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Novel Compounds Design of Acertannin, Hamamelitannin, and Petunidin-3-Glucoside Typical Compounds of African Leaves (Vernonia amygdalina Del) as Antibacterial Based on QSAR and Molecular Docking Kurniawan, Ilham; Ambarsari, Laksmi; Kurniatin, Popi Asri; Wahyudi, Setyanto Tri
Jurnal Jamu Indonesia Vol. 8 No. 2 (2023): Jurnal Jamu Indonesia
Publisher : Tropical Biopharmaca Research Center, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jji.v8i2.326

Abstract

Antibacterial secondary metabolites such as tannins and their derivatives are found in the Vernonia amygdalina Del. Antibiotic resistance can develop due to overuse, reducing the efficacy of drugs to prevent and treat infections. This research aims to use the Quantitative Structure-Activity Relationship (QSAR) and the semi-empirical method Austin Model 1 (AM1) to design a modified novel compound from African leaves that has improved antibacterial activity. This research includes a descriptor calculation of QSAR using AM1 MOE on typical compounds from African leaves, and calculation results are chosen based on a multilinear regression statistical analysis. The model equation represents the three primary parameters of QSAR, which are electronic, hydrophobic, and steric parameters, which will be used to measure modified compounds. Molecular docking using Autodock Tools (The Scripps Research Institute, USA), and analysis of results of docking Autodock Tools using Discovery Studio 3.5 Client. The best QSAR model obtained is LogEC50 = (0.829 x LogP) - (1,302 x AM1_HOMO) - (0.339 x AM1_dipole) - (5,128 x mr) + (0.145 x vol) - (11,355). The results showed that EC50 prediction of modified hamamelitannin has the best activity with the lowest ΔGbind -9.0 kcal/mol and inhibition constant of 0.249 μM. In summary, the novel compound's design calculation has better antibacterial activity, as indicated by a lower EC50, than fosfomycin or compounds without modification. The modified hamamelitannin compound was found to have better antibacterial activity (prediction EC50 = 0.1933 μM) than the original (experimental EC50 = 145.50 μM).
Molecular Docking Study of Bioactive Compounds from Curcuma aeruginosa Roxb. as Antioxidant and Anticancer Activities Ambarsari, Laksmi; Nurjanah, Siti; Artika, I Made; Fatriani, Rizka
Jurnal Jamu Indonesia Vol. 8 No. 2 (2023): Jurnal Jamu Indonesia
Publisher : Tropical Biopharmaca Research Center, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jji.v8i2.327

Abstract

Cancer is one type of dangerous disease that is increasing every year. Free radicals are the cause of gene mutations (cancer). Cancer will develop uncontrollably due to the occurrence of the cell cycle and the presence of compounds that trigger cell proliferation and inhibit the process of apoptosis. This cancer treatment is carried out by giving cyclin-dependent kinase2 (CDK2) and cyclooxygenase-2 (COX-2) inhibitor drugs to inhibit cancer development, as well as lipoxygenase (LOX) inhibitor drugs for the formation of free radicals. Curcuma aeruginosa RoxB., the plant, is known to have the potential for antioxidant and anticancer properties. This study aims to determine the molecular interaction between the dominant compound in the ethanol extract of C. aeruginosa with CDK2, COX-2, and LOX receptors. The type of ligand interaction with the receptor was determined through the parameters of affinity energy (∆G), inhibition constant (Ki), type of interaction, and percentage of binding site similarity (%BSS). The results showed that the gajutsulacton A had the best potential in inhibiting CDK2. The cucumenol may be a COX-2 inhibitor, and there are no compounds that can inhibit LOX as well as an antioxidant. Thus, our findings demonstrate the potential for C. aeruginosa bioactive to serve as anticancer candidate molecules against CDK2 and COX-2 receptors.
Cloning of the GOX-Xho Gene IPBCC 08.610 into Plasmid pTA2 and Its Characterization Aryani, Hanifah; Akbar, Nadhira Fathiaz; Fuad, Asrul Muhamad; Ambarsari, Laksmi; Kurniatin, Popi Asri
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 10, No. 2, November 2024
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v10i2.39602

Abstract

Glucose oxidase (GOX) from Aspergillus niger catalyzes the oxidation of β-D-glucose to δ-gluconolactone and hydrogen peroxide, making it valuable for industrial applications. Intracellular GOX exhibits higher activity than its extracellular counterpart. This study focuses on enhancing the extracellular production of GOX through recombinant DNA technology. This study aimed to reconstruct the GOX gene by adding XhoI sites at both ends, inserting a glu-ala-glu-ala spacer at the 5' end, and introducing an XbaI site at the 3' end. These modifications facilitate the cloning of the GOX-Xho gene into the pTA2 vector and its subsequent ligation into the pPICZαB expression vector, allowing for extracellular production of GOX through fusion with the α-mating factor (α-MF) signal peptide. The GOX-Xho gene was successfully amplified, cloned, and characterized. The pTA2-GOX-Xho recombinant plasmid was verified through sequencing and restriction analysis, confirming the present and correct orientation of the 1797 bp GOX-Xho gene. However, sequencing revealed several point mutations, necessitating further computational analysis to predict their impact on the enzyme's structure and function before recombinant protein expression.
POTENTIAL OF RED BETEL LEAVES (Piper crocatum) AS TYROSINASE INHIBITOR IN SILICO AND IN VITRO Mustopa, Syahrul; Safithri, Mega; Ambarsari, Laksmi
Indonesian Journal of Pharmaceutical Science and Technology Vol 11, No 1 (2024)
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/ijpst.v11i1.41575

Abstract

Melasma adalah kelainan pigmentasi yang diakibatkan sintesis melanin berlebih berupa bercak cokelat disekitar wajah atau leher. Melasma dapat mengenai semua kelompok ras, terutama daerah dengan radiasi ultraviolet tinggi seperti suku Hispanik/Latin dan Asia. Zat yang sering digunakan untuk mencegah hiperpigmentasi adalah asam kojat, asam azelat dan merkuri, akan tetapi zat tersebut bersifat karsinogen jika digunakan terus menerus. Sirih merah (Piper crocatum) memiliki senyawa aktif yang berperan sebagai antioksidan seperti flavonoid dan fenol. Penelitian ini bertujuan untuk mengetahui potensi senyawa aktif daun sirih merah terhadap penghambatan tirosinase. Penelitian ini dilakukan dengan metode in silico dan in vitro. Reseptor yang digunakan adalah tirosinase dengan kode PDB 5M8O, tropolon sebagai native ligand, dan asam kojat sebagai ligan pembanding. Sebanyak 34 senyawa aktif daun sirih merah hasil analisis LC-MS dan GC-MS.digunakan sebagai ligan uji. Penambatan molekuler dilakukan dengan menggunakan AutoDock Vina dan AutoDock Tools, serta divisualisasikan menggunakan Ligplot+ dan PyMOL. Penghambatan tirosinase secara in vitro menggunakan kit tyrosinase activity assay ab252899 dan asam kojat sebagai kontrol positif. Senyawa katekin memiliki energi bebas pengikatan (ΔG) terkecil, yaitu −6.7 kkal/mol, dan kinetika inhibisi sebesar 12.12 µM. Hasil pengujian in vitro, fraksi air memiliki aktivitas inhibisi tirosinase terbesar yaitu 84.84% dan asam kojat memiliki aktivitas sebesar 82.47%.
Evaluasi varietas, sumber eksplan dan strain Agrobacterium terhadap keberhasilan transformasi tebu dengan gen P5CS Evaluation of varieties, explant sources, and Agrobacterium strains for successful sugarcane transformation using P5CS gene Hayati MINARSIH; Dwi SUBIYARTI; Imron RIYADI; Soekarno Mismana PUTRA; Laksmi AMBARSARI
Menara Perkebunan Vol. 83 No. 1: 83 (1), 2015
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v83i1.7

Abstract

Abstract Genetic transformation can be used as an alter-native to develop sugarcane (Saccharum officinarum L.) tolerant to drought stress. P5CS gene has a role in biosynthesis of proline, an amino acid that accumulated under drought stress conditions. Transfer of a P5CS gene construct into plant cells in conjunction with regeneration of transgenic plantlets may develop sugarcane tolerant to drought stress. The aim of this research was to obtain an optimal transformation method which includes a suitable strain of Agrobacterium tumefaciens, and the best sugarcane explant and variety. The results showed that transfer of P5CS gene has been successfully carried out on sugarcane explants from solid media-derived calli, embryogenic calli and somatic embryos derived from temporary immersion system (TIS) culture. Whilst Agrobacterium strain LBA4404 was indicated as the most effective transformation vector. The regeneration of Kidang Kencana variety transformants from calli and somatic embryos was better than those of PS 881 and PS 891. The best performance of transformants based on the source of explants obtained from somatic embryos from TIS culture. Moreover, a succesfull Agrobacterium mediated transformation on sugarcane was indicated by transient expression of Gus gene and the ability of the transformants grew in a selection medium containing 50 ppm of kanamycin.Abstrak Transformasi genetik dapat digunakan sebagai upaya untuk merakit tebu (Saccharum officinarum L.) toleran terhadap cekaman kekeringan. Gen P5CS diketahui  berperan  dalam  biosintesis  prolin,  yaitu asam amino yang umumnya terakumulasi ketika tanaman mengalami cekaman kekeringan. Transfor-masi gen P5CS dan regenerasi transgeniknya mungkin dapat menghasilkan tanaman tebu trans-genik yang toleran terhadap cekaman kekeringan. Tujuan penelitian ini adalah untuk mendapatkan metode transformasi yang optimum yang mencakup strain Agrobacterium tumefaciens yang sesuai, sumber eksplan dan varietas tebu terbaik sebagai target transformasi. Hasil penelitian menunjukkan bahwa transformasi gen P5CS telah berhasil dilakukan ke eksplan tebu baik yang berupa kalus asal media padat maupun kalus embriogenik dan embrio somatik asal kultur sistem perendaman sesaat (SPS). Sementara itu strain A. tumefaciens LBA4404 menunjukkan hasil yang paling efektif sebagai vektor transformasi. Pertumbuhan transforman baik pada kalus maupun embrio somatik pada varietas Kidang Kencana terlihat paling baik dibandingkan dengan varietas PS 881 dan PS 891. Sumber eksplan yang paling efektif adalah embrio somatik yang diperoleh dari  kultur SPS. Keberhasilan transformasi tebu me-lalui Agrobacterium ditunjukkan oleh ekspresi transien dari gen GUS dan kemampuan dari trans-forman untuk tumbuh di media yang mengandung    50 ppm kanamisin.
Pemodelan protein dan analisis molecular docking enzim β-glukanase solat Bacillus subtilis W3.15: Ainia Hanifitri; Laksmi Ambarsari; Nisa Rachmania Mubarik
Menara Perkebunan Vol. 91 No. 1 (2023): 91 (1), 2023
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v91i1.523

Abstract

The β-glucanase enzyme is an enzyme protein that can hydrolyze β-glucan, one of the main components of the fungal cell wall. This enzyme protein is produced by several bacteria, one of which is B. subtilis. The three-dimensional (3D) structure of proteins is necessary to understand their properties and functions of proteins. Enzyme proteins can be analyzed for their structure and function using in silico method. This study aims to detect the β-glucanase gene from B. subtilis W3.15 and analyze it using the in silico method. The methods in this research are homology modeling and molecular docking analyses. Modeling was carried out using the SWISS-MODEL server and docking analysis using the PLANTS 1.1 program. Modeling the β-glucanase enzyme is based on the template of the β-glucanase enzyme protein model with PDB code 3o5s. The results of sequence alignment and model visualization were quite good as indicated by the model having a Ramachandran Plot value in the favored area of 91.10 %, a MolProbity score of 0.95, and a QMEAN value of 0.90 ± 0.06. The β-glucanase enzyme model was then docked using the PLANTS1.1 program with native ligand B3P, 1,4-β-D-Glucan, D-glucose, β-D-Glucan from oats, and N-Acetyl glucosamine. The results of docking analysis showed that the β-glucan ligand (β-D-glucan from oats) used as a substrate in the cultivation of isolate B. subtilis W3.15 had a better binding energy prediction value compared to the B3P ligand, which is a natural ligand in the template proteins.   [Keywords: β-Glucan, β-D-Glucan from oat, ligand, PLANTS 1.1, 3D structure, SWISS-MODEL]
In silico study: molecular docking of SARS-Cov-2 endoribonuclease on active compounds of Gmelina arborea Roxb. bark Shobiroh Nuur'Alimah; Agnia Nurul Jannati; Laksmi Ambarsari; Syamsul Falah
Menara Perkebunan Vol. 92 No. 1 (2024): 92(1), 2024
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v92i1.561

Abstract

Infection by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) triggers COVID-19 disease of the respiratory tract similar to pneumonia. The virus encodes four structural proteins and 16 non-structural proteins (nsp), one of which includes nsp15 or endoribonuclease (NendoU). NendoU plays an important role in viral replication and transcription and reduces the stimulation of immune cell responses. Active compounds in Gmelina arborea Roxb. bark have antioxidant properties that can inhibit the NendoU activity of SARS-CoV-2. This study aims to analyze the potential of compounds from Gmelina arborea Roxb. bark in inhibiting SARS-CoV-2 NendoU within in silico using the YASARA structure application. Balnophonin is the best test ligand based on binding ΔG value, dissociation constant (Kd), prediction of physicochemical characteristics, pharmacokinetics, and toxicity. Therefore, balanophonin can be developed as an effective alternative drug to inhibit SARS CoV-2 NendoU.
The In Silico Study of Bioactive Compounds from Some Tropical Trees as Inhibitors of Papain-Like Protease SARS-COV-2 Falah, Syamsul; Nuur’Alimah, Shobiroh; Ambarsari, Laksmi
Molekul Vol 20 No 2 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.2.9097

Abstract

ABSTRACT. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causal virus of the global COVID-19 pandemic. Furthermore, it is known to encode 4 structural and 16 non-structural proteins, one of which is Papain-Like protease (PLpro). This protein is an essential enzyme that plays a role in the maturation of viral polyproteins, the formation of replicate-transcriptase, and the signaling of the host's innate immune response to viral infections. To prevent the activities of PLpro, several compounds with inhibitory effects have been developed from natural sources. Flavonoid compounds from bay leaf (Syzygium polyanthum) and mahogany bark (Swietenia macrophylla), as well as phenolics from white teak bark (Gmelina arborea Roxb.), have been reported to have antiviral activities, but there are no studies on their potential as PLpro SARS-CoV-2 inhibitors. Therefore, this study aimed to investigate the PLpro SARS-CoV-2 inhibitory effects of 11 bay leaf, 3 mahogany bark, and 6 white teak bark test ligands within silico method using YASARA and PLANTS. The best test ligands obtained were epigallocatechin-3-gallate (-98.93 kcal/mol), catechin (-80.10 kcal/mol), epicatechin (-80.12 kcal/mol), and balanophonin (-83.36 kcal/mol) based on energy binding values surpassing the reference ligands ribavirin (-74.06 kcal/mol) and benserazide (-90.93 kcal/mol). Additionally, these four ligands satisfied physicochemical, pharmacokinetic, and toxicity predictions, in contrast to the natural ligand VIR251, which carries the risk of inhibiting hERG, potentially resulting in fatal outcomes. Based on the results, the compounds could be developed as effective alternative drugs in inhibiting PLpro SARS CoV-2. Keywords: Covid 19, molecular docking, Papain-Like protease, SARS CoV-
In Silico Analysis of Red Betel (Piper crocatum) Active Compounds as Xanthine Oxidase Inhibitors Safithri, Mega; Miantika, Shafillah; Ambarsari, Laksmi
Current Biochemistry Vol. 9 No. 2 (2022)
Publisher : IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/cb.9.2.1

Abstract

Asam urat jika diproduksi secara berlebih oleh tubuh dapat mengakibatkan pembengkakan, rasa nyeri dan kaku dipersendian. Pembentukkan asam urat di tubuh dapat dihambat dengan cara menginhibisi kerja enzim xantin oksidase. Penelitian ini bertujuan mengidentifikasi senyawa aktif sirih merah yang dapat menginhibisi aktivitas enzim xantin oksidase melalui penambatan molekuler (in silico). Metode in silico yang dilakukan yaitu penambatan terarah (site directed docking) dengan menggunakan AutoDock Tools 1.5.6. Ukuran pusat penambatan molekuler sebesar x=26,7853; y= 9,9800; z= 113,3917 dengan nilai dimensi x=14 ; y=14 ; z=18. Senyawa aktif sirih merah terpilih adalah asam protokatekuat, sofalkon, dan 2-(3,4-dimetoksi fenil)-6-etoksi-7- metoksi-1-naftol karena mempunyai nilai ∆G dan Ki yang lebih kecil dibanding allopurinol. Selain itu, senyawa-senyawa aktif tersebut memiliki interaksi residu asam amino yang kuat terhadap sisi aktif xantin oksidase.
In Silico Analysis of Active Compounds of Avocado Fruit (Persea americana Mill.) as Tyrosinase Enzyme Inhibitors Puspita, Puspa Julistia; Liliyani , Ni Putu Peggy; Ambarsari, Laksmi
Current Biochemistry Vol. 9 No. 2 (2022)
Publisher : IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/cb.9.2.3

Abstract

Melanocytes are an important component of skin pigmentation through their ability to produce melanin assisted by the enzyme tyrosinase which is a core enzyme in melanogenesis. The high phenolic and flavonoid compounds in the leaves, seeds and skin of avocados have potential as ligands (inhibitors) of tyrosinase related protein-1. This study aims to determine the active compounds from the leaves, seeds, and skin of avocados that play a role in inhibiting the activity of the tyrosinase enzyme in humans so that it can inhibit the formation of melanin. The research was conducted by molecular anchoring method using YASARA Structure software. The results showed that of the 68 active compounds of avocado leaves, seeds, and skins, there were 11 active compounds that had binding affinity for tyrosinase related protein-1, namely quarcetin, epicatechin, apigenin, 3-Hydroxytyrosol, scopoletin, abscisic acid, citric acid, coumaric acid. , quinic acid, vanillin, and caffeic acid. The active compound abscisic acid is the ligand with the best inhibitory potential with a bond free energy (∆G) of -2,645 kcal/mol which interacts with 17 amino acid residues. The research results can be used as a reference in in vitro and in vivo studies of the human tyrosinase enzyme.
Co-Authors -, Suryani . SURYANI A.E. Zainal Hasan Ade Heri Mulyati Adrian Adiva Aghnia, Diya Agnia Nurul Jannati Agung Isnanto Agustina L.N. Aminin Ahmad Irvan Pratama Ainia Hanifitri Aisyah Girindra Akbar, Nadhira Fathiaz Akhiruddin Maddu Akhmad Endang Zainal Hasan Alimah, Shobiroh Nuur Ambarsavitri, Rahmadhani ANINDA INDRIANI Anja Meryandini Annisa , Alifia Mutiara Annisa Dhiya Athiyyah Khanza Aqilah, Rifany Fairuz Aris Tri Wahyudi Arwansyah Arwansyah Aryani, Hanifah Asrul Muhamad Fuad, Asrul Muhamad Assifah Eryandini Asvarhoza, Genta AYU LESTARI Azhari, Muhammad Alwin Chelsea Chelsea, Chelsea Chelsy Narita Choirunnisa Miftahul Jannah Deki Geraldi Dewi Seswita Zilda Diana Widiastuti DIMAS ANDRIANTO Djarot Sasongko Hami Seno DWI NINGSIH SUSILOWATI DWI NINGSIH SUSILOWATI Dwi SUBIYARTI Dwicesaria, Maheswari Alfira Dwiningsih Susilowati Edy Djauhari Purwakusumah Edy Djauhari Purwakusumah Efi Sanfitri Harahap Elvaza, Azzara Putri Faliha Arinda Lestari Farhan Azhwin Maulana Fathin, Muhammad Faris Fatriani, Rizka Febrianti, Riska Febriyanto, Dimas G Jeni christi A GIA PERMASKU Giovanny, Lisa Gustini Syahbirin H. M. Mochtar Hamidah, Wanda Hanhan Dianhar Harahap, Efi Sanfitri HARTUTIK EKA SUSANTI Hasim - Hasim Hasim Hayati Minarsih Heri Purwoto Hidayat, Radika Evita Hudayanti, Martini Husnawati Husnawati Husnawati, . I MADE ARTIKA I Made Samudera I Made Samudera, I Made I MADE SAMUDRA Ifa Manzila Ifa Manzila Ika Yuni Astutik Ika Yuni Astutik, Ika Yuni Ike Wahyuni Putri Ilham Kurniawan Ilham Kurniawan Imelia Dewi Imron RIYADI Inayah, Mazidah Noer Inda Setyawati, Inda Irma Rahmayani Isnanto, Agung Jaya Hardi Kandi, Rizky Putra Kapitan, Origenes Boy Karichsa Hariana Komalasari, Nurma Angeliani Latifah K Darusman Lestari, Faliha Arinda Liliyani , Ni Putu Peggy Lisa Giovanny Made Suhandana Madyastuti, Rini Marfira, Nurul Mega Safithri Miantika, Shafillah Muhamad Rifai Muhamad Rifai Muhammad Alwin Azhari Muhammad Farhan Muhammad Faris Fathin Muhammad Halim, Muhammad Mustika Luthfia Mustika Permatasari Mustopa, Syahrul Nabila Nur Nafiati Natalia Marbun, Natalia NISA RACHMANIA MUBARIK Nur Qadri Rasyid Nurhidayat Nurhidayat Nurul Marfira Nuur'Alimah, Shobiroh Nuur’Alimah, Shobiroh Pratama, Ahmad Irvan Pratiwi, Anggita Aziz Purwantiningsih Sugita Purwanto, Ukhradiya Magharaniq Safira Purwatiningsih Sugita Puspa Julistia Puspita Putra, Adriansyah Nanda Putri, Ike Wahyuni Radika Evita Hidayah Rahayu, Dyah Utami Cahyaning Rahman, Syabilla Aulia Rasyid, Nur Qadri Ridho Pratama Rifany Fairuz Aqilah Riki Riki Riksa Nur Wahyuni Rini Kurniasih, Rini Rini Novita Riska Febrianti Rosyidah, Rara Annisaur Rury Eryna Putri Sanro Tachibana Sarmila, Sarmila Setyanto Tri Wahyudi Shobiroh Nuur' Alimah Shobiroh Nuur'Alimah Siti Nur'aeni Siti Nurjanah Siti Warnasih Slameut, Fitria Soekarno Mismana Putra Steffanus Gozales Suryani - Suryani Suryani Syamsul Falah TATI NURHAYATI Tirta Setiawan Tony Sumaryada Tri Puji Priyatno Tri Puji Priyatno Uswatun Hasanah Vino , Okta Wahyuni, Riksa Nur Waras Nurcholis Winarti, Novia Yadi Suryadi Yadi Suryadi Yudha, Trah Zahra Silmi Muscifa Zuniar Subastian