scholarly journals HKSA secara In-Silico Senyawa 1-Benzil-3- Benzoilurea dan Analognya sebagai Penghambat Reseptor Bruton Tyrosine Kinase (BTK)

2021 ◽  
Vol 3 (1) ◽  
pp. 35-47
Author(s):  
Denis Cristian Sudarno ◽  
Farida Suhud ◽  
Siswandono
Keyword(s):  
Tyrosine Kinase ◽  
Physicochemical Properties ◽  
In Silico ◽  
Quantitative Structure Activity Relationship ◽  
Tyrosine Kinase Receptor ◽  
Test Compound ◽  
Molegro Virtual Docker ◽  
Non Hodgkin Lymphoma ◽  
Bruton Tyrosine Kinase ◽  
Docking Approach

Abstract—In this study, a new anticancer drug design for non-Hodgkin’s lymphoma was carried out, with a molecular docking approach from the compound 1-benzyl-3-benzoylurea parent and its analog as an anticancer compound. The purpose of the study was to obtain the best quantitative structure-activity relationship (QSAR). The in-silico activity test was carried out on the new 1-benzyl-3-benzoilurea and its analog compound against the Bruton Tyrosine Kinase receptor (BTK) PDB code (5FBN) by using the Molegro Virtual Docker 5.5 program and producing a RS (Rerank Score) value for the test compound and Acalabrutinib was used as a comparison. This study also conducted bioavailability by predicting the value of F (intestinal human absorption) in the pkCSM program and toxicity studies by predicting LD50 values using the Protox II program. Correlation and regression were performed using the RS, F, and LD50 values that we obtained on the physicochemical properties of the test compound using the IBM SPSS version 24 program. The best equation is obtained as follows: (1) F = 0.851 Es Taft - 6.116 σ - 1.969 π² + 3.620 π + 90.809;  (2) RS = 4.376 Es Taft - 88.802; (3) LD50 = 672.518 CMR - 669.385 ClogP - 813.806. From the results of the best equation is obtained that the activity is influenced by the parameters of steric physicochemical properties (Es Taft). Keywords: 1-benzyl-3-benzoylurea, code pdb:5fbn, in-silico, non-hodgkin lymphoma Abstrak—Pada penelitian ini dilakukan rancangan obat baru antikanker Limfoma non-Hodgkin, dengan pendekatan penambatan molekul dari senyawa induk 1-benzil-3-benzoilurea dan analognya sebagai senyawa antikanker.Tujuan penelitian ini untuk mendapatkan persamaan hubungan struktur aktivitas (HKSA) terbaik. Uji aktivitas in-silico dilakukan terhadap senyawa baru 1-benzil-3-benzoilurea dan analognya terhadap reseptor Bruton Tyrosine Kinase (BTK) kode PDB 5FBN dengan menggunakkan program Molegro Virtual Docker 5.5 dan menghasilkan nilai RS (Rerank Score) untuk senyawa uji dan Acalabrutinib digunakan sebagai pembanding. Penelitian ini juga dilakukan studi bioavaibilitas dengan memprediksi nilai F (intestinal human absorbtion) pada program pkCSM dan studi toksisitas dengan memprediksi nilai LD50 menggunakan program Protox II. Korelasi dan regresi dilakukan menggunakan nilai RS, F dan LD50 yang telah diperoleh terhadap parameter sifat fisikokimia senyawa uji menggunakan program IBM SPSS versi 24. Persamaan terbaik yang diperoleh sebagai berikut: (1) F = - 1.969 π² + 0.851 Es Taft - 6.116 σ + 3.620 π + 90.809 (2) RS = 4.376 Es Taft - 88.802 (3) LD50 = 672.518 CMR - 669.385 ClogP - 813.806. Dari hasil persamaan terbaik tersebut diperoleh bahwa aktivitas dipengaruhi oleh parameter sifat fisikokimia sterik (Es Taft). Kata kunci: 1-benzil-3-benzoilurea, in-silico, kode pdb: 5fbn, limfoma non-hodgkin

scholarly journals Docking studies of Physalis peruviana ethanol extract using molegro virtual docker on insulin tyrosine kinase receptor as antidiabetic agent

2014 ◽  
Vol 3 (5) ◽  
pp. 265-269 ◽  
Author(s):  
Ayik Rosita Puspaningtyas
Keyword(s):  
Tyrosine Kinase ◽  
Ethanol Extract ◽  
Pharmaceutical Journal ◽  
Docking Studies ◽  
In Vivo Studies ◽  
Tyrosine Kinase Receptor ◽  
Molegro Virtual Docker ◽  
Physalis Peruviana ◽  
Urban People

Physalis peruviana Linn in Indonesia was better known as ciplukan, based on information from urban people in Indonesia is as antidiabetic. In the previeous studies, the levels of blood glucose in animals experimental of Physalis peruviana quantified with glucometer and compared with oral antidiabetic drugs gliclazide, showed that Gliclazide was decrease more levels of glucose significantly than ethanol extract of Physalis peruviana. We have done molecular docking using Molegro Virtual Docker (MVD) on ethanol extract of Physalis peruviana and gliclazide to compare between in silico and in vivo studies. Based on studies before the main content of the ethanol extract of Physalis peruviana were withanolide, 4-OH-withanolide, and perulactone. In this study the results showed that gliclazide had been better bond in insulin tyrosine kinase receptor than main content of Physalis peruviana which can be seen from Moldock score 105.217 and Rerank score -68,2931 means that the energy was lower and more stable binding. Moldock Score of main content Physalis peruviana (withanolide, 4-OH-withanolide, and perulactone) were -93.5472; 70.5843; 88.7881, respectively. Rerank score of main content Physalis peruviana (withanolide, 4-OH-withanolide, and perulactone) were -61.5149; -67.5345; -65.7979, respectively. The hydrogen bonds of withanolide, 4-OH-withanolide, perulactone and gliclazide with amino acid of insulin tyrosine kinase receptor were Phe 1186 and Thr 1186. Finally, in the 3D MVD visualization between main content of ethanol extract of Physalis peruviana and gliclazide can be concluded that interaction of gliclazide was more harmonious than main content of ethanol extract Physalis peruviana.DOI: http://dx.doi.org/10.3329/icpj.v3i5.18534 International Current Pharmaceutical Journal, April 2014, 3(5): 265-269

scholarly journals Study in Silico Compounds In 96% Ethanol Extract of Chrysanthemum cinerariifolium (Trev.) Leaves Towards Alfa Estrogen Receptors

2020 ◽  
Vol 11 (3) ◽  
pp. 144
Author(s):  
Roihatul Mutiah ◽  
Yen Yen Indrawijaya ◽  
Dwi Puspita
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptors ◽  
Metabolic Profiling ◽  
In Silico ◽  
Lethal Dose ◽  
Ethanol Extract ◽  
Good Activity ◽  
In Silico Prediction ◽  
Test Compound ◽  
Molegro Virtual Docker

Chrysanthemum cinerariifolium (Trev.) is a plant that has potential as an anticancer. This study aimed to predict the inhibitor of estrogen alpha and toxicity of compounds in 96% ethanol extract of C. cinerariifolium leaves in silico. Prediction of the activity of metabolic profiling compounds produced by UPLC QToF MS/MS ethanol extract 96% of C. cinerariifolium leaves towards alpha estrogen receptors (ER-α) (5W9C) was carried out using Molegro Virtual Docker. The docking results showed that the compound (2-Methyl-1,4-piperazinediyl) bis-[(3,4,5-trimethoxyphenyl)-methanone and Azoxystrobin have good activity compared to Tamoxifen, because these compounds have a lower Rerank Score. The activity of the test compound is also shown by the bonding of active amino acids (Arg 394, Asp351, Glu 353, and Val 533). As for the toxicity class based on Globally Harmonized System (GHS) and Lethal Dose 50 (LD50) values, the ten docking compounds had a relatively low toxicity.Keywords: C. cinerariifolium, breast cancer, alpha estrogen, cytotoxic activity, toxicity

scholarly journals Targeting phosphatidylinositol 3 kinase-β and -δ for Bruton tyrosine kinase resistance in diffuse large B-cell lymphoma

2020 ◽  
Vol 4 (18) ◽  
pp. 4382-4392
Author(s):  
Neeraj Jain ◽  
Satishkumar Singh ◽  
Georgios Laliotis ◽  
Amber Hart ◽  
Elizabeth Muhowski ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Phosphatidylinositol 3 Kinase ◽  
Non Hodgkin Lymphoma ◽  
Large B Cell Lymphoma ◽  
Bruton Tyrosine Kinase ◽  
Large B Cell ◽  
Resistant Cells

Abstract Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma; 40% of patients relapse after a complete response or are refractory to therapy. To survive, the activated B-cell (ABC) subtype of DLBCL relies upon B-cell receptor signaling, which can be modulated by the activity of Bruton tyrosine kinase (BTK). Targeting BTK with ibrutinib, an inhibitor, provides a therapeutic approach for this subtype of DLBCL. However, non-Hodgkin lymphoma is often resistant to ibrutinib or acquires resistance soon after exposure. We explored how this resistance develops. We generated 3 isogenic ibrutinib-resistant DLBCL cell lines and investigated the deregulated pathways known to be associated with tumorigenic properties. Reduced levels of BTK and enhanced phosphatidylinositol 3-kinase (PI3K)/AKT signaling were hallmarks of these ibrutinib-resistant cells. Upregulation of PI3K-β expression was demonstrated to drive resistance in ibrutinib-resistant cells, and resistance was reversed by the blocking activity of PI3K-β/δ. Treatment with the selective PI3K-β/δ dual inhibitor KA2237 reduced both tumorigenic properties and survival-based PI3K/AKT/mTOR signaling of these ibrutinib-resistant cells. In addition, combining KA2237 with currently available chemotherapeutic agents synergistically inhibited metabolic growth. This study elucidates the compensatory upregulated PI3K/AKT axis that emerges in ibrutinib-resistant cells.

scholarly journals Review of Bruton tyrosine kinase inhibitors for the treatment of relapsed or refractory mantle cell lymphoma

2019 ◽  
Vol 26 (2) ◽  
Author(s):  
C. Owen ◽  
N. L. Berinstein ◽  
A. Christofides ◽  
L. H. Sehn
Keyword(s):  
Tyrosine Kinase ◽  
Mantle Cell Lymphoma ◽  
First Generation ◽  
Kinase Inhibitors ◽  
Cell Lymphoma ◽  
Comparable Efficacy ◽  
Non Hodgkin Lymphoma ◽  
Mantle Cell ◽  
Bruton Tyrosine Kinase ◽  
Btk Inhibitors

Mantle cell lymphoma (mcl) is a rare subtype of aggressive B-cell non-Hodgkin lymphoma that remains incurable with standard therapy. Patients typically require multiple lines of therapy, and those with relapsed or refractory (r/r) disease have a very poor prognosis. The Bruton tyrosine kinase (btk) inhibitor ibrutinib has proven to be an effective agent for patients with r/r mcl. Although usually well tolerated, ibrutinib can be associated with unique toxicities, requiring discontinuation in some patients. Effective and well-tolerated alternatives to ibrutinib for patients with r/r mcl are therefore needed. Novel btk inhibitors such as acalabrutinib, zanubrutinib, and tirabrutinib are designed to improve on the safety and efficacy of first-generation btk inhibitors such as ibrutinib. Data from single-arm clinical trials suggest that, compared with ibrutinib, second-generation btk inhibitors have comparable efficacy and might have a more favourable toxicity profile. Those newer btk inhibitors might therefore provide a viable treatment option for patients with r/r mcl.

scholarly journals In Silico Screening of Potential Inhibitors of the Epidermal Growth Factor Receptor Kinase using Benzimidazole, Benzoxazole, Imidazole, and Tetrazole Derivatives

2021 ◽  
pp. 60-71
Author(s):  
Subramaniyan Arulmurugan ◽  
Helen P. Kavitha ◽  
Jasmine P. Vennila
Keyword(s):  
Molecular Docking ◽  
Tyrosine Kinase ◽  
In Silico ◽  
Heterocyclic Compounds ◽  
Docking Studies ◽  
Tyrosine Kinase Receptor ◽  
Binding Interaction ◽  
Docking Score ◽  
Molecular Docking Studies ◽  
Egfr Tyrosine Kinase

Background: Small molecule compounds are docked into receptor binding sites and the binding affinity of the complex is calculated using the structure-based drug design technique. Precise and quick docking processes, as well as the capacity to examine binding geometries and interactions, are required for a full knowledge of the structural principles that influence the strength of a protein/ligand complex. The present work deals with in-silico molecular docking studies of some heterocyclic compounds such as benzoxazole, benzimidazole, imidazole and tetrazole against the EGFR tyrosine kinase receptor. Methodology: Molecular docking studies of some heterocyclic compounds such as benzoxazole, benzimidazole, imidazole and tetrazole against the EGFR tyrosine kinase receptor using Schrodinger LLC (Maestro 9.2) software. Results: Our in silico observations reveal that, all the selected heterocyclic compounds (1-8) show good binding interaction and good docking score against selected target enzyme. Out of eight compounds selected for the study two compounds compound 3 and 7 shows higher glide score. Compound 3 binded to ASP855 with a docking score of −11.20 kcal/mol. Compound 7 binded to ASP855 with a docking score of −11.56kcal/mol. Conclusion: Docking results revealed that compounds (1-8) interact with EGFR kinase receptor active site. Among the compounds, compound 7 has shown the highest glide score of -11.56 kcal/mol.

In silico Discovery of Resveratrol Analogues as Potential Agents in Treatment of Metabolic Disorders

2019 ◽  
Vol 25 (35) ◽  
pp. 3776-3783
Author(s):  
Nebojša Pavlović ◽  
Maja Đanić ◽  
Bojan Stanimirov ◽  
Svetlana Goločorbin-Kon ◽  
Karmen Stankov ◽  
...  
Keyword(s):  
In Silico ◽  
Metabolic Disorders ◽  
Partial Agonist ◽  
Aqueous Solubility ◽  
Structural Similarity ◽  
Data Bank ◽  
Docking Studies ◽  
Binding Energies ◽  
Molegro Virtual Docker ◽  
Ppar Γ

Background: Resveratrol was demonstrated to act as partial agonist of PPAR-γ receptor, which opens up the possibility for its use in the treatment of metabolic disorders. Considering the poor bioavailability of resveratrol, particularly due to its low aqueous solubility, we aimed to identify analogues of resveratrol with improved pharmacokinetic properties and higher binding affinities towards PPAR-γ. Methods: 3D structures of resveratrol and its analogues were retrieved from ZINC database, while PPAR-γ structure was obtained from Protein Data Bank. Docking studies were performed using Molegro Virtual Docker software. Molecular descriptors relevant to pharmacokinetics were calculated from ligand structures using VolSurf+ software. Results: Using structural similarity search method, 56 analogues of resveratrol were identified and subjected to docking analyses. Binding energies were ranged from -136.69 to -90.89 kcal/mol, with 16 analogues having higher affinities towards PPAR-γ in comparison to resveratrol. From the calculated values of SOLY descriptor, 23 studied compounds were shown to be more soluble in water than resveratrol. However, only two tetrahydroxy stilbene derivatives, piceatannol and oxyresveratrol, had both better solubility and affinity towards PPAR-γ. These compounds also had more favorable ADME profile, since they were shown to be more metabolically stable and wider distributed in body than resveratrol. Conclusion: Piceatannol and oxyresveratrol should be considered as potential lead compounds for further drug development. Although experimental validation of obtained in silico results is required, this work can be considered as a step toward the discovery of new natural and safe drugs in treatment of metabolic disorders.

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