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All Journal VALENSI Jurnal Ilmiah Farmasi CHEMISTRY PROGRESS Mutiara Medika: Jurnal Kedokteran dan Kesehatan Jurnal Riset Industri Hasil Hutan Pharmascience 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 Gunung Djati Conference Series Herbal Medicine Journal Jurnal AGRISEP: Kajian Masalah Sosial Ekonomi Pertanian dan Agribisnis Jurnal Natural Scientiae Juragan (Jurnal Agroteknologi)
Noer Komari
Jurusan Kimia FMIPA Universitas Lambung Mangkurat
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Library & Information Science Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Public Health Social Sciences Other

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Skrining senyawa Eurycoma longifolia terhadap siklus sel dengan metode docking melalui interaksi cylcin Samsul Hadi; Khoerul Anwar; Noer Komari; Desiya Ramayanti Azhara; Diah Aulia Rosanti
Jurnal Ilmiah Farmasi Vol. 18 No. 2 (2022): Jurnal Ilmiah Farmasi
Publisher : Universitas Islam Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20885/jif.vol18.iss2.art15

Abstract

Background: The community has known pasak bumi for generations to increase sexual desire in men (aphrodisiac). Besides, it can improve the performance of sports athletes and as an antistress, reduce tension, anger, and confusion. Objective: This relatively large number of uses encourages researchers to want to do in silico screening of active compounds against antitumors by going through 2 stages, namely through online PASS and docking. Method: Docking method to see the stability interaction of compounds with cyclin. In this test, Pyrx was used as a docking tool with various cell cycle-related targets, namely cyclin D3 (PDB ID: 3G33), cyclin A (PDB ID: IJSU), cyclin A (PDB ID, cyclin C (1ZP2), cyclin D (ID PDB: 2W9F), cyclin H (PDB ID: 1KXU), and cyclin T (PDB ID: 3BLR). Results: The docking result showed that each cyclin showed the best interaction with these compounds: Cyclin A and 9-Methoxycanthin-6-one 3-N-oxide (-8.6 Kcal/mol), cyclin H and Niloticin (-8.0 Kcal/mol), cyclin D3 is 9-Methoxycanthin-6-one 3-N-oxide (-7.2 Kcal/mol), cyclin D is Eurycolactone F (-8.4 Kcal/mol), cyclin C is and Niloticin (-7.5 Kcal/mol), and cyclin T and Niloticin (-8.2 Kcal/mol). Conclusion: Based on the docking score obtained, the stability of the interaction is predicted to occur in cyclin A and 9-Methoxycanthin-6-one 3-N-oxide (ΔG: -8.6 Kcal/mol). Intisari Latar belakang: Pasak bumi telah dikenal oleh masyarakat secara turun-temurun untuk meningkatkan gairah seksual pada pria (afrodisiaka). Disamping itu dapat meningkatkan performa atlet olahraga dan sebagai antistress, menurunkan tegangan, kemarahan, dan kebingungan. Tujuan: Penggunaan yang relatif banyak ini mendorong peneliti berkeinginan melakukan skrining senyawa aktif terhadap antitumor secara in silico dengan melalui 2 tahap yaitu melalaui PASS online dan docking. Metode: Metode docking dipakai untuk melihat interaksi stabilitas senyawa dengan cylin. Dalam pengujian ini, Pyrx digunakan sebagai alat docking dengan berbagai target yang berhubungan dengan siklus sel, yaitu cyclin D3 (PDB ID: 3G33), cyclin A (PDB ID: IJSU), cyclin C (PDB ID: 1ZP2), cyclin D (ID PDB: 2W9F), cyclin H (ID PDB: 1KXU), dan cyclin T (ID PDB: 3BLR). Hasil: Hasil docking pada masing-masing cyclin menunjukkan interaksi terbaik dengan senyawa berikut ini: cyclin A dan 9-Methoxycanthin-6-one 3-N-oxide (-8,6 Kkal/mol), cyclin H dan Niloticin (-8,0 Kkal/mol), cyclin D3 dan 9-Methoxycanthin-6-one 3-N-oxide (-7,2 Kkal/mol), cyclin D dan Eurycolactone F (-8,4 Kkal/mol), cyclin C dan Niloticin (-7,5 Kkal/mol), serta cyclin T dan Niloticin (-8,2 Kkal/mol). Kesimpulan: Berdasarkan skor docking yang diperoleh, kestabilan interaksi diprediksi akan terjadi pada cyclin A dengan 9-Methoxycanthin-6-one 3-N-oxide (ΔG: -8.6 Kkal/mol).
Potensi Senyawa Kimia dari Herba Kelakai (Stenochlaena palustris) sebagai Antikanker: Kajian Molecular Docking NAFISAH; HANNA HABIBAH; SARMILA; INDAH SETIAWATI; INDAH SAPUTRI; NOER KOMARI
Gunung Djati Conference Series Vol. 15 (2022): Prosiding Seminar Nasional Kimia Tahun 2022
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (433.567 KB)

Abstract

Kelakai herb (Stenochlaena palustris) is a native fern from Borneo that grows wild on peatlands. This plant has been widely developed and is thought to have potential as an alternative to anticancer drugs. . The purpose of this study was to obtain chemical compounds from the antifungal herb that have the potential as anticancer with parameters in the form of Gibbs free energy data and residue interactions with protein and to determine the prediction of the toxicity of ten chemical compounds derived from the gibbon herb. This research method includes preparation of ligands and target protein, as well as docking of ten test compounds with target protein Anaplastic Lymphoma Kinase with swissdock, visualization of docking results using the USCF Chimera program and toxicity analysis using pkCSM and Protox online tool
Interaksi Asam Galat dan Metil Galat dari Tumbuhan Kasturi (Mangifera casturi) sebagai Inhibitor Protein Human Epidermal Growth Factor 2 (HER2): Evaluasi Molekular Docking NOER KOMARI; ROBIATUL ADAWIYAH; SAMSUL HADI; EKO SUHARTONO
Gunung Djati Conference Series Vol. 15 (2022): Prosiding Seminar Nasional Kimia Tahun 2022
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (293.647 KB)

Abstract

Kasturi (Mangifera casturi) is a endemic plant of Borneo. The polyphenol content of M. casturi leaves has antioxidant properties, including gallic acid and methyl gallic. The antioxidant potential of gallic acid and methyl gallate of M. casturi leaves is thought to inhibit the growth of breast cancer cells. Human Epidermal Growth Factor 2 (HER-2) protein is an important factor in the epidermal growth of breast cells and is also a target for breast cancer treatment. This study aims to investigate the potential of gallic acid and methyl gallic compounds from M. casturi as inhibitors of HER-2 protein. Molecular docking parameters in Gibbs free energy, interaction of gallic acid and methyl gallic ligands with HER-2 protein residues Kasturi (Mangifera casturi) is a endemic plant of Borneo. The polyphenol content of M. casturi leaves has antioxidant properties, including gallic acid and methyl gallic. The antioxidant potential of gallic acid and methyl gallate of M. casturi leaves is thought to inhibit the growth of breast cancer cells. Human Epidermal Growth Factor 2 (HER-2) protein is an important factor in the epidermal growth of breast cells and is also a target for breast cancer treatment. This study aims to investigate the potential of gallic acid and methyl gallic compounds from M. casturi as inhibitors of HER-2 protein. Molecular docking parameters in Gibbs free energy, interaction of gallic acid and methyl gallic ligands with HER-2 protein residues
Chemical composition comparison of n-hexane extract and essential oil kemenyan toba (Styrax sumatrana) sap from Tobasa North Sumatera by GC-MS and in silico study its compound as antiinflammatory Kamilia Mustikasari; Mardi Santoso; Nadia Sasanti; Maria Dewi Astuti; Taslim Ersam; Noer Komari
Jurnal Riset Industri Hasil Hutan Vol 14, No 2 (2022)
Publisher : Kementerian Perindustrian

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24111/jrihh.v14i2.7220

Abstract

The sap of kemenyan toba (Styrax sumatrana) is often used as a binder for perfumes, raw materials for cosmetics and medicines, so it is widely traded. However, not many studies have reported about its chemical composition. The process of extracting chemical compounds from kemenyan toba (S. sumatrana) sap quality one was carried out by maceration method using n-hexane and water distillation. The result of maceration was 25.3% of the n-Hexane extract, while the distillation yielded 0.13% (w/w) of a pale-yellow oil. The results of the GC-MS analysis showed that only benzoic acid was present in the extracts and essential oils. n-Hexane extract consists of styrene compounds, cinnamic acid, benzyl benzoate, 1,4-diphenyl-1.4-butanedione, benzyl cinnamates, methyl styrene, and cinnamyl cinnamate. In comparison, essential oil consists of 3-methylpentan-2-one, methyl palmitate, methyl stearate, methyl trans-9.10-epoxystearate, dioctyl hexanedioic, methyl oleic, and methyl-13.16-Octadecanoic. The in-silico test results of several compounds as antiinflammatory showed that the compounds cinnamyl cinnamate had potential as an anti-inflammatory.
Interaksi Kadmium dan Merkuri terhadap Enzim Kunci pada Glikolisis: Kajian In silico Eko Suhartono; Noer Komari; Salmon Charles Pardomuan Tua Siahaan
Jurnal Ilmiah Kedokteran Wijaya Kusuma Vol 10, No 2 (2021): SEPTEMBER 2021
Publisher : Universitas Wijaya Kusuma Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (453.747 KB) | DOI: 10.30742/jikw.v10i2.1599

Abstract

Glikolisis merupakan proses oksidasi glukosa yang melibatkan enzim hingga menghasilkan asam piruvat dalam kondisi aerob serta asam laktat dalam keadaan anaerob. Enzim-enzim yang terlibat di dalam glikolisis dapat berinteraksi dengan logam berat, melalui pengikatan secara kovalen terhadap residu asam amino dari enzim. Untuk membuktikan hal tersebut, digunakan metode in silico dengan menggunakan MIB: Metal Ion-Binding site prediction dan server docking dari Lu Lab@StructuralBioinformatics, China Medical University (http://bioinfo.cmu.edu.tw/MIB/). Enzim-enzim kunci pada glikolisis diperoleh dari RCSB Protein Data Bank (https://www.rcsb.org/search), yakni enzim glukokinase dengan kode PDB: 3FGU, enzim heksokinase dengan kode PDB: 4IXC, dan enzim piruvat kinase dengan kode PDB: 1ZJH. Protein disiapkan dengan menghilangkan residu ligan alami yang ada dalam protein. Persiapan ligan dan protein digunakan oleh program Chimera 1.15. Hasil penelitian mengungkapkan bahwa interaksi Hg terhadap enzim glukokinase, heksokinase, dan enzim piruvat kinase lebih reaktif dibanding Cd. Pada glikolisis, Cd banyak berinteraksi dengan residu asam glutamate dan residu histidine sedangkan Hg banyak berinteraksi dengan sistein pada enzim-enzim glikolisis. Pembentukkan kompleks Hg dengan resisdu sistein, menyebabkan Hg akan berikatan dengan gugus thiol bebas yang tersedia. Merkuri yang terikat pada gugus thiol pada residu sistein mengakibatkan fungsi residu sistein pada protein tidak berjalan dengan semestinya sehingga enzim tidak aktif dan glikolisis terganggu.
Three Dimension Structure Modeling of The Superoxide Dismutase (SOD) of Rice (Oryza sativa) Using Fold Recognition Method Using Phyre2 Web Server Noer Komari Komari
Jurnal Sains dan Terapan Kimia Vol 16, No 2 (2022)
Publisher : Program Studi Kimia, Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jstk.v16i2.11682

Abstract

Determining the 3D structure of proteins using laboratory instrumentation is time-consuming and expensive. The in silico method can be used as an alternative to predict the 3D structure of proteins, such as the fold recognition method. This study aims to create a 3D structural model of rice's (Oryza sativa) protein superoxide dismutase (SOD). The 3D structure modeling of the protein was carried out with the Phyre2 web server. The protein sequence was obtained from the UniProt KB database with the code A0A6F8FUX1. The results showed that the suitable template used to build the model was the template with the code c1unfX. The c1unfX template has a coverage value of 80%, 100% confidence, and i.d. of 51%. Validation of the model with the PROCHECK program showed that the most favored area on the Ramachandran Plot was 87.8%, and the disallowed area was 1.1%. The disallowed area, which is still below 15%, indicates that the three-dimensional structure model of the SOD protein built from the c1unfX template has good a value.
Effect of Kelakai (Stenochlaena palutris) Extract on Organophosphate Pesticide Exposure: Cytotoxic Studies in Ovo and in Silico Nafisah Nafisah; Sarmila Sarmila; Hanna Habibah; Indah Saputri; Indah Setiawati; Noer Komari
Jurnal Sains dan Terapan Kimia Vol 17, No 2 (2023)
Publisher : Program Studi Kimia, Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jstk.v17i2.14583

Abstract

Vegetable farmers in South Kalimantan use pesticides to protect crops from pests. The active ingredient of the pesticide has a broad toxic effect on target and non-target organisms. Continuous exposure to pesticides causes cancer. The plant of mantle (Stenochlaena palustris) is thought to have potential cytotoxic activity against cancer cell growth. The aim of this study was to examine the potential activity of chemical compounds in anaplastic lymphoma kinase (ALK) exposed to organophosphate pesticides in silico and in ovo. The in silico study used molecular docking and virtual screening methods. The methanol extract of malachite was obtained by maceration method. The in ovo study was carried out by injecting pesticide compounds and methanol extracts of methanol at doses of 0.5 and 1 ppm to free-range chicken eggs. The results of the in silico analysis showed that ethion and neophytadiene had the most negative G values, namely -8.62 kcal/mol and -8.39 kcal/mol, while the natural ligand 8 LY A 500 was -9.19 kcal/mol. The similarity of the type and number of residues in the binding complex between ethion and neophyadiene ligands with ALK protein indicates the potential for competition between ethion and neophyadiene when bound to ALK protein. Neofitadiene is suspected as a compound that has potential as anti-cancer by inhibiting the growth of ALK. Anchovy extract is considered to be able to slow down the rate of cell damage in chicken embryos caused by ethion with its inhibitory ability so that the cell surface is not damaged quickly.
Pemodelan Calponin Ikan Gabus (Channa striata) dengan Phyre2 dan Interaksi dengan Protein Lain Mirza Maulana Ahmad; Noer Komari
Jurnal Natural Scientiae Vol 2, No 1 (2022): Mei 2022
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jns.v2i1.4790

Abstract

Knowledge of the three-dimensional structure of proteins is very important to understand their character and function at the molecular level. Determination of protein structure in the laboratory is expensive and relatively difficult because it requires sophisticated instruments and takes a long time. As an alternative, an in silico approach can be used to predict the three-dimensional structure of proteins, namely the fold recognition method. The purpose of this study was to create a three-dimensional structure model of snakehead fish (Channa striata) calponin protein using the Phyre2 web server. The target protein sequence was obtained from UniProt KB with code K9LH64. The results of the study showed that the template for building the model was the c1wynA code. The results of the model (MP) evaluation obtained a coverage value was 45%, a confidence value was 100%, and an identity value was 69%. Validation of the model (MP) using the PROCHECK program showed the model was in the most favoured residue plot of 82.4%. This model deserves to be used as a model for calponin protein of snakehead fish, because the disallowed area was below 15%. The results of the analysis of interactions with other proteins using STRING-DB obtained the interaction model (MP) with Actin assembly-inducing protein (ACTA2) was 0.791; and Tropomyosin (TPM1) was 0.786. The results of molecular docking using PatchDock obtained the value of Atomic Contact Energy (ACE) for the calponin protein model (MP)-ACTA2 was 372.76 kJ/mol; Calponin model protein (MP)-TPM1 was 406.93 kJ/mol. The interactions that occured in the calponin model (MP)-ACTA2 were hydrogen bonds at residues Gly-41, Glu-60, Arg-64, Arg-66, Pro-67, Gly-68, Lys-71 and hydrophobic bonds at Arg-64, Lys- 71, Lys-72, Ile-73, Va-138. The interactions model of calponin model (MP)-TPM1 were hydrogen bonding at residues Ser-13, Lys-71, Ala-95, Tyr-96, Ser-136, Arg-137, Arg-150 and hydrophobic bonds at residues Leu-12, Ala-14, Lys-71, Ala-95, Val-138, Arg-150, Phe-152. Keywords: fold recognition, Phyre2 , 3D structure protein, calponin, protein-protein interaction
Analisis Hubungan Antar Parameter Kualitas Crude Palm Oil di PT. Laguna Mandiri Rantau Factory Tri Ayu Novelena; Noer Komari
Jurnal Natural Scientiae Vol 2, No 1 (2022): Mei 2022
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jns.v2i1.4864

Abstract

Analysis of the relationship between the quality parameters of crude palm oil (CPO) at PT. Laguna Mandiri Rantau Factory using a simple linear regression method and multiple linear regression has been carried out. This study was to determine the free fatty acid content, water content, and gross content of CPO and to compare the sample with company standards and SNI. The relationship between parameters was modeled with a simple linear regression mathematical model, Y = a + bx and multiple linear regression, Y = a + b1X1 + c2x2… + bnXn. The results showed that the average free fatty acid was 4.02%, the water content was 0.18%, and the impurities content was 0.018%. The fatty acid content has not met the company standard, while the water content and impurities have met the company and SNI. The relationship of water content (X) to free fatty acids (Y) in the equation Y = 3.328 + 3.804x. The relationship of free fatty acids (X) to water content (Y) in the equation Y = - 0.808 + 0.246x. The relationship between impurities (X) and free fatty acids (Y) in the equation Y = 3.569 + 25.399x. The relationship of free fatty acids (X) to the level of impurities (Y) in the equation Y = -0.124 + 0.035x. The relationship between dirt content (X) and water content (Y) in the equation Y = 0.070 + 6.315x. The relationship between water content (X) and dirt content (Y) in the equation Y = - 0.007 + 0.135x. The relationship of water content (X1) and dirt content (X2) to free fatty acids (Y) in the equation Y = 3.391 + 2.542 X1 + 9.344 X2. The relationship of impurities (X1) and free fatty acids (X2) to water content (Y) in the equation Y = - 0.737 + 0.572 X1 + 0.226X2. The relationship of free fatty acids (X1) and water content (X2) to the level of impurities (Y) in the equation Y = - 0.107 + 0.030X1 + 0.021X2.
Interaksi Senyawa Taxifolin dari Buah Kasturi (Mangifera casturi) sebagai Antikanker Payudara: Evaluasi Docking Molekular Rabiatul Adawiyah; Noer Komari
Jurnal Natural Scientiae Vol 1, No 1 (2021): November 2021
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jns.v1i1.4420

Abstract

Taxifolin also called dihydroquercetin is a flavonoid. Taxifolin is included in the flavonol subclass and polyphenol class. Taxifolin has been found in the leaves, bark and flesh of Mangifera casturi. Taxifolin is thought to have potential as an antibreast cancer through its activity as an anti-neoplastic agent. The occurrence of breast cancer begins with overexpression of the Human Epidermal Growth Factor Receptor 2 (HER-2) protein which can induce dimerization and autophosphorylation of the tyrosine kinase enzyme, resulting in migration and metastasis of breast cancer cells. This study aims to determine the interaction of taxifolin with HER-2 protein by molecular docking. Molecular docking using the SwissDock web server. Parameters of molecular docking include Gibbs free energy and interaction of taxifolin ligands and HER-2 residues. The results of docking molecular expressed by free energy Gibbs of taxifolin compounds with HER-2 protein is -7,99 kcal / mol, while the free energy Gibbs of the native ligand bond with HER-2 protein is -10.76 kcal / mol. The residues on HER-2 that interacts with taxifolin are GLY727, GLY804, LEU726, THR798, ASP863, ALA730, SER728, ARG849, GLY729, CYS805, THR862, VAL734, LEU852, LYS753, ALA751, ASP808, ARG849, ASN850. The value of Gibbs free energy and the interaction of residues indicate that taxifolin compounds have potential as anticancer breasts. Taxifolin as an inhibitor of HER-2 protein expression.
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 An’nisa, Windy Sidratul Awin Fauzi Azidi Irwan 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 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 Mukarramah Mukarramah, Mukarramah Nadia Sasanti NAFISAH Nafisah Nafisah Nafisah Nafisah Ningtyas Indah Sari Noor Malinda Nurhidayati Pratiwi Prahatama Putra, Aminuddin Puji Astuty Putra, Andifa Anugerah Putri, Amaris Nathania Hanindia Rabiatul Adawiyah Rahmat Eko Sanjaya Rahmi Hardini Retno Agnestisia ROBIATUL ADAWIYAH Rusdiana Rusdiana Rusdiana Rusdiana Salmon Charles Pardomuan Tua Siahaan 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 Tri Ayu Novelena Umi Baroroh Lili Utami Utami Irawati Veronica Shania Aprillia Widiyanto, Gregorius Yenny Era Nova