1,721,235 research outputs found
DFT study of guest-responsive cooperative effects: Inclusion complexation of alcohols with calix[4]pyrrole
No full textAbstract: Herein, we report guest-responsive structural changes and cooperative effects in inclusion complexes of meso-octamethylcalix[4]pyrrole. A series of lower alcohol guests were modeled using the density functional theory at B97D/6-311 + G* and ωB97D/6-311 + G* level of approximation to study their thermochemical properties and complexation geometries. Results of binding energies of CP:1-alcohol and CP:2-alcohol complexes indicated that the methylene glycol exhibited strongest binding, whereas ethane-1,2-diol has the highest cooperative effects. Attempts were also made to address the cooperative effects by correlating them with the partial charges (Hirshfeld, Atomic Dipole Corrected Hirshfeld) and the second-order energy interactions. Graphical abstract: [Figure not available: see fulltext.
Exploring Ruthenium-Based Organometallic Inhibitors against Plasmodium falciparum Calcium Dependent Kinase 2 (PfCDPK2): A Combined Ensemble Docking, QM/MM and Molecular Dynamics Study
No full textRecent advances in the metal-organic framework (MOF) have accelerated the discovery of novel metal-based anticancer, antibacterial and antimalarial compounds. This is substantiated by many serendipitously discovered metals (Ru, Rh, and Ir) based inhibitors that established the importance of metal inserted into the known organic scaffold. Conversely, it is possible to design novel bioactive compounds by mimicking hypervalent carbon atoms by transition metals. This process can be facilitated by computational drug discovery by treating metal centres using optimized parameters that can be used for molecular docking and molecular dynamics simulations. Further, the method can be plugged with high computational power and refined algorithms to interpret chemical phenomena with atomic-level insights. In the present work, we have demonstrated an approach for parameterizing three organometallic ligands (FLL, E52, and staurosporine) using MCPB.py. In particular, we report that E52 and FLL have a better shape complimentary and affinity compared to staurosporine identified inhibitor (staurosporine) against Calcium-dependent protein kinases 2 (CDPK2). This study also revealed that a flexible approach (ensemble) outperforms the given target with dynamic movements. The calculated MM-PBSA energies for staurosporine, FLL and E52 were −66.461±2.192, −67.182±1.971 and −91.339±2.745 kJ/mol, respectively
Understanding non-covalent interactions by NMR in urea- and thiourea-substituted calixarene complexes
No full textAbstract: High level quantum mechemical gauge-independent atomic orbital (GIAO)-DFT NMR calculations (B3LYP/6-311++G**) were performed to address the binding interactions of functionalized thiourea and urea substituted calixarenes. 1H NMR chemical shifts were evaluated for hydrogen-bonded protons of calixarenes (1,2) and their anionic-complexes with F−, Cl−, CN−, N3− and SCN−. Comparison of experimental vs. calculated anion binding geometries along with their chemical shift were made to decipher the structural features. The calculated chemical shift exhibit reasonable agreement with the experimental data. We showed that the substitution of C=O to C=S in calixarenes significantly affect the interaction with anions. In particular, urea substituted calixarenes-F− possess most deshielded hydrogens among the modeled inclusion complexes. Our study showed that NMR calculation in combination with calixarene structural models can be helpful in characterizing the non-covalent interactions. Graphic abstract: [Figure not available: see fulltext.]
Computational investigation of binding of chloroquinone and hydroxychloroquinone against PLPro of SARS-CoV-2
Get PDFNovel coronavirus SARS-CoV-2 has infected 18 million people with 700,000+ mortalities worldwide and this deadly numeric figure is rapidly rising. With very few success stories, the therapeutic targeting of this epidemic has been mainly attributed to main protease (Mpro), whilst Papain-like proteases (PLpro) also plays a vital role in the processing of replicase polyprotein. Multifunctional roles of PLpro such as viral polypeptide cleavage, de-ISGlyation and immune suppression have made it a promising drug target for therapeutic interventions. Whilst there have been a number of studies and others are on-going on repurposing and new-small molecule screening, albeit previously FDA approved drugs viz. Chloroquine (CQ) and Hydroxychloroquine (HCQ) have only been found effective against this pandemic. Inspired by this fact, we have carried out molecular docking and dynamics simulation studies of FDA approved CQ and HCQ against SARS-CoV-2 PLpro. The end aim is to characterise the binding mode of CQ and HCQ and identify the key amino acid residues involved in the mechanism of action. Further, molecular dynamics simulations (MDS) were carried out with the docked complex to search for the conformational space and for understanding the integrity of binding mode. We showed that the CQ and HCQ can bind with better binding affinity with PLpro as compared to reference known PLpro inhibitor. Based on the presented findings, it can be anticipated that the SARS-CoV-2 PLpro may act as molecular target of CQ and HCQ, and can be projected for further exploration to design potent inhibitors of SARS-CoV-2 PLpro in the near future
Investigation of structural and conformational equilibrium of Oxacalix[4]arene: A density functional theory approach
No full textHigh level theoretical calculations were employed to study the structural and conformational equilibrium of the Oxacalix[4]arenes. We have proposed that the replacement of methylene bridges with the oxygen atoms stabilizes 1,3-Alternate conformer predominantly. Furthermore, assessment of conformational equilibrium was explored in gaseous as well as solvation phases. The role of dispersion forces, possibility of complexation, distribution of electrostatic-potential, population analysis, substitution effects that are crucial for the analyte recognition were also discussed
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Recognition of anions using urea and thiourea substituted calixarenes: A density functional theory study of non-covalent interactions
No full textDesigning of new calixarene receptors for the selective binding of anions is an age-old concept; even though expected outcomes from this field are at premature stage. Herein, we have performed quantum chemical calculations to provide structural basis of anion binding with urea and thiourea substituted calixarenes (1, 2, and 3). In particular, spherical halides (F−, Cl−, Br−) and linear anions (CN−, N3−, SCN−) were modelled for calculating binding energies with receptor 1, 2 and 3 followed by their marked IR vibrations; taking the available experimental information into account. We found that the thiourea substitutions have better capability to stabilize the anions. Results have suggested that the structural behaviour of macrocyclic motifs were responsible for displaying the anion binding potentials. Moreover, second order “charge transfer” interactions of n‐σ∗NH and n‐σ∗OH type along the H‐bond axis played critical role in developing hydrogen bonds. The present work also examines the role of non-covalent interactions (NCI) and their effects on thermodynamic and chemical-reactivity descriptors
Designing of calixarene based drug carrier for dasatinib, lapatinib and nilotinib using multilevel molecular docking and dynamics simulations
No full textAbstract: Herein, an in-silico attempt was made to improve the pharmacological profile of second generation tyrosine kinase inhibitors (TKI’s) viz. dasatinib, lapatinib and nilotinib by forming their host–guest inclusion complexes with calixarene. We have investigated the energetics and binding behaviour of TKI’s with upper rim functionalised calix[n]arenes (n = 4,5,6 and 8) via appended groups (R=SO3H, tert-Butyl, iso-Propyl, COOH, C2H5OH, and C2H5NH2). For this, multilevel molecular docking approach with shape based fitting algorithms (Patchdock/Firedock and HexServer) followed by semiemperical PM3 calculations were employed to generate structural mode of complexes. Further, based on interaction energies and their structural integrity (dynamics behaviour), we concluded that the proposed drug carrier (host) for nilotinib (C2H5SO3H-calix[4]arene, and isopropyl/C2H5NH2-calix[8]arene), dasatinib (C2H5SO3H-calix[5]arene, C2H5COOH-calix[6]arene, tert-butyl-calix[6]arene) and lapatinib (C2H5SO3H/C2H5COOH-calix[6]arene and C2H5COOH-calix[8]arene) have the greater capability to form optimal complexes. Graphical abstract: [Figure not available: see fulltext.]
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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