Discovery anti-diabetic potent ofthiazolidinedione derivative based on virtual screening against aldose reducates

Thiazolidinedione (1) was used as a key intermediate for the synthesis of many therapeutic anti-diabetic molecule. Thus, Thiazolidinedione (1) was refluxed with aromatic aldehydes and phenol derivatives to afforded aryldine derivative (3). Moreover, the stereochemistry for compound 3 was discussed using Hartree-Fock theory geometries, and have been optimized at HF with 6-311G level of theory. The HOMO-LUMO energy gap of studied systems has been discussed. The molecular docking simulations into the active site of ALR2 were performed, and showed that, the compound 3 more suitable inhibitor against ALR2 and can used as anti- diabetic drug.

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In silicoidentification of putativeTrypanosoma cruzienolase inhibitors

10.1101/685206 ◽

2019 ◽

Author(s):

Edward A. Valera-Vera ◽

Melisa Sayé ◽

Chantal Reigada ◽

Mariana R. Miranda ◽

Claudio A. Pereira

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Virtual Screening ◽

Active Site ◽

Screening Strategy ◽

Glycolytic Enzyme ◽

Docking Simulations ◽

Enzyme Active Site ◽

Key Enzyme

AbstractEnolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids enolase was proposed as a key enzyme afterin silicoandin vivoanalysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroximate, triclofos, and aminohydroxybutyrate). Molecular docking simulations predicted acetohydroxamate and triclofos would not bind to the active site of the enzyme, and a re-scoring of the obtained poses signaled fosfomycin and aminohydroxybutyrate as bad enzyme binders. Docking poses obtained for etidronate, pamidronate, and PEP, were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a possibleTcENO inhibitor, and describe desirable and undesirable molecular motifs to be taken into account in the repurposing or design of drugs aiming this enzyme active site.

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A p–n fusion strategy to design bipolar organic materials for high-energy-density symmetric batteries

Journal of Materials Chemistry A ◽

10.1039/d1ta02059e ◽

2021 ◽

Author(s):

Jihyeon Kim ◽

Heechan Kim ◽

Sechan Lee ◽

Giyun Kwon ◽

Taewon Kang ◽

...

Keyword(s):

Energy Density ◽

Organic Material ◽

Energy Gap ◽

High Energy ◽

High Energy Density ◽

Lumo Energy ◽

Fusion Strategy ◽

Redox Active ◽

Bipolar Type ◽

Homo Lumo

A new bipolar-type redox-active organic material with a wide HOMO–LUMO energy gap is designed though the ‘p–n fusion’ strategy.

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STRUCTURES, ABSORPTION SPECTRA, AND ELECTRONIC PROPERTIES OF POLYFLUORENE AND ITS DERIVATIVES: A THEORETICAL STUDY

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633606002520 ◽

2006 ◽

Vol 05 (03) ◽

pp. 595-608 ◽

Cited By ~ 13

Author(s):

KRIENGSAK SRIWICHITKAMOL ◽

SONGWUT SURAMITR ◽

POTJAMAN POOLMEE ◽

SUPA HANNONGBUA

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Energy Gap ◽

Level Energy ◽

Excitation Energies ◽

Lumo Energy ◽

Functional Theory ◽

Local Energy Minimum ◽

Pi Systems ◽

Homo Lumo

The structural and energetic properties of polyfluorene and its derivatives were investigated, using quantum chemical calculations. Conformational analysis of bifluorene was performed by using ab initio (HF/6-31G* and MP2/6-31G*) and density functional theory (B3LYP/6-31G*) calculations. The results showed that the local energy minimum of bifluorene lies between the coplanar and perpendicular conformation, and the B3LYP/6-31G* calculations led to the overestimation of the stability of the planar pi systems. The HOMO-LUMO energy differences of fluorene oligomers and its derivatives — 9,9-dihexylfluorene (DHPF), 9,9-dioctylfluorene (PFO), and bis(2-ethylhexyl)fluorene (BEHPF) — were calculated at the B3LYP/6-31G* level. Energy gaps and effective conjugation lengths of the corresponding polymers were obtained by extrapolating HOMO-LUMO energy differences and the lowest excitation energies to infinite chain length. The lowest excitation energies and the maximum absorption wavelength of polyfluorene were also performed, employing the time-dependent density functional theory (TDDFT) and ZINDO methods. The extrapolations, based on TDDFT and ZINDO calculations, agree well with experimental results. These theoretical methods can be useful for the design of new polymeric structures with a reducing energy gap.

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Molecular Modeling Studies on 2,4-Disubstituted Imidazopyridines as Anti-Malarials: Atom-Based 3D-QSAR, Molecular Docking, Virtual Screening, In-Silico ADMET and Theoretical Analysis

Journal of Computational Biophysics and Chemistry ◽

10.1142/s2737416521500125 ◽

2021 ◽

pp. 2150012

Author(s):

Suraj N. Mali ◽

Anima Pandey

Keyword(s):

Molecular Docking ◽

Molecular Modeling ◽

Virtual Screening ◽

In Silico ◽

Energy Gap ◽

3D Qsar ◽

Modeling Studies ◽

In Vitro Investigation ◽

In Silico Admet ◽

Molecular Modeling Studies

Malarial parasites have been reported for moderate-high resistance towards classical antimalarial agents and henceforth development of newer novel chemical entities targeting multiple targets rather than targeting single target will be a highly promising strategy in antimalarial drug discovery. Herein, we carried out molecular modeling studies on 2,4-disubstituted imidazopyridines as anti-hemozoin formation inhibitors by using Schrödinger’s molecular modeling package (2020_4). We have developed statistically robust atom-based 3D-QSAR model (training set, [Formula: see text]; test set, [Formula: see text]; [Formula: see text] [Formula: see text]; root-mean-square error, [Formula: see text]; standard deviation, [Formula: see text]). Our molecular docking, in-silico ADMET analysis showed that dataset molecule 37, has highly promising results. Our ligand-based virtual screening resulted in top five ZINC hits, among them ZINC73737443 hit was observed with lesser energy gap, i.e. 7.85[Formula: see text]eV, higher softness value (0.127[Formula: see text]eV), and comparatively good docking score of [Formula: see text]10.2[Formula: see text]kcal/mol. Our in-silico analysis for a proposed hit, ZINC73737443 showed that this molecule has good ADMET, in-silico nonames toxic as well as noncarcinogenic profile. We believe that further experimental as well as the in-vitro investigation will throw more lights on the identification of ZINC73737443 as a potential antimalarial agent.

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5-Methyl-1,3-phenylene bis[5-(dimethylamino)naphthalene-1-sulfonate]: crystal structure and DFT calculations

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989019009058 ◽

2019 ◽

Vol 75 (7) ◽

pp. 1079-1083

Author(s):

Tanwawan Duangthongyou ◽

Ramida Rattanakam ◽

Kittipong Chainok ◽

Songwut Suramitr ◽

Thawatchai Tuntulani ◽

...

Keyword(s):

Dft Calculations ◽

Energy Gap ◽

Rotation Axis ◽

Three Dimensional ◽

Hydrogen Atoms ◽

Lumo Energy ◽

Compound C ◽

Dansyl Group ◽

Weak Hydrogen Bonds ◽

Homo Lumo

The title compound, C31H30N2S2O6, possesses crystallographically imposed twofold symmetry with the two C atoms of the central benzene ring and the C atom of its methyl substituent lying on the twofold rotation axis. The two dansyl groups are twisted away from the plane of methylphenyl bridging unit in opposite directions. The three-dimensional arrangement in the crystal is mainly stabilized by weak hydrogen bonds between the sulfonyl oxygen atoms and the hydrogen atoms from the N-methyl groups. Stacking of the dansyl group is not observed. From the DFT calculations, the HOMO–LUMO energy gap was found to be 2.99 eV and indicates n→π* and π→π* transitions within the molecule.

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Mulberrofuran G, a Potent Inhibitor of SPIKE Protein of SARS Corona Virus 2

Journal of Pharmaceutical Care ◽

10.18502/jpc.v9i2.6610 ◽

2021 ◽

Author(s):

Fatemeh Sadat Hosseini ◽

Mohammad Reza Motamedi

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

Active Site ◽

Potential Role ◽

Potent Inhibitor ◽

Screening Method ◽

Spike Protein ◽

Treatment Agent ◽

Approved Drugs ◽

Fda Approved Drugs

Background: At the onset of the 2020 year, Coronavirus disease (COVID-19) has become a pandemic and infected many people worldwide. Despite all efforts, no cure was found for this infection. Bioinformatics and medicinal chemistry have a potential role in the primary consideration of drugs to treat this infection. With virtual screening and molecular docking, some potent compounds and medications can be found and modified and then applied to treat disease in the next steps. Methods: By virtual screening method and PRYX software, some Food and Drug Administration (FDA) approved drugs and natural compounds have been docked with the SPIKE protein of SARS-CoV-2. Some more potent agents have been selected, and then new structures are designed with better affinity than them. After that, we searched for the molecules with a similar structure to designed compounds to find the most potent compound to our target. Results: Because of the study of structures and affinities, mulberrofuran G was the most potent compound in this study. The compound has interacted strongly with residues in the probably active site of SPIKE. Conclusion: Mulberrofuran G can be a treatment agent candidate for COVID-19 because of its good affinity to SPIKE of the virus and inhibition of virus-cell adhesion and entrance.

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SOLVENT EFFECTS ON THE ELECTRONIC STRUCTURE AND NON-LINEAR OPTICAL PROPERTIES OF PYRENE AND SOME OF ITS DERIVATIVES BASED ON DENSITY FUNCTIONAL THEORY

FUDMA Journal of Sciences ◽

10.33003/fjs-2020-0404-477 ◽

2021 ◽

Vol 4 (4) ◽

pp. 236-251

Author(s):

A. S. Gidado ◽

L. S. Taura ◽

A. Musa

Keyword(s):

Density Functional Theory ◽

Gas Phase ◽

Density Functional ◽

Energy Gap ◽

Chemical Reactivity ◽

Basis Set ◽

Lumo Energy ◽

Functional Theory ◽

Organic Optoelectronic ◽

Homo Lumo

Pyrene (C16H10) is an organic semiconductor which has wide applications in the field of organic electronics suitable for the development of organic light emitting diodes (OLED) and organic photovoltaic cells (OPV). In this work, Density Functional Theory (DFT) using Becke’s three and Lee Yang Parr (B3LYP) functional with basis set 6-311++G(d, p) implemented in Gaussian 03 package was used to compute total energy, bond parameters, HOMO-LUMO energy gap, electron affinity, ionization potential, chemical reactivity descriptors, dipole moment, isotropic polarizability (α), anisotropy of polarizability ( Δ∝) total first order hyper-polarizability () and second order hyperpolarizability (). The molecules used are pyrene, 1-chloropyrene and 4-chloropyrene in gas phase and in five different solvents: benzene, chloroform, acetone, DMSO and water. The results obtained show that solvents and chlorination actually influenced the properties of the molecules. The isolated pyrene in acetone has the largest value of HOMO-LUMO energy gap of and is a bit closer to a previously reported experimental value of and hence is the most stable. Thus, the pyrene molecule has more kinetic stability and can be described as low reactive molecule. The calculated dipole moments are in the order of 4-chloropyrene (1.7645 D) < 1-chloropyrene (1.9663 D) in gas phase. The anisotropy of polarizability ( for pyrene and its derivatives were found to increase with increasing polarity of the solvents. In a nutshell, the molecules will be promising for organic optoelectronic devices based on their computed properties as reported by this work.

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HOMO–LUMO Energy-Gap Tuning of π-Conjugated Zwitterions Composed of Electron-Donating Anion and Electron-Accepting Cation

The Journal of Organic Chemistry ◽

10.1021/acs.joc.0c02343 ◽

2020 ◽

Vol 86 (1) ◽

pp. 770-781

Author(s):

Akihiro Shimizu ◽

Yu Ishizaki ◽

Shun Horiuchi ◽

Takashi Hirose ◽

Kenji Matsuda ◽

...

Keyword(s):

Energy Gap ◽

Lumo Energy ◽

Homo Lumo

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Strategic design of thiophene-fused nickel dithiolene derivatives for efficient NLO response

Physical Chemistry Chemical Physics ◽

10.1039/c8cp01592a ◽

2018 ◽

Vol 20 (28) ◽

pp. 19007-19016 ◽

Cited By ~ 3

Author(s):

Manoj Majumder ◽

Anirban Misra

Keyword(s):

Energy Gap ◽

First Hyperpolarizability ◽

Lumo Energy ◽

Strategic Design ◽

Nlo Response ◽

Acceptor Group ◽

Donor Acceptor ◽

Homo Lumo

The zwitterionic donor–acceptor group significantly reduces the HOMO–LUMO energy gap resulting in an enormous increase in the first hyperpolarizability values.

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