Kajian in Silico Aktivitas Antioksidan Senyawa Bioaktif dalam Minyak Serai (Cymbopogon citratus)

stress oxidative is a factor promoting metabolic syndrome and other diseases. oxidative stress could be minimalized by exogen and endogen antioxidants. Essential oil from Cymbopogon citratus extract have potential activities as anti-inflammatory and relaxing. This study determined the potential activity as antioxidant through kelch ECH associating protein 1 (KEAP1) inhibition. Four phytosterol compounds from Cymbopogon citratus essential oil, including 3,7-dimethyl-1,3,6-octatriene, decanal, elemol, dan selina- 6-en-4-ol, were downloaded from PubChem database. four compounds were docked with KEAP1 protein and analyzed using Discovery studio ver. 19.0.0.  3,7-dimethyl-1,3,6-octatriene, decanal, elemol, and selina-6-en-4-ol bound to KEAP1 in certain amino acid residues with hydrophobic interaction and hydrogen bond. Interestingly, 3,7-dimethyl-1,3,6-octatriene proved five hydrophobic interaction, higher than decanal and selina-6-en-4-ol. The elemol, and selina-6-en-4-ol interacted with KEAP1 showing lower binding affinity and tight interaction. This study suggested that 3,7-dimethyl-1,3,6-octatriene, decanal, elemol, and selina-6-en-4-ol promoted antioxidant activity.

PENGEMBANGAN LEMBAR KERJA MAHASISWA (LKM) BERBASIS INKUIRI PADA MATERI INTERAKSI MOLEKULER

Molecular Biology is a problematic category of biology, and it is necessary to carry out innovative learning. One of the learning resources developed is Student worksheets (LKM) to support student activities. This study purpose to analyze inquiry-based student worksheets (LKM) on Molecular Interaction material. The research based on Research and Development with a 4D development model consisting of definition, design, development, and dissemination. The results showed that student worksheet is in the correct category based on three experts' opinions (media, material, and language). It is also included in the feasible category for use based on small-scale tests and large-scale tests with a feasible value. We concluded that student worksheet molecular interaction material is very valid and suitable for use in learning.        Abstrak. Biologi Molekuler cabang ilmu biologi yang dikategorikan sulit, oleh karena itu perlu untuk melakukan pengembangan materi yang inovatif. Salah satu sumber belajar yang dikembangkan adalah Lembar Kerja Mahasiswa (LKM) untuk menunjang kegiatan mahasiswa. Tujuan penelitian menganalisis kelayakan lembar kerja siswa (LKM) berbasis Inkuiri pada materi Interaksi Molekuler. Metode penelitian berupa Reseach and Development dengan model pengembangan 4D terdiri atas pendefinisian (Define), perancangan (Design), pengembangan (Develop), dan penyebaran (Disseminate). Hasil yang diperoleh LKM yang dikembangkan masuk dalam kategori valid berdasarkan pendapat tiga ahli (media, materi dan Bahasa). LKM juga masuk dalam kategori layak untuk digunakan berdasarkan uji skala kecil dan uji skala besar dengan nilai sangat layak. LKM materi interaksi molekuler sangat layak untuk diaplikasikan dalam pembelajaran

Molecular Docking Approach Of Brewed Coffee Compounds As Neuroprotective Agent

Coffee is the most popular beverage in the community and the main export commodity in Indonesia. coffee has a special flavor due to roasting and brewing techniques. This study identified the potential neuroprotective effect of eight compounds in brewed coffee through acetylcholinesterase inhibition by molecular docking. Molecular docking approach was conducted in this study. Eight compounds involved 2-Ethyl- 3,5 – dimethylpyrazine, Guaiacol, 2-Isobutyl-3- methoxypyrazine, 2- Methylpropanal, 3-Methyl – 2 – butene – 1 - thiol, 3- Methylbutanal, Furaneol, and 2 – Furfurylthiol were retrieved their structure from PubChem NCBI database and redocked with acetylcholinesterase by Molegro virtual docker version 5.0. then, the docking results were visualized and analyzed by PyMol 2.3 and Discovery Studio version 21.1.1. the docking studies performed that eight brewed coffee compound showed interaction with acetylcholinesterase at the protein gate and active sites. Even the interaction was not found in catalytic triad, the interaction of ligands – protein change the conformation and prevent the breaking down of acetylcholine to acetic acid and choline. This study suggested that eight brewed coffee compounds potentially as neuroprotective effect trough blocking acetylcholinesterase protein

Kajian Farmakoinformatika Senyawa Alkaloid Anggur Laut (Caulerpa racemose) Sebagai Inhibitor Collagenase Dalam Mekanisme Antiaging

Caulerpa racemosa or sea grape is an edible macroalgae, cultivated and wild species in Asia ocean. Sea grapes also well known as functional food source from marine, contains high protein, fibers and secondari metabolites. The biological functions  of sea grape also has been identified as antioxidant, antiinflammatory, antiobesity, and anticancer. However, the antiaging activity has not been known yet. This study investigated the potential antiaging activity of alkaloids compounds from sea grapes through inhibiting collagenase protein by farmacoinformatic study. six alkaloid structure of sea grapes including Caulerpin, Caulersin, Caulerchlorin, Racemosin A, Racemosin B, and Racemosin C, were retrieved from PubChem database and collagenase protein also was downloaded from Protein Data Bank with ID 2TCL. Six alkaloids of Caulerpa racemosa were redocked with collagenase at the specific site and were visualized by Discovery studio version 21.1.1. collagenase inhibitor compound also used as control for this study. farmacoinformatic analysis performed that six alkaloid of sea grapes and inhibitor compounds were showed at the same region of collagenase, which was identified as inhibitor sites. Several active residues of collagenase, involved SER139, PRO138, HIS128, and LEU81 were detected at six alkaloids compounds and control inhibitor, indicating six alkaloid of sea grapes potentially as collagenase inhibitor leading to antiaging properties. This study summarized that the six sea grape’s alkaloid has potential as collagenase inhibitor. Further in vivo analysis were required for further investigation

1-dehydrogingerdione, Senyawa volatil jahe sebagai agen sedatif subtitutif γ-aminobutyrate (GABA); Kajian biokomputasi

Gamma aminobutyrate (GABA) merupakan molekul penting dalam sistem saraf pusat. Ekspresi GABA yang tinggi menyebabkan abnormalitas sel saraf dan mengakibatkan beberapa penyakit termasuk penyakit mental. Penelitian ini bertujuan untuk menganalisis potensi tiga senyawa volatil yang terkandung di dalam jahe sebagai penenang melalui kajian biokomutasi. Pendekatan in silico digunakan dalam penelitian ini. Struktur senyawa volatil jahe didapatkan dari database PubChem dan struktur protein diperoleh dari database Protein Data Bank. Senyawa jahe, GABA diinteraksikan dengan protein target aminobutyrate aminotransferase dengan program Molegro virtual Docker 5 dan dianalisis menggunakan Discovery Studio ver 21.1.1. Senyawa 6-paradol, 6- gingerdione, dan 1-dehydrogingerdione berinteraksi dengan aminobutyrate aminotransferase pada beberapa sisi aktif, residu Phe217 teridentifikasi pada ketiga interaksi dan menunjukkan energi ikatan lebih rendah dari interaksi GABA dengan protein target. Jenis ikatan antara senyawa volatil jahe dan protein aminobutyrate aminotransferase yaitu ikatan hidrogen dan interaksi hidrofobik. Penelitian ini disimpulkan bahwa senyawa 1-dehydrogingerdione merupakan inhibitor aminobutyrate aminotransferase yang paling baik dan menunjukkan ikatan yang lebih kuat dari kompleks GABA-aminobutyrate aminotransferase. Kajian in vitro dan in vivo perlu dilakukan untuk analisis lebih lanjut

Phytochemical screening, in vitro and in silico antibacterial investigation of Elaeocarpus ganitrus extract

This study evaluated phytochemical composition, and in vitro and in silico antibacterial activity of Elaeocarpus ganitrus extract. Elaeocarpus ganitrus leaves, seed and fruit powder were extracted with absolute ethanol. Then, the extract was identified phytochemical compounds qualitatively and evaluated the antibacterial activity through in vitro against Staphylococcus aureus and E. coli. Molecular docking was conducted to evaluate the antibacterial mechanism of Elaeocarpus ganitrus extract. Elaeocarpus ganitrus leaves, seeds, and fruits extract presented positive tannin, saponin, cardiac glycoside, quinone, steroids, terpenoids, and anthocyanins. In vitro analysis performed Elaeocarpus ganitrus leaves strong inhibited Staphylococcus aureus growth and medium inhibition against E. coli. structure activity relationship revealed 14 of 72 compounds have high antibacterial activities. molecular docking of 7 compounds showed inhibition activity of D-alanin ligase of Staphylococcus aureus. Those compounds blocked the activity of D-alanine ligase at inhibitor sites of enzyme, and might be disrupted the cell wall synthesis. In conclusion, Elaeocarpus ganitrus contained several phytochemical compounds and has antibacterial activity both in vitro and in silico investigation

Berberine: A Potential Inhibitor of Dihydrofolate Reductase- Thymidylate Synthase (DHFR-TS) for Malaria

The goal of this study was to genetically link natural materials derived from Tinospora crispa L with Berberine to dihydrofolate reductase-thymidylate synthase (DHFR-TS). Method: The ligand berberine (CID: 2353) was obtained from Pubchem, while the protein DHFR-TS (PDB ID 2bl9) was obtained from Protein Data Bank. The ligands and proteins interacted with HEX 8.0.0.0 and were visualized with Discovery Studio. The researchers discovered a positive interaction between berberine and DHFR-TS, observed at four amino acid residues that bind to the protein TYR125, ILE121, LEU45, and MET54. Van der Waals interactions, hydrogen bonds, Pi-Sulfur, Pi-Alkyl, and Pi-Stalked interactions all contribute to strength and stability. In conclusion, berberine has the potential to act as a DHFR-TS inhibitor and thus prevent malaria.ABSTRAK: Tujuan penelitian ini adalah memanfaatkan bahan alam yang berasal dari Tinospora crispa L dengan kandungan utama Berberin dengan dihydrofolate reductase-thymidylate synthase (DHFR-TS) secara genetik. Metode, Ligan berberin (CID: 2353 ) diperoleh dari Pubchem sedangkan protein DHFR-TS (PDB ID 2bl9) diperoleh dari Protein Data Bank, ligan dan protein diinteraksikan menggunakan HEX 8.0.0.0 dan divisualisasikan menggunakan discovery studio. Ditemukan interaksi positif antara berberin dan DHFR-TS yang menunjukkan interaksi pada empat residu asam amino yang berikatan dengan protein. Mereka adalah TYR125, ILE121, LEU45 dan MET54. Beberapa interaksi yang dilakukan Van der Waals, ikatan hidrogen, Pi-Sulfur, Pi-Alkyl dan Pi-Stalked juga memberikan dukungan dalam rangka meningkatkan kekuatan dan stabilisasi. Kesimpulannya, berberin memiliki potensi fungsi sebagai penghambat DHFR-TS dan mengarah pada malaria

Potensi Asam kafeat pada Kopi sebagai Simultan Gen Peroxixme proliferator-activated receptor gamma (PPAR-γ): Studi In silico

Coffee plants are one of the cultivated plants of the Sikka Regency community. Coffee contains chemical compounds which is needed by humans. One of them is cafeic acid. Cafeic acid was recognized as having the potential as an anti-inflammatory, antioxidant, and healing type 2 diabetes mellitus (T2DM). The Peroxixme proliferator-activated receptor gamma gene (PPAR-γ) has a role in homeostasis regulation, so it can be used as hyperglycemia. But do not study on the interaction of cafeic acid as anti-diabetes molecularly. The purpose of this study was to analyze and predict the physico-chemical properties and potency of cafeic acid as anti-diabetes through the interaction of cafeic acid with PPAR- γ protein in silico. The method used consisted of downloading PPAR-γ protein through protein bank data (GDP) and cafeic acid through the PubChem database, protein preparation (PPAR-γ) and ligands (cafeic acid) with the PyRx program, protein analysis and ligand using the program using the Hex program 8.0 .0 and Discovery Studio V16.1.0.15360. The results showed that occur between cafeic acid and PPAR-γ show the role of anti-diabetes. This is evidenced by the presence of 11 amino acid residues (ASP441, LYS373, ASP396, LYS438, GLU407, PRO398, GLY399, ARG397, LEU400, GLY395, VAL403) which interacted with the chlorogenic acids and their energies of -168.5cal/mol. This function activates GLUT2 and GLUT4 as transportation routes inside and outside the cell. Caffeic acid is predicted to have potential as a natural ingredient in coffee which can be used for DMT2 therapy with genetic care (Nurtigenetics). We suggest further study is required in vivo experiment. Tanaman kopi merupakan salah satu tanaman budidaya masyarakat Kabupaten Sikka. Kopi memiliki kandungan senayawa yang sangat dibutuhkan oleh manusia. Salah satunya adalah asam kafeat.  Asam kafeat diketahui memiki potensi sebagai anti inflamasi, antioksidan, dan menyembuhkan penyakit Diabetes melitus tipe 2 (DMT2). Gen Peroxixme proliferator-activated receptor gamma (PPAR-γ) memiliki peran dalam regulasi homeostasis gula, sehingga dapat mecegah terjadinya kondisi hiperglikemia. Tetapi masih kurang studi molekuler tentang interaksi asam kafeat sebagai anti-diabetes secara molekuler. Tujuan penelitian ini untuk menganalisis dan memprediksi sifat fisiko kimia serta potensi asam kafeat sebagai anti-diabetes melalui interaksi asam kafeat dengan protein PPAR-γ secara in silico. Metode yang digunakan terdiri atas pengunduhan protein PPAR-γ melalui protein data bank (PDB) dan asam kafeat melalui database PubChem, persiapan protein (PPAR-γ) dan ligand (asam kafeat) dengan program PyRx, analisis interaksi protein dan ligand menggunakan program Hex 8.0 dan Discovery Studio 4.1. Hasil penelitian menunjukan interaksi yang terjadi antara asam kafeat dan PPAR-γ menunjukan peran sebagai anti-diabetes. Hal ini dibuktikan dengan adanya 11 residu asam amino (ASP441, LYS373, ASP396, LYS438, GLU407, PRO398, GLY399, ARG397, LEU400, GLY395, VAL403) yang mengikat asam klorogenat serta energinya -168,5cal/mol. Fungsi ini mengaktifkan GLUT2 dan GLUT4 sebagai jalur transportasi gula dalam dan di luar sel. Asam kafeat diprediksi memiliki potensi sebagai bahan alam dalam kopi yang dapat digunakan untuk terapi DMT2 dengan perawatan secara genetic (Nurtigenetik). Diperlukan penelitian lanjutan secara in vivo untuk mengetahui pengaruh asam kafeat terhadap penderita diabetes melitus tipe 2

Analisis In silico Heksosa, D-Manitol dan Asam Malat Kulit Kopi sebagai Penghambat Infeksi Virus Corona

COVID-19 merupakan penyakit infeksi saluran pernapasan yang disebabkan oleh virus corona, dan telah menjadi pandemik dari 2019 hingga 2022. Berbagai terapi telah dilakukan dan dikembangkan oleh banyak peneliti, termasuk pembuatan vaksin COVID-19. Penelitian ini bertujuan untuk menganalisis potensi senyawa pada kulit kopi sebagai agen penghambat kompleks antara spike glycoprotein SARS-CoV-2 dan Angiotensin-Converting Enzyme 2 (ACE2) secara in silico. Kajian in silico dilakukan dengan mengunduh struktur 3D senyawa yaitu heksosa, asam malat, dan D-manitol dari PubChem NCBI, serta kompleks spike glycoprotein SARS-CoV-2 – ACE2 dari Protein Data Bank. Interaksi masing-masing senyawa uji dan kompleks dianalisis dengan Molegro Virtual Docker dan divisualisasi dengan Discovery Studio. Hasil analisis menunjukkan bahwa heksosa, asam malat dan D-manitol mengikat bagian diantara spike glycoprotein SARS-CoV-2 dan ACE2. Residu sisi aktif ikatan antara kompleks dengan ketiga senyawa uji merupakan residu protein dari ACE2 dan spike glycoprotein SARS-CoV-2. Jenis ikatan yang terbentuk antara senyawa dan kompleks protein didominasi oleh ikatan hidrogen, dan beberapa gaya Van der Waals. Dari hasil analisis dapat disimpulkan bahwa senyawa heksosa, asam malat, dan D-manitol yang ada pada kulit kopi memiliki potensi sebagai anti SARS-CoV-2, namun demikian itu perlu dilakukan pembuktian secara in vitro dan in vivo.

In Silico Insight the Prediction of Chlorogenic Acid in Coffee through Cyclooxygenase-2 (COX2) Interaction

Inflammation was signs of pathological or abnormality in tissue to give an alert as a trouble signal to the system. Therapeutic using NSAIDs has some side effects. This research explored the potential role of chlorogenic acid as natural therapeutic compound to inhibit the inflammation target such as COX-2 by interaction model. The research method used in this study was the molecular docking approach, which binds ligand and protein. Protein data provided by Protein Data Bank (ID: 6cox) while, chlorogenic acid obtain from PubChem (CID: 1794427). We docked COX-2 and chlorogenic acid using Hex 8.0.0. Visualization and analysis of the molecular interactions of chlorogenic acid and COX-2 conducted by the Discovery Studio Client 4.1 software. Chlorogenic acid has a high permeability and is easily absorbed based on five Lipinski Rule. Interestingly, we found Fifteen amino acid was binding with chlorogenic acid that formed by hydrogen bond and van der Waals.The interaction between ligand-protein results in energy binding -327.59cal/mol. Chlorogenic acid has a potential role to inhibit inflammation pathway by inhibiting COX-2. We predicted chlorogenic acid has a potential as therapy anti-inflammatory to suppress COX-2 as mediator inflammation