Ligand Structure Research Articles

Unveiling a Hidden Pocket in HIV-1 Protease: New Insights Into Retroviral Protease Cantilever-Tip Region Characteristics.

The HIV-1 protease is critical for the process of viral maturation and as such, it is one of the most well characterized proteins in the Protein Data Bank. There is some evidence to suggest that the HIV-1 protease is capable of accommodating small molecule fragments at several locations on its surface outside of the active site. However, some pockets on the surface of proteins remain unformed in the apo structure and are termed "cryptic sites." To date, no cryptic sites have been identified in the structure of HIV-1 protease. Here, we characterize a novel cryptic cantilever pocket on the surface of the HIV-1 protease through mixed-solvent molecular dynamics simulations using several probes. Interestingly, we noted that several homologous retroviral proteases exhibit evolutionarily conserved dynamics in the cantilever region and possess a conserved pocket in the cantilever region. Immobilization of the cantilever region of the HIV-1 protease via disulfide cross-linking resulted in curling-in of the flap tips and the propensity for the protease to adopt a semi-open flap conformation. Structure-based analysis and fragment-based screening of the cryptic cantilever pocket suggested that the pocket may be capable of accommodating ligand structures. Furthermore, molecular dynamics simulations of a top scoring fragment bound to the cryptic pocket illustrated altered flap dynamics of the fragment-bound enzyme. Together, these results suggest that the mobility of the cantilever region plays a key role in the global dynamics of retroviral proteases. Therefore, the cryptic cantilever pocket of the HIV-1 protease may represent an interesting target for future in vitro studies.

Investigating flavonoids derived from Tribulus terrestris L. as prospective candidates for Alzheimer's disease treatment: Molecular docking modeling of their interactions with physiological system receptors

Alzheimer's disease (AD) stands as the primary cause of dementia, marked by its neurodegenerative essence, which results in cognitive impairment associated with memory and a decline in functionality. Currently there is no drug which can permanently cure the nervous lesions as well as completely eradicate this pathogenesis. The aim of this research is to examine the acetylcholinesterase activity of flavonoids identified in Tribulus terrestris L. (Tt) by predicting ligand-receptor binding. The research process begins with the preparation of protein and ligand structures. Subsequently, docking is performed, interaction between protein-ligands is then analyzed and visualized. Four phytoconstituents of Tt were chosen, and molecular docking simulations revealed that all four compounds exhibited good binding affinities. Based on the predicted ADMET values using the Lipinski rule, compounds with potentially good activity were identified. The results suggest that these compounds may exhibit anti-acetylcholinesterase activity.

Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling.

Accurate protein-ligand binding poses are the prerequisites of structure-based binding affinity prediction and provide the structural basis for in-depth lead optimization in small molecule drug design. However, it is challenging to provide reasonable predictions of binding poses for different molecules due to the complexity and diversity of the chemical space of small molecules. Similarity-based molecular alignment techniques can effectively narrow the search range, as structurally similar molecules are likely to have similar binding modes, with higher similarity usually correlated to higher success rates. However, molecular similarity is not consistently high because molecules often require changes to achieve specific purposes, leading to reduced alignment precision. To address this issue, we propose a new alignment method─Z-align. This method uses topological structural information as a criterion for evaluating similarity, reducing the reliance on molecular fingerprint similarity. Our method has achieved success rates significantly higher than those of other methods at moderate levels of similarity. Additionally, our approach can comprehensively and flexibly optimize bond lengths and angles of molecules, maintaining a high accuracy even when dealing with larger molecules. Consequently, our proposed solution helps in achieving more accurate binding poses in protein-ligand docking problems, facilitating the development of small molecule drugs. Z-align is freely available as a web server at https://cloud.zelixir.com/zalign/home.

Nickel-catalyzed regiodivergent hydrosilylation of α-(fluoroalkyl)styrenes without defluorination

The fluoroalkyl-containing organic molecules are widely used in drug discovery and material science. Herein, we report ligand regulated nickel(0)-catalyzed regiodivergent hydrosilylation of α-(fluoroalkyl)styrenes without defluorination, providing an atom- and step-economical synthesis route of two types of fluoroalkyl substituted silanes with exclusive regioselectivity. The anti-Markovnikov addition products (β-fluoroalkyl substituted silanes) are formed with monodentate phosphine ligand. Noteworthy, the bidentate phosphine ligand promote the generation of the more challenging Markovnikov products (α-fluoroalkyl substituted silanes) with tetrasubstituted saturated carbon centers. This protocol features with easy available starting materials and commercially available nickel catalysis, a wide range of substrates and excellent regioselectivity. The structure divergent products undergo a variety of transformations. Comprehensive mechanistic studies including the inverse kinetic isotope effects demonstrate the regioselectivity controlled by ligand structure through α-CF3 nickel intermediate. DFT calculations reveal a distinctive mechanism involving an open-shell singlet state, which is crucial for generating intricate tetra-substituted Markovnikov products.

Influence of Surface Chemistry on Metal Deposition Outcomes in Copper Selenide-Based Nanoheterostructure Synthesis.

The use of nanoparticle surface chemistry to direct metal deposition has been well-studied in the modification of metal nanoparticle substrates but is not yet well-established for metal chalcogenide particle substrates, although integration of these particles into nanoheterostructures is of high interest. In this report, we investigate the effect of Cu2-xSe surface chemistry on the morphology of metal deposition on these plasmonic semiconductor nanoparticles. Specifically, we functionalize Cu2-xSe nanoparticles with a suite of 12 different ligands and investigate how different aspects of the ligand structure do or do not impact the morphology and extent of subsequent metal deposition on the Cu2-xSe surface. Surprisingly, our results indicate that the morphology of the resulting metal deposits and the extent of metal deposition onto the existing Cu2-xSe particle substrate are indistinguishable for the majority of ligands tested. An exception to these findings is observed for particles functionalized by quaternary alkylammonium bromides, which exhibit statistically distinct metal deposition patterns compared to all other ligands tested. We hypothesize that this unique behavior is due to a cooperative binding mechanism of the quaternary alkylammonium bromides to the surface of copper selenide. Taken together, these results yield both new strategies for controlling postsynthetic modification of copper selenide nanoparticles and also reveal limitations of surface chemistry-based approaches for this system.

Counterion Effects in [Ru(bpy)3](X)2-Photocatalyzed Energy Transfer Reactions.

Photocatalysis that uses the energy of light to promote chemical transformations by exploiting the reactivity of excited-state molecules is at the heart of a virtuous dynamic within the chemical community. Visible-light metal-based photosensitizers are most prominent in organic synthesis, thanks to their versatile ligand structure tunability allowing to adjust photocatalytic properties toward specific applications. Nevertheless, a large majority of these photocatalysts are cationic species whose counterion effects remain underestimated and overlooked. In this report, we show that modification of the X counterions constitutive of [Ru(bpy)3](X)2 photocatalysts modulates their catalytic activities in intermolecular [2 + 2] cycloaddition reactions operating through triplet-triplet energy transfer (TTEnT). Particularly noteworthy is the dramatic impact observed in low-dielectric constant solvent over the excited-state quenching coefficient, which varies by two orders of magnitude depending on whether X is a large weakly bound (BArF 4 -) or a tightly bound (TsO-) anion. In addition, the counterion identity also greatly affects the photophysical properties of the cationic ruthenium complex, with [Ru(bpy)3](BArF 4)2 exhibiting the shortest 3MLCT excited-state lifetime, highest excited state energy, and highest photostability, enabling remarkably enhanced performance (up to >1000 TON at a low 500 ppm catalyst loading) in TTEnT photocatalysis. These findings supported by density functional theory-based calculations demonstrate that counterions have a critical role in modulating cationic transition metal-based photocatalyst potency, a parameter that should be taken into consideration also when developing energy transfer-triggered processes.

Novel hydroxy-tagged bis-dihydrazothiazole derivatives: Synthesis, antimicrobial capacity and formation of some metal chelates with iron, cobalt and zinc ions

Until today, microbialinfectionsepitomize a seriousuniversal health threat. Subsequently, developing a potential antimicrobialprototype remains an urgent, global necessity. Despite several reports discussing the biological utility of some bis-thiazoles, the use of bis-dihydrazothiazoles and their corresponding metal chelates as potent antimicrobials, is yet to be explored. The current report outlines an attempt to fill that void by representing a successful synthesis of a new class of bis-dihydrazothiazoles as well as three of their transition metal chelates and their use as potential antimicrobials. This report presents the design of some novel hydroxy-tagged bis-dihydrazothiazoles 6a-e and bis-dihydrazothiazolones 9a-evia the reaction of a bis-aldehyde thiosemicarbazone 3, as a common synthetic precursor, with two groups of hydrazonoyl halide derivatives 4a-e and 7a-e. The chelation affinity of these novel bis-dihydrazothiazoles to behave as neutral tridentate ligands coordinating to the metal ions; Fe(III), Co(II), or Zn(II) through azomethine-N, thiazole-S, and azo-N atoms to form metal complexes with a metal/ligand ratio of 2:1 was confirmed. In-vitro, antimicrobial screening of the novel hydroxy-tagged bis-dihydrazothiazole derivatives, as well as a selected group of their transition metal chelate complexes [M2L], was inspected, and the data weremeasured incomparisonto those of ketoconazole and gentamycin as antimicrobial reference standards. Most bis-dihydrazothiazoles 6a-e and bis-dihydrazothiazolones 9a-e showed decent to excellent antimicrobial activities against the screened microbes, but the chloro-substituted bis dihydrazothiazole derivatives 6c and 9c showed exceptional inhibition of Bacillus subtilis (20 mm), Escherichia coli (25 mm), and Candida albicans (19 mm), and Salmonella typhimurium (19 mm), respectively. Additionally, amongst the three synthesized metal complexes [M2L], only the zinc complex, [Zn2L] showed remarkable inhibition of both Staphylococcus aureus (21 mm) and Salmonella typhimurium (19 mm) compared to the reference standard Gentamycin, and was more potent than the free ligand, 6a itself (no activity and 11 mm respectively). Antimicrobial inspection was assessed by the agar well diffusion assay method against all bacterial and fungal strains. Magnetic moment, diffused reflectance, FT-IR, 1H NMR, molar conductivity, thermogravimetric analysis (TGA), X-ray diffraction (XRD), and scanning electron microscope(SEM) were among the many techniques used to elucidate the structures of all novel hydroxy-tagged bis-heterocyclic ligands and their metal chelate complexes.

Capturing the Effects of Single Atom Substitutions on the Inhibition Efficiency of Glycogen Synthase Kinase-3β Inhibitors via Markov State Modeling and Experiments.

Small modifications in the chemical structure of ligands are known to dramatically change their ability to inhibit the activity of a protein. Unraveling the mechanisms that govern these dramatic changes requires scrutinizing the dynamics of protein-ligand binding and unbinding at the atomic level. As an exemplary case, we have studied Glycogen Synthase Kinase-3β (GSK-3β), a multifunctional kinase that has been implicated in a host of pathological processes. As such, there is a keen interest in identifying ligands that inhibit GSK-3β activity. One family of compounds that are highly selective and potent inhibitors of GSK-3β is exemplified by a molecule termed COB-187. COB-187 consists of a five-member heterocyclic ring with a thione at C2, a pyridine substituted methyl at N3, and a hydroxyl and phenyl at C4. We have studied the inhibition of GSK-3β by COB-187-related ligands that differ in a single heavy atom from each other (either in the location of nitrogen in their pyridine ring, or with the pyridine ring replaced by a phenyl ring), or in the length of the alkyl group joining the pyridine and the N3. The inhibition experiments show a large range of half-maximal inhibitory concentration (IC50) values from 10 nM to 10 μM, implying that these ligands exhibit vastly different propensities to inhibit GSK-3β. To explain these differences, we perform Markov State Modeling (MSM) using fully atomistic simulations. Our MSM results are in excellent agreement with the experiments in that they accurately capture differences in the binding propensities of the ligands. The simulations show that the binding propensities are related to the ligands' ability to attain a compact conformation where their two aromatic rings are spatially close. We rationalize this result by sampling numerous binding and unbinding events via funnel metadynamics simulations, which show that indeed while approaching the bound state, the ligands prefer to be in their compact conformation. We find that the presence of nitrogen in the aromatic ring increases the probability of attaining the compact conformation. Protein-ligand binding is understood to be dictated by the energetics of interactions and entropic factors, like the release of bound water from the binding pockets. This work shows that changes in the conformational distribution of ligands due to atom-level modifications in the structure play an important role in protein-ligand binding.

A Systematic Hierarchical Virtual Screening Model for RhlR Inhibitors Based on PCA, Pharmacophore, Docking, and Molecular Dynamics.

RhlR plays a key role in the quorum sensing of Pseudomonas aeruginosa. The current structure-activity relationship (SAR) studies of RhlR inhibitors mainly focus on elucidating the functional groups. Based on a systematic review of previous research on RhlR inhibitors, this study aims to establish a systematic, hierarchical screening model for RhlR inhibitors. We initially established a database and utilized principal component analysis (PCA) to categorize the inhibitors into two classes. Based on the training set, pharmacophore models were established to elucidate the structural characteristics of ligands. Subsequently, molecular docking, molecular dynamics simulations, and the calculation of binding free energy and strain energy were performed to validate the crucial interactions between ligands and receptors. Then, the screening criteria for RhlR inhibitors were established hierarchically based on ligand structure characteristics, ligand-receptor interaction, and receptor affinity. Test sets were finally employed to validate the hierarchical virtual screening model by comparing it with the current SAR studies of RhlR inhibitors. The hierarchical screening model was confirmed to possess higher accuracy and a true positive rate, which holds promise for subsequent screening and the discovery of active RhlR inhibitors.

Impact of ligand structure and base bead pore size on host cell protein removal during monoclonal antibody purification using multimodal chromatography resin

Despite advancements in therapeutic monoclonal antibodies (mAbs) and cell line engineering, separating host cell proteins (HCPs) from mAbs during downstream purification remains challenging. Therefore, in this study, we developed a novel multimodal chromatography (MMC) resin to enhance HCP removal during mAb polishing processes. We evaluated the impact of both ligand structure and pore size of the MMC resin by purifying a post-protein A chromatography solution in flow-through mode. We observed that the efficiency of HCP clearance depended on the hydrophobic moiety structure of the ligand and predicted the mAb purification capability of MMC through linear salt-gradient elution experiments involving a mixture of transferrin, bovine serum albumin (BSA), and pepsin. Our findings revealed that the prototype immobilized 1,12-dodecanediamine via the formyl group exhibited the best performance attributed to its long alkyl chain. Furthermore, an investigation of effects of base bead pore size on HCP capacity using cellulose base beads of five different pore sizes showed that larger pore resin base beads had the highest HCP removal capacity. Specifically, MMC resins with a pore diameter exceeding 440 nm reduced the HCP level by three orders of magnitude under high mAb loading conditions (> 1000 mg/mL-resin). The MMC resin developed in this study, along with the insights gained into ligand structure and pore size, not only enhances mAb polishing efficiency but also contributes to improving downstream processes in mAb biopharmaceutical production.

Transformation of Metal-Organic Framework from Kinetic to Thermodynamic Product for Controlled Delivery of Vitamin C.

A biocompatible metal-organic framework (MOF), named HSTC-4, constructed using the flexible 4,4'-oxybis(benzoic acid) (OBA), was developed to enable efficient loading and controlled release of vitamin C (VC) through a combination of strategies involving ligand length, structure design, and metal selection. The kinetic product HSTC-4 demonstrates a propensity for transforming into the thermodynamically stable HSTC-5 under external stimuli, such as photoillumination and vacuum heating, as witnessed by single-crystal to single-crystal transformation. Density functional theory (DFT) calculations reveal that the VC guest molecules exhibit stronger binding affinity with HSTC-5 due to its narrower pores compared to HSTC-4, resulting in a slower release of VC from VC@HSTC-5. Furthermore, precise control over VC release can be achieved by introducing surface modifications involving SiO2 onto the structure of VC@HSCT-5, while simultaneously adjusting environmental factors such as pH and temperature conditions. Preliminary cell culture experiments and cytotoxicity assays highlight the biocompatibility of HSTC-5, suggesting that it is a promising platform for sustained drug delivery and diverse biomedical applications.

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs.

A Comprehensive Review of The Molecular Dynamic Study Of Chalcones, Coumarins and Chromones as Selective MAO‐B Inhibitors [2015‐Till Date

AbstractMolecular dynamics (MD) simulation is an in silico method used in the biomolecular level of research to study how the protein interacts with the target with time. It provides a detailed information of the protein dynamics and ligand structure with the crucial amino acid interactions. Monoamine oxidase B (MAO−B) is a crucial isoenzyme responsible for the catalyses of oxidative deamination of various biogenic amines in the brain and peripheral tissues. The selective inhibitors of MAO−B are considered as the management of symptoms of neurodegenerative disorders like Alzheimer's disease(AD) and Parkinson disease(PD). Recently the structural scaffolds containing chalcones, coumarins and chromones derived candidates shown potent, selective, competitive and reversible type of MAO−B inhibitors. The structural similarities between the above scaffolds can produce almost similar type of interactions in the inhibitor binding cavity of MAO−B. Numerous molecular simulation reports were supported by the above mentioned fact. The current review focus on the last ten year molecular dynamics report of chalcones, coumarins and chromones towards MAO−B inhibition. The review also focuses on the software details used in the MD dynamics simulation and the structural requirement from each class of compound for the recognition of MAO−B inhibitory activity.

Modulating the reduction potential and ligand basicity of Ni(II) HER catalysts with highly conjugated N2S2 ligands

Molecular catalysts with N2S2 chelates and earth abundant metals have been used in different applications. With their versatile nature to modulate activity through changes in the ligand framework, they are excellent candidates to generate low-cost and sustainable energy as electrocatalysts for the hydrogen evolution reaction (HER). Herein we demonstrate the modulation of the reduction potential and basicity across a series of six square planar Ni(II) complexes with bis(thiosemicarbazonato) (BTSC), hybrid thiosemicarbazonato-alkylthiocarbamato (TSTC), and bis(alkylthiocarbamato) (BATC) ligands and evaluate their activity as homogenous HER catalysts. The redox active ligands have been designed to modulate the electronic structure of the N2S2Ni core and to systematically alter their respective pKa values. Cyclic voltammograms of all six complexes show two reversible reduction events in acetonitrile that systematically shift to more anodic potentials when the pendent methylthiosemicarbazonato (–NN=C(S)NHMe) groups are substituted with ethylthiocarbamato (–NN=C(S)OEt) groups and/or when the 2,4-butanedione backbone is replaced by 1-phenyl-1,2-propandione. Ligand basicity was evaluated by spectroscopic titration in acetonitrile and found to vary systematically across the series. Within the series of complexes the reduction potentials vary over an ∼ 500 mV range and the ligand basicity over ∼ 7 pKa units. Density functional theory (DFT) computations are consistent with experimental changes in redox potential and pKa values across the series of complexes. The results demonstrate a unique example in which electronic properties of the complexes are modulated via small ligand structure variations. The complexes are stable under acidic conditions or upon reduction, but they degrade upon reduction in the presence of acid limiting their application as homogeneous HER electrocatalysts.

Lighting and rapid detection of the Coronavirus S protein using computationally speculated ligand and its application in SARS-CoV-2

Detection of key proteins has enormous medical potential, particularly during the initial phase of an outbreak of infectious diseases. For this purpose, we develop a research paradigm based on computational speculation. With the rapid development of computers, it is possible to analyze the structure of key proteins and screen specific fluorescent ligands through computational tools. This process resembles the production of antibodies but is more effective, and the resultant product is significantly cheaper. A proof of concept was demonstrated by studying the S protein of SARS-CoV-2. The structural data of the S protein enabled automated docking with fluorescent molecules. After two rounds of conditional screening and verification, the most effective fluorescent ligand, Protoporphyrin IX (PPIX), was identified. PPIX illuminates the S protein, recovers fluorescence upon binding. The illuminated complex is enriched by a single microsphere, allowing for the quantitative analysis of the proteins through fluorescence intensity. Finally, less than 1000 copies S protein-bearing pseudovirus can be detected in 20 minutes without amplification. Overall, we established a highly sensitive general method for protein detection based on single microsphere enrichment with the aid of computerised simulation. We hope this integrated approach will provide new insights for rapid screening in epidemic populations.

Investigating the effect of ligand structure on the anticancer properties of several new Co(II) complexes of vitaminB3-based phosphoramides

Nicotinamide, known as Vitamin-B3, has shown promising potential in improving various medical conditions. Carbacylamidophosphates (CAPh) are versatile phosphoramide ligands with a wide range of applications in both biochemistry and chemistry. Herein, to obtain compounds with enhanced anticancer activity and study the effect of the structure on this activity, four new Co(II) complexes of vitaminB3-based CAPh ligands with the formula of CoCl2[3-NC5H4CONHPO(NC5H10)2]2(C1), CoCl2[3-NC5H4CONHPO(NC5H9CH3)2]2(C2), CoCl2[3-NC5H4CONHPO(NC6H12)2]2(C3), and CoCl2[3-NC5H4CONHPO(NC4H10)2]2(C4) were designed and synthesized. FT-IR, UV–Vis, Atomic Absorption (AAS),1H, 13C, and 31PNMR, and Mass spectroscopies beside CHN and Molar conductivity methods were utilized to characterize the synthesized compounds. Using MTT-assay and Flow Cytometry, the anticancer effects of these complexes were studied on three distinct cell lines, including one normal cell line (MCF10A) and two cancer cell lines (MDA-MB-231, MCF-7). Results showed that our ligands could form complexes by coordinating with cobalt, which, not only have a very strong killing effect on cancer cells but also have a higher level of safety for normal cells and are more cost-efficient than Cisplatin. C3 was the most effective complex at inhibiting the growth of MCF-7 and MDA-MB-231 cells which exhibited a remarkable 97.5 % reduction in cancer cell growth and a Selectivity Index up to > 37. This is an impressive 93 and 54 times more selective and safer than commonly used drugs like Cisplatin and Doxorubicin, respectively.Flow Cytometry analysis shows complex-induced breast cancer cell apoptosis.The ligands’ amine structure and ring size can directly impact the complexes’ anticancer effect and safety for normal cells.

Green Fluorescence Property of Chromone-based Hydrazone Towards Zn2+ Ion

Excessive concentration of Zn in the environment may lead to bad toxicological responses that can affect human health and create numerous challenges in the environment. Therefore, it is very important to develop a sensitive method such as selective chemosensors based on fluorescence property which does not require laborious work in order to detect Zn metal ion. A formylchromone-thiosemicarbazide with two chloro derivatives namely DFCTSC was synthesized from reflux reaction of 6,8-dichloroformylchromone (DCF) and thiosemicarbazide (TSC) in ethanol. The characterisation of ligand structure was determined by using spectroscopic techniques such as Fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectroscopy (UV-VIS) and nuclear magnetic resonance spectroscopy (NMR). Meanwhile, the fluorescence property of DFCTSC in the presence of Zn ion was recorded using fluorescence spectrophotometer. The result showed DFCTSC has a good fluorescence behaviour towards Zn ion by giving turn-on green fluorescence at peak 500 nm and emit light when it observed under UV light. The behaviour displayed the ability of ligand to be used as a potential fluorescent chemosensor for detecting Zn2+.

Jahn-Teller effect and features of divalent copper ion behavior in multicomponent borate crystals

Crystals of YGa3(BO3)4, YAl3(BO3)4, EuGa3(BO3)4 and EuAl3(BO3)4 with copper alloy were studied by electron paramagnetic resonance and X-ray diffraction analysis. The lattice parameters and coordinates of copper-doped boron atoms were determined. The study of EPR spectra showed that copper is in the divalent state and replaces aluminum ions with C2 node symmetry. In YAl3(BO3)4:Cu crystals, a ligand structure exists due to the interaction of copper electrons with yttrium nuclei. The parameters of the spin Hamiltonian describing the behavior of the Cu2+ spectrum have been determined. The deviation of the Z-axis spectra from the C3 axis by 54(1)° is due to Jahn-Teller vibronic interaction and monoclinic distortion. In the EuGa3(BO3)4 crystal, a new spectrum 2 was found, which also belongs to divalent copper but is observed at an excited state 31 cm−1 away from the ground state. Above 70 K, an isotropic EPR line with a width of 450 Gs, g = 2.1, appears and exists up to room temperature.

Serine/Threonine Protein Kinases as Attractive Targets for Anti-Cancer Drugs-An Innovative Approach to Ligand Tuning Using Combined Quantum Chemical Calculations, Molecular Docking, Molecular Dynamic Simulations, and Network-like Similarity Graphs.

Serine/threonine protein kinases (CK2, PIM-1, RIO1) are constitutively active, highly conserved, pleiotropic, and multifunctional kinases, which control several signaling pathways and regulate many cellular functions, such as cell activity, survival, proliferation, and apoptosis. Over the past decades, they have gained increasing attention as potential therapeutic targets, ranging from various cancers and neurological, inflammation, and autoimmune disorders to viral diseases, including COVID-19. Despite the accumulation of a vast amount of experimental data, there is still no "recipe" that would facilitate the search for new effective kinase inhibitors. The aim of our study was to develop an effective screening method that would be useful for this purpose. A combination of Density Functional Theory calculations and molecular docking, supplemented with newly developed quantitative methods for the comparison of the binding modes, provided deep insight into the set of desirable properties responsible for their inhibition. The mathematical metrics helped assess the distance between the binding modes, while heatmaps revealed the locations in the ligand that should be modified according to binding site requirements. The Structure-Binding Affinity Index and Structural-Binding Affinity Landscape proposed in this paper helped to measure the extent to which binding affinity is gained or lost in response to a relatively small change in the ligand's structure. The combination of the physico-chemical profile with the aforementioned factors enabled the identification of both "dead" and "promising" search directions. Tests carried out on experimental data have validated and demonstrated the high efficiency of the proposed innovative approach. Our method for quantifying differences between the ligands and their binding capabilities holds promise for guiding future research on new anti-cancer agents.

Syntheses, crystal structures, luminescence properties and Hirshfeld surface analyses of two mononuclear 2,2′:6′,2′’-terpyridine lanthanide complexes with different β-diketones

Six ternary lanthanide complexes with different β-diketones as primary “antenna” ligand and 2,2’:6’,2’’-terpyridine as neutral ancillary ligand, namely [Ln(hfac)3(tpy)] [Ln(III) = Eu (1), Gd (2), Tb (3); hfac = hexafluoroacetylacetone; tpy = 2,2’:6’,2’’-terpyridine] and [Ln(btfa)3(tpy)] [Ln(III) = Eu (4), Gd (5), Tb (6); btfa = 4,4,4-trifluoro-1-phenyl-1,3-butanedione], were synthesized and characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, single crystal X-ray diffraction and powder X-ray diffraction. The three-dimensional Hirshfeld surface map and two-dimensional fingerprint analysis reveal that the substitution of hfac with btfa result in the decrease of the H···F/F···H and F···F interactions and the increase of the C···H/H···C and H···H interactions. Solid-state luminescence investigations indicate that the Eu(III) complexes (1-Eu and 4-Eu) and the Tb(III) complexes (3-Tb and 6-Tb) display the characteristic lanthanide-centered luminescence upon UV excitations. 1-Eu and 4-Eu emit red light at CIE: 0.6827, 0.3172 and CIE: 0.6819, 0.3179 with the quantum yields (QY) of 78.70 % and 68.85 % and the lifetimes (τ) of 0.768 and 0.808 ms, respectively. 3-Tb and 6-Tb emit green light at CIE: 0.2677, 0.7221 and CIE: 0.2680, 0.7217 with the QY values of 7.56 % and 1.38 % and the τ values of 0.076 and 0.022 ms, respectively. For the Eu(III) complexes, the substitution of hfac by btfa makes the QY value lower from 78.70 % to 68.85 % and slightly prolong the τ value from 0.768 to 0.808 ms, while for the Tb(III) complexes, both of the QY and τ values decrease. The results suggest that the structures of the primary β-diketone ligands could affect the luminescence performances such as QY and τ values of the Eu(III) and Tb(III) complexes.