Mathematical analysis based on eigenvalue approach to study liver metastasis disease with applied drug therapy

Mubarak, Saqib; Khanday, M. A.; Lone, Ahsan Ul Haq

doi:10.1007/s13721-020-00231-0

Cited by 8 publications

(8 citation statements)

References 7 publications

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“…Chemdraw compound preparation, Chem 3d structures, Chem 3D ultra 12.0 (Molecular Modeling and Analysis; Cambridge Soft Corporation) software, and MOPAC were enhanced and deposited in MDL MolFile (*.mol). All calculations were performed on a (1.80-1.99) GHz-based MS Windows 10 pro 64-bit operating system Intel (R) Core (TM) i7-8550 CPU [ 19 – 22 ]. A Protein Data Bank ( http://www.rcsb.org/ ) has been retrieved from protein structure generation and the crystal structures of the CXCR4 and CXCR7 receptors (PDB codes = 3ODU and 6K3F).…”

Section: Methodsmentioning

confidence: 99%

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Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

Murad

Alqurashi

Hussien

2022

BMC Complement Med Ther

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Background The chemokine CXCL12 and its two receptors (CXCR4 and CXCR7) are involved in inflammation and hematopoietic cell trafficking. This study was designed to investigate molecular docking interactions of four popular cardiovascular-active natural compounds; curcumin, resveratrol, quercetin, and eucalyptol; with these receptors and to predict their drug-like properties. We hypothesize that these compounds can modify CXCL12/CXCR4/CXCR7 pathway offering benefits for coronary artery disease patients. Methods Docking analyses were carried and characterized by Molecular Environment (MOE) software. Protein Data Bank (http://www.rcsb.org/) has been retrieved from protein structure generation and crystal structures of CXCR4 and CXCR7 receptors (PDB code = 3ODU and 6K3F). The active sites of these receptors were evaluated and extracted from full protein and molecular docking protocol was done for compounds against them. The presented parameters included docking scores, ligand binding efficiency, and hydrogen bonding. The pharmacokinetic/toxic properties (ADME/T) were calculated using SwissADME, ProTox-II, and Pred-hERG softwares to predict drug-like properties of the compounds. The thermochemical and molecular orbital analysis, and molecular dynamics simulations were also done. Results All compounds showed efficient interactions with the CXCR4 and CXCR7 receptors. The docking scores toward proteins 3ODU of CXCR4 and 6K3F of CXCR7 were − 7.71 and − 7.17 for curcumin, − 5.97 and − 6.03 for quercetin, − 5.68 and − 5.49 for trans-resveratrol, and − 4.88 and − 4.70 for (1 s,4 s)-eucalyptol respectively indicating that all compounds, except quercetin, have more interactions with CXCR4 than with CXCR7. The structurally and functionally important residues in the interactive sites of docked CXCR4-complex and CXCR7-complex were identified. The ADME analysis showed that the compounds have drug-like properties. Only (1 s,4 s)-Eucalyptol has potential weak cardiotoxicity. The results of thermochemical and molecular orbital analysis and molecular dynamics simulation validated outcomes of molecular docking study. Conclusions Curcumin showed the top binding interaction against active sites of CXCR4 and CXCR7 receptors, with the best safety profile, followed by quercetin, resveratrol, and eucalyptol. All compounds demonstrated drug-like properties. Eucalyptol has promising potential because it can be used by inhalation or skin massage. To our knowledge, this is the first attempt to find binding interactions of these natural agents with CXCR4 and CXCR7 receptors and to predict their druggability.

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Section: Methodsmentioning

confidence: 99%

“…The active sites were evaluated and extracted from the full protein. The energy minimization was done using MMFF94x force field [ 19 ]. London dG scoring was used as a function in the calculated docking score to rank the binding affinity of the synthesized compounds to the protein molecule [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

Murad

Alqurashi

Hussien

2022

BMC Complement Med Ther

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“…Drug preparation was compiled through ChemDraw, 3D structures were constructed using Chem 3D ultra 12.0 software (Molecular Modeling and Analysis; Cambridge Soft Corporation), then they were energetically minimized using MOPAC and saved as MDL MolFile (*.mol). All calculations were carried out on an Intel(R) Core(TM)i7, 3.8 GHz-based machine running MS Windows 10 as the operating system(Mubarak et al 2020 ; Naik 2020 ; Naik and Pardasani 2017 , 2018 ; Naik and Zu 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…Viruses use their proteases to break down their viral peptides into functional units essential for replication and packaging inside the host cells, and thus considered antiviral drug targets. Molecular docking is a popular bioinformatic modeling tool broadly used in structure-based drug design (Kitchen et al 2004 ; Mubarak et al 2020 ; Naik 2020 ; Naik and Pardasani 2017 , 2018 ; Naik and Zu 2020 ). It is an efficient way to predict the type of interaction, binding affinity and the appropriate target-binding sites between the drug and corresponding receptor using, for instance, scoring functions (Kitchen et al 2004 ; Lengauer and Rarey 1996 ).…”

Section: Introductionmentioning

confidence: 99%

Molecular docking suggests repurposing of brincidofovir as a potential drug targeting SARS-CoV-2 ACE2 receptor and main protease

Hussien

Abdelaziz

2020

Netw Model Anal Health Inform Bioinforma

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The current outbreak of the highly transmittable and life-threatening severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly and posed a global health emergency. Many clinical trials are now being conducted to test possible therapies. To assist this, virtual screening via molecular docking was performed on several FDA-approved drugs, previously used in epidemics, and the top ten compounds were selected. These ten well-characterized drugs, previously used to treat malaria and Ebola infections, were screened based on their interactions with the SARS-CoV-2 ACE2 receptor and 3C-like protease. Compared to the other nine medicines, brincidofovir, an ether lipid ester analog of cidofovir with potent antiviral activity, showed the highest docking scores and binding interactions. Therefore, brincidofovir is worth further investigations and clinical trials as a possible therapeutic agent for the COVID-19 disease caused by the novel SARS-CoV-2.

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“…The use of image processing techniques has spread across various applications, such as pattern recognition (Veerashetty et al , 2020; Virupakshappa et al , 2019), biomedical applications (Prasath et al , 2019; Virupakshappa et al , 2018), steganography (Ambika et al , 2019; Veerashetty et al , 2021), computer vision and so on (Ambika et al , 2020). On the basis of World Health Organization data, liver disease remains the ninth leading cause of death globally among women and fifth leading cause of death among men (Liu et al , 2017; Tierney et al , 2019; Abdelaziz et al , 2020; Mubarak et al , 2020). In order to diagnose liver disease, several imaging modalities are available such as Computerized Tomography (CT), Ultrasound, Magnetic Resonance Imagining (MRI), Histopathology, Positron Emission Tomography (PET), Angiography and so on (Ferraioli et al , 2018; Lin et al , 2018).…”

Section: Introductionmentioning

confidence: 99%

Ultrasound liver tumor segmentation using adaptively regularized kernel-based fuzzy C means with enhanced level set algorithm

Uplaonkar¹,

Virupakshappa²,

Patil³

2021

IJICC

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PurposeThe purpose of this study is to develop a hybrid algorithm for segmenting tumor from ultrasound images of the liver.Design/methodology/approachAfter collecting the ultrasound images, contrast-limited adaptive histogram equalization approach (CLAHE) is applied as preprocessing, in order to enhance the visual quality of the images that helps in better segmentation. Then, adaptively regularized kernel-based fuzzy C means (ARKFCM) is used to segment tumor from the enhanced image along with local ternary pattern combined with selective level set approaches.FindingsThe proposed segmentation algorithm precisely segments the tumor portions from the enhanced images with lower computation cost. The proposed segmentation algorithm is compared with the existing algorithms and ground truth values in terms of Jaccard coefficient, dice coefficient, precision, Matthews correlation coefficient, f-score and accuracy. The experimental analysis shows that the proposed algorithm achieved 99.18% of accuracy and 92.17% of f-score value, which is better than the existing algorithms.Practical implicationsFrom the experimental analysis, the proposed ARKFCM with enhanced level set algorithm obtained better performance in ultrasound liver tumor segmentation related to graph-based algorithm. However, the proposed algorithm showed 3.11% improvement in dice coefficient compared to graph-based algorithm.Originality/valueThe image preprocessing is carried out using CLAHE algorithm. The preprocessed image is segmented by employing selective level set model and Local Ternary Pattern in ARKFCM algorithm. In this research, the proposed algorithm has advantages such as independence of clustering parameters, robustness in preserving the image details and optimal in finding the threshold value that effectively reduces the computational cost.

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Mathematical analysis based on eigenvalue approach to study liver metastasis disease with applied drug therapy

Cited by 8 publications

References 7 publications

Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

Molecular docking suggests repurposing of brincidofovir as a potential drug targeting SARS-CoV-2 ACE2 receptor and main protease

Ultrasound liver tumor segmentation using adaptively regularized kernel-based fuzzy C means with enhanced level set algorithm

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