Density functional theory molecular modelling, DNA interactions, antioxidant, antimicrobial, anticancer and biothermodynamic studies of bioactive water soluble mixed ligand complexes

A versatile sensor capable of ratiometric fluorescence detection of trace water and turn-on detection of Cu2+ modulating the binding interaction of a Cu(II) complex with BSA and DNA complemented by docking studies

A fluorescent molecule, pyridine-coupled bis-anthracene (PBA), has been developed for the selective fluorescence turn-on detection of Cu2+. Interestingly, the ligand PBA also exhibited a red-shifted ratiometric fluorescence response in the presence of water. Thus, a ratiometric water sensor has been utilized as a selective fluorescence turn-on sensor for Cu2+, achieving a 10-fold enhancement in the fluorescence and quantum yield at 446 nm, with a lower detection limit of 0.358 μM and a binding constant of 1.3 × 106 M-1. For practical applications, sensor PBA can be used to detect Cu2+ in various types of soils like clay soil, field soil and sand. The interaction of the PBA-Cu(II) complex with transport proteins like bovine serum albumin (BSA) and ct-DNA has been investigated through fluorescence titration experiments. Additionally, the structural optimization of PBA and the PBA-Cu(II) complex has been demonstrated by DFT, and the interaction of the PBA-Cu(II) complex with BSA and ct-DNA has been analyzed using theoretical docking studies.

Phenanthroline and Schiff Base associated Cu(II)-coordinated compounds containing N, O as donor atoms for potent anticancer activity

As an inherent metal ion, copper has been the subject of investigation for developing a novel antitumoral compound that exhibits fewer adverse effects. Copper serves as a cofactor in multiple enzymes, generates reactive oxygen species (ROS), facilitates tumour evolution, metastasis and angiogenesis and has been detected at elevated concentrations in the serum and tissues of various human cancer types. In the given setting, utilising two methodologies in developing novel Copper-based pharmaceuticals for anti-cancer applications is standard practice. These approaches involve either the sequestration of unbound Copper ions or the synthesis of Copper complexes that induce cellular apoptosis. In the past four decades, the latter system has been used, leading to numerous reviews that have examined the anticancer characteristics of a wide range of Copper complexes. These analyses have consistently demonstrated that multiple factors frequently influence the efficacy of these compounds. This review examines the possible anticancer properties of copper and Cu(II) complexes that incorporate Schiff base ligands containing 1,10-phenanthroline. The present study will comprehensively analyse the examined cell lines and mechanistic research associated with each complex.

Exploring the antioxidant, antimicrobial, cytotoxic and biothermodynamic properties of novel morpholine derivative bioactive Mn(ii), Co(ii) and Ni(ii) complexes - combined experimental and theoretical measurements towards DNA/BSA/SARS-CoV-2 3CLPro

A novel class of bioactive complexes (1-3) [MII(L)2(bpy)], where, L = 2-(4-morpholinobenzylideneamino)phenol, bpy = 2,2'-bipyridine, MII = Mn (1), Co (2) or Ni (3), were assigned to octahedral geometry based on analytical and spectral measurements. Gel electrophoresis showed that complex (2) demonstrated significant DNA cleavage activity compared to the other complexes under the action of oxidation agent (H2O2). The DNA binding constant properties measured by various techniques were in the following sequence: (2) > (3) > (1) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is also supported by their biothermodynamic characteristics. The binding constant results for BSA from electronic absorption and fluorometric titrations demonstrate that complex (2) exhibits the highest binding effectiveness among them all, which means that all the compounds could interact with BSA through a static approach, additionally supported by FRET measurements. DFT and docking calculations were employed to realize the electronic structure, reactivity, and interaction capability of all substances with DNA, BSA, and the SARS-CoV-2 main protease. These binding energies fell within the ranges -7.7 to -8.5, -8.2 to -10.1 and -6.7 to -9.3 kcal mol-1, respectively. The higher reactivity of the complexes than the ligand is supported by FMO theory. The in vitro antibacterial, cytotoxicity, and radical scavenging characteristics revealed that complexes (2-3) have better biological efficacy than the others. The cytotoxicity and binding properties also show good correlation with the partition coefficient (log P), which is encouraging because all of the experimental findings are closely correlated with the theoretical measurements.

An Integrated Analysis of Mechanistic Insights into Biomolecular Interactions and Molecular Dynamics of Bio-Inspired Cu(II) and Zn(II) Complexes towards DNA/BSA/SARS-CoV-2 3CLpro by Molecular Docking-Based Virtual Screening and FRET Detection

Novel constructed bioactive mixed-ligand complexes (1b) [Cu^II(L)₂(phen)] and (2b) [Zn^II(L)₂(phen)] {where, L = 2-(4-morpholinobenzylideneamino)phenol), phen = 1,10-phenanthroline} have been structurally analysed by various analytical and spectroscopic techniques, including, magnetic moments, thermogravimetric analysis, and X-ray crystallography. Various analytical and spectral measurements assigned showed that all complexes appear to have an octahedral geometry. Agar gel electrophoresis's output demonstrated that the Cu(II) complex (1b) had efficient deoxyribonucleic cleavage and complex (2b) demonstrated the partial cleavage accomplished with an oxidation agent, which generates spreadable OH^● through the Fenton type mechanism. The DNA binding constants observed from viscosity, UV-Vis spectral, fluorometric, and electrochemical titrations were in the following sequence: (1b) > (2b) > (HL), which suggests that the complexes (1b-2b) might intercalate DNA, a possibility that is supported by the biothermodynamic measurements. In addition, the observed binding constant results of BSA by electronic absorption and fluorometric titrations indicate that complex (1b) revealed the best binding efficacy as compared to complex (2b) and free ligand. Interestingly, all compounds are found to interact with BSA through a static approach, as further attested by FRET detection. The DFT and molecular docking calculations were also performed to realize the electronic structure, reactivity, and binding capability of all test samples with CT-DNA, BSA, and the SARS-CoV-2 3CL^Pro, which revealed the binding energies were in a range of -8.1 to -8.9, -7.5 to -10.5 and -6.7--8.8 kcal/mol, respectively. The higher reactivity of the complexes than the free ligand is supported by the FMO theory. Among all the observed data for antioxidant properties against DPPH^᛫, ^᛫OH, O₂^-• and NO^᛫ free radicals, complex (1a) had the best biological efficacy. The antimicrobial and cytotoxic characteristics of all test compounds have been studied by screening against certain selected microorganisms as well as against A549, HepG2, MCF-7, and NHDF cell lines, respectively. The observed findings revealed that the activity enhances coordination as compared to free ligand via Overtone's and Tweedy's chelation mechanisms. This is especially encouraging given that in every case, the experimental findings and theoretical detections were in perfect accord.

Comprehensive Assessment of Biomolecular Interactions of Morpholine-Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2'-Bipyridine as Potential Anticancer and SARS-CoV-2 Agents: A Synergistic Experimental and Structure-Based Virtual Screening

A new class of pharmacologically active mixed-ligand complexes (1a-2a) [M^II(L)₂ (bpy)], where L = 2-(4-morpholinobenzylideneamino)phenol), bpy = 2,2'-bipyridine, M^II = Cu (1a), and Zn (2a), were assigned an octahedral geometry by analytical and spectral measurements. Gel electrophoresis showed that complex (1a) demonstrated the complete DNA cleavage mediated by H₂O₂. The overall DNA-binding constants observed from UV-vis, fluorometric, hydrodynamic, and electrochemical titrations were in the following sequence: (1a) > (2a) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is further supported by the biothermodynamic characteristics. The binding constant results of BSA by electronic absorption and fluorometric titration demonstrate that complex (1a) exhibits the highest binding effectiveness among others, which means that all compounds could interact with BSA through a static approach, additionally supported by FRET measurements. Density FunctionalTheory (DFT) and molecular docking calculations were relied on to unveil the electronic structure, reactivity, and interacting capability of all substances with DNA, BSA, and SARS-CoV-2 main protease (Mpro). These observed binding energies fell within the following ranges: -7.7 to -8.6, -7.2 to -10.2, and -6.7 to -8.2 kcal/mol, respectively. The higher reactivity of the complexes compared to free ligand is supported by the Frontier MolecularOrbital (FMO) theory. The in vitro antibacterial, cytotoxic, and radical scavenging characteristics revealed that complex (1a) has the best biological efficacy compared to others. This is encouraged because all experimental findings are closely correlated with the theoretical measurements.

Spectro-electrochemical, fluorometric and biothermodynamic evaluation of pharmacologically active morpholine scaffold single crystal ligand and its metal(II) complexes: A comparative study on in-vitro and in-silico screening towards DNA/BSA/SARS-CoV-19

A novel series of metal(II) complexes (1-5) [M^II(L)₂]{Where M = Cu (1), Co (2), Mn (3), Ni (4) and Zn (5)} constructed from 2-(4-morpholinobenzylideneamino)phenol Schiff base ligand (HL) in a 1:2 M ratio and the spectral and analytical results put forward square planar geometry. Spectro-electrochemical, hydrodynamic, gel electrophoresis, and DNA binding/cleavage results for all the compounds demonstrate that complex (1) had excellent DNA binding/cleavage properties compared to other compounds. The observation also suggests that test compounds could intercalate with DNA, and the biothermodynamic property more strongly supports the stabilizing of the double helix DNA with the complexes. BSA binding constant results show that complex (1) exposes the best binding property via a static mode, which is further confirmed by FRET calculations. The DFT calculations and docking results for all compounds towards DNA, BSA and SARS-CoV-19 main protease (3CLPro), reveal the binding energies were in the range of -7.8 to -9.4, -6.6 to -10.2 and - 6.1 - -8.2 kcal/mol for all test compounds respectively. In this case, complexes showed favorable binding energies compared to free ligand, which stimulates further studies aimed at validating the predicted activity as well as contributing to tackling the current and future viral pandemics. The in-vitro antioxidant, antimicrobial, and anticancer results for all compounds revealed that copper complex (1) has better activity compared to others. This might result in an effective anticancer drug for future research, which is especially promising since the observed experimental results for all cases were in close agreement with the theoretical calculations.

Biosynthesis and Characterization of Co3O4NPs Utilizing Prickly Pear Fruit Extract and its Biological Activities

In the current research, there is a low level of research and information about the interaction of cobalt oxide nanoparticles (Co3O4NPs) in biological systems. This research creates a very simple and cost-effective preparation of cobalt oxide nanoparticles by using prickly pear fruit extract as a reducing agent, which may be further used for biological applications like antimicrobial, antioxidant, DNA interaction and in-vitro anticancer activity. The use of prickly pear fruit extract acts as a good reducing agent and is responsible for easy preparation and reducing the toxicity of cobalt oxide nanoparticles. The fabricated biogenic nanoparticles were confirmed by microscopic and spectroscopic analytical techniques like Ultra Violet-Visible spectrometer, Fourier transforms infrared spectrometer (FTIR), X-ray Diffraction Method (XRD), Energy-dispersive X-ray spectroscopy (EDS), Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). The average size of the synthesized nanoparticles is 36.24 nm. In the MTT assay, the prepared cobalt oxide NPs haspotential mechanisms of cytotoxicity and in-vitro anticancer activity in Hepatocellular carcinoma cancer cells (HepG2). The microbial activities like antibacterial and antifungal studies of the biosynthesized nanoparticles were performed by the Disc method. The Co3O4NPs with DNA interaction were examined by UV-Visible and fluorescence spectroscopic methods. The binding constant value of biogenic Co3O4NPs with CT-DNA was observed by UV-Visible spectroscopy with a result of 2.57x105mol-1. The binding parameters and quenching constants were observed by fluorescence spectroscopic methods having values of Ksv=7.1x103, kq=7.1x108, Ka=3.47.1x105, n=0.9119. From the findings, Co3O4NPs may be utilized as a medicinal aid for their antibacterial, antifungal, antioxidant, DNA binding and in-vitro anticancer activities.

Spectrophotometric and fluorometric detection of DNA/BSA interaction, antimicrobial, anticancer, antioxidant and catalytic activities of biologically active methoxy substituted pyrimidine-ligand capped copper nanoparticles

New Schiff base ligand (DPMN) was synthesized from the condensation of 2-hydroxy-5-nitrobenzaldehyde and 2-amino-4,6-dimethoxypyrimidine which was confirmed by spectroscopic and analytical methods. Solid air stable copper nanoparticles (DPMN-CuNPs) were synthesized from its copper chloride salt and it is stabilized by the prepared Schiff base ligand by phase transfer assisted synthesis which is a modified Brust-Schiffrin technique. The formation of ligand stabilized copper nanoparticles was confirmed by UV-Visible and FT-IR spectroscopic techniques. The size, surface morphology and quality of DPMN-CuNPs were analyzed by SEM and TEM techniques. Antioxidant activities of DPMN and DPMN-CuNPs with DPPH, SOD, peroxide and nitrous oxide were analyzed by electronic absorption spectroscopy. DNA interaction between DPMN and DPMN-CuNPs with CT-DNA was carried out using electronic absorption, fluorescence, viscometric measurements and cyclic voltammetric techniques. Interaction between BSA and the synthesized compounds analyzed by electronic absorption spectroscopy, Antimicrobial studies confirmed that the synthesized DPMN-CuNPs possess significant biological activities than DPMN. Anticancer results suggest that prepared DPMN-CuNPs have significant anticancer activity against different cancer cell lines and least toxic effect against the normal (NHDF) cell line. Other than the positive response in biological evaluation, our DPMN-CuNPs possess good catalytic activity in methyl orange reduction, methylene blue degradation and nitro phenol reduction.

Analysis of DNA interactions and GC content with energy decomposition in large-scale quantum mechanical calculations

GC content is a contributing factor to the stability of nucleic acids due to hydrogen bonding. More hydrogen bonding generally results in greater stability. Empirical evidence, however, has suggested that the GC content of a nucleic acid is a poor predictor of its stability, implying that there are sequence-dependent interactions besides what its GC content indicates. To examine how much such sequence-dependent interactions affect the interaction energies of double-stranded DNA (dsDNA) molecules, dsDNA molecules of different sequences are generated and examined in silico for variabilities in the interaction energies within each group of dsDNA molecules of the same GC content. Since the amount of hydrogen bonding depends on the GC content, holding the GC content fixed when examining the differences in interaction energies allows sequence-dependent interactions to be isolated. The nature of sequence-dependent interactions is then dissected using energy decomposition analysis (EDA). By using EDA, the components of the interactions that depend on the neighboring base pairs help explain some of the variability in the interaction energies of the dsDNA molecules despite having the same GC content. This work provides a new paradigm and tool for the study and analysis of the distributions of interaction components in dsDNA with the same GC content using EDA within large-scale quantum chemistry calculations.

Bioactive platinum complex of ligand bearing pyrimidine skeleton: DNA/BSA binding, molecular docking, anticancer, antioxidant and antimicrobial activities

A new octahedral platinum complex [PtLCl₄] of Schiff base ligand containing pyrimidine and morpholine skeleton (where, L is 4,6-dichloropyrimidin-5-yl)methylene)-2-morpholinoethanamine) was isolated and characterized by elemental analysis, ¹H-NMR, FTIR, UV-visible and ESI-MS techniques. DNA interaction of isolated compounds with calf thymus (CT-DNA) was explored by UV-vis absorption, fluorescence, cyclic voltametric and viscometric methods. The result shows that prepared compounds can interact with CT-DNA through electrostatic interactions. Bovine serum album (BSA) binding behavior of isolated compounds was also studied by UV-vis absorption and fluorescence techniques. Both the spectroscopic results suggest that the isolated ligand and its complex bind with BSA through static quenching. The optimized structure of ligand and platinum complex were achieved by the DFT calculations. Moreover, molecular docking of ligand and its complex were studied. These analysis results reveal that ligand has low binding affinity on DNA and BSA molecules in contrast to its complex. In vitro anticancer activity of isolated compounds toward normal cell line (NHDF) as well as cancer cell lines (MCF-7, HepG2, HeLa and A549) was studied by MTT assay. The results supports that isolated platinum complex can control the growth of cancer cells (MCF-7, 20.12 ± 1.00 µg/mL; HepG2, 32.2 ± 1.69 µg/mL; HeLa, 24.68 ± 1.29 µg/mL; A549, 23.46 ± 1.17 µg/mL) without inhibiting the normal cell line (NHDF, 109.26 ± 5.46 µg/mL). Antioxidant and antimicrobial activities of isolated compounds indicate that ligand and Pt complex are found to have good radical scavenging against four different free radicals and antimicrobial abilities on E. coli and C. albicans antimicrobial species. HighlightsPlatinum complex of Schiff base with pyrimidine and morpholine linkage was synthesized.Pt complex has better biomolecular interaction with DNA and BSA.Molecular docking of Pt complex with DNA and BSA has been studiedPt complex has good anticancer activities.Pt complex has better antioxidant and antimicrobial activities.

Cell apoptosis induced by ciprofloxacin based Cu(II) complexes: cytotoxicity, SOD mimic and antibacterial studies

The current cancer research focuses on the design and synthesis of chemical compounds that can modulate cell apoptosis or programmed cell death. So we synthesized and characterized ciprofloxacin based copper(II) complexes and studied their anticancer activity against HCT 116 cancer cells by MTT assay. We further investigated the influence of compound-2 (better IC₅₀ value than cisplatin) on cancer cells to know the exact mechanism of anticancer activity. The distinct morphological change of cells due to compound-2 was observed in bright field microscopy. The trypan blue assay clearly demonstrated inhibition of cell viability. The clonogenic ability inhibition assay showed a low percentage of the plating efficiency of HCT 116 cells. The mechanism of cell death, either apoptotic or necrotic was distinguished by annexin V-FITC/PI (propidium iodide) staining assay and LDH (lactate dehydrogenase) release assay. The positive annexinV/PI cells in presence of compound-2 and absence of LDH in the LDH release assay confirmed the cell apoptotic mechanism of cell death. We also checked in vitro antibacterial activity of compounds against Gram^(-ve) and Gram^(+ve) bacteria in terms of MIC (minimum inhibitory concentration) and the data were in good agreement with the standard drug data. SOD mimic activity of synthesized Cu(II) complexes was also studied in terms of IC₅₀ value. The brine shrimp lethality bioassay was also performed to evaluate the cytotoxic properties of the Cu(II) complexes.Communicated by Ramaswamy H. Sarma.

Pyrimidine Derivative Schiff Base Ligand Stabilized Copper and Nickel Nanoparticles by Two Step Phase Transfer Method; in Vitro Anticancer, Antioxidant, Anti-Microbial and DNA Interactions

Pyrimidine derivative Schiff base ligand (DPMC) stabilized metal nanoparticles of copper (DPMC-CuNPs) and nickel (DPMC-NiNPs) were synthesized by modified Brust-Schiffrin technique, which is a two-step phase transfer assisted synthesis. The prepared metal nanoparticles were confirmed by UV-Visible and Infrared spectroscopy. The size, surface morphology and the quality of the DPMC and its MNPs were analyzed by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) methods respectively. Electrochemical behavior of the DPMC-CuNPs and DPMC-NiNPs was analyzed by cyclic voltammetry method. DNA binding studies of the synthesized compounds with CT-DNA were examined by four different techniques such as UV-Visible and emission spectroscopy, cyclic voltametry and viscometric measurments. Thermal denaturation and sono-chemical denaturation studies of DNA with the DPMC, DPMC-CuNPs and DPMC-NiNPs results also suggest the synthesized compounds have good DNA binding ability. Various antioxidant scavenging studies results shows that DPMC and its copper and nickel nanoparticles have significant antioxidant activity. Antimicrobial studies of the DPMC and its MNPs were studied by Agar-Agar well diffusion method. Anticancer studies of the DPMC and its MNPs show that the DPMC-CuNPs and DPMC-NiNPs have significant anticancer activity with least toxicity than the standard drug cis-platin. Graphical Abstract.

A new chiral boron-dipyrromethene (BODIPY)-based fluorescent probe: molecular docking, DFT, antibacterial and antioxidant approaches

A new chiral BODIPY-based fluorescent compound, 5-bromo-4,4-difluoro-3(S)-1-phenylethyl)amino) BODIPY, 4 was synthesized for biomedical applications. Optical, antimicrobial, antioxidant properties of the compound 4 are investigated. The partition coefficient suggested that the compound 4 has the potential to be developed as an active antibacterial and antioxidant candidate. In this context, antibacterial assay was carried out for compound 4 against various bacterial strains, revealing maximum inhibition zone (24 ± 2.19 mm) in Escherichia coli. Moreover, results of antioxidant activity of compound 4 revealed IC₅₀ values to be greater than ascorbic acid. Molecular docking has given brief insight about the binding of the compound 4, suggesting that it has a strong potential to inhibit bacterial target enzymes viz., DNA gyrase, enzymes in the type II fatty acid synthesis and Ddl (d-alanine: d-alanine ligase) in peptidoglycan synthesis. The molecular geometry and electrostatic potential of compound 4, was established by DFT (Density Functional Theory) calculations.AbbreviationsBBBblood‒brain barrierBDEbond dissociation energyBODIPYboron-dipyrromethaneDdlD-alanine:D-alanine ligaseDDQ2,3-dichloro-5,6-dicyano-1,4-benzoquinoneDFTdensity functional theoryDNAdeoxyribonucleic acidDPPH1,1‒diphenyl‒2‒picrylhydrazylNBSN-bromo succinimideROSreactive oxygen speciesUV-visultraviolet-visibleFMOfrontier molecular orbitalsHOMOhighest occupied molecular orbitalLUMOlowest unoccupied molecular orbitalCommunicated by Ramaswamy H. Sarma.

Spectro-electrochemical assessments of DNA/BSA interactions, cytotoxicity, radical scavenging and pharmacological implications of biosensitive and biologically active morpholine-based metal(ii) complexes: a combined experimental and computational investigation

Biosensitive and biologically active morpholine-based transition metal(ii) complexes (1-5) were constructed as [MII(L) AcO]·nH2O {where M = Cu (1) n = 1; Co (2), Mn (3), Ni (4), n = 4 and Zn (5) n = 2}, which were synthesized from 2-(-(2-morpholinoethylimino) methyl)-4-bromophenol ligand (HL) and structurally characterized by various analytical and spectroscopic techniques, which proposed a square planar and tetrahedral geometry around the central metal ion with lattice water molecules. The gel electrophoresis results revealed that complexes 1 and 5 had more potent DNA cleavage efficacy in the presence of an oxidizing agent (H2O2) as compared to the others. The observed DNA binding results for all the compounds as determined by spectro-electrochemical and hydrodynamic techniques were in the order 3.36 (1) > 3.06 (2) > 2.73 (4) > 2.61 (5) > 1.84 (3) > 1.00 (HL) × 104 M-1. The obtained bovine serum albumin (BSA) protein binding constant (K b) results put forward the following order 2.38 (1) > 2.21 (2) > 2.18 (5) > 1.76 (4) > 1.40 (3) > 1.26 (HL) × 104 M-1. Also, the biothermodynamic parameters (, , ΔH° and ΔS°) and binding results divulged that all the complexes (1-5) could bind to DNA via intercalation in a spontaneous manner. Density functional theory calculations were employed to optimize the structure of ligand (HL) and its complexes (1-5) to gain insights into their electronic structures. Molecular docking analysis was carried out to identify the preferential binding modes of these complexes toward DNA and BSA protein. The theoretical observations of all cases were found to be very close to the experimental observations. Among the radical scavenging activity results for all the cases toward DPPH, hydroxyl radical, superoxide, nitric oxide and ferric reducing agents, complex (1) revealed a superior scavenging potency over the other compounds. In the screened antimicrobial reports against 10 different selected pathogenic species, although all the complexes (1-5) exhibited a greater significant inhibitory effect than the free ligand, complexes 4 and 5 achieved the best potency over standard drugs. The observed percentage of growth inhibition for all the compounds against the A549, HepG2, MCF-7 and NHDF cell lines suggested that complex 1 had enhanced growth-inhibitory potency over the other compounds and slightly affected normal cells as compared to the standard drug cisplatin, which may lead to its investigation as a promising anticancer agent in future research.