system, we were able to ascertain the limiting amount of sulfur that can be covalently bonded by terpene, as well as determine the average length of polysulfide chains under the assumption of equal reactivity and complete depletion of all double bonds. The side reaction of limonene aromatization, as indicated by the MALDI-TOF spectrum of the product resulting from its interaction with elemental sulfur, was corroborated by ¹H and ¹³C NMR spectroscopy. Consequently, the registration and interpretation of MALDI-TOF spectra of inverse vulcanization products, either independently or in conjunction with the application of ¹H and ¹³C NMR spectroscopy methods, as well as the determination of the limiting number of sulfur atoms that can be bound to one molecule of an unsaturated compound, paves the way for new avenues of investigation into the structure and side reactions involved in the synthesis of high-sulfur polymers. Full article

As a promising polymer for the production of biomaterials and drug delivery systems, poly(lactic acid) (PLA) is characterized by its relative hydrophobicity, as well as its chemical and biological inertness. Here, we aimed to improve the biological properties of PLA-based materials via the covalent attachment of a hydrophilic biocompatible glycopolymer, namely poly(2-deoxy-N-methacrylamido-D-glucose) (PMAG) on their surface. PMAG is a water-soluble polymer that contains glucose units in its side chains, which are responsible for good biocompatibility and the ability to attach bioactive molecules. In the developed protocol, PMAG was synthesized by controlled radical polymerization in the presence of a reversible addition–fragmentation chain transfer (RAFT) agent, followed by the conversion of glycopolymer terminal dithiobenzoate functionality into a primary amino group (PMAG-NH₂). PLA-based films served as model aliphatic polyester materials for developing the surface biofunctionalization protocol. According to that, PMAG-NH₂ covalent immobilization was carried out after alkali treatment, allowing the generation of the surface-located carboxyl groups and their activation. The developed modification method provided a one-point attachment of hydrophilic PMAG to the hydrophobic PLA surface. PMAG samples, which differed by the degree of polymerization, and the variation of polymer concentration in the reaction medium were applied to investigate the modification efficacy and grafting density. The developed single-point polymer grafting approach provided the efficient functionalization with a grafting density in the range of 5–23 nmol/cm². The neat and modified polymer films were characterized by a number of methods, namely atomic force microscopy, thermogravimetric analysis, ellipsometry, and contact angle measurements. In addition, an ArgGlyAsp-containing peptide (RGD peptide) was conjugated to the PMAG macromolecules grafted on the surface of PLA films. It was shown that both surface modification with PMAG and with PMAG-RGD peptide enhanced the adhesion and growth of mesenchymal stem cells as compared to a neat PLA surface. Full article