scholarly journals Studi Interaksi Senyawa Turunan Saponin dari Daun Bidara Arab (Ziziphus spina-christi L.) sebagai Antiseptik Alami secara In Silico

2020 ◽  
Vol 7 (3) ◽  
pp. 229
Author(s):  
Fitrianti Darusman ◽  
Taufik Muhammad Fakih
Keyword(s):  
Candida Albicans ◽  
Staphylococcus Epidermidis ◽  
In Silico ◽  
Discovery Studio ◽  
Autodock 4.2

Christinin merupakan senyawa turunan glikosida saponin yang paling banyak terdapat dalam daun bidara arab (Ziziphus spina-christi L.). Terdapat empat tipe christinin yaitu christinin-A, B, C, dan D yang diduga memiliki aktivitas sebagai antimikroba yang efektif terhadap bakteri dan jamur, seperti Staphylococcus epidermidis, Echerichia coli, dan Candida albicans yang sering menyebabkan infeksi pada permukaan kulit yang biasanya dapat diatasi dengan penggunaan cairan antiseptik. Penelitian ini bertujuan untuk mengidentifikasi, mengevaluasi serta mengeksplorasi afinitas dan interaksi molekular antara senyawa christinin-A, B, C, dan D terhadap makromolekul target pada Staphylococcus epidermidis, Echerichia coli dan Candida albicans dengan menggunakan simulasi penambatan molekular secara in silico. Molekul senyawa uji terlebih dahulu dioptimasi geometri dengan menggunakan perangkat lunak GaussView 5.0.8 dan Gaussian09. Konformasi terbaik dipilih untuk dilakukan studi interaksi terhadap makromolekul target dengan menggunakan perangkat lunak MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Interaksi yang terbentuk selanjutnya diamati dengan menggunakan perangkat lunak BIOVIA Discovery Studio 2020.  Berdasarkan hasil dari simulasi penambatan molekular, senyawa christinin memiliki afinitas yang baik terhadap makromolekul target pada Staphylococcus epidermidis, Echerichia coli dan Candida albicans. Dengan demikian, senyawa tersebut diprediksi dapat digunakan sebagai kandidat komponen utama dari antiseptik alami.

Studi Interaksi Senyawa Turunan Saponin dari Daun Bidara Arab (Ziziphus spina-christi L.) sebagai Antiseptik Alami secara In Silico

2020 ◽  
Vol 7 (3) ◽  
pp. 233
Author(s):  
Fitrianti Darusman ◽  
Taufik Muhammad Fakih
Keyword(s):  
Candida Albicans ◽  
Staphylococcus Epidermidis ◽  
In Silico ◽  
Discovery Studio ◽  
Autodock 4.2

Christinin merupakan senyawa turunan glikosida saponin yang paling banyak terdapat dalam daun bidara arab (Ziziphus spina-christi L.). Terdapat empat tipe christinin yaitu christinin-A, B, C, dan D yang diduga memiliki aktivitas sebagai antimikroba yang efektif terhadap bakteri dan jamur, seperti Staphylococcus epidermidis, Echerichia coli, dan Candida albicans yang sering menyebabkan infeksi pada permukaan kulit yang biasanya dapat diatasi dengan penggunaan cairan antiseptik. Penelitian ini bertujuan untuk mengidentifikasi, mengevaluasi serta mengeksplorasi afinitas dan interaksi molekular antara senyawa christinin-A, B, C, dan D terhadap makromolekul target pada Staphylococcus epidermidis, Echerichia coli dan Candida albicans dengan menggunakan simulasi penambatan molekular secara in silico. Molekul senyawa uji terlebih dahulu dioptimasi geometri dengan menggunakan perangkat lunak GaussView 5.0.8 dan Gaussian09. Konformasi terbaik dipilih untuk dilakukan studi interaksi terhadap makromolekul target dengan menggunakan perangkat lunak MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Interaksi yang terbentuk selanjutnya diamati dengan menggunakan perangkat lunak BIOVIA Discovery Studio 2020.  Berdasarkan hasil dari simulasi penambatan molekular, senyawa christinin memiliki afinitas yang baik terhadap makromolekul target pada Staphylococcus epidermidis, Echerichia coli dan Candida albicans. Dengan demikian, senyawa tersebut diprediksi dapat digunakan sebagai kandidat komponen utama dari antiseptik alami.

Role of 4-O Galloylchlorogenic Acid in Lung Cancer- An Insilico Approach

2017 ◽  
Vol 9 (5) ◽  
Author(s):  
Jaynthy C. ◽  
N. Premjanu ◽  
Abhinav Srivastava
Keyword(s):  
Lung Cancer ◽  
Cell Proliferation ◽  
In Silico ◽  
Computational Study ◽  
Regulation Mechanism ◽  
Down Regulation ◽  
Fruit Extract ◽  
In Vitro Techniques ◽  
Discovery Studio

Cancer is a major disease with millions of patients diagnosed each year with high mortality around the world. Various studies are still going on to study the further mechanisms and pathways of the cancer cell proliferation. Fucosylation is one of the most important oligosaccharide modifications involved in cancer and inflammation. In cancer development increased core fucosylation by FUT8 play an important role in cell proliferation. Down regulation of FUT8 expression may help cure lung cancer. Therefore the computational study based on the down regulation mechanism of FUT8 was mechanised. Sapota fruit extract, containing 4-Ogalloylchlorogenic acid was used as the inhibitor against FUT-8 as target and docking was performed using in-silico tool, Accelrys Discovery Studio. There were several conformations of the docked result, and conformation 1 showed 80% dock score between the ligand and the target. Further the amino acids of the inhibitor involved in docking were studied using another tool, Ligplot. Thus, in-silico analysis based on drug designing parameters shows that the fruit extract can be studied further using in-vitro techniques to know its pharmacokinetics.

Novel Thiazole-Based Thiazolidinones as Potent Anti-infective Agents: In silico PASS and Toxicity Prediction, Synthesis, Biological Evaluation and Molecular Modelling

2020 ◽  
Vol 23 (2) ◽  
pp. 126-140 ◽  
Author(s):  
Christophe Tratrat
Keyword(s):  
In Silico ◽  
Antimicrobial Agents ◽  
Target Identification ◽  
Biological Evaluation ◽  
Microbial Infection ◽  
Toxicity Prediction ◽  
Discovery Studio ◽  
Bacteria And Fungi ◽  
Multiple Drugs ◽  
Antibacterial And Antifungal

Aims and Objective: The infectious disease treatment remains a challenging concern owing to the increasing number of pathogenic microorganisms associated with resistance to multiple drugs. A promising approach for combating microbial infection is to combine two or more known bioactive heterocyclic pharmacophores in one molecular platform. Herein, the synthesis and biological evaluation of novel thiazole-thiazolidinone hybrids as potential antimicrobial agents were dissimilated. Materials and Methods: The preparation of the substituted 5-benzylidene-2-thiazolyimino-4- thiazolidinones was achieved in three steps from 2-amino-5-methylthiazoline. All the compounds have been screened in PASS antibacterial activity prediction and in a panel of bacteria and fungi strains. Minimum inhibitory concentration and minimum bacterial concentration were both determined by microdilution assays. Molecular modeling was conducted using Accelrys Discovery Studio 4.0 client. ToxPredict (OPEN TOX) and ProTox were used to estimate the toxicity of the title compounds. Results: PASS prediction revealed the potentiality antibacterial property of the designed thiazolethiazolidinone hybrids. All tested compounds were found to kill and to inhibit the growth of a vast variety of bacteria and fungi, and were more potent than the commercial drugs, streptomycin, ampicillin, bifomazole and ketoconazole. Further, in silico study was carried out for prospective molecular target identification and revealed favorable interaction with the target enzymes E. coli MurB and CYP51B of Aspergillus fumigatus. Toxicity prediction revealed that none of the active compounds was found toxic. Conclusion: Substituted 5-benzylidene-2-thiazolyimino-4-thiazolidinones, endowing remarkable antibacterial and antifungal properties, were identified as a novel class of antimicrobial agents and may find a potential therapeutic use to eradicate infectious diseases.

scholarly journals Studi Interaksi Molekuler Aktivitas Antimikroba Peptida Bioaktif terhadap Staphylococcus aureus Secara In silico

2020 ◽  
Vol 7 (2) ◽  
pp. 93
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Staphylococcus Aureus ◽  
In Silico ◽  
Binding Protein ◽  
Pelteobagrus Fulvidraco ◽  
Penicillin Binding Protein ◽  
Discovery Studio

Pendahuluan: Lendir kulit ikan lele kuning (Pelteobagrus fulvidraco), mengandung peptida bioaktif dan banyak dimanfaatkan dalam pengobatan berbagai penyakit karena memiliki aktivitas biologis, diantaranya sebagai antimikroba. Beberapa peptida bioaktif tersebut, antara lain pelteobagrin, myxinidin, pleurocidin, dan pardaxin-P1 dan telah terbukti mampu menghambat Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus. Tujuan: Penelitian ini bertujuan untuk mengidentifikasi aktivitas antimikroba molekul peptida bioaktif secara in silico terhadap makromolekul Penicillin-Binding Protein 3 (PBP3) dari Staphylococcus aureus dan interaksi peptida bioaktif tersebut yang terlibat dalam mekanisme aksi antimikroba. Metode: Sekuensing peptida bioaktif terlebih dahulu dilakukan pemodelan ke dalam bentuk konformasi 3D menggunakan software PEP-FOLD. Konformasi terbaik hasil pemodelan dipilih untuk kemudian dilakukan studi penambatan molekuler terhadap makromolekul dari Staphylococcus aureus menggunakan software PatchDock. Interaksi molekuler yang terbentuk selanjutnya diidentifikasi lebih lanjut menggunakan software BIOVIA Discovery Studio 2020. Hasil: Berdasarkan hasil penambatan molekuler menunjukkan bahwa peptida bioaktif myxinidin memiliki afinitas paling baik dengan ACE score −2497,26 kJ/mol. Kesimpulan: Peptida bioaktif lendir kulit ikan lele kuning (Pelteobagrus fulvidraco) dapat dipertimbangkan sebagai kandidat antimikroba alami.

scholarly journals Kaempferol-Mediated Sensitization Enhances Chemotherapeutic Efficacy of Sorafenib Against Hepatocellular Carcinoma: An In Silico and In Vitro Approach

2020 ◽  
Vol 10 (3) ◽  
pp. 472-476
Author(s):  
Bhagyalakshmi Nair ◽  
Ruby John Anto ◽  
Sabitha M ◽  
Lekshmi R. Nath
Keyword(s):  
Hepatocellular Carcinoma ◽  
Multidrug Resistance ◽  
Liver Cancer ◽  
In Silico ◽  
Culture Media ◽  
Positive Control ◽  
Advanced Hepatocellular Carcinoma ◽  
Discovery Studio ◽  
Toxic Concentrations

Purpose : Sorafenib is the sole FDA approved drug conventionally used for the treatment of advanced hepatocellular carcinoma (HCC). Despite of the beneficial use of sorafenib in the treatment of HCC, multidrug resistance still remains a challenge. HCC is inherently known as chemotherapy resistant tumor due to P-glycoprotein (P-gp)-mediated multidrug resistance. Methods: We studied the interaction energy of kaempferol with human multidrug resistance protein-1 (RCSB PDB ID: 2CBZ) using in silico method with the help of BIOVIA Discovery Studio. HepG2 and N1S1 liver cancer cell lines were treated in suitable cell culture media to evaluate the efficacy of kaempferol in chemo-sensitizing liver cancer cells towards the effect of sorafenib. Cell viability study was performed by MTT assay. Results: In silico analysis of kaempferol showed best docking score of 23.14 with Human Multi Drug Resistant Protein-1 (RCSB PDB ID: 2CBZ) compared with positive control verapamil. In in-vitro condition, combination of sub-toxic concentrations of both kaempferol and sorafenib produced 50% cytotoxicity with concentration of 2.5 µM each which indicates that kaempferol has the ability to reverse the MDR by decreasing the over-expression of P-gp. Conclusion: Kaempferol is able to sensitize the HepG2 and N1S1 against the sub-toxic concentration of sorafenib. Hence, we consider that the efficacy of sorafenib chemotherapy can be enhanced by the significant approach of combining the sub-toxic concentrations of sorafenib with kaempferol. Thus, kaempferol can be used as a better candidate molecule along with sorafenib for enhancing its efficacy, if validated through preclinical studies.

In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

2021 ◽  
Vol 24 ◽  
Author(s):  
Ashis Kumar Goswami ◽  
Hemanta Kumar Sharma ◽  
Neelutpal Gogoi ◽  
Ankita Kashyap ◽  
Bhaskar Jyoti Gogoi
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Discovery Studio ◽  
North East ◽  
Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

scholarly journals Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels

2020 ◽  
Author(s):  
Mohammad H. Mirhakkak ◽  
Sascha Schäuble ◽  
Tilman E. Klassert ◽  
Sascha Brunke ◽  
Philipp Brandt ◽  
...  
Keyword(s):  
Candida Albicans ◽  
In Silico ◽  
Human Subjects ◽  
Bacterial Species ◽  
Fungal Growth ◽  
Metagenomic Sequencing ◽  
Growth Data ◽  
Predictive Capacity ◽  
Fungal Abundance ◽  
A Genome

AbstractCandida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance. We optimized the predictive capacity of our model using wild type and mutant C. albicans growth data and used it for in silico metabolic interaction predictions. Our analysis of more than 900 paired fungal–bacterial metabolic models predicted key gut bacterial species modulating C. albicans colonization levels. Among the studied microbes, Alistipes putredinis was predicted to negatively affect C. albicans levels. We confirmed these findings by metagenomic sequencing of stool samples from 24 human subjects and by fungal growth experiments in bacterial spent media. Furthermore, our pairwise simulations guided us to specific metabolites with promoting or inhibitory effect to the fungus when exposed in defined media under carbon and nitrogen limitation. Our study demonstrates that in silico metabolic prediction can lead to the identification of gut microbiome features that can significantly affect potentially harmful levels of C. albicans.

Chlorinated plastoquinone analogs that inhibit Staphylococcus epidermidis and Candida albicans growth

2020 ◽  
Vol 65 (5) ◽  
pp. 785-795
Author(s):  
Emel Mataracı Kara ◽  
Nilüfer Bayrak ◽  
Hatice Yıldırım ◽  
Mahmut Yıldız ◽  
Berna Ozbek Celik ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Staphylococcus Epidermidis
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