Preferred Binding Mode Research Articles

4,4-Nitrophenoxyaniline derived Azo ester: Structural elucidation, DFT simulation, and DNA interactional studies via wet and in silico methods

A new ester namely,1-((4-(4-nitrophenoxy)phenyl)diazenyl)biphenyl benzoate, has been synthesized by esterification reaction between reported nitro terminated azo alcohol and benzoyl chloride. Complete structural elucidation of the synthesized ester was done by different spectroscopic techniques including (FT-IR), (Proton and Carbon-13 NMR), (UV/VIS) spectroscopy, and single-crystal XRD analysis and cyclic voltammetry. XRD structural elucidation revealed the ester 1a to be in Triclinic crystal system with P-1 space groups, showing two-dimensional supramolecular structure, involving only one intermolecular interaction between O4-O9…H9. DFT simulations were also performed to illustrate structural ramification of synthesized ester.Further, Drug DNA interaction was used to determine the biological significance of the produced ester. UV–VIS spectroscopy, hydrodynamic measurement, and molecular docking were used to determine the preferred binding mode of interaction of the synthesized ester with Salmon Sperm (SS) DNA and found that molecule interacts in groove binding fashion with DNA molecule. 2021 Elsevier Ltd. All rights reserved.

N1 neuraminidase of H5N1 avian influenza A virus complexed with sialic acid and zanamivir – A study by molecular docking and molecular dynamics simulation

Development of antiviral drugs is an urgent need to control and prevent the presently circulating H5N1 avian influenza virus which is affects the human respiratory tract. The complex crystal structure of N1–N–acetylneuranamic acid (sialic acid, SIA) is not available as complex and hence SIA and zanamivir (ZMR) are docked into the binding site of N1 neuraminidase. Based on the analysis, the initial complex structures have been simulated for 120 ns to get insight into the binding modes and interaction between protein–ligand complex systems. NAMD pair interaction energy and MM–PBSA binding free energy are calculated and show that there are two possible binding modes (BM1 and BM2) for N1–SIA and a single binding mode (BM1) for and N1–ZMR complex structures respectively. BM1 of N1–SIA is the most preferred binding mode. On contrary to the currently available drugs in which the chair conformation is distorted, in both the binding modes of N1–SIA, the binding pocket of N1 neuraminidase is able to accommodate SIA in 2C5 chair conformation which is the preferred conformation of SIA in solution state. In N1–ZMR complex, ZMR is bind in a distorted chair conformation. The neuraminidase binding pocket is also able to accommodate galactose of SIAα(2→3)GAL and SIAα(2→6)GAL. RMSD, RMSF and hydrogen bonding analyses have been carried out to identify the conformational flexibility and structural stability of each complex system. All the analyses show that SIA can be used as an inhibitor for N1 neuraminidase of H5N1 influenza viral infection. Communicated by Ramaswamy H. Sarma

Understanding the interaction between carboxylates and coinage metals from first principles.

Carboxylate groups have recently been explored as a new type of ligand to protect superatomic copper and silver nanoclusters, but little is known of the interfacial structure and bonding. Here, we employ density functional theory to investigate the interfaces of a model carboxylate group, CH3COO, on the coinage metal surfaces and clusters. We found that μ2-CH3COO is the most preferred binding mode on the three M(111) surfaces (M = Cu, Ag, and Au), while μ3-CH3COO is also stable on Cu(111) and Ag(111). The saturation coverage was found to be about seven CH3COO groups per nm2 for all surfaces. CH3COO has the strongest binding on Cu and weakest on Au. Moving from the flat surfaces to the icosahedral M13 clusters, we found that the eight-electron superatomic [M13(CH3COO)6]- nanoclusters also prefer the μ2-CH3COO mode on the surface. The icosahedral kernel in [Cu13(CH3COO)6]- and [Ag13(CH3COO)6]- was well maintained after geometry optimization, but a larger deformation was found in [Au13(CH3COO)6]-. Given the broad availability and variety of carboxylic acids including amino acids, our work suggests that carboxylate groups could be the next-generation ligands to further expand the universe of atomically precise metal clusters, especially for Cu and Ag.

Hg(II) Binding to Thymine Bases in DNA.

The compounds of mercury can be highly toxic and can interfere with a range of biological processes, although many aspects of the mechanism of toxicity are still obscure or unknown. One especially intriguing property of Hg(II) is its ability to bind DNA directly, making interstrand cross-links between thymine nucleobases in AT-rich sequences. We have used a combination of small molecule X-ray diffraction, X-ray spectroscopies, and computational chemistry to study the interactions of Hg(II) with thymine. We find that the energetically preferred mode of thymine binding in DNA is to the N3 and predict only minor distortions of the DNA structure on binding one Hg(II) to two cross-adjacent thymine nucleotides. The preferred geometry is predicted to be twisted away from coplanar through a torsion angle of between 32 and 43°. Using 1-methylthymine as a model, the bis-thymine coordination of Hg(II) is found to give a highly characteristic X-ray spectroscopic signature that is quite distinct from other previously described biological modes of binding of Hg(II). This work enlarges and deepens our view of significant biological targets of Hg(II) and demonstrates tools that can provide a characteristic signature for the binding of Hg(II) to DNA in more complex matrices including intact cells and tissues, laying the foundation for future studies of mechanisms of mercury toxicity.

Illustration of a computational pipeline for evaluating cyclodextrin host-guest complex formation through conformational capture of bullvalene.

Cyclodextrins have a diverse range of applications, including as supramolecular hosts, as enzyme active-site analogs, in improving drug solubility and delivery, and in molecular selection. We have investigated their ability to form stable complexes with bullvalenes, unusual organic cage molecules that spontaneously interconvert between numerous degenerate isomers. The shape-shifting nature of substituted bullvalenes raises the potential for dynamic adaptive binding to biological targets. We tested whether β- and γ-cyclodextrins can capture particular bullvalene isomers and whether the preferred binding mode(s) differ between isomers. We first applied our computational host-guest interaction potential energy profiling to determine the best binding mode(s) of unsubstituted bullvalene and each isomer of methylenehydroxybullvalene to β- and γ-cyclodextrin. Subsequent molecular dynamics simulations of the predicted host-guest complexes showed that while unsubstituted bullvalene has a single, albeit ill-defined, binding mode with either cyclodextrin, each isomer of methylenehydroxybullvalene has two possible modes of binding to β-cyclodextrin but only a single, nebulous mode of binding to γ-cyclodextrin. Experimental determination of the binding free energy of each methylenehydroxybullvalene-cyclodextrin complex showed that methylenehydroxybullvalene is more likely to bind to β-cyclodextrin than to γ-cyclodextrin, despite its smaller cavity. Together, our results suggest that β-cyclodextrin, but not γ-cyclodextrin, shows promise for conformational capture of mono-substituted bullvalenes. More broadly, our computational pipeline should prove useful for rapid characterization of cyclodextrin host-guest complexes, avoiding the need for costly synthesis of guest molecules that are unlikely to bind stably, as well as providing detailed atomic-level insight into the nature of complexation.

Exploring the Potential Mechanism of Costunolide-Induced MCF-7 Cells Apoptosis by Multi-Spectroscopy, Molecular Docking and Cell Experiments.

Breast cancer is one of the most common cancer with high morbidity and mortality in women. This study aimed to explore the potential mechanism of costunolide inducing MCF-7 cells apoptosis by multi-spectroscopy, molecular docking, and cell experiments. The results manifested that costunolide interacted with calf thymus DNA (ct-DNA) in a spontaneous manner, and the minor groove as the preferential binding mode. Furthermore, costunolide inhibited cell proliferation and colony formation. Hoechst 33258 staining showed that cell apoptosis induced by costunolide might be related to DNA damage. The apoptosis mechanism relied on regulating the protein expression of Bax, Bcl-2, p53, Caspase-3 and the activation of p38MAPK and nuclear factor κB (NF-κB) pathways. This study will provide some experimental basis and potential therapeutic strategy for breast cancer treatment.

Computational Analysis of the Interactions between the S100B Extracellular Chaperone and Its Amyloid β Peptide Client.

S100B is an astrocytic extracellular Ca2+-binding protein implicated in Alzheimer’s disease, whose role as a holdase-type chaperone delaying Aβ42 aggregation and toxicity was recently uncovered. Here, we employ computational biology approaches to dissect the structural details and dynamics of the interaction between S100B and Aβ42. Driven by previous structural data, we used the Aβ25–35 segment, which recapitulates key aspects of S100B activity, as a starting guide for the analysis. We used Haddock to establish a preferred binding mode, which was studied with the full length Aβ using long (1 μs) molecular dynamics (MD) simulations to investigate the structural dynamics and obtain representative interaction complexes. From the analysis, Aβ-Lys28 emerged as a key candidate for stabilizing interactions with the S100B binding cleft, in particular involving a triad composed of Met79, Thr82 and Glu86. Binding constant calculations concluded that coulombic interactions, presumably implicating the Lys28(Aβ)/Glu86(S100B) pair, are very relevant for the holdase-type chaperone activity. To confirm this experimentally, we examined the inhibitory effect of S100B over Aβ aggregation at high ionic strength. In agreement with the computational predictions, we observed that electrostatic perturbation of the Aβ-S100B interaction decreases anti-aggregation activity. Altogether, these findings unveil features relevant in the definition of selectivity of the S100B chaperone, with implications in Alzheimer’s disease.

Deciphering the effect of hydrophobicity on protein binding interaction in cobalt(II) complexes by multispectroscopic and computational methods

In the present work, we report the synthesis, characterization of two cobalt complexes (1 and 2) and their HSA binding studies by multispectroscopic methods. Hirshfeld surfaces analysis and fingerprint plot analysis were carried out to identify intermolecular interactions viz., N–H···O, O–H···O and C–H···O linkages in crystal framework of the complexes. Density functional theory (DFT) studies were carried out to ascertain the electronic structure and molecular geometry of the complexes 1 and 2, and determine the localization of HOMO and LUMO in the complexes. A comparative in vitro interaction study of complex 1 and 2 with human serum albumin protein was carried out by employing UV-vis, fluorescence, circular dichroism, FTIR and molecular docking techniques. Interestingly, the HSA binding affinity of complex 2 was found to be more than complex 1 which was evidenced from the higher binding constant values owing to its strong hydrophobic topology. Further, a significant conformational change in microenvironment of HSA was noticed upon binding with complexes 1 and 2, nevertheless more perturbations were noticed in presence of complex 1. Molecular docking studies were carried out to validate the spectroscopic results and ascertain the preferential binding mode of complexes at the specific target site of HSA. Communicated by Ramaswamy H. Sarma

Identification of the molecular determinants driving the substrate specificity of fungal lytic polysaccharide monooxygenases (LPMOs)

Understanding enzymatic breakdown of plant biomass is crucial to develop nature-inspired biotechnological processes. Lytic polysaccharide monooxygenases (LPMOs) are microbial enzymes secreted by fungal saprotrophs involved in carbon recycling. LPMOs modify biomass by oxidatively cleaving polysaccharides, thereby enhancing the efficiency of glycoside hydrolases. Fungal AA9 LPMOs are active on cellulose, but some members also display activity on hemicelluloses and/or oligosaccharides. Although the active site subsites are well defined for a few model LPMOs, the molecular determinants driving broad substrate specificity are still not easily predictable. Based on bioinformatic clustering and sequence alignments, we selected seven fungal AA9 LPMOs that differ in the amino-acid residues constituting their subsites. Investigation of their substrate specificities revealed that all these LPMOs are active on cellulose and cello-oligosaccharides, as well as plant cell wall–derived hemicellulosic polysaccharides, and carry out C4 oxidative cleavage. The product profiles from cello-oligosaccharide degradation suggest that the subtle differences in amino-acid sequence within the substrate-binding loop regions lead to different preferred binding modes. Our functional analyses allowed us to probe the molecular determinants of substrate binding within two AA9 LPMO subclusters. Many wood-degrading fungal species rich in AA9 genes have at least one AA9 enzyme with structural loop features that allow recognition of short β-(1,4)–linked glucan chains. Time-course monitoring of these AA9 LPMOs on cello-oligosaccharides also provides a useful model system for mechanistic studies of LPMO catalysis. These results are valuable for the understanding of LPMO contribution to wood decaying process in nature and for the development of sustainable biorefineries.

Computational Investigation of the Preferred Binding Modes of N2O in Group 8 Metal Complexes.

Nitrous oxide (N2O) is a potentially important oxidant for green chemistry applications but thus far has shown limited examples as a ligand for transition metal complexes. Given the lack of reported N2O complexes, density functional theory was utilized to study the potential binding effects in multiple group 8 metal complexes. N2O is found to be a very weakly π-accepting ligand (approximately 1/3 as effective as CO). With the weak π-accepting character, the N2O is predicted to be bound through the nitrogen atom in a linear geometry. In all calculated ruthenium and osmium complexes, the nitrogen bound mode of binding is preferred. Only by introduction of a very weak π-donor metal (such as iron) can the N2O be found to slightly prefer binding through the oxygen atom in a purely σ-donor fashion.

Synthesis and Glycosidase Inhibition Properties of Calix[8]arene-Based Iminosugar Click Clusters

A set of 6- to 24-valent clusters was constructed with terminal deoxynojirimycin (DNJ) inhibitory heads through C6 or C9 linkers by way of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions between mono- or trivalent azido-armed iminosugars and calix[8]arene scaffolds differing in their valency and their rigidity but not in their size. The power of multivalency to upgrade the inhibition potency of the weak DNJ inhibitor (monovalent DNJ Ki being at 322 and 188 µM for C6 or C9 linkers, respectively) was evaluated on the model glycosidase Jack Bean α-mannosidase (JBα-man). Although for the clusters with the shorter C6 linker the rigidity of the scaffold was essential, these parameters had no influence for clusters with C9 chains: all of them showed rather good relative affinity enhancements per inhibitory epitopes between 70 and 160 highlighting the sound combination of the calix[8]arene core and the long alkyl arms. Preliminary docking studies were performed to get insights into the preferred binding modes.

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)-dipicolylamine complexes.

Gold nanoparticles covered with a mixture of ligands of which one type contains solubilizing triethylene glycol residues and the other peripheral zinc(II)–dipicolylamine (DPA) complexes allowed the optical detection of hydrogenphosphate, diphosphate, and triphosphate anions in water/methanol 1:2 (v/v). These anions caused the bright red solutions of the nanoparticles to change their color because of nanoparticle aggregation followed by precipitation, whereas halides or oxoanions such as sulfate, nitrate, or carbonate produced no effect. The sensitivity of phosphate sensing depended on the nature of the anion, with diphosphate and triphosphate inducing visual changes at significantly lower concentrations than hydrogenphosphate. In addition, the sensing sensitivity was also affected by the ratio of the ligands on the nanoparticle surface, decreasing as the number of immobilized zinc(II)–dipicolylamine groups increased. A nanoparticle containing a 9:1 ratio of the solubilizing and the anion-binding ligand showed a color change at diphosphate and triphosphate concentrations as low as 10 μmol/L, for example, and precipitated at slightly higher concentrations. Hydrogenphosphate induced a nanoparticle precipitation only at a concentration of ca. 400 μmol/L, at which the precipitates formed in the presence of diphosphates and triphosphates redissolved. A nanoparticle containing fewer binding sites was more sensitive, while increasing the relative number of zinc(II)–dipicolylamine complexes beyond 25% had a negative impact on the limit of detection and the optical response. Transmission electron microscopy provided evidence that the changes of the nanoparticle properties observed in the presence of the phosphates were due to a nanoparticle crosslinking, consistent with the preferred binding mode of zinc(II)–dipicolylamine complexes with phosphate anions which involves binding of the anion between two metal centers. This work thus provided information on how the behavior of mixed monolayer-protected gold nanoparticles is affected by multivalent interactions, at the same time introducing a method to assess whether certain biologically relevant anions are present in an aqueous solution within a specific concentration range.

9,10-Bis[(4-(2-hydroxyethyl)piperazine-1-yl)prop-2-yne-1-yl]anthracene: Synthesis and G-quadruplex Selectivity

G-quadruplex DNA is the target of several natural and synthetic small molecules with antiproliferative and antiviral activity. We here report the synthesis through Sonogashira reaction and A3 coupling of a disubstituted anthracene derivative, 9,10-bis[(4-(2-hydroxyethyl)piperazine-1-yl)prop-2-yne-1-yl]anthracene. The binding of this compound to G-quadruplex and double stranded DNA sequences was evaluated using electrospray ionization mass spectrometry (ESI-MS), demonstrating selectivity for the first structure. The interaction pattern of the ligand with G-quadruplex was investigated by molecular docking and stacking was found to be the preferred binding mode.

Interactions of Ionophoric Polyphenols with Human Serum Albumin

The distribution of a drug is determined, at least in part, by its interactions with serum proteins. Human serum albumin (HSA), the most abundant blood plasma protein, serves as the most common mode of transport for drugs to their target. In our previous work, we have synthesized and studied important characteristics of a series of ionophoric polyphenols as potential anti‐Alzheimer’s disease agents. As part of our ongoing investigations on the biological activity of these compounds, we are now exploring possible transport mechanisms. In our current work, the interactions of the ionophoric polyphenols with HSA were studied via in vitro and in silico methods. In line with in vitro studies, the interaction of the ionophoric polyphenols with HSA were studied by fluorescence and circular dichroism (CD) spectroscopies to obtain binding affinities, bimolecular quenching constants, theoretical number of binding sites and HSA secondary structural changes. Moreover, in line with in silico studies, a preferred mode of binding was predicted by molecular docking and the predicted systems were subject to a 5 ns MD simulation; consequently, RMSD studies were performed to attest for stability of the systems, MM/GBSA binding free energies were calculated to correlate with experimental binding affinities and per‐residue energy decomposition analyses were carried out to analyze residues critical to binding. Using resveratrol, a polyphenolic compound which has demonstrated strong neuroprotective and anti‐Alzheimer disease properties, as a control, in vitro results showed the formation of adducts (static quenching), one theoretical binding site, binding constants (Ka) ranging 104 to 106 M−1 and only slight secondary structure modifications between HSA and the ionophoric polyphenols. Further, in silico results revealed the ionophoric polyphenols and resveratrol favorably binding subdomain IIA of HSA, forming critical interactions to Trp 214 and Asp451. RMSD studies showed the HSA‐IIA system plateauing after a short time indicating stable binding events; in addition, a Pearson correlation coefficient of R=0.80 between the experimental binding affinity and computational binding free energies showed a strong correlation between in vitro and in silico results. Overall, our results seem to indicate that there is a ionophoric polyphenol‐serum albumin interaction, which could have a potential impact on the use of ionophoric polyphenols as therapeutics for Alzheimer’s disease.Support or Funding InformationThis research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE‐AC02‐05CH11231.

Exploring Interactions of Nucleosome via Interactome Analysis and Integrative Modeling

Interactions between nucleosome and various chromatin factors play key role in chromatin regulation such as histone modification and chromatin remodeling. Taking advantage of advances in a number of experimental techniques such as cro-EM, NMR and crosslinking mass spectrometry, we constructed three comprehensive human nucleosome interactomes using high-resolution experimental structures from PDB, recent crosslinking mass spectrometry data in human nuclei and experimental data form APID database. We explored the interactions of nucleosomes with binding partners via network analysis at different levels of details including residue-level, domain-level and protein-level. Residue level interactome allowed us to identify well-defined binding hotspots on histones and nucleosomal DNA. In addition, we performed extensive all atom molecular dynamic simulations to explore the histone tail dynamics and conformations in the context of nucleosomes with linker DNA. Histone tails were found to interact with nucleosomal DNA and histones via preferred binding modes affecting DNA solvent accessibility and thus potentially competing with other nucleosome binding partners.

Innovative Three-Step Microwave-Promoted Synthesis of N-Propargyltetrahydroquinoline and 1,2,3-Triazole Derivatives as a Potential Factor Xa (FXa) Inhibitors: Drug Design, Synthesis, and Biological Evaluation.

The coagulation cascade is the process of the conversion of soluble fibrinogen to insoluble fibrin that terminates in production of a clot. Factor Xa (FXa) is a serine protease involved in the blood coagulation cascade. Moreover, FXa plays a vital role in the enzymatic sequence which ends with the thrombus production. Thrombosis is a common causal pathology for three widespread cardiovascular syndromes: acute coronary syndrome (ACS), venous thromboembolism (VTE), and strokes. In this research a series of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives as a potential factor Xa (FXa) inhibitor were designed, synthesized, and evaluated for their FXa inhibitor activity, cytotoxicity activity and coagulation parameters. Rational design for the desired novel molecules was performed through protein-ligand complexes selection and ligand clustering. The microwave-assisted synthetic strategy of selected compounds was carried out by using Ullmann-Goldberg, N-propargylation, Mannich addition, Friedel-Crafts, and 1,3-dipolar cycloaddition type reactions under microwave irradiation. The microwave methodology proved to be an efficient way to obtain all novel compounds in high yields (73–93%). Furthermore, a thermochemical analysis, optimization and reactivity indexes such as electronic chemical potential (µ), chemical hardness (η), and electrophilicity (ω) were performed to understand the relationship between the structure and the energetic behavior of all the series. Then, in vitro analysis showed that compounds 27, 29–31, and 34 exhibited inhibitory activity against FXa and the corresponding half maximal inhibitory concentration (IC50) values were calculated. Next, a cell viability assay in HEK293 and HepG2 cell lines, and coagulation parameters (anti FXa, Prothrombin time (PT), activated Partial Thromboplastin Time (aPTT)) of the most active novel molecules were performed to determine the corresponding cytotoxicity and possible action on clotting pathways. The obtained results suggest that compounds 27 and 29 inhibited FXa targeting through coagulation factors in the intrinsic and extrinsic pathways. However, compound 34 may target coagulation FXa mainly by the extrinsic and common pathway. Interestingly, the most active compounds in relation to the inhibition activity against FXa and coagulation parameters did not show toxicity at the performed coagulation assay concentrations. Finally, docking studies confirmed the preferential binding mode of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives inside the active site of FXa.

Unveiling the Antimicrobial Activities of Dicationic Carbazoles and Related Analogs Through Computational Docking

Computational docking is a globally used tool now-a-days in bioinformatics. All the drugs/ligands generate their effect only when they interact/bind with the target molecule, here DNA. The potential drugs/ligands can only be identified by the study of their relative binding energies and preferential binding modes. Due to availability of huge numbers of such drugs/ligands; the evaluation of their relative potency is a challenging task. In the present work, carbazoles and its derivatives were studied for their DNA binding abilities using computational molecular docking. All the docked ligands had planar structures which allowed them to adopt crescent shape and thus minor groove binding to DNA was preferred by most of them. Computational docking revealed that DNA binding energies of carbazoles and its analogs followed the same trend as their thermal melting values. Also the drugs/ligands preferred themselves to bind at AT-rich regions of the minor groove of the selected DNA sequences.

Adsorption behavior of β-cyclodextrin onto gold nanoparticles

Native and modified cyclodextrins (CDs) are routinely used as a capping agent upon the preparation of gold nanoparticles (AuNP); however, their role in the synthesis remains unresolved. Here, the adsorption behavior of β-cyclodextrin (β-CD) onto AuNP was studied by all-atom molecular dynamics (MD) simulations. We found that β-CD binding onto the AuNP surface occurs through multiple non-covalent interactions, among which non-covalent binding of the aliphatic carbon moieties and the hydroxyl oxygen atoms plays a vital role. Surprisingly, the MD analysis revealed that the most preferred binding mode of the β-CD molecules onto the gold surface corresponds to the toroid side geometry. Only minor populations of β-CD molecules were observed, in which the adsorbate molecules are bound onto AuNP by either its primary or secondary rims, respectively. The adsorbed β-CDs formed the multiple-layer coating on AuNP, composed up to three adsorbate layers. We found that for AuNP of the size of 2.9 nm, the maximum water-protecting efficiency of the adsorbate coating occurs upon reaching a value of 40 β-CD molecules, the further increase in the adsorbate content resulted in some self-aggregation of β-CD molecules onto the gold surface. Our findings provide the molecular-level understanding of the adsorption behavior of β-CD onto gold, which is relevant for various applications of CD-capped gold nanostructures.

Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6–311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg2+ (−49.6 kcal/mol), Zn2+ (−45.3 kcal/mol) and Cu2+ (−148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg2+ and Cu2+ prefer to bind with the PNA-Cytosine (−32.9 kcal/mol & −132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn2+ (−29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu2+ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg2+ and Zn2+ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu2+ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg2+, Zn2+, and Cu2+ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg2+ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn2+, Cu2+) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu2+ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Screening cyclooxygenase-2 inhibitors from Andrographis paniculata to treat inflammation based on bio-affinity ultrafiltration coupled with UPLC-Q-TOF-MS

The cyclooxygenase-2 (COX-2) is a key enzyme in the synthesis of prostaglandins, its inhibitors are effective for the treatment of inflammation. In this study, an analytical method based on bio-affinity ultrafiltration coupled with ultra performance liquid chromatography and quadrupole-time-of-flight mass spectrometry (BAUF-UPLC-Q-TOF-MS) was established for rapidly screening and identifying COX-2 ligands. Meanwhile, the specificity of the method was verified by denatured COX-2 and inactive compound. Next, the biological activity of ligands screened was proved by enzyme inhibition assay. The preferred binding modes for these COX-2 inhibitors were then determined by molecular docking. Finally, network pharmacology was used to explore the pathways involved anti-inflammatory effects. As a result, five COX-2 inhibitors were selected in the extract of Andrographis Herba (AH), including andrographolide (1), 14-deoxy-11,12-didehydroandrographiside (2), andrographidine E (3), andrographidine D (4), and deoxyandrographolide (5). Among them, compounds 2, 3, 4 and 5 were reported to have COX-2 inhibitory activity for the first time. The result of COX-2 inhibition assay showed that compound 3 had an IC50 of 19 μM, compounds 2 and 5 had an IC50 of >200 μM. And each ligand could bind to multiple amino acid residues of COX-2 based on molecular docking. At last, combined with network pharmacology, these ligands could exert anti-inflammatory effects through three pathways related to COX-2, arachidonic acid metabolism, synthesis of prostaglandins, and prostanoid ligand receptors. The method established in the study could be used to rapidly screen other enzyme inhibitors in complex mixtures, and help to understand the mechanism of action.