scholarly journals DOCKING MOLEKULER SENYAWA AKTIF BUAH DAN DAUN JAMBU BIJI (Psidium guajava L.) TERHADAP PROTEIN SARS-CoV-2

FORTE JOURNAL ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 77-84
Author(s):  
Rosario Manalu
Keyword(s):  
In Silico ◽  
Psidium Guajava ◽  
Antivirus Software ◽  
Native Ligand

Pada akhir 2019, terjadi wabah pneumonia baru berasal dari Wuhan, Provinsi Hubei yang disebabkan oleh virus SARS-CoV-2. Sehingga perlu dilakukan penghambatan protein virus tersebut sebagai salah satu penemuan kandidat obat baru. Tujuan penelitian untuk mencari bahwa senyawa metabolit sekunder yang terdapat dalam pada buah dan daun jambu biji (Psidium guajava L) mempunyai aktivitas sebagai antivirus dengan cara menghambat protein SARS-CoV-2. Metode penambatan molekul (docking molecular) untuk prediksi struktur kompleks senyawa-protein yang dinamakan docking ligan-protein. Penelitian dilakukan dengan cara analisis secara In Silico senyawa metabolit sekunder tanaman jambu biji dan memodelkan interaksi senyawa pada protein SARS-CoV-2 yang berperan sebagai antivirus. Software yang digunakan adalah PLANTS, YASARA, ChemSketch, dan Ligplus. Penelitian diawali dengan validasi internal pada salah satu reseptor SARS-CoV-2 dengan kode protein PDB.ID 6LU7. Proses docking dilakukan terhadap native ligand, senyawa kimia pada tanaman jambu biji, dan senyawa pembanding sebagai kontrol positif. Hasil penelitian menunjukkan bahwa score docking dari tiga senyawa metabolit sekunder terbaik masih lebih tinggi dibandingkan dengan ligan native-nya. Score docking kaemferol, kuersetin dan hyperin adalah -90.399, -92.012 dan -92.231 kkal/mol. Ikatan kompleks dengan ligan native masih lebih stabil (kuat) dibandingkan dengan kompleks antara protein dan senyawa aktif dari Jambu Biji.

scholarly journals Molecular Docking Senyawa Asam Askorbat dan Kuersetin pada Tumbuhan Jambu Biji Merah (Psidium guajava L.) Sebagai Pencegah COVID-19

2021 ◽  
Vol 9 (2) ◽  
Author(s):  
Inggrid V. Gandu ◽  
Fona D. H. Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
Aaltje Manampiring ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Ascorbic Acid ◽  
Molecular Docking ◽  
Immune System ◽  
Binding Affinity ◽  
In Silico ◽  
Preventive Measure ◽  
Psidium Guajava ◽  
Positive Control ◽  
Important Thing

Abstract: Coronavirus Disease 2019 or COVID-19 is an infectious disease first identified in Wuhan, China in December 2019. Prevention of COVID-19 infection is an important thing to do in reducing the spread of this virus. Boosting the body's immune system can be done as a preventive measure, one of which is by consuming natural plants such as red guava. This study aims to determine the molecular docking of red guava (Psidium guajava L.) as a plant to prevent COVID-19. This was an in silico with computerized methods. The samples in this study were ascorbic acid and quercetin compounds in red guava plants obtained from the PubChem website. The results showed that the binding affinity of ascorbic acid is -5.4 and the binding affinity of quercetin is -7.6. Remdesivir which was used as a positive control had a binding affinity of -7.3. In conclusion, quercetin compounds have better results than ascorbic acid compounds and remdesivir.Keywords: COVID-19, red guava, molecular docking  Abstrak: Coronavirus Disease 2019 atau COVID-19 merupakan suatu penyakit menular yang pertama kali ditemukan di Wuhan, Tiongkok pada Desember 2019. Pencegahan infeksi COVID-19 merupakan hal yang penting untuk dilakukan dalam mengurangi penyebaran dari virus ini. Meningkatkan sistem imun tubuh dapat dilakukan sebagai tindakan pencegahan salah satunya dengan mengonsumsi tumbuhan-tumbuhan alami seperti jambu biji merah. Penelitian ini bertujuan untuk mengetahui molecular docking jambu biji merah (Psidium guajava L.) sebagai tanaman pencegah COVID-19. Jenis penelitian ialah in silico dengan metode komputerisasi. Sampel penelitian yaitu senyawa asam askorbat dan kuersetin pada tumbuhan jambu biji merah yang diperoleh dari website pubchem. Hasil penelitian mendapatkan binding affinity dari senyawa asam askorbat yaitu -5.4 dan binding affinity dari senyawa kuersetin yaitu -7.6. Remdesivir yang dijadikan sebagai kontrol positif mendapatkan hasil binding affinity yaitu -7.3. Simpulan penelitian ini ialah senyawa kuersetin memiliki hasil yang lebih baik daripada senyawa asam askorbat dan juga obat remdesivir.Kata kunci: COVID-19, jambu biji merah, molecular docking

scholarly journals In vitro and in silico anti-dengue activity of compounds obtained from Psidium guajava through bioprospecting

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Andrea Isabel Trujillo-Correa ◽  
Diana Carolina Quintero-Gil ◽  
Fredyc Diaz-Castillo ◽  
Winston Quiñones ◽  
Sara M. Robledo ◽  
...  
Keyword(s):  
Gallic Acid ◽  
Treatment Strategy ◽  
In Silico ◽  
Antiviral Effect ◽  
Psidium Guajava ◽  
Caribbean Coast ◽  
Ethanolic Extracts ◽  
Pharmacological Potential ◽  
Experimental Strategies

Abstract Background For decades, bioprospecting has proven to be useful for the identification of compounds with pharmacological potential. Considering the great diversity of Colombian plants and the serious worldwide public health problem of dengue—a disease caused by the dengue virus (DENV)—in the present study, we evaluated the anti-DENV effects of 12 ethanolic extracts derived from plants collected in the Colombian Caribbean coast, and 5 fractions and 5 compounds derived from Psidium guajava. Methods The cytotoxicity and antiviral effect of 12 ethanolic extracts derived from plants collected in the Colombian Caribbean coast was evaluated in epithelial VERO cells. Five fractions were obtained by open column chromatography from the ethanolic extract with the highest selectivity index (SI) (derived from P. guajava, SI: 128.2). From the fraction with the highest selectivity (Pg-YP-I-22C, SI: 35.5), five compounds were identified by one- and two-dimensional nuclear magnetic resonance spectroscopy. The antiviral effect in vitro of the fractions and compounds was evaluated by different experimental strategies (Pre- and post-treatment) using non-toxic concentrations calculated by MTT method. The DENV inhibition was evaluated by plate focus assay. The results were analyzed by means of statistical analysis using Student’s t-test. Finally the antiviral effect in Silico was evaluated by molecular docking. Results In vitro evaluation of these compounds showed that three of them (gallic acid, quercetin, and catechin) were promising antivirals as they inhibit the production of infectious viral particles via different experimental strategies, with the best antiviral being catechin (100% inhibition with a pre-treatment strategy and 91.8% with a post-treatment strategy). When testing the interactions of these compounds with the viral envelope protein in silico by docking, only naringin and hesperidin had better scores than the theoretical threshold of − 7.0 kcal/mol (− 8.0 kcal/mol and − 8.2 kcal/mol, respectively). All ligands tested except gallic acid showed higher affinity to the NS5 protein than the theoretical threshold. Conclusion Even though bioprospecting has recently been replaced by more targeted tools for identifying compounds with pharmacological potential, our results show it is still useful for this purpose. Additionally, combining in vitro and in silico evaluations allowed us to identify promising antivirals as well as their possible mechanisms of action.

scholarly journals The Active Compound of Bangle Essential Oil as Cyclooxygenase-2 (Cox-2) Inhibitor: In Silico Approach

2020 ◽  
Vol 6 (2) ◽  
pp. 156-168
Author(s):  
Richa Mardianingrum ◽  
Ruswanto Ruswanto ◽  
Gina Septiani Agustien ◽  
Aas Nuraisah
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Body Temperature ◽  
In Silico ◽  
Cyclooxygenase 2 ◽  
The Body ◽  
Cox 2 ◽  
Amino Benzoic Acid ◽  
Native Ligand ◽  
Methyl Phenyl

Fever is a condition where the body temperature rises above normal or more than 37o C and also tend to be an initial clinical manifestation of the use of antipyretic drugs thatcause toxicity such as on the liver due to prolonged usage. Particularly, the bangle (Zingiber purpureum Roxb.) is one of the Zingiberaceae plants that contain essential oils used for the treatment of fever. Therefore, this researchaimed to identify active compounds which have antipyreticspotential with the in silico approach. The simulation of molecular docking showed 1,4-naphthalenedione-2-ethyl-3-hydroxy was able to attach to the binding site of cyclooxygenase-2 (COX-2) and interact withmain residues that constituted the active cavity of COX-2. While the simulation of molecular dynamics suggested thatthe bound compound was stable at 4 ns, that is the time taken. The binding free energiesexpected by the MM-PBSA method indicated the 1,4-naphthalenedione-2-ethyl-3-hydroxy had a higher affinity than a native ligand (2-[(2,6-dichloro-3-methyl-phenyl)-amino] benzoic acid, JMS) and paracetamol. This suggested its capacity for advancing as a new COX-2 inhibitor.

scholarly journals In Silico Activity Identification of Cyclo Peptide Alkaloids from Zizyphus Spina-Christi Species Against Sars-Cov-2 Main Protease

2021 ◽  
Vol 6 (1) ◽  
pp. 71-81
Author(s):  
Taufik Muhammad Fakih ◽  
Dwi Syah Fitra Ramadhan ◽  
Fitrianti Darusman
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Docking Simulation ◽  
Functional Theory ◽  
Main Protease ◽  
Docking Method ◽  
Promising Target ◽  
Cyclopeptide Alkaloids ◽  
Prediction Server ◽  
Native Ligand

The COVID-19 has spread worldwide and become an international pandemic. The promising target for drug discovery of COVID-19 was SARS-CoV-2 Main Protease (Mpro), that has been successfully crystallized along with its inhibitor. The discovery of peptide-based inhibitors may present better options than small molecules for inhibitor SARS-CoV-2 Mpro. Natural compounds have such a wide potential and still few explored, Zizyphus spina-christi is one of the medicinal plants that have many pharmacological activities and contains a peptide compound from alkaloids class, i.e. cyclopeptide alkaloids, that is interesting to explore as SARS-CoV-2 Mpro inhibitor. The compound structure was drawn and optimized using density functional theory 3-21G method. The protein chosen was the high resolution of SARS-CoV-2 MPro receptor (1.45 Å) with PDB ID: 6WNP, in complex with boceprevir. Molecular docking simulation was performed using Autodock4 with 100 numbers of GA run, the validation methods assessed by RMSD calculation. Furthermore, the prediction of pharmacological activity spectra was carried out using the PASS Prediction server. The results showed RMSD value was 1.98 Å, this docking method was valid. The binding energy of all compounds showed better results than the native ligand (Boceprevir). The in silico PASS prediction results indicated that all compounds showed antiviral activity. Some compounds showed protease inhibitory activity, i.e Ambiphibine-H, Franganine, and Mauritine-A, and the highest Pa (Predicted activity) value showed by Mauritine-A compounds. It can be concluded that the cyclopeptide compounds of Zizyphus spina-christi were indicated to have a potential as COVID-19 therapy targeting SARS-CoV-2 Mpro.

scholarly journals Molecular docking of lutein as anti-photoaging agent in silico

2021 ◽  
Vol 1 (1) ◽  
pp. 15
Author(s):  
I Gede Bayu Krisnayana ◽  
Putu Dewi Febyani ◽  
Ida Ayu Yadnyaningtias Permata Sari ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Uv Exposure ◽  
Type I ◽  
Fibrillar Collagen ◽  
Matrix Metalloproteinase 1 ◽  
High Antioxidant Activity ◽  
In Silico Molecular Docking ◽  
Native Ligand ◽  
Autodock 4.2

The accumulation of UV exposure resulted in the loss of skin elasticity, and the appearance of wrinkles on the skin is commonly known as photoaging. Matrix metalloproteinase-1 (MMP-1) is an enzyme that degrades type I and III fibrillar collagen. This study aims to determine the mechanism of MMP-1 inhibition by lutein, a carotenoid compound with high antioxidant activity, using in silico molecular docking. This study was conducted by optimization of lutein structure using HyperChem 8, preparation of MMP-1 (PDB ID: 966C) using Chimera 1.10.1, validation of the method, and docking lutein against MMP-1 using Autodock 4.2. The results showed lutein had binding energy of -12.28 kcal/mol, lower than RS2 native ligand (-10.83 kcal/mol). The hydrogen bond formed between lutein and MMP-1 through HIS228 residue. To conclude, lutein may be developed as an anti-photoaging agent by inhibiting the MMP-1.

scholarly journals In Silico Approach of Potential Phytochemical Inhibitor from Moringa oleifera, Cocos nucifera, Allium cepa, Psidium guajava, and Eucalyptus globulus for the treatment of COVID-19 by Molecular Docking

2020 ◽  
Author(s):  
Ika Nur Fitriani ◽  
Wiji Utami ◽  
Adi Tiara Zikri ◽  
Pugoh Santoso
Keyword(s):  
Molecular Docking ◽  
Medicinal Plants ◽  
Oleanolic Acid ◽  
Allium Cepa ◽  
Bioactive Compounds ◽  
In Silico ◽  
Eucalyptus Globulus ◽  
Moringa Oleifera ◽  
Cocos Nucifera ◽  
Psidium Guajava

Abstract Background Coronavirus disease 2019 (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2. COVID-19 has devastating effects on people in all countries and getting worse. We aim to investigate an in-silico docking analysis of phytochemical compounds from medicinal plants that used to combat inhibition of the COVID-19 pathway. There are several phytochemicals in medicinal plants, however, the mechanism of bioactive compounds remains unclear. These results are obtained from in silico research provide further information to support the inhibition of several phytochemicals. Methods Molecular docking used to determine the best potential COVID-19 M pro inhibitor from several bioactive compounds in Moringa oleifera, Allium cepa, Cocos nucifera, Psidium guajava, and Eucalyptus globulus. Molecular docking was conducted and scored by comparison with standard drugs remdesivir. ADME properties of selected ligands were evaluated using the Lipinski Rule. The interaction mechanism of the most recommended compound predicted using the STITCH database. Results There was no recommended compound in Moringa oleifera as a potential inhibitor for COVID-19. Oleanolic acid in Allium cepa, α-tocotrienol in Cocos nucifera, asiatic acid in Psidium guajava and culinoside in Eucalyptus globulus were the most recommended compound in each medicinal plant. Oleanolic acid was reported to exhibit anti-COVID-19 activity with binding energy was − 9.20 kcal/mol. This score was better than remdesivir as standard drug. Oleanolic acid interacted through the hydrogen bond with HIS41, THR25, CYS44, GLU166. Oleanolic acid binding with CASP-3, CASP-9, and XIAP signaling pathway. Conclusions Oleanolic acid in Allium cepa found as a potential inhibitor of COVID-19 M-pro that should be examined in future studies. These results suggest that oleanolic acid may be useful in COVID-19 treatment.

scholarly journals In silico molecular docking of quercetin as anti-colorectal cancer agents by inhibiting LT4AH

2021 ◽  
Vol 1 (2) ◽  
pp. 16
Author(s):  
Made Agus Widiana Saputra ◽  
Anak Agung Istri Rani Mahaswari ◽  
Ni Ketut Sri Anggreni ◽  
Wahyu Nadi Eka Putri ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Malignant Neoplasm ◽  
Docking Method ◽  
Leukotriene A4 Hydrolase ◽  
Leukotriene A4 ◽  
In Silico Molecular Docking ◽  
Native Ligand

Colorectal cancer is a malignant neoplasm originating from the colon or rectum. Overexpression of leukotriene A4 hydrolase (LTA4H) increases the growth of HCT116 colon cancer cells, therefore, this enzyme becomes an attractive target for commercial drug bestatin. Meanwhile, quercetin is a member of flavonoids possessing a wide variety of anticancer. This study aimed to determine the potential of quercetin as anti-colorectal cancer by inhibiting LTA4H through in silico molecular docking. The docking process involved optimizing quercetin structure, preparing LTA4H protein (PDB ID: 3U9W), validating the molecular docking method, and docking quercetin and bestatin on LTA4H. The binding energy of quercetin to LTA4H was -9.57 kcal/mol, while 28P native ligand and bestatin yielded -10.22 kcal/mol and -9.10 kcal/mol, respectively. Based on the binding energy value, quercetin has a potential inhibitory against the LTA4H.

scholarly journals STUDI POTENSI SIANIDIN DAN PEONIDIN DARI UBI JALAR UNGU (ipomoea batatas L.) SEBAGAI AGEN DEPIGMENTASI SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
N. P.L. Laksmiani ◽  
I G.P. Putra ◽  
I P.W. I P. W. Nugraha ◽  
I W. Suwartawan ◽  
N. K.S. Ani
Keyword(s):  
Molecular Docking ◽  
Sweet Potato ◽  
In Silico ◽  
Target Protein ◽  
Program Optimization ◽  
Test Compound ◽  
Docking Method ◽  
Purple Sweet Potato ◽  
Native Ligand ◽  
Molecular Docking Method

Hyperpigmentation is caused by enhancement of melanin production that causes skin darkening. Purple sweet potato is one of the plants that is potentially developed as skin depigmentation agent because it contains anthocyanin. The most common types of anthocyanins in purple sweet potato are cyanidin and peonidin which are in vitro proven to be used as skin lightening. The objective of this study is to determine the potential of cyanidin and peonidin as skin depigmentation agent against target protein D-Dopachrome taumerase  through in silico molecular docking method. The research steps include the preparation of target protein using Chimera 1.10.1 program, optimization of cyanidine and peonidin 3D structures using Hyperchem 8 program, validation of molecular docking method, and docking of cyanidine and peonidine on target protein using Autodock 4.2 program. The bond energy between cyanidin and peonidin with the target protein D-Dopachrome taumerase are -7.75 kcal / mol and -8.38 kcal / mol. The cyanidin and peonidin bond values ??are smaller than the native ligand, suggesting that the bond between the test compound (cyanidin and peonidin) with the target protein are stronger and more stable than the native ligand, so that the affinity of the test compound was greater than the native ligand. This suggests that the cyanidin and peonidin compounds in purple sweet potato have potential as a depigmentation agent by inhibiting D-Dopachrome taumerase protein.

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