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: Tripeptide Combination Molecular Docking Study of Matrix Metalloproteinase-1
Abstrak: Matrix metalloproteinase-1 (MMP-1) merupakan enzim yang menginduksi photoaging dan photocarcinogenesis dan mendegradasi kolagen tipe I dan tipe III. Tripeptida diketahui berpotensi menginhibisi MMP-1 secara in silico. Penelitian ini bertujuan mengetahui lebih lanjut potensi tripeptida dalam menginhibisi MMP-1 dengan pendekatan situs pengikatan kolagen dan menyaring tripeptida dengan teknik kombinasi penambatan molekuler dengan aplikasi PLANTS. Terdapat empat ligan terbaik dari 332 tripeptida yang memiliki skor penambatan lebih baik dari batimastat yang menghambat aktivitas MMP-1 secara in silico, yaitu TRR, ARR, GRR, dan PRR. Skor penambatan terbaik adalah -117,154 pada tripeptida TRR. Penambatan kombinasi dari empat ligan terbaik dilakukan dan didapatkan skor terbaik kombinasi 2 tripeptida TRR_ARR, -120,242 dan kombinasi 3 tripeptida TRR_ARR GRR, -121,486. Ligan kombinasi berbeda nyata dari ligan alami, akan tetapi tidak berbeda nyata terhadap tripeptida tunggal secara statistika. Ligan alami, ligan pembanding, TRR, PRR, kombinasi 2 ligan dan kombinasi 3 ligan menginhibisi MMP-1 melalui pengikatan dengan Zn katalitik serta residu pengikat substrat, sedangkan dua tripeptida lainnya, yaitu ARR dan GRR menginhibisi kolagenase-1 melalui pengikatan dengan residu pengikat substrat dan situs katalitik., Matrix metalloproteinase-1 (MMP-1) is an enzyme that induces photoaging and photocarcinogenesis and degrades type I and type III collagen. Tripeptides are known to have the potential to inhibit MMP-1 in silico. This study aims to further investigate the potential of tripeptides in inhibiting MMP-1 with a collagen binding site approach and screen tripeptides with a combination technique of molecular tethering with PLANTS application. There are four best ligands from 332 tripeptides that have better tethering scores than batimastat that inhibit MMP- 1 activity in silico, namely TRR, ARR, GRR, and PRR. The best docking score was -117,154 on the TRR tripeptide. Docking combinations of the four best ligands were carried out and the best score was obtained for the combination of 2 TRR_ARR tripeptides, -120,242 and the combination of 3 TRR_ARR GRR tripeptides, -121,486. The combined ligands were significantly different from the natural ligand, but not statistically significantly different from the single tripeptide. The natural ligand, comparator ligand, TRR, PRR, combination of 2 ligands and combination of 3 ligands inhibited MMP-1 through binding to catalytic Zn as well as substrate-binding residues, while the other two tripeptides, namely ARR and GRR inhibited collagenase-1 through binding to substrate-binding residues and catalytic sites.
Keyword: matrix metalloproteinase-1, photoaging, photocarcinogenesis, tripeptide, molecular docking, combined molecular docking, tripeptida, penambatan molekul, penambatan molekul kombinasi

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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