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All Journal Journal of Food and Pharmaceutical Science VALENSI JURNAL KIMIA SAINS DAN APLIKASI Pharmaciana: Jurnal Kefarmasian Biology, Medicine, & Natural Product Chemistry Biopropal Industri Journal of Islamic Pharmacy JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Chimica et Natura Acta ALCHEMY Jurnal Penelitian Kimia JMM (Jurnal Masyarakat Mandiri) Journal of Pharmacopolium MATAPPA: Jurnal Pengabdian Kepada Masyarakat Jurnal Inovasi Hasil Pengabdian Masyarakat (JIPEMAS) Jurnal Kreativitas PKM Molekul: Jurnal Ilmiah Kimia Jurnal Ilmu Kefarmasian Indonesia Jurnal Farmasi Sandi Karsa Kumawula: Jurnal Pengabdian Kepada Masyarakat Jurnal Analis Farmasi Pharmacoscript Jurnal Ilmiah Farmako Bahari Jurnal Farmagazine Agrinimal Jurnal Ilmu Ternak dan Tanaman Jurnal Farmasi dan Sains Indonesia (JFSI) JAF (Jurnal Analis Farmasi) JIFI (Jurnal Ilmiah Farmasi Imelda) Jurnal Riset Rumpun Ilmu Kesehatan (JURRIKES) Jurnal Pengabdian Pada Masyarakat Media Informasi Journal of Food and Pharmaceutical Sciences Pharmaceutical Science Journal Prosiding Seminar Nasional Unimus
Richa Mardianingrum
Universitas Perjuangan Tasikmalaya
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 1 
The Active Compound of Bangle Essential Oil as Cyclooxygenase-2 (Cox-2) Inhibitor: In Silico Approach Richa Mardianingrum; Ruswanto Ruswanto; Gina Septiani Agustien; Aas Nuraisah
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 6, No. 2, November 2020
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v6i2.16943

Abstract

Fever is a condition where the body temperature rises above normal or more than 37o C and also tend to be an initial clinical manifestation of the use of antipyretic drugs thatcause toxicity such as on the liver due to prolonged usage. Particularly, the bangle (Zingiber purpureum Roxb.) is one of the Zingiberaceae plants that contain essential oils used for the treatment of fever. Therefore, this researchaimed to identify active compounds which have antipyreticspotential with the in silico approach. The simulation of molecular docking showed 1,4-naphthalenedione-2-ethyl-3-hydroxy was able to attach to the binding site of cyclooxygenase-2 (COX-2) and interact withmain residues that constituted the active cavity of COX-2. While the simulation of molecular dynamics suggested thatthe bound compound was stable at 4 ns, that is the time taken. The binding free energiesexpected by the MM-PBSA method indicated the 1,4-naphthalenedione-2-ethyl-3-hydroxy had a higher affinity than a native ligand (2-[(2,6-dichloro-3-methyl-phenyl)-amino] benzoic acid, JMS) and paracetamol. This suggested its capacity for advancing as a new COX-2 inhibitor.
Desain dan Studi In Silico Senyawa Turunan Kuwanon-H sebagai Kandidat Obat Anti-HIV Ruswanto Ruswanto; Tifa Nofianti; Richa Mardianingrum; Tresna Lestari
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 4, No. 1, Mei 2018
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1038.7 KB) | DOI: 10.15408/jkv.v4i1.6867

Abstract

Kuwanon-H merupakan senyawa flavonoid dari kulit akar  murbei (Morus alba L) yang secara in vitro berpotensi sebagai anti-HIV dibanding senyawa flavonoid lainnya yang terkandung dalam kulit akar murbei seperti morusin dan morusin 4′-glucosida. Telah dilakukan penelitian desain senyawa, penambatan molekular menggunakan ArgusLab 4.0.1 dengan metode ArgusDock, penerapan aturan Lipinski’s Rule of Five menggunakan Marvin Sketch 5.2.5.1dan uji toksisitas menggunakan aplikasi Toxtree secara in silico terhadap turunan senyawa kuwanon-H. Desain enam puluh senyawa turunan kuwanon-H dilakukan dengan cara model pendekatan Topliss pada rantai samping alifatiknya. Hasil penambatan ke-60 turunan senyawa pada reseptor HIV-1 Reverse Transcriptase (1REV) menunjukkan bahwa senyawa terbaik yaitu 3-[(2Z)-3-(siklopropilmetil)but-2-en-1-il]-8-[6-({3-[(2Z)-3-(siklopropilmetil)but-2-en-1-il]-2,4-dihidroksifenil}karbonil)-5-(2,4-di-hidroksilfenil)-3-metilsiklohek-2-en-1-il]-2-(2,4-dihidroksilfenil),7-dihidroksi-4H-kromen-4-on dengan nilai energi bebas yang lebih rendah (-12.5798 kkal/mol) dibandingkan ligan asli (-11.0445 kkal/mol) dan kuwanon-H (-11.0189 kkal/mol). Senyawa terbaik ini tidak memenuhi aturan Lipinski’s Rule of Five. Hasil prediksi uji toksisitas senyawa terbaik menurut parameter Cramer Rules termasuk kategori III, yaitu diprediksi memiliki toksisitas tinggi, menurut parameter Benigni/Bossa Rulebase diprediksi senyawa yang diuji tidak bersifat karsinogenik, genotoksik, dan nongenotoksik, sedangkan menurut parameter Kroes TTC decision tree diprediksi senyawa uji berpotensi toksik.DOI:http://dx.doi.org/10.15408/jkv.v4i1.6867 
Synthesis, Characterization and In Silico Study of Fe(III) Complex with N'-(4-Chlorobenzoyl)-Isonicotino-Hydrazide as Anti Tuberculosis Candidate Ruswanto Ruswanto; Fajar Setiawan; Nur Rahayuningsih; Richa Mardianingrum; Nur Laili Dwi Hidayati; Elsi Eryanti
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 6, No. 1, May 2020
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1586.366 KB) | DOI: 10.15408/jkv.v6i1.11788

Abstract

The synthesis of Fe(III) complexes with ligands N'-(4-Chlorobenzoyl)isonicotinohydrazide can be synthesized through mixing metal and ligand dissolved in ethanol by reflux at ± 75oC for 5 hours. The instruments for the characterization of the complex were used UV-Visible and Infrared Spectrophotometry. The aims of the study are: to determine the synthesis method, characterize of the complex, and to study the interaction of the complex with target receptors. The weight of the synthesized compound was obtained by 38.1 mg. The purity of the complex has been tested using the determination of melting point and got a melting point range was 196-198oC. The maximum wavelength of Fe(III)N'-(4-Chlorobenzoyl)isonicotinohydrazid) complex was  261.0 nm and provide absorption of Fe-O vibrations at wavenumbers 530.42 cm-1. The docking process was done using AutodockTools-1.5.6 software which shows that the Fe(III)N'-(4-Chlorobenzoyl) isonicotinohydrazide complex can interact with Enoyl-Acyl Carrier Protein Reductase from Mycobacterium Tuberculosis and it has better  interaction than isoniazid or N'-(4-Chlorobenzoyl)isonicotinohydrazide compound with the acquisition of free energy binding (ΔG) -9.80 kcal/mol and inhibition constant (Ki ) 0.06529 μM.
Computational Study of 1-(3-Nitrobenzoyloxymethyl)-5-Fluorouracyl Derivatives as Colorectal Cancer Agents Richa Mardianingrum; Delis Susilawati; Ruswanto Ruswanto
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 8, No. 2, November 2022
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v8i2.25489

Abstract

Cancer is one of the chronic diseases with a reasonably high increase at this time. One type of cancer with the highest mortality rate is colorectal cancer. Colorectal cancer is cancer that occurs in the colon and rectum. Based on GLOBOCAN data (2018), cases of colorectal cancer in Indonesia reached 8.6% or 30,017 people and were the second most common cause of death in men and the third in women. The development of cancer drugs to obtain drugs with better activity, lower toxicity, and working more selectively through structural modifications is still being carried out until now. This study aims to determine the pharmacokinetic properties and stable interactions between the thymidylate synthase and one of the 78 derivatives of 1-(3-nitrobenzoiloximethyl)-5-fluorouracyl (NB5FU) by in silico, namely molecular docking, and molecular dynamics simulations. The result shows that the NB5FU78 derivative compounds have better pharmacokinetic properties than NB5FU. Lipinski's rules of five criteria that fill the requirements have a smaller free bond energy value than NB5FU. Based on the results of molecular dynamics simulations carried out for 5 ns, the NB5FU78 derivative has a stable interaction with the thymidylate synthase (TS) receptor with total bond energy of -36.36 kcal/mol.
The Potency of Alkaloid Derivates as Anti-Breast Cancer Candidates: In Silico Study Renadi, Sedin; Pratita, Anindita Tri Kusuma; Mardianingrum, Richa; Ruswanto, Ruswanto
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 9, No. 1, May 2023
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v9i1.31481

Abstract

Breast cancer is the most frequent malignancy in women worldwide. One of the target receptors for the treatment of breast cancer are estrogen, progesterone, and HER2 receptors. An alternative treatment using natural ingredients has been developed, one of which is alkaloid compounds. This study aims to determine the activity of alkaloid compounds as anti-breast cancer agents through an in-silico method. Virtual screening (AutoDock Vina), molecular docking (AutoDock Tools), molecular dynamics (Desmond), scanning Lipinski's rule of five, as well as pharmacokinetic and toxicity parameters, were performed. The results of virtual screening, molecular docking, and molecular dynamics show that the compounds daurisoline, solasodine, and sambutoxin have stable interactions with the HER2 receptor, with the lowest values of RMSD (Root Mean Square Deviation) and RMSF (Root Mean Square Fluctuation) compared to other compounds. Based on the results of the study conducted, it was shown that daurisoline, solasodine, and sambutoxin were predicted to be used as anti-HER2 candidates for the treatment of breast cancer.
The Virtual Screening of Flavonoid Derivatives on Progesterone, Estrogen, and HER-2 Receptor for Breast Cancer Treatment Candidate Septian, Ade Dwi; Wardani, Gatut Ari; Mardianingrum, Richa; Ruswanto, Ruswanto
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 9, No. 1, May 2023
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v9i1.31482

Abstract

Cancer is defined as a disease caused by progressive and abnormal cell proliferation in the body. This condition is caused by deoxyribonucleic acid (DNA) changes, which causes cells to lose their normal function. The aim of this study is to find that flavonoid compounds have a more stable interaction than tamoxifen as anti-cancer candidates. Research has been conducted in silico with molecular docking (AutodockTools-1.5.7) and molecular dynamics of 200 flavonoid compounds. Furthermore, pharmacokinetic parameters, toxicity, and the application of the Lipinski Rule of Five were investigated. Based on molecular docking results, the compounds eriocotrin, glabrol, kaempferitrin, linarin, and narirutin have more stable interactions with lower binding energy (∆G) than tamoxifen. From the results of molecular docking, molecular dynamics, and pharmacokinetic studies, it is predicted that the kaempferitrin compound can be used as an anti-cancer candidate and does not cause toxicity through further research.
Papain-like Protease Peptides as Construction Material for the SARS-CoV-2 Vaccine Design Candidate: In-silico Study Mardianingrum, Richa; Pertiwi, Nur Ihsani; Rizkuloh, Lina Rahmawati; Ikram, Nur Kusaira Khairul; Ruswanto, Ruswanto
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 11, No. 1, May 2025
Publisher : Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v11i1.42748

Abstract

COVID-19 remains a major global health threat. In addition to implementing health protocols and consuming supplements, proactive prevention strategies are essential to limit the spread of the virus. One of the most promising approaches is the use of vaccines, particularly peptide-based vaccines, which are under active development. This study aimed to design a peptide vaccine derived from the SARS-CoV-2 papain-like protease (PLpro) and evaluate its interaction with key components of the human immune system, namely Toll-like receptor 3 (TLR3), major histocompatibility complex class I (MHC-I), and class II (MHC-II). The research employed an immunoinformatics approach utilizing NetCTL, IEDB Tepitool, PEP-FOLD3, trRosetta, HDOCK, GalaxyRefine2, and other molecular modeling tools. The designed vaccine construct was visualized in 3D using trRosetta and validated through ERRAT2, achieving a 100% quality score, indicating excellent structural integrity. The docking simulations demonstrated stable interactions between the vaccine and the immune receptors, suggesting strong immunogenic potential. In conclusion, the in silico-designed peptide vaccine based on SARS-CoV-2 PLpro shows promise in triggering immune responses through stable binding with TLR3, MHC-I, and MHC-II, highlighting its potential as a candidate for further experimental validation in COVID-19 vaccine development.
Co-Authors Aas Nuraisah Aas Nuraisah Aas Nuraisah Adinda Putri Amanda Afriliani, Sindy Aguslina Kirtishanti Agustien, Gina Septiani Ai Teni Siti Robi`ah Amelia, Widya Puspitasari Andri Kusmayadi Arif Budiman Arry Yanuar AYU RAHMAWATI Bachtiar, Kamiel Roesman Delis Susilawati Diah Lia Aulifa Dudi Nurmalik Elis Nurul Ikhlas Elsi Eryanti Fajar Setiawan Falya, Yuniarti Feri Sandria Firiani, Yuli Gatut Ari Wardani Gina Septiani Agustien Gina Septiani Agustien Gina Septiani Agustien Ginna Sri Nuryani Gramita, Widya Siva Hadiwijaya, Nathannael Adrya Harfiah Nur Aini Hartono, Sugianto Ayudha Ikram, Nur Kusaira Khairul Imam Mustaqim Garna Indah Cantika Indri Rahmawati Irma Andriani Isti Daruwati Jhoni, I Made Kamiel Roesman Bachtiar Korry Novitriani, Korry Kuncoro, Aditiya Kurniawan, Rian Liawardi, Petra Pahlawanda Chrisanto Lilis Tuslinah Lilis Tuslinah Lilis Tuslinah, Lilis Lina Rahmawati Rizkuloh Makiyatuzahro, Dede Avissa Mardhiah Mardhiah Mardhiah Mardhiah Mas'ud, Ibnu Meylany Sity Rossy Lestary Mia Nurfazriah Mida Hamidah Mochamad Herdi Nurzaman Monikasari, Hesti Muchtaridi Muchtaridi Nahariyah, St. Rohmani Napitupulu, Gloria Neta Ekayanti Suganda Nisa Uswatun Khasanah Nitya Nurul Fadilah Nofianti, Tita Nofriyaldi, Ali Nur Aji Nur Aji Nur Ihsani Pertiwi Nur Laeli Dwi Hidayati Nur Laili Dwi Hidayati Nur Rahayuningsih Nur Rahayuningsih, Nur Nurlaila, Putri Saniah Nurmalik, Dudi Nurmalik, Dudi Nursuhud Nursuhud Nursuhud Nurul Frasiska Oktariani, Anisa Pertiwi, Nur Ihsani Pratama, Rizki Pratita, Anindita Tri Kusuma Pratomo, Muhammad Fadhil Rahmawati, Syifa Sri Renadi, Sedin Rizgy Anggia Ruswanto, Ruswanto Ryan Apriandi Sa'banah, Nonah Sarwatiningsih, Yunia Sarwatiningsih, Yunia Septian, Ade Dwi Setyawati, Luthfi Utami Sindy Afriliani Siswandono, Siswandono Srie Rezeki Nur Endah Srie Rezeki Nur Endah Suhardiana, Eddy Suharyani, Ine Suharyani SUSANTI Susanti Susanti Susanti Susanti Susanti Susanti Syifa Alifia Lukman Tammy Riyanda Julianti Tati Herlina Tati Herlina Tifa Nofianti Tita Nofianti Tita Nofianti Tita Nofianti, Tita Tresna Lestari, Tresna Tuslinah, Lilis Unang Supratman Vikandari, Sonya Nurizki Walid, Rifan Afrian Nur Winda Trisna Wulandari, Winda Trisna Wirantono, Sebastian Nathanoel Yuliawati, Sri Yunia Sarwatiningsih