Judul: Penambatan Molekuler Senyawa Aktif Temu Kunci (Boesenbergia pandurata) Sebagai Inhibitor Matrix Metalloproteinase-1
Abstrak: Matrix metalloproteinase-1 (MMP-1) merupakan enzim pendegradasi kolagen yang aktivitasnya dipicu oleh sinar ultraviolet (UV). MMP-1 memiliki pengaruh langsung dalam photoaging, sehingga diperlukan inhibitor untuk menghambat aktivitas MMP-1 untuk mencegah penuaan kulit. Temu kunci (Boesenbergia pandurata) diketahui memiliki senyawa aktif yang potensial dalam menghambat penuaan kulit, namun potensi dari masing-masing senyawa bioaktif temu kunci sebagai inhibitor MMP-1 secara in silico belum diketahui. Penelitian ini bertujuan menguji potensi tanaman temu kunci sebagai inhibitor MMP-1 melalui penambatan molekuler dan analisis jenis interaksi yang terbentuk. Pada tahap awal, senyawa aktif temu kunci diseleksi melalui penapisan virtual menggunakan YASARA Structure serta prediksi bioavailabilitas dan toksisitas melalui pkCSM dan Protox online tool. Selanjutnya, dilakukan penambatan molekuler menggunakan YASARA Structure serta visualisasi 2D dan 3D menggunakan Discovery Studio Visualizer. Sebanyak enam ligan terbaik dipilih sebagai kandidat terbaik berdasarkan hasil penapisan virtual, prediksi bioavailabilitas, serta prediksi toksisitas. Ligan-ligan uji tersebut meliputi helichrysetin, panduratin D, pinocembrin chalcone, cardamonin, 5,7-dimethoxyflavone, dan tectochrysin. Hasil terbaik penambatan molekuler ditunjukkan oleh tectochrysetin dengan nilai ΔGbind sebesar -9,59 kkal/mol dan Kd sebesar 0,094 μM., Matrix metalloproteinase-1 (MMP-1) is a collagen-degrading enzyme whose activity is triggered by ultraviolet (UV) light. MMP-1 has a direct effect on photoaging, so an inhibitor is needed to inhibit MMP-1 activity to prevent skin aging. Fingerroot (Boesenbergia pandurata) are known to have active compounds that have the potential to inhibit skin aging. However, there is no study regarding the potency of each fingerroot bioactive compound as MMP-1 inhibitor through in silico research yet. This study aims to test the potential of fingerroot as an MMP-1 inhibitor through molecular docking and analysis of the types of interactions formed. In the early stages, the active compounds of fingerroot were selected through virtual screening using the YASARA Structure and checked for bioavailability and toxicity prediction through pkCSM and Protox online tools. The ligand selected were subjected to molecular docking using YASARA Structure and 2D and 3D visualization using Discovery Studio Visualizer. Six ligands were selected as best candidate based on virtual screening, bioavailability, and toxicity result. Those ligands are helichrysetin, panduratin D, pinocembrin chalcone, cardamonin, 5,7-dimethoxyflavone, dan tectochrysin. The best results are shown by tectochrysetin with -9,59 kcal/mol ΔGbind score dan Kd 0,094 μM.
Keyword: fingerroot, MMP-1, molecular docking, photoaging, YASARA Structure

Judul: Virtual Screening Natural Polyphenol Compounds as Inhibitor of Matrix Metalloproteinase-1 for Anti Photoaging and Photocarcinogenesis
Abstrak: Matrix metalloproteinase-1 (MMP-1) menjadi enzim yang paling banyak dipicu aktivitasnya oleh sinar UV dan bertanggung jawab terhadap degradasi kolagen. Degradasi kolagen menjadi penyebab utama photoaging dan photocarcinogenesis. Berbagai senyawa aktif telah diteliti aktivitasnya sebagai inhibitor MMP-1, termasuk senyawa polifenol. Saat ini, lebih dari 8000 jenis polifenol telah diidentifikasi di berbagai tanaman dan belum semuanya diteliti. Penelitian ini bertujuan menyaring polifenol alami dari database sebagai inhibitor MMP-1 terbaik. Tahap awal penelitian yaitu dilakukan penapisan virtual 408 polifenol alami menggunakan PyRx dan prediksi bioavailabilitas serta toksisitas menggunakan pkCSM dan Protox online tool, dilanjutkan dengan penambatan molekuler menggunakan AutoDock Vina serta visualisasi 2D dengan LigPlot+ dan 3D dengan PyMol. Terdapat empat senyawa yang diprediksi potensial sebagai inhibitor MMP-1 untuk anti photoaging dan photocarcinogenesis, yaitu luteolinidin, hispidulin, demetoksikurkumin, dan kurkumin. Luteolinidin dan hispidulin menghambat dengan mengkelat Zn katalitik, sedangkan demetoksikurkumin dan kurkumin tanpa mengkelat Zn katalitik, tetapi membentuk interaksi lebih banyak pada kantong S1’. Demetoksikurkumin memiliki kemampuan menghambat terbaik dengan ΔG -10,0 kkal/mol, Ki 0,05 µM, dan BSS 66,77%., Matrix metalloproteinase-1 (MMP-1) is the enzyme that is mostly triggered by UV rays and it is responsible for collagen degradation. Degradation of collagen is the main cause of photoaging and photocarcinogenesis. Various active compounds have been studied for their activity as MMP-1 inhibitors, including polyphenol compounds. Recently, more than 8000 types of polyphenols have been identified in various plants and not all of them have been studied. The research aims to screen virtualy natural polyphenols from database as the best MMP-1 inhibitors. First step of the research is virtual screening of 408 natural polyphenols using PyRx and prediction of bioavailability also toxicity using pkCSM and Protox online tool, followed by molecular docking using AutoDock Vina and 2D visualization with LigPlot+ also 3D with PyMol. There are four compounds predicted as potential MMP-1 inhibitors for anti photoaging and photocarcinogenesis, such as luteolinidin, hispidulin, demethoxicurcumin, and curcumin. Luteolinidin and hispidulin are inhibit by chelating catalytic Zn, whereas demethoxycurcumin and curcumin do not chelate catalytic Zn, but they are form more interactions in the S1' pocket. Demethoxycurcumin has the best inhibitory ability with ΔG -10,0 kcal/mol, Ki 0,05 M, and BSS 66,77%.
Keyword: MMP-1, penapisan virtual, photoaging, photocarcinogenesis, polifenol alami

Judul: Construction of Strongly Optimal Binary Linear Code with Minimum Distance 9 and 11
Abstrak: A binary linear code of length n over q F is a subspace of n q F . A code has three parameters that attached to it, namely length, dimension, and minimum distance. A code with length n, dimension k and minimum distance d is often called [n, k, d ]-code. Usually, when two parameters are given, then we want to find a code that has the best value for the last parameter. Based on Gilbert- Varshamov bound, if a [n, k, d ]-code exists and can not be expanded, we call it a strongly optimal code. In this paper, we construct strongly optimal code with minimum distance 9 and 11. In constructing the code, we created a theorem and algorithm based on Gilbert-Varshamov bound before we implement the algorithm to MAPLE programming language. Because of computational limitations, the program can only construct up to k = 10 for d = 9 and k = 12 for d = 11.
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