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All Journal Bionatura Indonesian Journal of Applied Sciences Chimica et Natura Acta Indonesian Journal of Chemistry Jurnal Riset Sains dan Kimia Terapan Jurnal Ilmiah Berkala: Sains dan Terapan Kimia al Kimiya : Jurnal Ilmu Kimia dan Terapan Journal of Tropical Pharmacy and Chemistry Kimia Padjadjaran
R. Ukun M.S. Soedjanaatmadja
Departemen Kimia, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Universitas Padjadjaran
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology

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Journal : Indonesian Journal of Chemistry

 1 
Exploring the Potency of Nigella sativa Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations Ari Hardianto; Muhammad Yusuf; Ika Wiani Hidayat; Safri Ishmayana; Ukun Mochammad Syukur Soedjanaatmadja
Indonesian Journal of Chemistry Vol 21, No 5 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.65951

Abstract

Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening campaigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments.
Selection of the Parameters in the Synthesis of Ethylenediamine-Folate Using the Plackett Burman Design Erianti Siska Purnamasari; Linda Septiana; Ari Hardianto; Ukun Mochammad Syukur Soedjanaatmadja; Anni Anggraeni; Husein Hernadi Bahti
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.68313

Abstract

This study is concerned with synthesizing ethylenediamine-folate (EDA-Folate), which will then be used as a precursor in synthesizing Gd-PEG-DOTA-Folate, a novel targeted-contrast agent for the diagnosis of cancer, employing the Magnetic Resonance Imaging method. This study aims to determine all the parameters affecting the synthesis of EDA-Folate using the Plackett Burman design. The synthesis method included activation of folic acid using dicyclohexylcarbodiimide and N-Hydroxysuccinimide to result in NHS-Folate, followed by conjugation of ethylenediamine with NHS-Folate to produce EDA-Folate. Analysis of the reaction product confirmed that the reaction product was EDA-Folate. From the resulted data, it can also be concluded that there were four significant parameters (out of the ten parameters studied) in the synthesis of EDA-Folate (with its value presented in the bracket), i.e., time inactivation of NHS-Folate (24 h), stirring rate inactivation of NHS-Folate (300 rpm), the mole of EDA (12 moles), and time of EDA-Folate (12 h). Moreover, the value or desirability of the experimental design was found to be 0.875 (which is < 1.0), meaning that the design will produce optimal conditions and thus the optimal yield of the reaction.
Co-Authors Abdul Muis Abdul Mutalib Abdul Mutalib Abdul Mutalib Abdul Mutalib Ace Tatang Hidayat Ade Sholeh Hidayat Agus Safari Amin Setiawan - Anggraeni, Nenden Indrayati Anni Anggraeni Anni Anggraeni Anni Anggraeni Anni Anggraeni, Anni Ari Hardianto Astrid, Dewi Bayu Shiddiq Widhi Pratama Devi, Puspitasari Rosiana Dewi Astrid DWIRYANI ARIZONA Erianti Siska Purnamasari Fadhlillah, Muhammad Fahruddin, Muhammad Fahmi Fauzi, Muhammad Ryan Febrianti, Inky Fitriani Fitriani Fitriani Fitriani Ginting, Sani D. R. Br Hafiz, Ersanda Herman Herman Hidayat, Ade Sholeh Horasio, Debora Tamaris Husein Hernadi Bahti Ika Wiani IMAN PERMANA MAKSUM IMAN PERMANA MAKSUM Iman Permana Maksum Iman Rahayu Inky Febrianti Janitra, Regaputra Satria Juliandri Juliandri Linda Septiana Linda Yuniar Martalena Ramli Muhammad Yusuf Muhammad Yusuf Muhammad Yusuf Muhammad Yusuf Muhammad Yusuf Muhammad Yusuf Mukhtari, Zakiyah Mulyasari, Rita Nurrusyda, Fajriana Shafira O. Suprijana - Pusaka, Semerdanta Rachman, Saadah Diana Retna Putri Fauzia Rita Mulyasari Saadah Diana Rachman Saadah Diana Rachman Safri Ishmayana Safri Ishmayana Saryono Shabarni Gaffar Supriyatna Supriyatna Syafruddin Syafruddin TATI NURHAYATI Umi Baroroh Yurika Sastyarina Yurika Sastyarina Zakiyah Mukhtari Zuhrotun Nafisah Zuhrotun Nafisah