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All Journal HAYATI Journal of Biosciences JURNAL KIMIA SAINS DAN APLIKASI Current Biochemistry Indonesian Journal of Pharmaceutical Science and Technology ALCHEMY Jurnal Penelitian Kimia Indonesian Journal of Chemistry QARDHUL HASAN: MEDIA PENGABDIAN KEPADA MASYARAKAT Jurnal Farmamedika (Pharmamedica Journal) Indonesian Journal of Applied Research (IJAR)

Rini Kurniasih, Rini

Department Of Biochemistry, Faculty Of Mathematics And Natural Sciences, Bogor Agricultural University, Kampus IPB Dramaga, Bogor 16680, West Java

Author-ID : 552891

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Education Energy Engineering Environmental Science Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Medicine & Pharmacology Social Sciences Other

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Structure Identification and Quality Assessment of Laccase (Lac InaCC) from Neurospora crassa by Using a Structure Prediction Rini Kurniasih; Laksmi Ambarsari; Setyanto Tri Wahyudi
HAYATI Journal of Biosciences Vol. 28 No. 1 (2021): January 2021
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.28.1.1

Laccases are multi-copper oxidase enzyme, developed for being applied widely. The laccase gene in this study was isolated from local isolates of Neurospora crassa (LAC inaCC). The structure of this enzyme has not been known and there is no laccase structure of Neurospora crassa based on protein structure development in database. Here, we aimed to analyze the characteristics of the sequence and prediction structure, the structure quality after refinement through the molecular dynamics (MD) simulation method. LAC inaCC has been identified with typical sequence motifs (HWH, HSH, HXXH) which played role in copper-binding on 274(HWH)G-DG-T-CP on CBL-1, 314GT-WY(HSH)FS-QYG-G on CBL-2, and 607HPIHL on CBL-3. The four copper atoms have an important role in the catalytic activity. LAC inaCC is a multi-subunit enzyme consisted of three functional domains with structural motifs of Greek-key β barrel which is typical structure motif. Refinement in the prediction structure through the MD simulation showed that this method was proven to be able to improve the structure quality. The increase on the most favoured area on Ramachandran plot, clashcore percentile score, and molprobity score showed that the laccase structure headed to conformation change, to be more stable conformation with better resolution compared to earlier prediction structure.

In Silico, to Determine The Active Compounds of Black Tea and Turmeric In Increasing The Activity of The Enzyme Sod Akhmad Endang Zainal Hasan; Mega Safithri; Aziz Syamsul Huda; Rini Kurniasih
Indonesian Journal of Applied Research (IJAR) Vol. 3 No. 1 (2022): Indonesian Journal of Applied Research (IJAR)
Publisher : Universitas Djuanda

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30997/ijar.v3i1.187

Damage to cells caused by stress can be reduced by the presence of antioxidants, one of which is Superoxide dismutase (SOD). The role of the active ingredients of black tea and turmeric will be studied using the in-silico method to identify the active compounds as components in SOD activation. The bioavailability and toxicity of the active compounds of black tea and turmeric were studied and followed by molecular docking and virtual games. The parameters studied are Gibbs's free energy (∆G) and binding site similarity (BSS). The results were analyzed using Gibbs's free energy (∆G) and binding site similarity (BSS) parameters. It was found that those that could increase the activity of Cu/Zn SOD enzymes were Epicatechin gallate (black tea) and curcumin (turmeric), with values of -9.5 and -7.4 Kcal/mol and the same BSS value of 81.8%. The control ligand used was beta amyrin. According to Lipinski's rules, Epicatechin gallate and curcumin compounds can be absorbed well and are safe for consumption. This study concludes that Epicatechin gallate, an active compound of black tea, and curcumin, an active compound of turmeric rhizome, have the best potential to increase the activity of Cu/Zn SOD enzymes based on the results of virtual screening and molecular docking. Epicatechin gallate and curcumin are predicted to be well absorbed by the body because they qualify Lipinski's rules and are not toxic and safe for consumption.

Immobilization of Glucose Oxidase on Modified-Carbon-Paste-Electrodes for Microfuel Cell Laksmi Ambarsari; Inda Setyawati; Rini Kurniasih; Popi Asri Kurniatin; Akhiruddin Maddu
Indonesian Journal of Chemistry Vol 16, No 1 (2016)
Publisher : Universitas Gadjah Mada

Glucose oxidase (GOx) is being developed for many applications such as an implantable fuel cell, due to its attractive property of operating under physiological conditions. This study reports the functional immobilization of glucose oxidase onto polyaniline-nanofiber-modified-carbon-paste-electrodes (GOx/MCPE) as bioanodes in fuel cell applications. In particular, GOx is immobilized onto the electrode surface via a linker molecule (glutaraldehyde). Polyaniline, synthesized by the interfacial polymerization method, produces a morphological form of nanofibers (100-120 nm) which have good conductivity. The performance of the polyaniline-modified-carbon-paste-electrode (MCPE) was better than the carbon- paste-electrode (CPE) alone. The optimal pH and temperature of the GOx/MCPE were 4.5 (in 100 mM acetate buffer) and 65 °C, respectively. The GOx/MCPE exhibit high catalytic performances (activation energy 16.4 kJ mol-1), have a high affinity for glucose (Km value 37.79 µM) and can have a maximum current (Imax) of 3.95 mA. The sensitivity of the bioelectrode also was high at 57.79 mA mM-1 cm-2.

In Silico Screening of Cinnamon (Cinnamomum burmannii) Bioactive Compounds as Acetylcholinesterase Inhibitors Zatta Yumni Ihdhar Syarafina; Mega Safithri; Maria Bintang; Rini Kurniasih
Jurnal Kimia Sains dan Aplikasi Vol 25, No 3 (2022): Volume 25 Issue 3 Year 2022
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Alzheimer’s is a progressive and neurodegenerative disease that mainly affects people aged 65 years and older. The pathophysiology of Alzheimer’s is possibly related to the depletion of the neurotransmitter acetylcholine (ACh) due to beta-amyloid plaques and neurofibrillary tangles. Secondary metabolites found in cinnamon bark (Cinnamomum burmannii) have the potential as anticholinesterases to treat Alzheimer’s symptoms. This study aimed to identify the potency of bioactive compounds from cinnamon bark as AChE inhibitors in silico through analysis of binding energy, inhibition constants, and types of interactions. The research was conducted by screening virtually 60 test ligands using the PyRx program and molecular docking using the Autodock Tools program. The results of the ligand-receptor interaction analysis showed that 12 of the 15 tested ligands had potential as AChE inhibitors. Epicatechin and medioresinol are the ligands with the best potential for AChE inhibition with affinity close to the natural ligand or donepezil. Epicatechin has a binding energy of −10.0 kcal/mol and inhibition constant of 0.0459 M, with four hydrogen bonds and seven hydrophobic bonds. Meanwhile, medioresinol has −9.9 kcal/mol binding energy and inhibition constant of 0.0543 M, with one hydrogen bond and thirteen hydrophobic bonds.

PENAPISAN VIRTUAL SENYAWA AKTIF SIRIH MERAH (Piper Crocatum) SEBAGAI INHIBITOR ANGIOTENSIN CONVERTING ENZYME Riyan Alifbi Putera Irsal; Djarot Sasongko Hami Seno; Mega Safithri; Rini Kurniasih
Jurnal Farmamedika (Pharmamedika Journal) Vol 7 No 2 (2022): Jurnal Farmamedika (Pharmamedica Journal)
Publisher : Sekolah Tinggi Teknologi Industri dan Farmasi Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47219/ath.v7i2.157

Lisinopril (Angiotensin Converting Enzyme inhibitor) merupakan obat pilihan lini pertama dalam pengobatan hipertensi, namun obat tersebut masih memiliki banyak efek samping. Sirih merah telah banyak digunakan dalam pengobatan herbal dan diharapkan berpotensi menghambat aktivitas ACE (Angiotensin Converting Enzyme). Penelitian ini bertujuan untuk menemukan senyawa aktif yang berpotensi menghambat ACE in silico dengan metode molecular anchoring. Enzim ACE memiliki sisi pengikatan Metal binding yang mengikat di logam zinc, interaksi tersebut melibatkan asam amino HIS383, HIS387, dan GLU411. Situs aktif dari enzim ACE terletak pada asam amino GLU384. Ion zinc merupakan komponen penting dari ACE karena terikat pada situs aktif. Terdapat 7 ligan yang berinteraksi dengan asam amino penting sesuai ligan alami dan bernilai (bebas Gibbs dan Ki) lebih negatif dari ligan alaminya. Terdapat 1 ligan yang menjadi terbaik diantara 7 ligan yaitu, 3S,5R,8R,9R,10R,12R,13R,14R,17S)-17-[(2S)-5-[2-(3,4-dimethoxyphenyl)ethylamino]-2-hydroxypentan-2-yl]- 4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,12- diol.

Penambatan Molekuler Senyawa Aktif Sirih Merah (Piper crocatum) pada Butirilkolinesterase sebagai Kandidat Antialzheimer Rahmadi Ganesha Putri; Mega Safithri; Husnawati Husnawati; Rini Kurniasih
ALCHEMY Jurnal Penelitian Kimia Vol 19, No 1 (2023): March
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.19.1.59676.68-85

Alzheimer adalah salah satu penyakit neurodegeneratif kronis dan menjadi penyakit yang sering dialami oleh orang lanjut usia. Perubahan yang terjadi dari penyakit Alzheimer, yakni penurunan fungsi kognitif, memori, dan perubahan perilaku secara permanen. Senyawa aktif pada daun sirih merah memiliki kesamaan kandungan dengan daun sirih hijau untuk menghambat butirilkolinesterase (BChE). Butirilkolinesterase adalah salah satu enzim yang berperan dalam penanganan penyakit Alzheimer dikaitkan dengan terbentuknya Alzheimer, yakni hipotesis kolinergik. Penelitian dilakukan menguji daya inhibisi senyawa aktif yang terkandung dalam daun sirih merah terhadap aktivitas butirilkolinesterase melalui pendekatan simulasi penambatan molekuler. Penelitian menggunakan dua metode, yakni penggabungan penapisan virtual dan penambatan molekuler sebagai tahapan awal pengembangan daun sirih merah terhadap aktivitas penghambatan butirilkolinesterase. Hasil dalam penelitian diperoleh, daya inhibisi terbaik ditemukan pada 1,2,3,4,5,6,7-heptazacycloicosane sebesar 0,4888 µM dan energi bebas pengikatan sebesar -8,6 kkal∙mol-1. Residu yang berperan dalam menghambat butirilkolinesterase, yakni pada pengikatan substrat oleh ligan uji, yakni Tyr-332 dan Trp-82. Hasil penelitian ini dapat dijadikan sebagai sumber referensi dalam menemukan alternatif pengobatan penyakit Alzheimer. Molecular Docking of the Active Compound of Red Betel (Piper crocatum) on Butyrylcholinesterase as an Antialzheimer's Candidate. Alzheimer's is a chronic neurodegenerative disease often experienced by the elderly. Changes that occur from Alzheimer's disease such as permanent decline in cognitive function, memory, and behavioral changes. The active compounds in red betel leaves have similar contents with green betel leaves to inhibit butyrylcholinesterase (BChE). Butyrylcholinesterase is an enzyme that may play an important role in the treatment of Alzheimer's disease associated with the formation of Alzheimer's, the cholinergic hypothesis. The study tested the inhibition power of the active compounds contained in red betel leaves against the activity of butyrylcholinesterase through a molecular docking simulation approach. The method in the study used the merger of virtual screening and molecular docking as the initial stage for the development of red betel leaves against the inhibitory activity of butyrylcholinesterase. The result in the study found the best inhibitiron power was found at 1,2,3,4,5,6,7-heptazacycloicosane of 0.4888 µM and binding free energy of -8.6 kkal∙mol-1. The residues that play a role in the inhibition of butyrylcholinesterase on substrate binding by test ligands were Tyr-332 and Trp-82. The research result can be used as a reference in finding alternative treatments for Alzheimer's disease.

Molecular Docking of Red Betel Leaf Bioactive Compounds (Piper crocatum) as Lipoxygenase Inhibitor Fernanda Chairunisa; Mega Safithri; Dimas Andrianto; Rini Kurniasih; Riyan Alifbi Putera Irsal
Indonesian Journal of Pharmaceutical Science and Technology Vol 10, No 2 (2023)
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24198/ijpst.v10i2.38934

Degenerative diseases occurred due to several risk factors that are directly related to inflammationwhich affected several diseases such as coronary heart disease (CHD) and diabetes. One of theinflammatory causative agents is leukotrienes produced by the lipoxygenase enzyme (LOX) so thatit takes anti-inflammatory drugs made from herbal plants. Red betel leaf (Piper crocatum) potentiallyinhibited the lipoxygenase enzyme because it contains potential phytochemical compounds suchas alkaloids, flavonoids, eugenol, saponins, and tannins. This research aimed to test the inhibitionof active compounds from extract and fractions of red betel leaves that have the best inhibition forlipoxygenase enzymes causing malondialdehyde formed through molecular docking simulations. Thisresearch used lipoxygenase enzyme as receptor (PRB code: 4NRE), C8E as natural ligand and activecompound from extract and fractions of red betel leaves as a ligand. The highest inhibition regarded toNandrolone phenylpropionate and Sofalcone ligand with -10.4 kcal/mol and -9.1 kcal/mol of affinityenergy. Amino acid residues that played a role in ligand and receptor interaction were HIS373 andHIS378. The receptor structure with the best ligands was declared stable based on molecular dynamicssimulations.

The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis Syamsul Falah; Laksmi Ambarsari; Dimas Andrianto; Rini Kurniasih; Sanro Tachibana
Jurnal Kimia Sains dan Aplikasi Vol 26, No 5 (2023): Volume 26 Issue 5 Year 2023
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jksa.26.5.166-177

A Flavonoid glycoside compound, isolated and identified from E. polyantha as myricitrin, was analyzed as a ligand for its molecular binding activity against SARS-CoV-2 protein (receptor binding domain on Spike/RBD, main protease/nsp5, EndoRNAse, RNA-dependent-RNA-polymerase/RdRp), and its receptor, ACE2, and computationally assessed via molecular docking method. This study aims to determine the potential of myricitrin in E. polyantha from Indonesia as an antiviral drug for SARS-CoV-2 through molecular docking and molecular dynamic simulation analysis. The results showed that the myricitrin had the strongest binding affinity energy towards the three important SARS-CoV-2 proteins, namely endoRNAse, main protease (3CLpro), and RdRp with ∆G values of −9.60 kcal/mol, −8.40 kcal/mol, and −8.30 kcal/mol, respectively. These values are stronger than the comparator ligands of favipiravir (−5.60 kcal/mol), atazanavir (−7.20 kcal/mol), and remdesivir (−7.70 kcal/mol). This indicated that the compound has the potential as an inhibitor against 3CLpro, endoRNAse, and RdRp of SARS-CoV-2 proteins. This result was supported by the prediction made according to the Molprobity and PASS Online web servers, which showed that myricitrin has high bioactivity potential as an enzyme inhibitor (with a score of 0.38) and antiviral (with a score of 0.704).

INHIBISI EKSTRAK DAUN SIRIH MERAH TERHADAP LIPASE PANKREAS SEBAGAI ANTIOBESITAS SECARA IN SILICO Mega Safithri; Nur Azizah; Maria Bintang; Rini Kurniasih
Jurnal Farmamedika (Pharmamedika Journal) Vol 8 No 2 (2023): Jurnal Farmamedika (Pharmamedica Journal)
Publisher : Sekolah Tinggi Teknologi Industri dan Farmasi Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47219/ath.v8i2.214

A Obesity triggers the emergence of various degenerative diseases, such as stroke, heart disease, type 2 diabetes, and insulin resistance. Pancreatic lipase inhibitors are anti-obesity drug agents that work by inhibiting pancreatic lipase enzymes. This study aims to search and predict the inhibitory activity of pancreatic lipase from the active compound of red betel leaf. The research began with virtual screening of 60 test ligands, prediction of ligand stability and toxicity, validation method of molecular docking, molecular docking, 2D and 3D visualization. The results showed that benzethonium octyloxyacetate, salicylic acid beta-D-glucopyranosyl ester, and anthocyanins had the best potential in inhibiting pancreatic lipase enzymes based on virtual screening, ligand stability, ligand toxicity, energy affinity, number of hydrogen bonds with active site, bond distance, and constants inhibition (Ki). Benzethonium octyloxyacetate has an affinity value of -8 kcal/mol, has a hydrogen bond interaction on the His349 residue on the active site of the pancreatic lipase receptor (6KSM) with a bond distance of 2,94 Å and Ki value of 1,347 μM.

Minyak atsiri Kapulaga (Elettaria cardamomum) sebagai inhibitor Sap 5 Candida albicans penyebab kandidiasis vulvovaginalis (KVV) secara in silico Gusnia Meilin Gholam; Rini Kurniasih; I Made Artika
Current Biochemistry Vol. 11 No. 1 (2024)
Publisher : IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/cb.11.1.5

ABSTRACT Vulvovaginal candidiasis (VVC) is a disease caused by the inflammatory process of the vulva and vaginal mucosa caused by Candida sp., mainly Candida albicans. This study aimed to analyze the molecular interaction between the volatile oil in cardamom and Sap 5 as an inhibitor of Candida albicans causing VVC through In silico molecular interaction analysis. The methods used are analysis of homology, structural quality, and essential areas, receptor and ligand preparation, gridbox validation, virtual screening, Lipinski prediction and toxicity, and ligand-receptor interaction visualization analysis. The results showed that essential oils have the potential to inhibit Sap 5 through molecular bonding and produce interactions in the form of hydrogen bonds, electrostatic bonds, and hydrophobic interactions. The best test ligands were Geranyl acetate (-6.78 kcal/mol), Alpha-terpinyl acetate (-6.07 kcal/mol), 1,8-Sineol (-5.47 kcal/mol), and Linalool (-5.06 kcal/mol). The test ligands have contact with catalytic residues on Asp32/Asp218. In addition, the properties of these ligands also meet the Lipinski and Toxicity rules, so they can be predicted to be safe. Keywords: Candida albicans, Cardamom, Essential oil, In silico, Sap 5 ABSTRAK Kandidiasis vulvovaginalis (KVV) merupakan penyakit akibat dari proses inflamasi vulva dan mukosa vagina yang disebabkan oleh Candida sp. utamanya Candida albicans. Penelitian ini bertujuan untuk menganalisis interaksi molekuler antara minyak atsiri yang terkandung pada kapulaga dengan Sap 5 sebagai inhibitor Candida albicans penyebab KVV melalui analisis interaksi molekuler secara In silico. Metode yang digunakan yaitu analisis homologi, kualitas struktur, dan daerah penting, preparasi reseptor dan ligan, validasi gridbox, penapisan virtual, prediksi Lipinski dan toksisitas, dan analisis visualisasi interaksi ligan-reseptor. Hasil penelitian menunjukkan bahwa minyak atsiri mempunyai potensi menghambat Sap 5 melalui penambatan molekuler dan menghasilkan interaksi berupa ikatan hidrogen, ikatan elektrostatik, dan interaksi hidrofobik. Golongan ligan uji yang terbaik yaitu Geranil asetat (-6.78 kkal/mol), Alfa-terpinil asetat (-6.07 kkal/mol), 1,8-Sineol (-5.47 kkal/mol), dan Linalool (-5.06 kkal/mol). Ligan uji tersebut mempunyai kontak residu katalitik pada Asp32/Asp218. Selain itu, sifat ligan tersebut juga memenuhi aturan Lipinski dan Toksisitas, sehingga dapat diprediksi aman. Kata kunci: Candida albicans, Kapulaga, Minyak atsiri, In silico, Sap 5

Co-Authors Achyar, Catellia Auliany Akhiruddin Maddu Akhmad Endang Zainal Hasan Aziz Syamsul Huda Destiandani, Khansa Dimas Andrianto DIMAS ANDRIANTO Djarot Sasongko Hami Seno Dwicesaria, Maheswari Alfira Febrina, Adella Fernanda Chairunisa Fitrilia, Tiana Gholam, Gusnia Meilin Gusnia Meilin Gholam Heri Saptadi Ismanto Hudayanti, Martini Husnawati Husnawati I MADE ARTIKA Inda Setyawati, Inda LAKSMI AMBARSARI M.A. Primaningrum Dian, M.A. Primaningrum Maria Bintang MARIA BINTANG Mega Safithri Nur Azizah Nusyarah, Ayu Tri Purwanto, Ukhradiya Magharaniq Safira Rahmadi Ganesha Putri Raisyadikara, Fadila Riyan Alifbi Putera Irsal Riyan Alifbi Putera Irsal Rosyidah, Rara Annisaur Sanro Tachibana Setyanto Tri Wahyudi Syamsul Falah Zatta Yumni Ihdhar Syarafina

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