Identification of 4-acrylamido-<i>N</i>-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Sepay, Nayim; Chakrabarti, Sukanya; Afzal, Mohd; Alarifi, Abdullah; Mal, Dasarath

doi:10.1039/d2ra04333e

Cited by 11 publications

(6 citation statements)

References 51 publications

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“…On the other hand, areas with the lowest probability of finding an electron show the minimum Pauli repulsion. The ELF value for this region is 0, represented by the color blue. , It is worth noting that the area with well-localized electrons, such as lone pairs, chemical bonds, and atomic shells, shows the most significant Pauli repulsion. The ELF helps to identify the regions with the highest and lowest electron densities, which can provide valuable insights into the molecular structure and bonding in chemical reactions.…”

Section: Resultsmentioning

confidence: 99%

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure

Paul,

Das,

Sepay

et al. 2024

Crystal Growth & Design

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The development of a novel transition metal carbon oxyfluoride, Co 3 Sb 4 CO 6 F 6 , i.e., an [M-L-C-O-F]-type compound, leads to the formation of a 2-fold ∼(√2a × √ 2b × c) pseudo-superstructure compared to the basic structure (a × b × c) of Co 3 Sb 4 O 6 F 6 , i.e., an [M-L-O-F]-type compound, and a unique C−Sb covalent bond has been revealed for the first time. The covalent bond parameter, i.e., distance between carbon and antimony, not only could be included in the directory of the chemical bond in the bond valence sum (BVS) model of Brese and O'Keeffe [Acta Crystallogr. B47, 1991, 192−197] but also can open up research in inorganic chemistry. A single crystal of Co 3 Sb 4 CO 6 F 6 has been obtained by employing a greener hydrothermal synthetic technique, and table sugar (sucrose, C 12 H 22 O 11 ) acted as the source of carbon while incorporating into Co 3 Sb 4 O 6 F 6 , a transition metal oxyfluoride system comprising a stereochemically active lone pair cation (Sb 3+ ). The smallest atomic radii of carbon were perfectly suited to occupy the tetrahedral sites of the Sb 4 pseudo tetrahedron in Co 3 Sb 4 O 6 F 6 and generated distortion in the structure, which resulted in lowering the symmetry to Fmm2 from I4̅ 3m. The participation of one electron from the lone pair of antimony cation and one electron from carbon led to the formation of a CSb 4 covalent unit, which is well supported by the electron localization function (ELF) study. The DFT study also confirmed the lowering of the band gap energy (E g = 1.16 eV) in Co 3 Sb 4 CO 6 F 6 compared to Co 3 Sb 4 O 6 F 6 (E g = 1.48 eV).

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Section: Resultsmentioning

confidence: 99%

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure

Paul,

Das,

Sepay

et al. 2024

Crystal Growth & Design

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“…Moreover, other studies have combined molecular docking, MD simulation and MMGBSA with advance techniques such as large-scale density functional tight binding (DFTB) to investigate drug-protein interaction at a quantum level [21,37,38].…”

Section: Discussionmentioning

confidence: 99%

ADME, Molecular Targets, Docking, and Dynamic Simulation Studies of Phytoconstituents of Cymbopogon citratus (DC.)

Ajayi,

Fatoki,

Alonge

et al. 2024

MEDIN

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Cymbopogon citratus (DC) Stapf., is utilized in both culinary and medicinal contexts, wherein its extracts demonstrate a range of therapeutic properties, including antidiabetic, antioxidant, and anti-inflammatory activities. This investigation aimed to computationally analyze phytochemicals of C. citratus, evaluating their pharmacokinetics and binding dynamics. The findings revealed a combination of high and low gastrointestinal absorption (GIA) for C. citratus (DC.) phytochemicals, with some exhibiting permeability across the blood-brain barrier (BBB). Xanthine dehydrogenase/oxidase (XDH) emerged as the primary human molecular target of C. citratus phytocompounds, while XDH and Matrix metalloproteinase-9 (MMP9) have central connectivity in the protein interaction network. Orientin has best binding affinity with XDH (-9.083 kcal.mol-1) and MMP9 (-9.051 kcal.mol-1). Molecular dynamic (MD) simulations indicated the favorable stability and interactions of XDH with Orientin and Quercetin, respectively. In summary, this investigation underscores the potential of twenty-six (26) in C. citratus extract to combating cancer and neurodegenerative diseases through mechanisms targeting XDH and MMP9.

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“…In previous studies, the binding energy between effective molecule and SARS-CoV-2 M pro protein was calculated by density functional tight binding (DFTB), and the free-energy surfaces/thermodynamics of large biochemical systems was accurately and efficiently predicted using GPU-based DFTB approach [ 31 , 32 ]. Although DFTB was used to understand large biomolecular systems, the molecular docking was performed in this study.…”

Section: Discussionmentioning

confidence: 99%

Identification of biomarkers related to tryptophan metabolism in osteoarthritis

Yang,

Zhou,

et al. 2024

Biochemistry and Biophysics Reports

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Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Abstract: An anti COVID-19 molecule have been identified from the ZINC-15 database with the help of molecular docking, DFTB, and molecular dynamics method.

Cited by 11 publications

References 51 publications

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure

ADME, Molecular Targets, Docking, and Dynamic Simulation Studies of Phytoconstituents of Cymbopogon citratus (DC.)

Identification of biomarkers related to tryptophan metabolism in osteoarthritis

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Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Abstract: An anti COVID-19 molecule have been identified from the ZINC-15 database with the help of molecular docking, DFTB, and molecular dynamics method.

Cited by 11 publications

References 51 publications

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co3Sb4CO6F6 Pseudo-superstructure

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co3Sb4CO6F6 Pseudo-superstructure

ADME, Molecular Targets, Docking, and Dynamic Simulation Studies of Phytoconstituents of Cymbopogon citratus (DC.)

Identification of biomarkers related to tryptophan metabolism in osteoarthritis

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Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure

Unraveling an Unusual Covalent C–Sb Bond Formation in a Co₃Sb₄CO₆F₆ Pseudo-superstructure