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All Journal JURNAL KIMIA SAINS DAN APLIKASI Pharmaciana: Jurnal Kefarmasian Indonesian Journal of Cancer Chemoprevention MPI (Media Pharmaceutica Indonesiana) Jurnal Kedokteran Gigi Universitas Padjadjaran Acta Pharmaciae Indonesia : Acta Pharm Indo Pharmacy Reports Mandala of Health : A Scientific Journal Molekul: Jurnal Ilmiah Kimia Journal of Applied Science for Pharmaceuticals and Health
Fareza, Muhamad Salman
Pharmacy Department, Jenderal Soedirman University
Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Dentistry Engineering Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Nursing Public Health

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Evaluation of natural compounds as VEGFR-2 inhibitors for breast cancer therapy: insights from molecular docking and drug-likeness analysis Aprilia, Vika; Sarmoko; Fareza, Muhamad Salman; Baroroh, Hanif Nasiatul; Choironi, Nur Amalia
Pharmacy Reports Vol. 4 No. 2 (2024): Pharmacy Reports
Publisher : Indonesian Young Scientist Group and UPN Veteran Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.51511/pr.82

Abstract

Breast cancer remains one of the most common cancers worldwide, with VEGFR-2 (KDR) playing a key role in tumor angiogenesis. Inhibiting VEGFR-2 is a promising therapeutic strategy. Natural compounds are increasingly studied for their potential to inhibit VEGFR-2. This study aims to assess the binding affinity of 11 natural compounds (andrographolide, alpha-mangostin, pinostrobin, pinocembrin, ethyl-p-methoxycinnamate (EPMS), xanthorrhizol, galangin, gamma-mangostin, curcumin, cinnamaldehyde, and alashanoid B) to the VEGFR-2 protein through molecular docking and Lipinski's rule analysis, identifying promising candidates for breast cancer treatment. Molecular docking simulations were performed for 11 compounds and sunitinib as a control, with binding energies and interactions analyzed. The compounds were also evaluated for drug-likeness using Lipinski’s rule of five. Curcumin showed the highest binding affinity to VEGFR-2 with a binding energy of -9.9 kcal/mol, surpassing sunitinib (-9.4 kcal/mol). Key interactions were observed with active site residues Cys919 and Asp1046. All tested compounds met the criteria for oral bioavailability per Lipinski’s rules. Curcumin demonstrates potential as a VEGFR-2 inhibitor due to its favorable binding affinity and drug-like properties. Enhancing curcumin’s bioavailability is recommended for effective therapeutic application.
Optimizing Ultrasound-Assisted Extraction Methods of Etlingera elatior Using Response Surface Methodology for High Performance Liquid Chromatography Fingerprinting Wasito, Hendri; Ridha, Kirana Shafa; Fareza, Muhamad Salman
Jurnal Kimia Sains dan Aplikasi Vol 28, No 7 (2025): Volume 28 Issue 7 Year 2025
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jksa.28.7.355-361

Abstract

Kecombrang flower (Etlingera elatior) is widely used in traditional medicine and contains various metabolites. High-performance liquid chromatography (HPLC) fingerprinting can be employed as an analytical technique to comprehensively reveal the metabolite profile, while ultrasound-assisted extraction (UAE) was developed to optimize metabolite extraction. This study aims to determine the optimal extraction conditions for E. elatior and apply these conditions in HPLC fingerprinting. This study utilized central composite design (CCD) and response surface methodology (RSM) to optimize the extraction of E. elatior flowers, focusing on extraction time and the simplicia-to-solvent ratio. The optimal extraction results were applied to HPLC fingerprints of the flowers, leaves, and stems of E. elatior. The chromatograms were further analyzed using chemometric methods, namely principal component analysis (PCA), partial least squares discriminant analysis (PLSDA), and hierarchical cluster analysis (HCA) to classify and interpret the variability of metabolite profiles in different parts of E. elatior. The optimal UAE conditions were determined to be a time of 46 minutes and a simplicia-to-solvent ratio of 1:25 (g/mL). Chemometric analysis revealed that the samples were well clustered, which reflects the similarity of metabolites among them. The HCA further showed that the metabolite profile of E. elatior flowers is closely related to that of the stems.
Bioinformatics Analysis of Rho GTP-ase Activating Protein 35 (ARHGAP35) in Breast Cancer Migration Febrian, Dicky Rizky; Setyono, Joko; Fareza, Muhamad Salman; Choironi, Nur Amalia; Fadlan, Arif; Sarmoko, Sarmoko
Indonesian Journal of Cancer Chemoprevention Vol 12, No 3 (2021)
Publisher : Indonesian Society for Cancer Chemoprevention

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14499/indonesianjcanchemoprev12iss3pp161-169

Abstract

Breast cancer is a second deadly cancer after lung cancer worldwide. Progression of cancer is driven by mutated cancer drive gene such as ARHGAP35. This study aims to analyze the role of ARHGAP35 in the growth and development of breast cancer cells. ARHGAP35 expression level was analyzed using Oncomine (p-value<1E-4; gene rank top 10%). Overall survival (OS) and disease-free survival (DFS) were evaluated by using GEPIA (median cutoff; HR displayed with 95% CI). STRING was used for analyzing the protein-protein interaction network, while WEBGESTALT for KEGG pathway and gene ontology (GO) of ARHGAP35 and associated proteins and cBioPortal for gene mutation. ARHGAP35 was overexpressed in several types of breast cancer, namely invasive ductal breast carcinoma (IDC), invasive ductal and lobular breast carcinoma (IDLC), invasive lobular breast carcinoma (ILC), male breast carcinoma, and mixed ductal and lobular carcinoma (MDLC). High expression of ARHGAP35 had significantly lower OS (p=0.045) compared to low expression of ARHGAP35 and the difference in DFS was not significant (p=0.98). ARHGAP35 interacted with RHOA, RHOB, RHOC, RHOD, RASA1, RND1, RAC1, CDC42, FYN and SRC. KEGG pathway and GO analysis showed that these proteins are highly involved in actin-based processes through adherent junction, axon guidance, focal adhesion, regulation of actin cytoskeleton, and tight junction. Mutation rate analysis showed 34 missense, 29 truncating, 3 fusion, and 1 in frame on ARHGAP35. Taken together, ARHGAP35 may involve in the growth and development of breast cancer through regulation of actin cytoskeleton pathway.Keywords: ARHGAP35, breast cancer, KEGG pathway, mutation rate, actin cytoskeleton.
Synthesis and Cytotoxic Activity of Methoxylated Chalcones in Breast Cancer MCF-7 and Prostate Cancer DU-145 Cell Lines Fareza, Muhamad Salman; Samudra, Genta Hafied Naga; Asrada, Syahdan; Fischellya, Dafi; Wijaya, Triyadi Hendra; Choironi, Nur Amalia; Wasito, Hendri; Suhesti, Tuti Sri; Mustikaningtyas, Ika; Rehana, Rehana; Setiyabudi, Lulu; Sarmoko, Sarmoko
Molekul Vol 20 No 3 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.3.13612

Abstract

Chalcones, a class of naturally occurring compounds, exhibit a broad spectrum of biological activities, including anticancer properties. In this study, a series of methoxylated chalcones were synthesized via Claisen-Schmidt condensation and evaluated for cytotoxic activity against breast cancer MCF-7 and prostate cancer DU-145 cell lines. The synthetic route involved Claisen-Schmidt condensation, leading to various methoxy-substituted chalcone derivatives. The structures of the synthesized chalcones were confirmed through NMR and mass spectrometry. Cytotoxicity was assessed using the PrestoBlue assay, with 4-bromochalcone (compound 2) displaying the highest cytotoxic activity against MCF-7 cancer cell lines (IC50 = 26.99 µM). These results indicate that methoxylated chalcones hold promise as potential lead compounds for the development of new anticancer agents targeting breast and prostate cancer.
Analisis Target Protein Pada Penyakit Kanker Serviks dari Senyawa Ethyl Para Methoxy Cinnamate Secara In Silico Ayunda Tasya Hapsari; Muhamad Salman Fareza; Nur Amalia Choironi
Journal of Applied Science for Pharmaceuticals and Health Vol 1 No 2 (2024): Journal of Applied Science for Pharmaceuticals and Health (Desember)
Publisher : Centre of Applied Science for Pharmaceutical Science Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jasph.2024.1.2.14999

Abstract

Kasus kanker serviks merupakan kanker tertinggi ke-5 diantara kanker lainnya di dunia. Amplifikasi DNA adalah salah satu mekanisme terjadinya kanker ini. Karena itu, keparahan penyakit ini bisa berkembang. Gen yang berperan dalam perkembangan kanker serviks adalah CCNB1, CCNB2, CDK, dan MMP. Terdapat masalah pada beberapa obat yang menargetkan beberapa protein tersebut seperti erlotinib, alvocidib, marimastat, dan lain-lain. Oleh karena itu, penemuan obat baru untuk mengatasi kasus ini perlu dilakukan. Senyawa Ethyl Para Methoxy Cinnamate (EPMC) mempunyai aktivitas sitotoksik IC50 sebesar 35 μg/ml yang bersifat sangat sitotoksik terhadap sel HeLa. Penelitian ini bertujuan untuk mengetahui potensi target dan profil docking molekul senyawa EPMC yang berpotensi menghambat kanker serviks. Pencarian data menggunakan database Pubchem, SWISS Target Prediction, PubMed, STRING, dan PDB. Situs Webgestalt dilakukan untuk analisis Geneontologi, jalur KEGG, dan asosiasi obat. Hasil PTTGs digunakan untuk melihat interaksi antara protein menggunakan STRING dan gen hub 10 teratas dengan cystoscape. Simulasi docking dilakukan untuk menentukan profil mooring. Hasil: Target potensial EPMC adalah EGFR, CCND1, CDK4, CDK2, CCNA1, HGF, MMP9, CCNE1, CCNB1, CDH1. Hasil simulasi docking menunjukkan MMP9 memiliki energi ikatan yang lebih rendah dibandingkan kontrol positif, yaitu sekitar -6,9 kkal/mol. Oleh karena itu, MMP9 berpotensi menjadi target EPMC melalui jalur persinyalan PI3K-Akt. Kesimpulan: Senyawa EPMC dapat menghambat pertumbuhan sel kanker dengan menargetkan MMP9 melalui jalur pensinyalan PI3K-Akt.
Efek Penambatan Senyawa Demetoksikurkumin Dan Bisdemetoksikurkumin Terhadap Protein LSD1 Nadia Sayyidadah Aulia; Muhamad Salman Fareza; Triyadi Hendra Wijaya; Nahrul Hasan; Putri Khaerani Cahyaningrum; Ari Wahyudi
Journal of Applied Science for Pharmaceuticals and Health Vol 2 No 1 (2025): Journal of Applied Science for Pharmaceuticals and Health (June)
Publisher : Centre of Applied Science for Pharmaceutical Science Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jasph.2025.2.1.16466

Abstract

Beta-talasemia merupakan penyakit genetik pada sintesis hemoglobin di dalam sel darah merah yang ditandai dengan menurunnya produksi β-globin. Senyawa kurkumin diketahui dapat meningkatkan kadar HbF pada sel K562. Senyawa demetoksikurkumin dan bisdemetoksikurkumin diketahui memiliki stabilitas dan bioavaibilitas yang lebih baik dari kurkumin. Penelitian ini bertujuan untuk melihat interaksi senyawa demetoksikurkumin dan bisdemetoksikurkumin pada protein LSD1 secara in silico. Penelitian eksperimental yang dilakukan terbagi dalam dua tahap. Pertama, validasi metode yang meliputi pengunduhan struktur LSD1 (PDB ID: 6KGP), preparasi struktur protein dengan menghilangkan molekul air dan memisahkan molekul protein dan ligan natif, penambatan kembali dengan Ligan natif menggunakan AutoDock Vina dan penghitungan nilai RMSD. Kedua, penambatan molekuler senyawa demetoksikurkumin dan bisdemetoksikurkumin dengan protein LSD1 menggunakan koordinat hasil validasi yang valid dan visualisasi penambatan dengan menggunakan BIOVIA Discovery Studio 2020. Hasil validasi menunjukkan nilai RMSD yaitu 1,402 Å. Energi ikatan terendah untuk protein LSD1 yaitu -10,4 kkal/mol dan -10,2 kkal/mol untuk senyawa demetoksikurkumin dan bisdemetoksikurkumin. Residu asam amino pada LSD1 yang berperan pada pengikatan senyawa uji demetoksikurkumin yaitu Thr624; Val288 dan Arg316. Residu asam amino pada LSD1 yang berperan pada pengikatan senyawa uji demetoksikurkumin yaitu Thr624; Leu659; Val811; Arg316; Leu625; Tyr761 dan Trp751. Penelitian ini menunjukkan bahwa senyawa demetoksikurkumin menunjukkan hasil yang lebih baik dan interaksi yang lebih potensial pada protein LSD1 dibandingkan bisdemetoksikurkumin
Co-Authors . Harwoko Ade Martinus Anggraeni, Vina Juliana Aprilia, Vika Ari Asnani Ari Wahyudi Asrada, Syahdan Ayunda Tasya Hapsari Choironi, Nur Amalia Dina Parika Dody Novrial Dody Novrial, Dody Dwi Utami Anjarwati Fadlan, Arif Fajar Wahyu Pribadi Febrian, Dicky Rizky Fischellya, Dafi Hanif Nasiatul Baroroh Harwoko Harwoko Hasan, Nahrul HENDRI WASITO Irse Priyaganda Bani Musa Joko Setyono Kaefiyah Nurul Insani Lela Lailatul Khumaisah Mustikaningtyas, Ika Nadia Sayyidadah Aulia Nur Amalia Choironi Nur Amalia Choironi Putri Khaerani Cahyaningrum Putri Nur'afni Sa'adah Rehana Rehana Rehana, Rehana Ridha, Kirana Shafa Rizka Hidayati Rizki Akbar Ramadhan Samudra, Genta Hafied Naga Sarmoko Sarmoko Setiyabudi, Lulu Siagian, Defi Srium Sri Sutji Susilowati Sunarto Sunarto Sunarto Sunarto Sunarto Sunarto Sunarto, Sunarto Thianti Sylviningrum Triyadi Hendra Wijaya Triyadi Hendra Wijaya Tuti Sri Suhesti Wahyu Dwi Kusdaryanto Yuliasari, Agnes