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All Journal HAYATI Journal of Biosciences VALENSI International Journal of Renewable Energy Development JURNAL KIMIA SAINS DAN APLIKASI Jurnal Sains Materi Indonesia Science and Technology Indonesia Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Chimica et Natura Acta Indonesian Journal of Chemistry Jurnal Jamu Indonesia Kappa Journal Molekul: Jurnal Ilmiah Kimia International Journal of Renewable Energy Development Borneo Journal of Pharmacy Indonesian Journal of Jamu

Setyanto Tri Wahyudi

Department Of Physics, Faculty Of Mathematical And Natural Sciences, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia

Author-ID : 748784

Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Earth & Planetary Sciences Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Physics 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 Design of Novel Glucagon-Like Peptide 1 Mutants as Candidate for New Peptide Agonist Drugs Tony Sumaryada; Ajeng Widya Roslia; Alfi Afifah; Setyanto Tri Wahyudi; Agus Kartono
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.28.1.92

The binding of glucagon-like peptide 1 (GLP-1) incretin hormone and its receptor GLP-1R plays an important role in the human body. The GLP-1 acts as the insulin secretion stimulator through a GLP-1R agonist activation to avoid the type 2 diabetes mellitus problem. A recent development in computational sciences has enabled us to design a new GLP-1 mutant which has a better binding stability to GLP-1R. In this paper, we have conducted an in-depth analysis of protein-protein docking of GLP-1 and GLP-1R receptor to determine the responsible factors affecting the binding stability. The protein-protein binding stability was analyzed by performing the point mutations on the GLP-1 structure and running the molecular dynamics simulation of the docked structures. Five mutants, Lys20Arg, Lys20His, Lys20Ser, Lys20Gly, and Lys20Ala, has been created computationally and docked with GLP-1R and tested via a molecular dynamics simulation and the free energy perturbation calculation to search for the best-binding mutant. Our results have shown that the Lys20His mutant design has the best potential to be developed as a new peptide agonist drug based on its binding affinity and structural integrity as compared to other mutants and the peptide agonist drugs available in the market exenatide, and liraglutide.

Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates Fikry Awaluddin; Irmanida Batubara; Setyanto Tri Wahyudi
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 7, No. 2, November 2021
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v7i2.21634

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.

NANOSERAT POLIANILIN SEBAGAI CLADDING TERMODIFIKASI PADA SENSOR SERAT OPTIK UNTUK DETEKSI UAP ASETON Akhiruddin Maddu; Hamdani Zain; Ahmad Aminuddin; Setyanto Tri Wahyudi
Jurnal Sains Materi Indonesia Vol 9, No 3: JUNI 2008
Publisher : Center for Science & Technology of Advanced Materials - National Nuclear Energy Agency

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17146/jsmi.2008.9.3.4701

NANOSERAT POLIANILIN SEBAGAI CLADDING TERMODIFIKASI PADA SENSOR SERAT OPTIK UNTUK DETEKSI UAP ASETON. Pada penelitian ini digunakan bahan nanoserat polianilin sebagai cladding termodifikasi pada sistem sensor serat optik untuk mendeteksi uap aseton. Sensor ini dirancang berdasarkan perubahan absorpsi medan evanescent pada bidang batas inti-cladding polianilin akibat perubahan sifat optiknya ketika diekspos dengan uap aseton. Nanoserat polianilin yang disintesis dengan metode polimerisasi interfasial, dilapiskan pada bagian inti serat optik yang telah dilepas cladding aslinya dan berfungsi sebagai bagian penginderaan (sensing element). Respon sensor serat optik diuji dengan mengukur intensitas transmisi cahaya yang melewati sistem sensor serat optik saat diekspos dengan uap aseton. Berdasarkan kurva respon sensor diperoleh waktu respon 30 detik dan waktu pemulihan (recovery) 10 detik. Sensor serat optik ini juga memperlihatkan kemampuan balik (reversibility) dan pengulangan (repeatability) yang cukup baik. Sensitivitas sensor terhadap tekanan uap aseton dihasilkan sebesar 1,25 %/mmHg, artinya besar perubahan intensitas transmisi untuk setiap perubahan 1 mmHg adalah 1,25 %.

PENUMBUHAN FILM CdO DENGAN METODE CHEMICAL BATH DEPOSITION (CBD) Akhiruddin Maddu; Johan D. Sirait; Setyanto Tri Wahyudi
Jurnal Sains Materi Indonesia Vol 10, No 1: OKTOBER 2008
Publisher : Center for Science & Technology of Advanced Materials - National Nuclear Energy Agency

PENUMBUHAN FILM CdO DENGAN METODE CHEMICAL BATH DEPOSITION (CBD). Film CdO ditumbuhkan pada supstrat kaca dalam dua tahap, yaitu deposisi dengan metode Chemical Bath Deposition (CBD) dan dilanjutkan dengan pemanasan pada 250 oC dan 400 oC. Morfologi film CdO memperlihatkan bentuk bongkahan berukuran sekitar 1 μm, sedangkan ketebalan filmsekitar 1 μm berdasarkan hasil SEM. Hasil analisis XRD memperlihatkan bahwa fasa kristal mengalami transformasi akibat pemanasan. Film yang dipanaskan pada 250 oC didominasi oleh fasa CdCO3 dan pemanasan lanjutan pada 400 oC berubah fasa CdCO3 menjadi fasa CdO. Fasa kristal CdO memiliki struktur FCC dengan nilai parameter kisi yang diperoleh sebesar 4,70 Å. Nilai celah pita energi (Eg) ditentukan berdasarkan spektrum transmisi film CdO,diperoleh nilai Eg sebesar 2,1 eV untuk kedua film.

The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G Tony Ibnu Sumaryada; Kania Nur Sawitri; Setyanto Tri Wahyudi
Indonesian Journal of Chemistry Vol 18, No 1 (2018)
Publisher : Universitas Gadjah Mada

Molecular dynamics simulations of the B1 fragment of protein G (56 residues) have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance) of the salt-bridge pairs E27–K31 (in the α-helix) and E56–K10 (connecting β4 and β1) has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained

Homology Modeling and Structural Dynamics of the Glucose Oxidase Farhan Azhwin Maulana; Laksmi Ambarsari; Setyanto Tri Wahyudi
Indonesian Journal of Chemistry Vol 20, No 1 (2020)
Publisher : Universitas Gadjah Mada

Glucose oxidase from Aspergillus niger IPBCC.08.610 (GOD_IPBCC) is a locally sourced flavoenzyme from Indonesia that can potentially be developed in a variety of industrial processes. Although this enzyme has a high activity in catalyzing the redox reactions, the use of this enzyme was still limited to be applied as glucose biosensor. Using information from the amino acid sequences, a computational structure of GOD_IPBCC was therefore designed by homology modeling method using two homologous structures of GOD from protein data bank (1CF3 and 5NIT) as the templates. The quality of the resulting structures was evaluated geometrically for selection of the best model, and subsequently, 50 ns of MD simulations were carried out for the selected model as well as the corresponding template. Results obtained from the validation analysis showed that the 1CF3 template-built structure was selected as the best reliable model. The structural comparison exhibited that the best-modeled structure consisted of two functional domains and three catalytic residues similarly to the corresponding experimental structure. The overall dynamic behavior of the 50 ns of the structure was structurally stable and comparable with that of the positive control both from globally and locally observations. Implications of these stable nature within the best-modeled structure unfold the possibilities in search of notable residues and their roles to enhance enzyme thermostability.

Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus Muhammad Arba; Andry Nur-Hidayat; Ida Usman; Arry Yanuar; Setyanto Tri Wahyudi; Gilbert Fleischer; Dylan James Brunt; Chun Wu
Indonesian Journal of Chemistry Vol 20, No 6 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.56120

The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-dependent RNA polymerase. It is the key enzyme in the viral replication machinery, and it does not exist in human beings, therefore its targeting has been considered as a strategic approach. Here we describe the identification of potential hits from Indonesian Herbal and ZINC databases. The pharmacophore modeling was employed followed by molecular docking and dynamics simulation for 40 ns. 151 and 14480 hit molecules were retrieved from Indonesian herbal and ZINC databases, respectively. Three hits that were selected based on the structural analysis were stable during 40 ns, while binding energy prediction further implied that ZINC1529045114, ZINC169730811, and 9-Ribosyl-trans-zeatin had tighter binding affinities compared to Remdesivir. The ZINC169730811 had the strongest affinity toward RdRp compared to the other two hits including Remdesivir and its binding was corroborated by electrostatic, van der Waals, and nonpolar contribution for solvation energies. The present study offers three hits showing tighter binding to RdRp based on MM-PBSA binding energy prediction for further experimental verification.

Antioxidant Analysis of Kawa Daun (Coffea canephora) Beverage by In Vitro and In Silico Approaches Ifwarisan Defri; Nurheni Sri Palupi; Setyanto Tri Wahyudi; Nancy Dewi Yuliana
Indonesian Journal of Chemistry Vol 22, No 2 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.69422

In Tanah Datar Regency, West Sumatra, Indonesia, the waste of pruning coffee leaves (Coffea canephora) is utilized as a traditional beverage called "Kawa Daun". For a consistent quality of Kawa Daun functional beverage, we evaluated the effect of different smoking times (0, 2, 4, and 6 h) on its in vitro DPPH antioxidant activity. Estimation of antioxidant components from the coffee leaf was conducted in silico using Peroxiredoxin V (PrxV) with 3MNG code as a receptor, and 33 phytochemicals were reported to be present in the coffee leaves as ligands. As a result, Kawa Daun, with a 2-h smoking time, had the highest antioxidant activity. Molecular docking between PrxV and the 33 compounds resulted in the ten most potential compounds based on the affinity energy. They were xanthone (-4.9 kcal/mol), uric acid (-4.8 kcal/mol), xanthosine (-4.8 kcal/mol), caffeine (-4.6 kcal/mol), 3-methylxanthine (-4.6 kcal/mol), 7-methylxanthosine (-4.6 kcal/mol), theobromine (-4.5 kcal/mol), theophylline (-4.5 kcal/mol), caffeic acid (-4.5 kcal/mol), and xanthine (-4.4 kcal/mol). These ten ligands had stronger interactions than the control ligand 1.2-dithiane-4.5-diol (-3.6 kcal/mol). This research showed the potential of Kawa Daun as a functional beverage with antioxidant activity. Further confirmation on the antioxidant potential of this beverage using an in vivo method is recommended.

Potential Adenostemma lavenia and Muntingia calabura Extracts to Inhibit Cyclooxygenase-2 Activity as a Therapeutic Strategy for Anti-inflammation: Experimental and Theoretical Studies Bagaskoro Tuwalaid; Dyah Iswantini; Setyanto Tri Wahyudi
Indonesian Journal of Chemistry Vol 22, No 3 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.70794

Continuous inflammation can cause new and more severe diseases, thus effective treatments are needed. One of the common inflammation treatments is given by reducing prostaglandins' production through the inhibition of COX-2 activity. This experiment aims to examine the potential application of plant extracts of Adenostemma lavenia and Muntingia calabura (Jamaica cherry) as anti-inflammatory agents in inhibiting COX-2 activity through in silico and in vitro assays. Molecular docking and molecular dynamics simulation were accomplished to evaluate the stability of the complex between COX-2 and ligands. The COX-2 inhibition was determined using the COX-2 Inhibitor Screening Assay KIT. Based on the docking results, the active compound from A. lavenia, ligand 1a,9b-dihydro-1H-cyclopropa[a]anthracene, has the lowest binding energy of -8.7 kcal/mol. In comparison, M. calabura contains 7-hydroxyflavone ligand with a Gibbs free energy of -9.1 kcal/mol. The molecular dynamics study demonstrates that COX-2 maintains its stability when forming interactions with selected compounds from all the tested extracts. The results of the COX-2 inhibition test showed that 96% EtOH extract of A. Lavenia at concentrations of 25 and 100 ppm had an inhibitory activity of 98%; meanwhile, 70% and 96% EtOH extracts of M. calabura at 1000 ppm concentration could inhibit COX-2 activity up to 100%. The results demonstrate that both plants show potential anti-inflammatory activity.

Co-Authors Abdulloh Rifai Agus Kartono Ahmad Aminuddin Ahmad, Faozan Ajeng Widya Roslia Akhiruddin Maddu Alfi Afifah Andry Nur-Hidayat Arba, Muhammad Arba, Muhammad Ardian Arif Arry Yanuar Asoka, Shadila Fira Auliya Ilmiawati Ayu Rahmania Lestari Badrunanto, Badrunanto Bagaskoro Tuwalaid Charlena Chun Wu Dwi Iryani, Ryscha Dyah Iswantini Dylan James Brunt Farhan Azhwin Maulana Fikry Awaluddin Fikry Awaluddin Gilbert Fleischer Hamdani Zain Harry Noviardi Ida Usman Ifwarisan Defri Ilham Kurniawan Ilham Kurniawan Irmanida Batubara Johan D. Sirait Joni Prasetyo, Joni Kania Nur Sawitri LAKSMI AMBARSARI Muhammad Farid Muscifa, Zahra Silmi Nancy Dewi Yuliana Nurmawan, Cucu Putri Palupi, Nurheni Sri Rini Kurniasih, Rini Sianipar, Rut Novalia Rahmawati Sri Mulijani Sulaeman, Ahmad Sofyan Tatik Khusniati Tony Sumaryada Wulan Tri Wahyuni Yuantoro, Yandra Zahra Silmi Muscifa

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