Ligand Structure Research Articles

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.

The Role of the Polyethylene Glycol in the Organization of Gold Nanorods at the Air-Water and Air-Solid Interfaces.

The organization of metallic nanoparticles into assembled films is a complex process. The type of nanoparticle stabilizing ligand and the method for creating an organized layer can profoundly affect the optical properties of the resulting nanoparticle assembly. Investigations of the ligand structure and nanoparticle interactions can provide a greater understanding of the design of the assembly process and the quality of the resulting materials. One of the functionalization methods in the preparation of specific gold nanorods is the utilization of thiol-terminated poly(ethylene glycol). This generates gold nanorods capable of forming stable monolayers at the air-water interface upon dispersion in a suitable organic solvent. Herein, we show that depending on the molecular weight of the poly(ethylene glycol), the structures obtained at the air-water and air-solid interfaces differ in the arrangement. The studied structures were characterized by using spectroscopic and microscopic techniques, and the structural type was correlated with the polymer type. Insoluble and stable Langmuir monolayers composed of higher-molecular-weight gold nanorods with poly(ethylene glycol) were formed only in the presence of an additional stabilizer that prevented the formation of gold nanorods in aqueous solutions. At the air-solid interface, conformational changes in poly(ethylene glycol) induced the aggregation of gold nanorods, which became closely packed under the influence of surface pressure. The presented results suggested that the arrangement of two-dimensional layers of gold nanorods could be tailored using poly(ethylene glycol) of various molecular weights.

Phytochemical Targeting of Nerve Growth Factor by Thymoquinone and Cuscutin: A Molecular Dynamics Simulation Study.

Background Nerve growth factor (NGF) is a novel target of pain therapeutics for oral cancer, and it plays a main role in the nociception of chronic pain. Surgery, along with chemotherapy or radiotherapy, is the gold standard for treating patients, but the side effects are significant as well. Newer effective interventions with natural phytochemicals could improve patient compliance and enhance the quality of life among patients with oral cancer. A literature search revealed a positive correlation between NGF and oral cancer pain. Nigella sativa (N. sativa) and Cuscuta reflexa (C. reflexa) have proven anticancer effects, but their activity with NGF is unexplored. Aims and objectives We aimed to identify the potential phytochemicals in N. sativa and C. reflexa. We also checked the NGF-blocking activity of the phytochemicals. Molecular docking and molecular dynamic (MD) simulations evaluated the binding energy and stability between the NGF protein and selected phytochemical ligands. Materials and methods We obtained protein NGF structure from UniProt (ID: 4EDX, P01138, Beta-nerve growth factor), ligand (thymoquinone) structure using PubChem ID: 10281, and ligand (cuscutin) structure using PubChem ID: 66065. Maestro protein (Schrödinger Inc., Mannheim, Germany) was used for molecular docking. Desmond Simulation Package (Schrödinger Inc., Mannheim, Germany) was used to model MDfor 100 nanoseconds (ns). We have assessed the interaction between the protein and ligands by root mean square deviation (RMSD) values. Results The interaction of thymoquinone and cuscutin with NGF was assessed. While interacting with thymoquinone, there was mild fluctuation from 0.6 Å to 2.5 Å up to 80 ns and ended up at 4.8 Å up to 100 ns. While interacting with cuscutin, mild fluctuation was seen from 0.8 Å to 4.8 Å till 90 ns and ended at 6.4 Å up to 100 ns. We found a stable interaction between our drug combination and the NGF receptor. Conclusion We have identified a stable interaction between thymoquinone, cuscutin, and NGF by our MD simulations. Hence, it could be used as an NGF inhibitor for pain relief and to control tumor progression. Further in vitro and in vivo evaluations of this novel drug combination with phytochemicals will help us understand their biological activities and potential clinical applications in oral cancer therapeutics.

The Chameleon Strategy-A Recipe for Effective Ligand Screening for Viral Targets Based on Four Novel Structure-Binding Strength Indices.

The RNA viruses SARS-CoV, SARS-CoV-2 and MERS-CoV encode the non-structural Nsp16 (2'-O-methyltransferase) that catalyzes the transfer of a methyl group from S-adenosylmethionine (SAM) to the first ribonucleotide in mRNA. Recently, it has been found that breaking the bond between Nsp16 and SAM substrate results in the cessation of mRNA virus replication. To date, only a limited number of such inhibitors have been identified, which can be attributed to a lack of an effective "recipe". The aim of our study was to propose and verify a rapid and effective screening protocol dedicated to such purposes. We proposed four new indices describing structure-binding strength (structure-binding affinity, structure-hydrogen bonding, structure-steric and structure-protein-ligand indices) were then applied and shown to be extremely helpful in determining the degree of increase or decrease in binding affinity in response to a relatively small change in the ligand structure. After initial pre-selection, based on similarity to SAM, we limited the study to 967 compounds, so-called molecular chameleons. They were then docked in the Nsp16 protein pocket, and 10 candidate ligands were selected using the novel structure-binding affinity index. Subsequently the selected 10 candidate ligands and 8 known inhibitors and were docked to Nsp16 pockets from SARS-CoV-2, MERS-CoV and SARS-CoV. Based on the four new indices, the best ligands were selected and a new one was designed by tuning them. Finally, ADMET profiling and molecular dynamics simulations were performed for the best ligands. The new structure-binding strength indices can be successfully applied not only to screen and tune ligands, but also to determine the effectiveness of the ligand in response to changes in the target viral entity, which is particularly useful for assessing drug effectiveness in the case of alterations in viral proteins. The developed approach, the so-called chameleon strategy, has the capacity to introduce a novel universal paradigm to the field of drugs design, including RNA antivirals.

Photo-assisted selective oxidation of monoterpenes by a covalently supported dioxo-molybdenum complex on TiO2: Effect of electron donor ligands

High-valent dioxo-Mo species have demonstrated the ability to catalyze industrially interesting alkene-to-epoxide transformations via oxygen atom transfer (OAT) reactions. The impact of electron donor ligands of dioxo-molybdenum complexes [MoO2Ln] covalently supported on TiO2 nanotubes (MoO2Ln/TiO2NT) on OAT to α-pinene, β-pinene, (R)-limonene and camphene has been investigated through the use of UV–vis radiation and molecular oxygen. Molybdenum complexes with electron donor ligands, such as bipyridine, bispyrazole, and terpyridine, exhibited high conversion and selectivity towards epoxide formation. This suggests that electron donation enhances the efficiency of photostimulated OAT. The photonic efficiency (ξ) demonstrates a linear correlation between the ligand structure and the OAT activity, indicating that the electron donation of the ligands enhances electron mobility towards the Mo=O bond. This correlation is evident in the position of the IR and Raman νsym(O=Mo=O) and vasym(O=Mo=O) vibrations of the complex Mo.

Identification of Potential Lead Compounds against BCL-2 through In-silico Screening of Phytochemicals of Nigella sativa and Cuscuta reflexa for Oral Squamous Cell Carcinoma Management

Significance of the study: In silico analysis is frequently used in physicochemical characterisation, the discovery and improvement of novel compounds with affinity to a target, and the elucidation of absorption, distribution, metabolism, excretion, and toxicity features. Aim and Objective: The aim of this study is to assess the efficacy of Nigella sativa and Cuscuta reflexa in targeting Bcl2-antiapoptotic protein in Oral Squamous Cell Carcinoma through in silico analysis. Materials and Methods: The present study was designed to formulate a drug against Oral Squamous cell carcinoma against the target protein Bcl-2. Protein Database (PDB) was used to select and analyse the protein. Based on the literature search, the original molecules selected were thymoquinone, tannin pyrogallol, Cuscutin, kaempferol, nigellicine and the ligand structures were obtained ZINC15 database. Target protein structure was recognised through Protein sequence from PB (Protein Data Bank). Swiss ADME was used for assessing the properties of the molecules. Twenty new molecules were identified from zinc pharmer and docking was done for all the 20 using Swiss dock. Binding energy was assessed and compared with the original molecules.ZINC73690300 and ZINC73690304 had better binding energy than that of original molecules. Both molecules can be potential candidates for Bcl2 inhibition to prevent OSCC. Results: ZINC73690300 and ZINC73690304 had better binding energy than that of the original molecules. Both molecules can be potential candidates for Bcl-2 inhibition to prevent OSCC. Conclusion: The present study evaluated the binding energy and bioavailability of the combined extract, thus attempting to predict the target ligand binding between the compounds in OSCC before attempting in vitro studies.-

Bis(imino)pyridyliron incorporated with NO2, F and benzhydryl substituents as thermostable precatalysts for vinyl-terminated polyethylenes

The electronic and steric properties of ligands are of great importance in late transition metal catalyst mediated ethylene polymerization to tune the catalytic performance. In this contribution, strong electron-withdrawing groups—fluoro and nitro—along with benzhydryl as a steric component, were incorporated into the parent bis(imino)pyridine ligand structure to prepare a series of iron (II) chloride complexes: 2-[MeC=N{2-(Ph2CH)-4-NO2-6-F}C6H2]-6-[MeC=N(Ar)C6H2]C5H3N–FeCl2 (Ar = 2,6-Me2C6H3Fe2Me, 2,6-Et2C6H3Fe2Et, 2,6-iPr2C6H3Fe2iPr, 2,4,6-Me3C6H2Fe3Me and 2,6-Et2-4-MeC6H2Fe2Et,Me). Apart from the structural characterization of all complexes executed via FTIR and elemental analysis, X-ray diffraction analysis unveiled distorted square pyramidal geometry for Fe2Me (τ5 = 0.21) and Fe2Et (τ5 = 0.28). Upon in situ activation with either MAO or MMAO cocatalysts, all iron complexes displayed distinguished polymerization performance, especially in terms of thermo-stability. In particular, the less hindered Fe2Me exhibited high activity: 20.4 × 106 g mol−1 h−1 at 70 °C, 1.5 × 106 g mol−1 h−1 at 110 °C, and 0.6 × 106 g mol−1 h−1 at 120 °C. Whereas, the sterically more hindered Fe2iPr proved to be more productive in generating high molecular weight polyethylene (Mw up to 410.7 kg mol−1 at 70 °C). Moreover, by adjusting the reaction temperature and ligand structure, the chain termination reaction could be modulated from a high proportion of vinyl-terminated polyethylene to saturated polyethylene rich product [CH2CH(CH2)nCH3/CH3(CH2)nCH3 = 0.7/0.3–0.39/0.61], as confirmed by high-temperature 1H/13C NMR spectra. Low molecular weight vinyl-terminated polyethylenes are of significant importance in the synthesis of functional polymers and can serve as valuable additives in lubricants.

Novel Schiff's base-assisted synthesis of metal-ligand nanostructures for multi-functional applications: Detection of catecholamines/antibiotics, removal of tetracycline, and antifungal treatment against plant pathogens

The development of nanozymes (NZ) for the simultaneous detection of multiple target chemicals is gaining paramount attention in the field of food and health sciences, and waste management industries. Nanozymes (NZ) effectively compensate for the environmental vulnerability of natural enzymes. Considering the development gap of NZ with diverse applications, we synthesized versatile Schiff’s base ligands following a facile route and readily available starting reagents (glutaraldehyde, aminopyridines). DPDI, one of the synthesized ligands, readily reacted with transition metal ions (Cu+2, Ag+1, Zn+2 in specific) under ambient conditions, yielding the corresponding nanoparticles/MOF. The structures of ligands and their products were confirmed using various analytical techniques. The enzymatic efficacy of DPDI-Cu (km 0.25 mM=, Vmax = 10.75 µM/sec) surpassed Tremetese versicolor laccase efficacy (km 0. 5 mM=, Vmax = 2.15 µM/sec). Additionally, DPDI-Cu proved resilient to changing pH, temperature, ionic strength, organic solvent, and storage time compared to laccase and provided reusability. DPDI-Cu proved promising for colorimetric detection of dopamine, epinephrine, catechol, tetracycline, and quercetin. The mechanism of oxidative detection of TC was studied through LC/MS analysis. DPDI-Cu-bentonite composite efficiently adsorbed tetracycline with maximum Langmuir adsorption of 208 mg/g. Moreover, DPDI/Cu and DPDI-Ag nanoparticles possessed antifungal activity exhibiting a minimum inhibitory concentration of 400 µg/mL and 3.12 µg/mL against Aspergillus flavus. Florescent dye tracking and SEM/TEM analysis confirmed that DPDI-Ag caused disruption of the plasma membrane and triggered ROS generation and apoptosis-like death in fungal cells. The DPDI-Ag coating treatment of wheat seeds confirmed the non-phytotoxicity of Ag-NPs.

Identifying High-Quality Leads among Screened Anticancerous Compounds Using SMILES Representations.

Cancer is a lethal disease that affects numerous people worldwide. Chemotherapy stands as one of the most effective treatment regimens to combat cancer. Nevertheless, anticancer drugs face a high failure rate due to safety and efficacy issues. Drug failure could be subdued by instigating drug leads with reduced toxicity and enhanced efficacy. Computer-aided drug discovery endorses drug leads in manoeuvring protein and ligand structures or representations. Simplified molecular input line entry system (SMILES) is a linear notation representing the three-dimensional structure of a molecule using symbols and alphanumeric characters. SMILES representation hoards rings and scaffold structures in its depiction. Mining ring and scaffold patterns from molecular SMILES would assist in ascertaining biological properties based on molecular patterns. Moreover, the emergence of artificial intelligence (AI) technologies would accelerate identification of efficient anticancer drug leads. AI algorithms proclaimed for their pattern recognition ability could be employed for identifying molecular patterns from SMILES representation, thereby enabling property prediction. Consequently, we developed a multilayer perceptron (MLP) model for the prediction of anticancer activity using SMILES of NCI-60 cancer growth inhibition data. Furthermore, the top 8 frequent scaffolds were identified on preliminary analysis of cancer growth inhibition data and ChEMBL drugs. The developed MLP model classified anticancer and nonanticancer compounds with a classification accuracy of 0.92. Also, benchmarking of the developed model with machine learning algorithms exhibited better performance of the MLP model.

Exploring Structural Requirements for Sigma-1 Receptor Linear Ligands: Experimental and Computational Approaches.

Sigma-1 receptor (S1R) is involved in a large array of biological functions due to its ability to interact with various proteins and ion channels. Crystal structures of human S1R revealed the trimeric organization for which each protomer comprises the ligand binding pocket. This study applied a multistep computational procedure to develop a pharmacophore model obtained from molecular dynamics simulations of available cocrystal structures of well-known S1R ligands. Apart from the well-established positive ionizable and hydrophobic features, the obtained model included an additional specific hydrophobic feature and different excluded volumes, thus increasing the selectivity of the model as well as a more detailed determination of the distance between two essential features. The obtained pharmacophore model passed the validation test by receiver operating characteristic (ROC) curve analysis of active and inactive S1R ligands. Finally, the pharmacophoric performance was experimentally investigated through the synthesis and binding assay of new 4-phenylpiperazine-based compounds. The most active new ligand 2-(3-methyl-1-piperidyl)-1-(4-phenylpiperazin-1-yl)ethanone (3) showed an S1R affinity close to the reference compound haloperidol (Ki values of 4.8 and 2.6 nM, respectively). The proposed pharmacophore model can represent a useful tool to design and discover new potent S1R ligands.

Discovery of the Next-Generation Platinum-Based Anticancer Agents for Combating Oxaliplatin-Induced Drug Resistance.

Oxaliplatin-based chemotherapy has proven to be one of the most effective treatments for advanced or metastatic colorectal cancer. However, increasing clinical resistance to oxaliplatin poses unprecedented challenges for both patients and clinicians. Despite extensive efforts to combat this issue, to date, no new molecules have been discovered that can successfully replace oxaliplatin. With the aim of developing a new generation of Pt(II)-based anticancer agents in response to the challenges of oxaliplatin-induced drug resistance, we performed a systematic screening of new Pt(II)-complexes with a quantitative structure-activity relationship (QSAR) study based on their antiresistance activity against oxaliplatin-resistant colon cancer cells. The results revealed that both the structure and chirality of the chelating ligand had a significant impact on the antiresistance properties of the Pt(II)-complexes. Our study culminated in the identification of chiral R-binaphthyldiamine-ligated Pt(II)-malonatoglycoconjugates that can completely counteract oxaliplatin resistance with excellent in vitro and in vivo potency.

The Binding Capacity of the Lead Phytochemical Molecule to Cancer Cell Target Proteins and its Potential Anticancer Properties with Respect to Standard Drugs

Molecular docking is an important tool for connecting molecular biological structure to computer-aided drug design. The purpose of this blind docking experiment is to compare the binding energies of these three drugs and to predict the most likely binding poses of a ligand with a known three dimensional structure of a protein. To substantiate our previous in vitro study findings, an in silico model was chosen to compare the binding properties of the three drugs. The work is entirely bioinformatics in nature. Blind docking was accomplished with the help of free software/(s). A comparison was made among the three drgus, used primarily in cancer treatment, namely, anastrazole, capecitabine and quercetin. In our in vitro study, these three drugs were extremely effective. CB dock-2 to blind dock, SwissTargetPrediction to choose the targets, PubChem and Protein Data Base to obtain 3D structures of ligand and target respectively were used. Absorption, Distribution, Metabolism, and Excretion (ADME) from SwissADME, drug likeness from MolSoft L.L.C. software, and Liponski’s rule was used to check the “Rule of five (RO5)”. The crystallographic structures have resolution values ranging from 1 Å to 3 Å. Lipinski’s rule of five, Swiss ADME and drug likeness were used to compare the three drugs. For all of the targets studied, quecetin appeared to have the highest AutoDock vina scores. To summarize the current findings and publicly available data, quercetin is chemoprotective and radioprotective to healthy/ normal cells and it can be used during cancer treatment.