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Pemodelan Farmakofor untuk Identifikasi Inhibitor Heat Shock Proteins-90 (HSP-90): Pharmacophore Modeling to Identify Heat Shock Proteins-9 (HSP-90) Inhibitors Muhammad Arba; Arfan; Ayu Trisnawati; Desi Kurniawati
Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) Vol. 6 No. 2 (2020): (October 2020)
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22487/j24428744.2020.v6.i2.15036

Abstract

Heat shock proteins-90 (HSP-90) is a protein that plays an important role in the life cycle of normal and cancer cells for their self protection from thermal stress, oxidative damage, and cell hypoxia. Inhibition of HSP90 is one way to suppress the growth of cancer cells. In this study, pharmacophore modeling and molecular docking were conducted to identify hit compounds as inhibitors of HSP-90. The pharmacophore feature consists of three hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic feature with Area Under Curve of Receiver Operating Characteristics (AUCROC) is 0.5 and the Goodness of Hit (GH) value is 0.752. Screening in the ZINC database generated 1,500 hit compounds, were subjected to molecular docking to determine their binding energy and interactions with HSP-90. The range of binding energy (E) of all hit compounds is -5.68 to -12.24 kcal/mol and there are four best hit compounds namely lig_543, lig_527, lig_1337 and lig_337, when compared to native ligands (PU2, E=-8.25 kkal/mol) based on the binding energy and orientation, which indicate their potential as new HSP-90 inhibitors.
Activity Prediction of Bioactive Compounds Contained in Etlingera elatior Against the SARS-CoV-2 Main Protease: An In Silico Approach Dwi Syah Fitra Ramadhan; Taufik Muhammad Fakih; Arfan Arfan
Borneo Journal of Pharmacy Vol 3 No 4 (2020): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v3i4.1634

Abstract

The COVID-19 pandemic has become a serious problem today, with its prevalence increasing every day. The SARS-CoV-2 main protease (MPro) is a promising therapeutic target to inhibit replicating and spreading the virus that causes COVID-19. The compounds contained in the Etlingera elatior plant has the potential. This study aimed to examine the compounds' activity in E. elatior against SARS-CoV-2 MPro using in silico methods. A total of seven compounds contained in E. elatior were obtained from the Knapsack database. The compounds were then docked into the SARS-CoV-2 MPro receptor's active site with the PDB ID 6LU7. Afterward, the biological activities were predicted by the PASS prediction webserver. The molecular docking results showed that ergosterol peroxide and sitostenone had the best binding energy with -10.40 kcal/mol and -9.17 kcal/mol, respectively. The in silico PASS prediction showed it has potential as antiviral therapy. It concluded ergosterol peroxide and sitostenone has the potential as SARS-CoV-2 MPro inhibitor candidate.
Insight on Estrogen Receptor Alpha Modulator from Indonesian Herbal Database: An in-silico analysis Muhammad Arba; Nadhifatul Aslikah; Arfan Arfan; Ruslin Ruslin; Arry Yanuar
PHARMACY: Jurnal Farmasi Indonesia (Pharmaceutical Journal of Indonesia) Jurnal Pharmacy, Vol. 17 No. 02 Desember 2020
Publisher : Pharmacy Faculty, Universitas Muhammadiyah Purwokerto

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30595/pharmacy.v17i2.7592

Abstract

Estrogen receptor α (ERα) is liable for regulating transcription factors which are an important part of hormonal signaling in breast cancer. This study intends to find hit compounds that are considered capable of inhibiting ERα by utilizing structure-based pharmacophores and molecular docking. Pharmacophore of the original ERα ligand (E4D600) has one hydrogen bond acceptor and three hydrogen bond donors which are used to select compounds from the Indonesian herbal database. This pharmacophore model had an Area under Curve of the Receiver Operating Characteristics (AUC-ROC) value is 0.80 and the Goodness of Hits (GH) value is 0.81. The selection process generated 330 compounds which proceed to the molecular docking stage to analyze their binding energy and interactions to ERα. The results indicated potential hit compounds seen from their binding energies in the range -5.42 to -10.01 kcal/mol. four of the best compounds including Lig57/(-)-Bidwillon A, Lig47/Quercetin 3-(6''-galloylgalactoside), Lig197/Multifloroside and Lig83/Erythrabyssin II provide promising information for their detailed analysis as ERα inhibitors.
Comparative analysis of the stability features of human alpha-defensins as candidates for the future COVID-19 therapy through molecular dynamics Taufik Muhammad Fakih; Dwi Syah Fitra Ramadhan; Arfan Arfan
Pharmaciana Vol 12, No 3 (2022): Pharmaciana
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (425.827 KB) | DOI: 10.12928/pharmaciana.v12i3.22616

Abstract

Coronavirus 19 (COVID-19) is still a global health issue to date, SARS-CoV-2 is a novel coronavirus that is responsible for this sickness. The receptor-binding domain of the SARS-CoV-2 virus associates with angiotensin-converting enzyme 2 (ACE-2) and allows the virus to enter human cells. Natural peptides such alpha-defensin are thought to attach to the SARS-CoV-2 RBD and prohibit it from engaging with ACE-2. Molecular dynamics simulations using a computational approach are utilized to understand the stability of six alpha-defensin macromolecules using the Gromacs 2016 software. The trajectories formed are then analyzed using VMD 1.9.4 and BIOVIA Discovery Studio 2020 software. Finally, the free energy is estimated using the MM/PBSA method. The alpha-defensins 2 macromolecules were found to have the best stability based on numerous study results (trajectory visualization, RMSD, RMSF, and free energy calculations). As a result, these macromolecules could be used to build new antiviral treatments for COVID-19 infectious disease candidates.
PENINGKATAN KUALITAS KESEHATAN MASYARAKAT ERA PANDEMIC COVID-19 MELALUI PEMANFAATAN TANAMAN OBAT KELUARGA SEBAGAI SUMBER IMMUNOMODULATOR Sunandar Ihsan; Yamin Yamin; Muhammad Handoyo Sahumena; Wa Ode Sitti Zubaydah; Arfan Arfan
Jurnal Pengabdian NUSANTARA Vol 2, No 2 (2022): Juli - Desember
Publisher : Universitas Halu Oleo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33772/jpnus.v2i2.28443

Abstract

Coronavirus Diseases 2019 (COVID-19) is a disease caused by a new coronavirus strain (SARS-CoV-2) which then mutates into various variants including the omicron variant, alpha variant, beta variant, and gamma variant. Where, transmission will pose a high risk when the body's immunity is low. The purpose of this activity is to provide information on various "Family Medicine Gardens" that can function as Immunomodulators to the general public, as well as students, both junior high school (SMP) and elementary school (SD) students. The implementation of this activity is carried out face-to-face and is packaged in the form of socializing the benefits of the Family Medicinal Garden (TOGA) as a source of immunomodulators, together with the community practicing making Family Medicinal Plant gardens in the Poasia and Kambuh Districts as well as the School Environment. In addition, this is also done by distributing leaflets containing information on the types of plants that act as immunomodulators and how to make them.
Phytochemical Profile and Biological Activities of Ethylacetate Extract of Peanut (Arachis hypogaea L.) Stems: In-Vitro and In-Silico Studies with Bibliometric Analysis Idin Sahidin; N. Nohong; Marianti A. Manggau; A. Arfan; W. Wahyuni; Iren Meylani; M. Hajrul Malaka; Nur Syifa Rahmatika; Agung W. M. Yodha; Nur Upik En Masrika; Abdulkadir Kamaluddin; Andini Sundowo; Sofa Fajriah; Rathapon Asasutjarit; Adryan Fristiohady; Rina Maryanti; Nur Indri Rahayu; M. Muktiarni
Indonesian Journal of Science and Technology Vol 8, No 2 (2023): (ONLINE FIRST) IJOST: September 2023
Publisher : Universitas Pendidikan Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17509/ijost.v8i2.54822

Abstract

The utilization of the stems, leaves, and hulls of peanuts (Arachis hypogea) is not as popular as the seeds. This study aimed to investigate the chemical contents and pharmacological activities of A. hypogaea stems in-vitro and in-silico. This study was also completed with bibliometric analysis. The methanol extract (ME) was reextracted by ethylacetate to get ethyl acetate extract (EAE). The chemical contents of EAE were analyzed by phytochemical screening, Liquid Chromatography-Mass Spectroscopy (LC-MS/MS), TPC (Total Phenolic Content), and TFC (Total Flavonoid Content). In-vitro and in-silico studies evaluated antioxidant potency, toxicity, and cytotoxicity toward MCF-7 cell lines. The results showed that EAE contained terpenoids, flavonoids, alkaloids, and phenolics which were supported by LC-MS/MS data. The EAE was categorized as a very strong antioxidant and moderately active in both cytotoxicity and toxicity.
Penambatan Molekul dan Dinamika Molekul beberapa Fitokimia dari Acalypha Indica L. sebagai Inhibitor Matriks Metalloproteinase9 Aiyi Asnawi; Ellin Febrina; Widhya Aligita; Anne Yuliantini; Arfan Arfan
Jurnal Sains Farmasi & Klinis Vol 10, No 1 (2023): J Sains Farm Klin 10(1), April 2023
Publisher : Fakultas Farmasi Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jsfk.10.1.62-70.2023

Abstract

Berbagai efek farmakologis telah dikaji terhadap ekstrak dan islolat dari Acalypha Indica L. terutama terkait dengan aktifitas anti kanker. Matrix metalloproteinases MMP9 merupakan contoh yang sangat baik dari kelompok proteinase terpenting yang terlibat dalam sel metastatic/kanker. MMP9 telah dikaitkan dengan berbagai macam penyakit, termasuk sistem pernapasan, sistem autoimun, dan bahkan kanker. Maka dari itu, makalah ini bertujuan untuk mendapatkan senyawa pemandu dari beberapa fitokimia Acalypha Indica L. yang bertanggung jawab dalam migrasi sel dengan menggunakan penambatan molekul dan dinamika molekul. Ligan ditambatkan ke situs aktif struktur kristal MMP9 (PDB ID: 5UE4) menggunakan aplikasi AutoDock Release 4.2.6. Proses penambatan molekul divalidasi dengan melakukan penambatan ulang ligan alami pada sisi aktif MMP9. Selanjutnya, menggunakan GROMACS dilakukan simulasi dinamika molekul (MD) ditandem dengan algoritma gmx_MMGBSA dan gmx_MMGBSA_ana untuk menghitung energi ikatan dan kontribusi residu terhadap terhadap kestabilan kompleks. Hasil menunjukkan hanya satu ligan dari 36 ligan yang dievaluasi tidak mampu berikatan dengan sisi aktif MMP9, dan enam dari ligan mampu mengikatnya lebih negatif daripada ligan alami. Kompleks dengan ligan S54 dan S56 yang memiliki energi paling negatif tetapi dari sisi parameter lainnya, kompleks S56 paling stabil. Dapat disimpulkan, g-sitosterol asetat (S56) memiliki potensi untuk berfungsi sebagai senyawa pemandu untuk MMP9
Pencarian Inhibitor DYRK2 dari Database Bahan Alam Zinc15: Analisis Farmakofor, Simulasi Docking dan Dinamika Molekuler La Ode Aman; Mangara Sihaloho; Arfan Arfan
Jurnal Sains Farmasi & Klinis Vol 10, No 1 (2023): J Sains Farm Klin 10(1), April 2023
Publisher : Fakultas Farmasi Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jsfk.10.1.100-113.2023

Abstract

DYRK2 (Dual-specificity tyrosine phosphorylation-regulated kinase 2) merupakan protein kinase yang memiliki banyak peranan dalam berbagai proses biologis, termasuk pembelahan sel, proliferasi sel, diferensiasi sel, dan apoptosis. DYRK2 diantaranya terlibat dalam regulasi siklus sel dengan cara mengatur aktivitas proteasom 26S sehingga inhibisi aktivitas DYRK2 dapat menghambat fungsi proteasom 26S dan mengurangi proliferasi sel kanker. Secara in vitro, kurkumin menunjukan kemampuan mengurangi proliferasi sel kanker melalui penghambatan enzim DYRK2. Pada penelitian ini, analog kurkumin telah diskrining dari database bahan alam Zinc15 dengan menggunakan model farmakofor yang diperoleg dengan pendekatan berbasis ligan. Hasil skrining kemudian dievaluasi dengan menerapkan teknik docking molekuler dan dinamika molekuler berdasarkan energi interaksi, rata-rata energi pengikatan bebas dan stabilitas interaksi antara ligan dan situs aktif DYRK2. Skrining terhadap 270.547 molekul dari database bahan alam Zinc15 menghasilkan 110 senyawa hit terpilih. Dengan mempertimbangkan hasil simulasi docking dan dinamika molekuler, tiga analog kurkumin prospektif telah dipilih yaitu ZINC000085597244, ZINC000217945958, dan ZINC000217643970. Molekul-molekul ini memiliki kriteria yang lebih baik dibandingkan kurkumin pada beberapa kriteria, seperti energi interaksi, energi pengikatan bebas, dan stabilitas interaksi dengan target. Disimpulkan, senyawa-senyawa ZINC000085597244, ZINC000217945958, dan ZINC000217643970 diprediksi sebagai kandidat potensial untuk obat anti-kanker dengan mekanisme aksi spesifik terhadap DYRK2.
PENYULUHAN KESEHATAN PADA MASYARAKAT DI KELURAHAN PURIRANO, SEBAGAI UPAYA MENINGKATKAN PEMAHAMAN TENTANG BAHAYA STUNTING Muhammad Ilyas Y.; Sahidin Sahidin; Arfan Arfan; Asnita Hafsani; Firman Oktivendra; Nur Aisyah Abdullah; Nur Salma; Titin Syafiransyah; Nirwati Rusli; Nurhikma Nurhikma; Sulsiah Sulsiah
EJOIN : Jurnal Pengabdian Masyarakat Vol. 1 No. 6 (2023): EJOIN : Jurnal Pengabdian Masyarakat, Juni 2023
Publisher : LPPM Institut Pendidikan Nusantara Global

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55681/ejoin.v1i6.1074

Abstract

Stunting is a growth disorder experienced by toddlers which results in delays in child growth that is not in accordance with the standards, resulting in an impact on cognitive development due to disruption of brain development so that it can reduce children's intelligence. The main causes of stunting include insufficient intake of nutrients and nutrients that meet the needs of children, wrong parenting due to lack of knowledge and education for pregnant women and nursing mothers, poor environmental sanitation such as lack of clean water facilities and limited access to health facilities needed for pregnant women, nursing mothers, and toddlers. The purpose of this activity is to provide education and knowledge about the dangers of stunting to the Purirano Village community. Through this socialization, it is hoped that it can provide information and education to the community, especially to mothers about the dangers of stunting. This activity was carried out by a team of lecturers from the Fakultas Farmasi UHO, Politeknik Bina Husada Kendari, RSUD Bahteramas Kendari and pharmacist students of the Faculty of Pharmacy UHO in collaboration with the National Population and Family Planning Agency of Southeast Sulawesi Province as resource persons in this activity. The results of the socialization activities carried out by gathering residents consisting of adolescent girls, pregnant women, and mothers who have toddlers in the Puirano village hall are expected to provide new insights for both residents and the village and can be realized independently in everyday life and play an active role in meeting the target of reducing stunting rates, especially in Southeast Sulawesi. so that participants in this socialization are expected to participate in reducing stunting rates in Indonesia, especially in Southeast Sulawesi.
The Potential of Clerodendrum paniculatum Leaves Fraction as a 3-Chymotrypsin-Like (3CL) Protease Inhibitor of SARS-CoV-2 Muhammad Arba; Arfan Arfan; Yamin Yamin; Muhammad Sulaiman Zubair
Indonesian Journal of Chemistry Vol 23, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.81447

Abstract

We described the biological activity of the Clerodendrum paniculatum leaf fraction against the SARS-CoV-2 3-Chymotrypsin-like 3CL protease at the molecular level. This study applied LC-MS/MS to identify bioactive compounds from fractions, computational studies, and fluorescence resonance energy transfer (FRET) assays to ascertain their inhibitory activity. LC-MS/MS analysis of the three samples revealed that sample 1 contained 18 compound peaks. In samples 2 and 3, there were 23 and 25 compounds with different molecular weights, respectively. Docking's study identified that the alkaloids (komarovicine and roemerine) have lower binding energies than other metabolites and standard compounds, with values of -33.47 and -32.63 kJ/mol, respectively. Roemerine demonstrated excellent stability based on dynamic simulation results and confirmed its affinity for 3CL protease predicted by the MM-PBSA approach of -89.44 kJ/mol. The FRET method for testing 3CL protease activity revealed that sample 2 had an enzyme inhibitory activity of 94.3%, which was close to that of GC376 (98.19%). Meanwhile, samples 1 and 3 yielded satisfactory inhibition activity by 89.64% and 85.24%, respectively. The antiviral activity of C. paniculatum leaves was discovered for the first time by inhibiting the 3CL protease SARS-CoV-2, providing an excellent opportunity for its development as an anti-SARS-CoV-2.