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Imam Siswanto
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CORRELATION BETWEEN MISSING LOOP PROXIMITY TO THE BINDING SITE AND GRID SCORE CHANGES AFTER MISSING LOOP REFINEMENT Chelsea Christabel William; Muhammad Farhan Naufal Ibrahim; Daanish Farras Ahmad; Imam Siswanto
Integrative Perspectives of Social and Science Journal Vol. 3 No. 06 Juni (2026): Integrative Perspectives of Social and Science Journal
Publisher : PT Wahana Global Education

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Abstract

This study investigated whether missing loops and ligand distance is associated with grid score changes after refinement. Total of 23 protein and ligand complexes were selected from the Protein Data Bank based on resolution of ≤ 2.5 Å, presence of a co-crystallized ligand, and missing loop regions. The structures were classified into close, moderate, and far groups using UCSF Chimera 1.16. Missing loops were reconstructed using MODELLER 10.8, followed by molecular docking refinement using DOCK6. ΔGrid Score were calculated using Microsoft Excel, ligand-receptor interactions were visualized using BIOVIA Discovery Studio Visualizer 2025, and statistical analysis was performed using IBM SPSS Statistics. The close group showed the highest mean absolute grid score change at 18.7741 kcal/mol, followed by the moderate group at 2.2939 kcal/mol and the far group at 0.7025 kcal/mol. Spearman analysis showed a significant negative relationship between missing loop and ligand distance and absolute grid score change, with a correlation coefficient of -0.430 and a p-value of 0.040. These findings indicate that missing loops located closer to ligands tend to produce larger docking score changes after refinement, although score direction is also influenced by local interaction patterns.
MOLECULAR DOCKING AND MM/GBSA BINDING FREE ENERGY EVALUATION OF NAPROXEN-AZETIDINONE HYBRID DERIVATIVES AS POTENTIAL PREFERENTIAL COX-2 INHIBITORS: COMPARATIVE STUDY WITH MELOXICAM, ISORHAMNETIN, AND NAPROXEN FOR OSTEOARTHRITIS Moch Ghozi Falih Ar Rammi; Niqia Romah; Imam Siswanto
Integrative Perspectives of Social and Science Journal Vol. 3 No. 06 Juni (2026): Integrative Perspectives of Social and Science Journal
Publisher : PT Wahana Global Education

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Osteoarthritis (OA) is a prevalent chronic inflammatory joint disease in which cyclooxygenase-2 (COX-2) plays a central role in mediating pain and inflammation. Selective COX-2 inhibition offers therapeutic benefit while minimizing gastrointestinal adverse effects associated with non-selective NSAIDs. Naproxen-azetidinone hybrids represent a promising scaffold for developing improved COX-2 inhibitors. Molecular docking was performed against the COX-2 crystal structure (PDB ID: 4M11) using AutoDock Vina, with protocol validation confirmed by redocking (RMSD = 1.0764 Å). MM/GBSA rescoring was applied to estimate binding free energies (ΔGbind). Six naproxen-azetidinone derivatives (N4a-N4f) were evaluated alongside meloxicam, isorhamnetin, and naproxen as references. All derivatives exhibited superior COX-2 binding affinity (docking score: -10.07 to -10.89 kcal/mol; Ki: 0.01032 - 0.04122 µM) and ΔGbind (-51.495 to -55.217 kcal/mol) compared to all references. Arg120 served as the universal hydrogen bond anchor across all derivatives. N4a (docking score: -10.89 kcal/mol: Ki 0.01032 µM) and N4b (ΔGbind : -55.217 kcal/mol) were identified as lead candidates. Naproxen-azetidinone derivatives, particularly N4a and N4b, demonstrate strong in silico potential as selective COX-2 inhibitors superior to meloxicam and isorhamnetin. Experimental validation through enzymatic COX-1/COX-2 inhibition assays and ADMET profiling is warranted.
Screening In Silico dan Penambatan Molekuler Senyawa Turunan 4-Hydroxytamoxifen (OHT) sebagai Kandidat Agen Anti Kanker Payudara terhadap Estrogen Receptor Alpha (ER-????) Alfian Valentino Fernanda Putra Subhakti; Nindita Dwi Ambarwati; Nurul Qomaryah Kiswa; Dea Qoiril Ana; Nur Hanna Fahimah; Intan Asmi Saharani; Mutia Kafaa Ghania; Aleind Aloysius Gonzaga; Najma Tatsbita Satria; Putri Andini Sutejo; Imam Siswanto
JOURNAL SAINS STUDENT RESEARCH Vol. 4 No. 4 (2026): Agustus: Jurnal Sains Student Research
Publisher : CV. KAMPUS AKADEMIK PUBLISING

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.61722/jssr.v4i4.11274

Abstract

Luminal breast cancer subtypes expressing Estrogen Receptor Alpha (ER-α) account for approximately 70% of breast cancer cases globally. Although hormonal therapy using the active ligand 4-hydroxytamoxifen (OHT) has been widely employed, its long-term efficacy is frequently hampered by drug resistance and adverse side effects. This study aims to design and evaluate, in silico, the potential of structurally modified OHT derivatives as more effective and selective ER-α inhibitor candidates. Ligand geometry optimization was performed using the semi-empirical PM6 method in Gaussian software. Molecular docking simulations were conducted using DOCK6 against the ER-α crystal structure (PDB ID: 3ERT), validated through a re-docking procedure of the reference ligand. Molecular interaction analysis was visualized in 2D/3D using BIOVIA Discovery Studio. Method validation showed high accuracy, with a Root Mean Square Deviation (RMSD) value of 1.032 Å (< 2.0 Å). Docking results revealed that the native ligand OHT-opt exhibited the best grid score (−59.47 kJ/mol), followed by pyrrolidine-OHT (−58.47 kJ/mol) and mono-fluoro-OHT (−56.11 kJ/mol). Interaction analysis showed that the mono-fluoro-OHT modification retains the essential hydrogen bond with the anchoring residue ARG101.A (2.716 Å) while forming a new hydrogen bond with GLU60 (2.668 Å) on helix 3 (H3). This new interaction may disrupt the receptor's allosteric conformation, potentially preventing transcriptional activation. This study concludes that structural modifications of OHT derivatives, particularly pyrrolidine-OHT and mono-fluoro-OHT, exhibit competitive binding affinities and hold strong potential to be developed as novel therapeutic agents for breast cancer, pending further validation through molecular dynamics simulations and in vitro experiments.
Co-Authors Aleind Aloysius Gonzaga Alfian Valentino Fernanda Putra Subhakti Chelsea Christabel William Daanish Farras Ahmad Dea Qoiril Ana Intan Asmi Saharani Moch Ghozi Falih Ar Rammi Muhammad Farhan Naufal Ibrahim Mutia Kafaa Ghania Najma Tatsbita Satria Nindita Dwi Ambarwati Niqia Romah Nur Hanna Fahimah Nurul Qomaryah Kiswa Putri Andini Sutejo