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The growth of micro-organisms that acquire resistance to most commercially available antibiotics is occurring rapidly. Consequently, a pressing necessity exists to identify and detect new antimicrobial substances. This study aimed to analyze the antioxidant and antibacterial activity of nanoemulsion clove extract and grape seed oil. This research was conducted in June 2023 using experimental methods at the Research Laboratory of the Universitas Islam Bandung Pharmaceutical Study Program by developing a nanoemulsion preparation containing clove extract (Syzygium aromaticum L.) and grape seed oil (Vitis vinifera L.). Antioxidant activity was tested using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. Antibacterial activity was tested using the agar diffusion method by measuring the growth inhibitory diameter of Staphylococcus aureus and Streptococcus mutans bacteria and divided into four groups formulas based on the addition of clove extract with different concentrations in the nanoemulsion base (FA=0.25%, FB=0.5%, FC=0.75%, and FD=1%) to see the best results. The result shows nanoemulsion preparations have antioxidant properties in the DPPH test. The FA formula has the highest IC50, namely 1,117.56 ppm. The antibacterial activity of Staphylococcus aureus and Streptococcus mutans has an inhibition zone, although it is still in the category of inhibiting bacterial growth, but does not kill growth. The nanoemulsion formulation, comprising clove extract and grape seed oil, has exhibited exceptional antioxidant properties and substantial antimicrobial efficacy against prevalent oral bacterial strains.

The 2019 coronavirus pandemic disease (COVID-19) is still declared a global pandemic by the World Health Organization (WHO). Therefore, an effort that is considered effective in finding therapeutic agents is needed to prevent the spread of COVID-19 infection. One of the steps that can be chosen is by utilizing antimicrobial peptides (AMPs) from animal venom by targeting the specific receptor of SARS-CoV-2, namely the main protease (Mpro). Through this research, a computational approach will be conducted to predict antiviral activity, including protein-peptide docking using PatchDock algorithm, to identify, evaluate, and explore the affinity and molecular interactions of four types of antimicrobial peptides (AMPs), such as Mucroporin, Mucroporin-M1, Mucroporin-S1, and Mucroporin-S2 derived from scorpion venom (Lychas mucronatus) against main protease (Mpro) SARS-CoV-2. These results were then confirmed using protein-peptide interaction dynamics simulations for 50 ns using Gromacs 2016 to observe the molecular stability to the binding site of SARS-CoV-2 Mpro. Based on protein-peptide docking simulations, it was proven that the Mucroporin S-1 peptides have a good affinity against the active site area of SARS-CoV-2 Mpro, with an ACE score of −779.56 kJ/mol. Interestingly, Mucroporin-S1 was able to maintain the stability of its interactions based on the results of RMSD, RMSF, and MM/PBSA binding free energy calculations. The results of the computational approach predict that the Mucroporin-S1 peptide is expected to be useful for further research in the development of new antiviral-based AMPs for the COVID-19 infectious disease.

Coronavirus infection (COVID-19) caused by SARS-CoV-2 appears as a pandemic that has spread to almost all countries in the world. Antiviral therapy using natural compounds is one alternative approach to overcome this infectious disease. The therapeutic mechanism is proven effective against the main protease (Mpro) of SARS-CoV-2. This research aims to perform bioinformatics studies, including ligand-docking simulations and protein-protein docking simulations, to identify, evaluate, and explore five compounds' activity on SARS-CoV-2 Mpro and their effects against Angiotensin-Converting Enzyme 2 (ACE-2). Protein-ligand docking simulations show kaempferol, flavonol, and their glycosides (Afzelin and Juglanin) and other flavonoids (Quercetin, Naringenin, and Genistein) have a high affinity towards SARS-CoV-2 Mpro. These results were then confirmed using protein-protein docking simulations to observe the ability of five compounds to prevent the attachment of ACE-2 to the active site. Based on the results of the bioinformatics studies, Quercetin has the best affinity, with a binding free energy value of −33.18 kJ/mol. The five compounds are predicted to be able to interact strongly with SARS-CoV-2. The results in this research are useful for further studies in the development of novel anti-infective drugs for COVID-19 that target SARS-CoV-2 Mpro.

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.

Resistensi antibiotika muncul sebagai polemik yang dapat mempengaruhi kesehatan manusia. Kemajuan teknologi membuka peluang dalam penemuan molekul senyawa baru yang mampu mencegah perkembangan mikroba patogen, seperti Pseudomonas aeruginosa yang resisten terhadap beberapa jenis antibiotika. Terapi fotodinamika dengan memanfaatkan penggunaan fotosensitizer yang berasal dari senyawa yang membentuk kompleks dengan besi merupakan salah satu pendekatan alternatif untuk mengatasi penyakit infeksi dengan risiko resistensi mikroba yang lebih rendah. Penelitian yang dilakukan secara in silico ini bertujuan untuk mengamati, mengeksplorasi, dan mengevaluasi mekanisme aksi berbasis struktural dari molekul senyawa yang membentuk kompleks dengan besi, yaitu besi-ftalosianina dan besi-salofen terhadap protein hemofor HasAp serta pengaruh molekularnya terhadap bagian situs aktif pengikatan dari protein hemofor HasR. Identifikasi interaksi molekuler dan afinitas antara molekul senyawa besi-ftalosianina dan besi-salofen terhadap protein hemofor HasAp dilakukan dengan simulasi ligan-protein docking mempergunakan software MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Di samping itu, dilakukan juga simulasi protein-protein docking terhadap sistem kompleks ligan-protein untuk memastikan pengaruh molekularnya terhadap bagian situs aktif pengikatan dari protein hemofor HasR dengan mempergunakan software PatchDock. Berdasarkan simulasi ligan-protein docking diperoleh hasil bahwa senyawa besi-ftalosianina memiliki afinitas paling baik terhadap kedua protein hemofor HasAp, dengan nilai energi bebas pengikatan masing-masing sebesar −68,45 kJ/mol dan −65,23 kJ/mol. Menariknya, hasil simulasi protein-protein docking antara kompleks molekul senyawa besi-ftalosianina dan protein hemofor HasAp-besi-ftalosianina terhadap protein hemofor HasR memiliki nilai energi kontak atom yang positif sebesar 556,56 kJ/mol. Dari penelitian ini dapat diprediksikan bahwa perbedaan struktur molekul senyawa yang membentuk kompleks dengan besi mampu mempengaruhi mekanisme aksi berbasis structural terhadap protein hemofor target.

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.

The recent public health crisis is threatening the world with the emergence of the spread of the new coronavirus 2019 (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus originates from bats and is transmitted to humans through unknown intermediate animals in Wuhan, China in December 2019. Advances in technology have opened opportunities to find candidates for natural compounds capable of preventing and controlling COVID-19 infection through inhibition of spike proteins of SARS-CoV-2. This research aims to identify, evaluate, and explore the structure of spike protein macromolecules from three coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using computational studies. Based on the identification of the three spike protein macromolecules, it was found that there was a similarity between the active binding sites of ACE-2. These observations were then confirmed using a protein-docking simulation to observe the interaction of the protein spike to the active site of ACE-2. SARS-COV-2 spike protein has the strongest bond to ACE-2, with an ACE score of ?1341.85 kJ/mol. Therefore, some of this information from the results of this research can be used as a reference in the development of competitive inhibitor candidates for SARS-CoV-2 spike proteins for the treatment of COVID-19 infectious diseases.

Copyright of Journal of Agroindustrial Technology / Jurnal Teknologi Industri Pertanian is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Jurnal Fitopatologi Indonesia is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Jurnal Fitopatologi Indonesia is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Jurnal Fitopatologi Indonesia is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)