Binding Energies of N-Bearing Astrochemically-Relevant Molecules on Water Interstellar Ice Models. A Computational Study

Background: Malaria is endemic in various parts of India particularly in the North- Eastern states with Plasmodium falciparum-the most prevalent human malaria parasite. Plantderived compounds have always received tremendous importance in the area of drug discovery and development and scientific study of traditional medicinal plants are of great importance to mankind. Objective: The present work deals with the computational study of some antimalarial compounds obtained from a few medicinal plants used by the tribal inhabitants of the North-Eastern region of India for treating malaria. Methods: In silico methodologies were performed to study the ligand-receptor interactions. Target was identified based on the pharmacophore mapping approach. A total of 18 plant-derived compounds were investigated in order to estimate the binding energies of the compounds with their drug target through molecular docking using Autodock 4.2. ADMET filtering for determining the pharmacokinetic properties of the compounds was done using Mobyle@RPBS server. Subsequent Quantitative-Structure Activity Relationship analysis for bioactivity prediction (IC50) of the compounds was done using Easy QSAR 1.0. Results: The docking result identified Salannin to be the most potent Plasmepsin II inhibitor while the QSAR analysis identified Lupeol to have the least IC50 value. Most of the compounds have passed the ADME/Tox filtration. Conclusion: Salannin and Lupeol were found to be the most potent antimalarial compounds that can act as successful inhibitors against Plasmepsin II of P. falciparum. The compounds Salannin and Lupeol are found in Azadirachta indica and Swertia chirata plants respectively, abundantly available in the North-Eastern region of India and used by many inhabiting tribes for the treatment of malaria and its symptoms.

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Combinatorial Library Designing and Virtual Screening of Cryptolepine Derivatives against Topoisomerase II by Molecular Docking

10.1101/2020.06.08.141176 ◽

2020 ◽

Author(s):

Maria ◽

Zahid Khan

Keyword(s):

Molecular Docking ◽

Cell Division ◽

Binding Energy ◽

Cancer Cells ◽

Anticancer Agents ◽

Combinatorial Library ◽

Topoisomerase Ii ◽

Computational Study ◽

Binding Energies ◽

Potential Inhibitors

AbstractComputational approaches have emerging role for designing potential inhibitors against topoisomerase 2 for treatment of cancer. TOP2A plays a key role in DNA replication before cell division and thus facilitates the growth of cells. This function of TOP2A can be suppressed by targeting with potential inhibitors in cancer cells to stop the uncontrolled cell division. Among potential inhibitors cryptolepine is more selective and has the ability to intercalate into DNA, effectively block TOP2A and cease cell division in cancer cells. However, cryptolepine is non-specific and have low affinity, therefore, a combinatorial library was designed and virtually screened for identification of its derivatives with greater TOP2A binding affinities.A combinatorial library of 31114 derivatives of cryptolepine was formed and the library was virtually screened by molecular docking to predict the molecular interactions between cryptolepine derivatives and TOP2A taking cryptolepine as standard. The overall screening and docking approach explored all the binding poses of cryptolepine for TOP2A to calculate binding energy. The compounds are given database number 8618, 907, 147, 16755, and 8186 scored lowest binding energies of −9.88kcal/mol, −9.76kcal/mol, −9.75kcal/mol, −9.73kcal/mol, and −9.72kcal/mol respectively and highest binding affinity while cryptolepine binding energy is −6.09kcal/mol. The good binding interactions of the derivatives showed that they can be used as potent TOP2A inhibitors and act as more effective anticancer agents than cryptolepine itself. The interactions of derivatives with different amino acid residues were also observed. A comprehensive understanding of the interactions of proposed derivatives with TOP2A helped for searching more novel and potent drug-like molecules for anticancer therapy. This Computational study suggests useful references to understand inhibition mechanisms that will help in the modification of TOP2A inhibitors.

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Adsorption of PAHs on interstellar ice viewed by classical molecular dynamics

Physical Chemistry Chemical Physics ◽

10.1039/c8cp00593a ◽

2018 ◽

Vol 20 (13) ◽

pp. 8753-8764 ◽

Cited By ~ 11

Author(s):

Eric Michoulier ◽

Jennifer A. Noble ◽

Aude Simon ◽

Joëlle Mascetti ◽

Céline Toubin

Keyword(s):

Molecular Dynamics ◽

Low Temperature ◽

Electronic State ◽

Binding Energies ◽

Ground Electronic State ◽

Barrier Heights ◽

Classical Molecular Dynamics ◽

Interstellar Ice

The present work represents a complete description of PAH–ice interaction in the ground electronic state and at low temperature, providing the binding energies and barrier heights necessary to the ongoing improvement of astrochemical models.

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Computational study of Mg insertion into amorphous silicon: advantageous energetics over crystalline silicon for Mg storage

MRS Proceedings ◽

10.1557/opl.2013.1036 ◽

2013 ◽

Vol 1540 ◽

Cited By ~ 1

Author(s):

Fleur Legrain ◽

Oleksandr I. Malyi ◽

Teck L. Tan ◽

Sergei Manzhos

Keyword(s):

Density Functional ◽

Nearest Neighbor ◽

Defect Formation ◽

Crystalline Silicon ◽

Computational Study ◽

Binding Energies ◽

Functional Theory ◽

Wide Range ◽

Insertion Sites ◽

Formation Energies

ABSTRACTWe show in a theoretical density functional theory study that amorphous Si (a-Si) has more favorable energetics for Mg storage compared to crystalline Si (c-Si). Specifically, Mg and Li insertion is compared in a model a-Si simulation cell. Multiple sites for Mg insertion with a wide range of binding energies are identified. For many sites, Mg defect formation energies are negative, whereas they are positive in c-Si. Moreover, while clustering in c-Si destabilizes the insertion sites (by about 0.1/0.2 eV per atom for nearest-neighbor Li/Mg), it is found to stabilize some of the insertion sites for both Li (by up to 0.27 eV) and Mg (by up to 0.35 eV) in a-Si. This could have significant implications on the performance of Si anodes in Mg batteries.

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Pyrazole Schiff Base Hybrids as Anti-Malarial Agents: Synthesis, In Vitro Screening and Computational Study

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207321666180213092911 ◽

2018 ◽

Vol 21 (3) ◽

pp. 194-203 ◽

Cited By ~ 9

Author(s):

Shilpy Aggarwal ◽

Deepika Paliwal ◽

Dhirender Kaushik ◽

Girish Kumar Gupta ◽

Ajay Kumar

Keyword(s):

Schiff Base ◽

Antimalarial Activity ◽

Computational Study ◽

Docking Study ◽

Docking Studies ◽

Binding Energies ◽

Study Results ◽

Wide Range ◽

Parasite Plasmodium Falciparum

Background: Malaria is one of the most vital infectious diseases caused by protozoan parasites of the Plasmodium genus. As P. falciparum, the cause of most of the severe cases of malaria, is increasingly resistant to available drugs such as amodioquine, chloroquine, artemisinin, and antifolates, there is an urgent need to identify new targets for chemotherapy. Objective: This study screened novel pyrazole derivatives carrying iminium & benzothiazole group for antimalarial potential against P. falciparum chloroquine sensitive (3D7) strain. Materials & Methods: Several pyrazole schiff base hybrids with a wide range of substitution have been synthesized via condensation of substituted aniline with substituted 4-formylpyrazole and evaluated for their in vitro antimalarial activity against asexual blood stages of human malaria parasite, Plasmodium falciparum. The interaction of these conjugate hybrids was also investigated by molecular docking studies in the binding site of P. falciparum cystein protease falcipain-2. The pharmacokinetic properties were also studied using ADME prediction. Results: Among all compounds, 6bf and 6bd were found to be potential molecules with EC50 1.95µg/ml and 1.98µg/ml respectively. Docking study results reveal that the pyrazole schiff base derivatives occupy the PfFP binding sites and they show good interactions with significant values of binding energies. Conclusion: We provide evidence which implicates pyrazole Schiff base hybrids as potential prototypes for the development of antimalarial agents.

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Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking

RSC Advances ◽

10.1039/c6ra12084a ◽

2016 ◽

Vol 6 (69) ◽

pp. 64756-64768 ◽

Cited By ~ 13

Author(s):

Camila Muñoz-Gutierrez ◽

Francisco Adasme-Carreño ◽

Eduardo Fuentes ◽

Iván Palomo ◽

Julio Caballero

Keyword(s):

Computational Study ◽

Protein Flexibility ◽

Docking Study ◽

Binding Energies ◽

Induced Fit ◽

Cross Docking ◽

Pparγ Agonists ◽

Differential Binding ◽

Binding Orientation ◽

Crystal Receptor

A cross-docking study for describing differential binding energies of PPARγ and agonists was successful after the inclusion of protein flexibility through the use of several crystal receptor conformations.

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On the binding energies and configurations of vacancy and copper–vacancy clusters in bcc Fe–Cu:a computational study

The Philosophical Magazine A Journal of Theoretical Experimental and Applied Physics ◽

10.1080/14786430500156930 ◽

2006 ◽

Vol 86 (2) ◽

pp. 141-172 ◽

Cited By ~ 18

Author(s):

D. Kulikov§ ◽

L. Malerba ◽

M. Hou

Keyword(s):

Computational Study ◽

Binding Energies ◽

Vacancy Clusters

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Exchange of Cl+ between Lone-Pair Donors and π-Donors: A Computational Study

European Journal of Mass Spectrometry ◽

10.1255/ejms.335 ◽

2000 ◽

Vol 6 (2) ◽

pp. 153-160 ◽

Cited By ~ 6

Author(s):

Theis I. Sølling ◽

Leo Radom

Keyword(s):

Ab Initio ◽

Computational Study ◽

Lone Pair ◽

Binding Energies ◽

Lewis Base ◽

Molecular Orbital Calculations ◽

Reaction Energy ◽

Lewis Bases ◽

Donor Ability ◽

Reaction Energies

The chemistry of mono-adducts ([Cl–X]+) between Cl+ and a Lewis base (X = NH3, H2O, HF, PH3, H2S or HCl) has been investigated using ab initio molecular orbital calculations at the G2 level. The reactions of such mono-adducts with additional Lewis bases (Y) are found to give [Y–Cl]+ plus X, generally without an intermediate barrier, via a bis-adduct [Y–Cl–X]+. The binding energies of the bis-adduct and the reaction energies are related to the donor properties of the Lewis bases. The reactions between the mono-adducts [Cl–X]+ and the π-donors ethylene and acetylene yield chloriranium and chlorirenium ions, respectively. These reactions proceed via complexes that resemble either the reactants or products depending on the sign of the reaction energy, the latter in turn being determined by the donor ability of the Lewis base. Results for the chlorine systems are compared with those for the corresponding phosphorus systems investigated previously.

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Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

Molecules ◽

10.3390/molecules25040798 ◽

2020 ◽

Vol 25 (4) ◽

pp. 798

Author(s):

Iñigo Iribarren ◽

Goar Sánchez-Sanz ◽

Cristina Trujillo

Keyword(s):

Density Functional ◽

Computational Study ◽

Halogen Bond ◽

Anion Recognition ◽

Lone Pair ◽

Halogen Bonding ◽

Binding Energies ◽

Bond Critical Point ◽

Density Values ◽

Intramolecular Hydrogen

A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X⋯I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

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A Computational Study on SnO2 Au-Doped Grains: CO Adsorption

MRS Proceedings ◽

10.1557/proc-0915-r06-02 ◽

2006 ◽

Vol 915 ◽

Author(s):

Anna Mazzone

Keyword(s):

Grain Size ◽

Computational Study ◽

Co Adsorption ◽

Adsorption Properties ◽

Binding Energies ◽

Current Transport ◽

Hartree Fock ◽

Grain Surface ◽

Semi Empirical

AbstractIn this study an analysis is made of the adsorption properties of nanocrystalline SnO2 containing a metallic dopant. The analysis is based on semi-empirical Hartree-Fock and scattering theories and the structures considered are SnO2 grains with a rutile lattice and a size comparable with the experimental ones. The grains contain rows of gold atoms located on the grain surface or in an endohedral position, in the grain interior, and the adsorbed system is generated by depositing a CO molecule on the grain surface. The calculations illustrate the dependence of the binding energies and ofthe conductance on the grain size, on the location of the metallic additives in both the clean and in the CO-adsorbed grains. New mechanisms of adsorption and of current transport are proposed.

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