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All Journal VALENSI Jurnal Ilmiah Farmasi CHEMISTRY PROGRESS BIOTROPIA - The Southeast Asian Journal of Tropical Biology Mutiara Medika: Jurnal Kedokteran dan Kesehatan Jurnal Riset Industri Hasil Hutan Berkala Kedokteran Jurnal Ilmiah Kedokteran Wijaya Kusuma Jurnal Teknologi Agro-Industri Chemistry Indonesian Journal of Chemical Research Acta Biochimica Indonesiana Jurnal Pengabdian Kepada Masyarakat (Mediteg) Jurnal Jejaring Matematika dan Sains Jurnal Ilmiah Berkala Sains dan Terapan Kimia Jurnal Informasi, Perpustakaan, dan Kearsipan (JIPKA) Gunung Djati Conference Series Herbal Medicine Journal Jurnal AGRISEP: Kajian Masalah Sosial Ekonomi Pertanian dan Agribisnis Jurnal Natural Scientiae Juragan (Jurnal Agroteknologi) Journal of Pharmascience
Noer Komari
Jurusan Kimia FMIPA Universitas Lambung Mangkurat
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STRUCTURAL DYNAMICS OF BACTERIAL NITROREDUCTASE ENZYMES FROM A MINING-IMPACTED ENVIRONMENT IN SOUTH KALIMANTAN, INDONESIA: ARCHITECTURE FOR SUSTAINABLE CHROMIUM BIOREMEDIATION Anugerah Putra, Andifa; Ramadhani, Munandar; Komari, Noer; Badruzsaufari
BIOTROPIA Vol. 33 No. 1 (2026): BIOTROPIA Vol. 33 No. 1 January 2026
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2026.33.1.2532

Abstract

ARTICLE HIGLIGHTS- New bacterial enzymes found in Indonesian soil can neutralize toxic chromium waste.- These unique bacteria show great promise for bioremediation in polluted mining soils.- One of the newly found enzymes from these bacteria has a superior, highly stable structure.- This superior stability is key, coming from a rigid core with flexible moving loops.- This research provides a molecular blueprint for engineering enzymes to clean up chromium.ABSTRACTHexavalent chromium [Cr(VI)], a soluble and carcinogenic industrial pollutant, poses a significant threat to both the environment and human health, necessitating effective remediation strategies. Microbial enzymatic reduction of Cr(VI) to its less toxic trivalent state, Cr(III), is a promising approach. However, growing evidence suggests that many enzymes involved in this process are flavin mononucleotide (FMN)-dependent reductases, which likely reduce Cr(VI) adventitiously via a reduced flavin intermediate, rather than through direct enzymatic catalysis. This study presents a comparative computational analysis of two novel FMN-dependent reductases, designated M2Cr10 and M54Cr10, derived from chromium-tolerant bacteria Acinetobacter radioresistens and Bacillus tropicus, respectively, which were isolated from Indonesian serpentine soil. Phylogenetic and sequence analyses classified both enzymes as members of the FMN-dependent nitroreductase superfamily. High-quality homology models were generated and validated, with over 95% of residues occupying the most favored regions of the Ramachandran plot, confirming their stereochemical integrity. Molecular docking simulations predicted strong binding affinities for the FMN cofactor, with binding energies of -7.1 kcal/mol for M2Cr10 and -8.1 kcal/mol for M54Cr10. These interactions are stabilized by a network of hydrogen bonds and hydrophobic contacts, with residue Tyr¹³¹ identified as a key anchor for the FMN isoalloxazine ring in both enzymes. Extensive 10-nanosecond molecular dynamics simulations revealed that the A. radioresistens M2Cr10 enzyme exhibits superior structural architecture characterized by greater global stability, as indicated by lower average root mean square deviation (RMSD) and solvent-accessible surface area (SASA). However, it also displays greater localized flexibility (higher RMSF) in functional loop regions critical for catalysis. This combination of a rigid scaffold and dynamic functional loops suggests that M2Cr10 may be a more robust and potentially efficient biocatalyst. These findings provide a detailed molecular blueprint for understanding the structural determinants of stability in FMN-dependent reductases and offer a rational basis for engineering these enzymes for more effective adventitious bioremediation of Cr(VI).
Penambatan Molekul Kandungan Eurycoma longifolia Jack. (Pasak bumi) terhadap Human Phosphodiesterase 5 Samsul Hadi; Khoerul Anwar; Amalia Khairunnisa; Noer Komari
Journal of Pharmascience Vol. 7 No. 2 (2020): Jurnal Pharmascience
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jps.v7i2.8731

Abstract

Pasak bumi sebagai obat tradisional pria telah digunakan oleh masyarakat melayu, khususnya orang Sumatra dan kalimantan, akan tetapi mekanisme secara molekuler belum dikatahui dengan jelas. Salah satu pendekatan yang dapat digunakan untuk mengetahui mekanisme pasak bumi sebagai obat tradisional yang bermanfaat mengatasi disfungsi ereksi adalah penambatan molekul. Penambatan melekul dilakukan dengan cara melihat interaksi ligand dengan reseptor. Ligand yang berasal dari pasak bumi adalah 5-methoxycanthin-6-one, 9-methoxycanthin-6-one, eurycomalactone, eurycomalide A, eurycomanone, eurycomaoside, laurycolactone A, longilactone, niloticin, picrasidine O. Sehingga kesepuluh ligand ini didocking menggunakan salah satu aplikasi docking yaitu PLANTS 1.1 untuk melihat ikatan dengan PDE5. Sebelum dilakukan docking terhadap ligand pasak bumi, terlebih dahulu dilakukan docking terhadap ligand Sildenafil untuk melhat nilai RMSD. RMSD ini diperlukan sebagai alat validasi metode, berdasarkan percobaan, nilai RMSD dari Sildenafil adalah 1,2517 A0. Hasil terbaik dari penambatan molekul pasak bumi adalah niloticin dengan skor doking -97,8802, sehingga nilai interaksinya terhadap reseptor sebesar 93,71% dari Sildenafil.Pasak bumi as traditional male medicine has been used by Malay people, especially Sumatra and Borneo people, but the molecular mechanism is not yet known clearly. One approach that can be used to determine the mechanism of the Pasak Bumi as a traditional medicine that is useful to overcome erectile dysfunction is docking molecules. Molecular docking is done by looking at the interaction of ligands with receptors. Ligands originating from the Pasak Bumi are 5-methoxycanthin-6-one, 9-methoxycanthin-6-one, eurycomalactone, eurycomalide A, eurycomanone, eurycomaoside, laurycolactone A, longilactone, niloticin, picrasidine O. docking application namely PLANTS 1.1 to see the bond with PDE5. Before docking Pasak Bumi ligand, it is first docking Sildenafil ligand to see the RMSD value. The RMSD is needed as a method validation method, based on experiments, the RMSD value of Sildenafil is 1.2517 A0. The best results from docking of the Pasak bumi molecule is niloticin with a doctor score of -97.8802, so interaction skor to the receptor is 93.71% of Sildenafil.Keywords: Pasak Bumi, PDE5, PLANTS
Evaluasi Docking Molekular Potensi β-Sitosterol dari Kelakai (Stenochlaena palustris) sebagai Inhibi-tor Estrogen Receptor Noer Komari; Tazkia Safarina; Mirza Maulana Ahmad; Nugi Maulana; Eko Suhartono; Samsul Hadi
Journal of Pharmascience Vol. 9 No. 2 (2022): Jurnal Pharmascience
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jps.v9i2.13412

Abstract

 Tumbuhan khas rawa Kalimantan yang banyak dikaitkan dengan kesehatan adalah Kelakai (Stenochlaena palustris). Kelakai mengandung senyawa kimia antioksidan, antibakteri, antijamur, antianemia dan antiinflamasi. β-sitosterol adalah fitosterol penting di tumbuhan kelakai. β-sitosterol dikatakan mampu menekan pertumbuhan sel kanker payudara. Protein penting dalam perkembangan sel kanker payudara adalah Estrogen Receptor (ER) yang juga merupakan target protein untuk kerja obat. Penelitian ini bertujuan melihat potensi senyawa β-sitosterol sebagai inhibitor ER secara in silico. Energi bebas Gibbs (ΔG), koefisien inhibisi (Ki) dan interaksi ligan dengan residu ER dianalisis sebagai parameter docking. Sifat farmakokinetik β-sitosterol diprediksi menggunakan server web pkCSM dan SwissADME. Hasil molekular docking menunjukkan bahwa β-sitosterol membentuk kompleks dengan ER dengan energi bebas Gibbs (ΔG) = -5,27 kkal/mol dan raloxifene = -5,71 Kkal/mol. β-sitosterol berinteraksi dengan residu Gln-441, Asn-439, Met-438, Ala-493, Leu-495, Arg-503, Gln-499, Gln-502, Gln-506 dan raloxifene berinteraksi dengan residu Phe-425, Met-421, Leu-428, Ile-424, Met-388, Leu-391, Leu-387, Phe-404, Met-502, Met 348, Leu-525, Leu-346, Asp-347, Glu-348, Ala-350, Pro-515, Asp547, Trp-383, Met-383, Glu-524, Val-528, Trp-383, Asn-502, Pro-508, Leu-589, Val-524, Val-327. β-sitosterol tidak bersifat hepatotoksik dan tidak menyebabkan alergi kulit. Protein ER berinteraksi stabil dengan β-sitosterol dengan Sembilan residu. β-sitosterol berpotensi sebagai kandidat obat antikanker dengan menghambat pertumbuhan ER. Kata kunci: raloxifene, kanker payudara, in silico, target protein, SwissADME   A typical plant of the Borneo swamp that is widely associated with health is Kelakai (Stenochlaena palustris). Kelakai contains antioxidant, antibacterial, antifungal, antianemic and anti-inflammatory chemical compounds. β-sitosterol is an important phytosterol in Stenochlaena palustris. β-sitosterol is said to be able to suppress the growth of breast cancer cells. An important protein in the development of breast cancer cells is the Estrogen Receptor (ER) which is also a protein target for drug action. This study aims to see the potential of β-sitosterol compounds as ER inhibitors in silico. Gibbs free energy (ΔG), inhibition coefficient (Ki) and ligand interaction with ER residues were analyzed as docking parameters. The pharmacokinetic properties of β-sitosterol were predicted using pkCSM and SwissADME web servers. The results of molecular docking showed that β-sitosterol formed a complex with ER with Gibbs free energy (ΔG) = -5.27 kcal/mol and raloxifene = -5.71 kcal/mol. β-sitosterol interacts with Gln-441, Asn-439, Met-438, Ala-493, Leu-495, Arg-503, Gln-499, Gln-502, Gln-506 residues and raloxifene interacts with Phe-425, Met-421, Leu-428, Ile-424, Met-388, Leu-391, Leu-387, Phe-404, Met-502, Met 348, Leu-525, Leu-346, Asp-347, Glu-348 , Ala-350, Pro-515, Asp547, Trp-383, Met-383, Glu-524, Val-528, Trp-383, Asn-502, Pro-508, Leu-589, Val-524, Val-327 residues. β-sitosterol is not hepatotoxic and does not cause skin allergies. The ER protein interacts stably with β-sitosterol with nine residues. β-sitosterol has potential as an anticancer drug candidate by inhibiting ER growth.
Co-Authors A.A. Ketut Agung Cahyawan W Abdullah Abdullah Adi Rahmadi Afdella, Nor Afni Ahmad Budi Junaidi Akmal Rizky Harun Amalia Khairunnisa Aminuddin Prahatama Putra Anang Kadarsah Anang Kadarsah, Anang Anjang Yudistri Annisa Rizqi Dwi Oktaviani Anugerah Putra, Andifa An’nisa, Windy Sidratul Asnah Asnah Awin Fauzi Azidi Irwan Badruzsaufari Bambang Setiawan Dahlena Ariyani Desiya Ramayanti Azhara Dewi Umaningrum Diah Aulia Rosanti Dona Marisa, Dona Dwi Rasy Mujiyanti Dwi Rasy Mujiyanti Dwi Rasy Mujiyanti Eko Suhartono Eko Suhartono Erfanur Adlhani Etty Novita Fahruraji, Fahruraji Febriyanti, Nur Fatma Fitri Hady Amrullah Habibah, Hanna HANNA HABIBAH Hanna Habibah Ina Risnawati INDAH SAPUTRI Indah Saputri INDAH SETIAWATI Indah Setiawati Kamilia Mustikasari Karlina Karlina Khoerul Anwar Kholifatu Rosyidah Laksono Trisnantoro Lisda Hayatie, Lisda Lusi Thenios Mardi Santoso Maria Dewi Astuti Marisa Shellyanti Megayulia Nooryaneti Melina Arini Sylvia Dewi Mirza Maulana Ahmad Mirza Maulana Ahmad Mukarramah Mukarramah, Mukarramah Nadia Sasanti NAFISAH Nafisah Nafisah Nafisah Nafisah Ningtyas Indah Sari Noor Malinda Noorliana Noorliana Nugi Maulana Nurhidayati Pratiwi Prahatama Putra, Aminuddin Puji Astuty Putra, Andifa Anugerah Putri, Amaris Nathania Hanindia Rabiatul Adawiyah Rahmat Eko Sanjaya Rahmi Hardini Ramadhani, Munandar Retno Agnestisia ROBIATUL ADAWIYAH Rusdiana Rusdiana Rusdiana Rusdiana Salmon Charles Pardomuan Tua Siahaan Samsul Hadi Samsul Hadi Samsul Hadi Samsul Hadi Saputri, Indah SARMILA Sarmila Sarmila Sarmila, Sarmila Siti Juliati Siti Ratna Jinan F Sri Hendriani Sujatmiko Sujatmiko Sujatmiko Sujatmiko Sunardi Sunardi Sunardi sunardi sunardi Sunardi, Ph.D., Sunardi Taslim Ersam Tazkia Safarina Tri Ayu Novelena Umi Baroroh Lili Utami Utami Irawati Veronica Shania Aprillia Widiyanto, Gregorius Yenny Era Nova