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Roy, Kunal; Kar, Supratik; Das, Rudra Narayan

doi:10.1016/b978-0-12-801505-6.00010-7

Cited by 29 publications

(12 citation statements)

References 103 publications

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“…Each pose is then examined for its compatibility with the target in terms of shape, electrostatics, and other properties to generate a corresponding dock score. A favorable dock score indicates that the ligand has the potential to be a strong binder [73] …”

Section: Resultsmentioning

confidence: 99%

“…A favorable dock score indicates that the ligand has the potential to be a strong binder. [73] The binding interaction of Zn and Mn complexes with DNA (1Z3F) and BSA (6QS9) receptor proteins were studied by in silico molecular docking. The Zn-Complex showed a more docking score (5566), docking area (737.10), and lowest atomic contact energy (ACE = À 586.77 kJ/mol) with DNA than Mn-Complex and piroxicam (Table 6).…”

Section: In Silico Docking Analysismentioning

confidence: 99%

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Comprehensive Biological, Photodegradation, Density Functional Theory, and Docking Exploration of Zn(II) and Mn(II) complexes of Piroxicam

Maha,

Tajammal,

Samra

et al. 2023

ChemistrySelect

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The biological evaluation of coordination complexes is an active research area ascribed to structural modification and synergistic action due to metal ions. The mononuclear complexes of Zn(II) and Mn(II) piroxicam were evaluated for their encyclopedic biological activities, DFT, and docking exploration. Different antioxidant methods were used to assess their antioxidant potential. DNA cleavage and protein binding properties of the complexes were monitored through gel electrophoresis and UV‐visible spectrophotometry. The low IC50 value of both complexes implies more potency than the piroxicam. The percent cleavage and binding constant values indicated that the complexes bind with DNA and BSA more efficiently than the piroxicam. In SD rats, complexes were screened for analgesic, anti‐anxiety, anti‐inflammatory, and anti‐hyperglycemic effects. The complexes demonstrated statistically significant results for in‐vivo analysis. Photodegradation results of the metal complexes under UV lamp exhibited abrupt degradation than the piroxicam. Docking results also validate a better propensity of both complexes to bind with DNA and BSA. Hydrogen bonding and Van der Waals forces play a key role in stabilizing complexes in DNA and BSA binding pockets. These metal complexes have evident therapeutic potential more than piroxicam and could be promising drugs for relieving pain, anxiety, inflammation, and associated comorbidities with good pharmacodynamic properties.

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Section: Resultsmentioning

confidence: 99%

Section: In Silico Docking Analysismentioning

confidence: 99%

Comprehensive Biological, Photodegradation, Density Functional Theory, and Docking Exploration of Zn(II) and Mn(II) complexes of Piroxicam

Maha,

Tajammal,

Samra

et al. 2023

ChemistrySelect

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show abstract

“…Molecular docking is the evaluation of the way that two or more molecular structures such as protein, enzyme and drugs fit together ( 34 ). The final protein structures for best docked complex showed docking score, area, ACE, and transformation of 12864, 1594.40, 137.01, 0.57, and -0.48 -0.04 84.68 -20.55 42.63.…”

Section: Resultsmentioning

confidence: 99%

Serum soluble Fas ligand is a severity and mortality prognostic marker for COVID-19 patients

et al. 2022

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Finding cytokine storm initiator factors associated with uncontrolled inflammatory immune response is necessary in COVID-19 patients. The aim was the identification of Fas/Fas Ligand (FasL) role in lung involvement and mortality of COVID-19 patients. In this case-control study, mild (outpatient), moderate (hospitalized), and severe (ICU) COVID-19 patients and healthy subjects were investigated. RNA isolated from PBMCs for cDNA synthesis and expression of mFas/mFasL mRNA was evaluated by RT-PCR. Serum sFas/sFasL protein by ELISA and severity of lung involvement by CT-scan were evaluated. Also, we docked Fas and FasL via Bioinformatics software (in silico) to predict the best-fit Fas/FasL complex and performed molecular dynamics simulation (MDS) in hyponatremia and fever (COVID-19 patients), and healthy conditions. mFasL expression was increased in moderate and severe COVID-19 patients compared to the control group. Moreover, mFas expression showed an inverse correlation with myalgia symptom in COVID-19 patients. Elevation of sFasL protein in serum was associated with reduced lung injury and mortality. Bioinformatics analysis confirmed that blood profile alterations of COVID-19 patients, such as fever and hyponatremia could affect Fas/FasL complex interactions. Our translational findings showed that decreased sFasL is associated with lung involvement; severity and mortality in COVID-19 patients. We think that sFasL is a mediator of neutrophilia and lymphopenia in COVID-19. However, additional investigation is suggested. This is the first report describing that the serum sFasL protein is a severity and mortality prognostic marker for the clinical management of COVID-19 patients.

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“…Docking is a molecular technique that determines the interaction between protein and small molecules (ligands, nanoparticles, peptides, etc.) [34]. The docking study was carried out using the MM-GBSA method of MAESTRO BioLuminate with an OPLS2005 force field and VSGB2.0 solvent model for measuring the difference in the binding energy of protein (1IYT & 2MXU) with different peptide inhibitors.…”

Section: Molecular Dockingmentioning

confidence: 99%

In silico identification of novel peptides as potential modulators of Aβ42 Amyloidogenesis

Kundal

Paramasivam

Mitra

et al. 2022

Preprint

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Alzheimer’s Disease is a neurodegenerative disease for which no cure is available at present. The presence of amyloid plaques in the extracellular space of neural cells is the key feature of this fatal disease. Amyloid-Beta (Aβ) is a 40-42 amino acid peptide and the main component of amyloid plaques. This peptide is produced by the proteolysis of Amyloid Precursor Protein by presenilin. Deposition of 42 residual Aβ peptides forms fibrils structure, leading to disruption of neuron synaptic transmission, inducing neural cell toxicity, ultimately leading to neuron death. To modulate the amyloidosis of Aβ peptides, various novel peptides have been investigated via molecular docking and molecular dynamic simulation studies. The sequence-based peptides were designed and investigated for their interaction with Aβ42 monomer and fibril using the molecular docking method, and their influence on the structural stability of target proteins was studied using molecular simulations. According to the docking results, amongst all the synthetic peptides, the peptide YRIGY (P6) has the highest binding affinity with Aβ42 fibril, and the peptide DKAPFF (P12) shows better binding with Aβ42 monomer. Moreover, simulation results also suggest that the higher the binding affinity, the better the inhibitory action. From these findings, it is suggested that both the peptides can modulate the amyloidogenesis, but peptide (P6) has better potential for the disaggregation of the fibrils, whereas peptide P12 stabilizes the native structure of the Aβ42 monomer more effectively and hence can serve as a potential amyloid inhibitor. Thus, these peptides can be explored as therapeutic agents against Alzheimer’s Disease.

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Cited by 29 publications

References 103 publications

Comprehensive Biological, Photodegradation, Density Functional Theory, and Docking Exploration of Zn(II) and Mn(II) complexes of Piroxicam

Comprehensive Biological, Photodegradation, Density Functional Theory, and Docking Exploration of Zn(II) and Mn(II) complexes of Piroxicam

Serum soluble Fas ligand is a severity and mortality prognostic marker for COVID-19 patients

In silico identification of novel peptides as potential modulators of Aβ42 Amyloidogenesis

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