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Journal : Jurnal Natural Scientiae

 1 
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.
Kajian Molecular Docking Senyawa Karwinaphthol B dari Tanaman Bawang Dayak (Eleutherine palmifolia (L.) Merr) sebagai Inhibitor Enzim Glukokinase Puji Astuty; 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.v2i1.5412

Abstract

Karwinaphthol B is a compound of the naphthoquinone group. Karwinaphthol B is a chemical compound found in Bawang Dayak. Karwinaphthol B is one of the compounds considered to have antidiabetic effects. Diabetes Mellitus is a chronic disease that occurs when the body cannot produce enough insulin or cannot use insulin (insulin resistance) which causes blood glucose levels to rise (hyperglycaemia) under normal conditions. This study aims to see the potential of karwinaphthol B as a glucokinase inhibitor with parameters such as ∆G value and interaction of amino acid residues with molecular docking and pharmacophore studies using filter Lipinski, pkCSM, and SwissADME. The results of molecular docking showed that karwinaphthol B compound had potential as antidiabetic based on the ∆G value of -8.39 kcal/mole. Karwinaphthol B compound has an LD50 value of 2.168 mole/kg which is included in the non-toxic category; does not have hepatotoxicity, skin sensitization, and has a good bioavailability value. The interaction of Karwinaphthol B compounds with glucokinase enzymes at amino acid residues VAL62, ARG63, SER64,THR65, PRO66,  GLU67, GLY68, SER69, GLN98, MET210 , ILE211, TYR214, TYR215, CYS220, GLU221, MET235,  CYS252, LEU451, VAL452, and VAL455.
Pembuatan dan Karakterisasi Arang Aktif dari Kayu Alaban (Vitex Pinnata L.) Menggunakan Asam Asetat Marisa Shellyanti; Noer Komari
Jurnal Natural Scientiae Vol 3, No 2 (2023): November 2023
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jns.v3i2.9892

Abstract

Kayu alaban merupakan pohon yang dapat tumbuh di berbagai jenis tanah. Jenis arang kayu alaban memiliki karakteristik yang unggul dibandingkan dengan jenis arang lainnya. Arang kayu alaban memiliki kandungan karbon yang tinggi, yaitu sekitar 90%, sehingga arang kayu alaban menjadi salah satu bahan bakar yang sangat efisien dan ramah lingkungan. Arang kayu alaban cukup tersedia di pasar dan warung serta toko kelontong dan biasanya dipakai untuk kegiatan di dapur. Salah satu kelemahan arang tersebut adalah belum diaktivasi. Penelitian ini untuk mengetahui kualitas arang aktif dari kayu alaban dengan asam asetat sebagai aktivator. Hasil penelitian menunjukkan bahwa arang tanpa aktivasi dan sesudah aktivasi memenuhi aturan yang mengacu SNI 06-3730-95 untuk kadar air (3,955% dan 3,345%) dan kadar abu (1,865% dan 2,895%). Arang setelah aktivasi memiliki daya serap iodium sebesar 761,58 mg/g telah memenuhi syarat SNI 06-3730-95.
Kajian Molecular Docking Senyawa Quercetin dari Buah Terong Pokak (Solanum torwum Swartz) sebagai Antiinflamasi pada Protein Tumor Necrosis Factor-α (TNF-α) Lusi Thenios; 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.v2i1.4462

Abstract

Quercetin is a polyphenolic flavonoid with potential chemopreventive activity. Quercetin is a chemical compound found in Solanum torvum Sw fruit. Quercetin is one of the compounds that are considered to have anti-inflammatory effects. Inflammation is a localized protective response elicited by tissue damage caused by physical trauma, damaging chemicals, or microbiology. Tumor Necrosis Factor-α (TNF-α) is a proinflammatory cytokine that functions in mediating the innate immune response. Irregular production of cytokines can lead to various immunopathological conditions, including auto-inflammatory, autoimmune, and cancer-causing diseases. This study aims to determine the potential of quercetin compounds derived from turkey berry (Solanum torvum Sw.) which have the potential as anti-inflammatory drugs with parameters such as ∆G, the interaction of residues on TNF-α protein (PDB ID: 6X85) with molecular docking, and pharmacophore studies using Lipinski, pkCSM, and SwissADME filters. The molecular docking simulation results showed that the quercetin compound had a ∆G value of -8.55 kcal/mol and had amino acid residue interactions in the form of ILE155; TYR59; GLY121; TYR119; GLN61; TYR151; VAL123; LEU157; ILE58; GLY122; SER60; LEU120; LEU157. Quercetin has the potential as an anti-inflammatory drug on TNF- α protein with an LD50 value of 2.471; bioavailability value of 0.55; does not have hepatotoxicity and skin sensitization properties and has passed the Lipinski test.
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 Mukarramah Mukarramah, Mukarramah Nadia Sasanti NAFISAH Nafisah Nafisah Nafisah Nafisah Ningtyas Indah Sari Noor Malinda Noorliana Noorliana 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 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