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Discovery of SARS-CoV-2 RNA-dependent-RNA-polymerase (RdRp) Inhibitor from Sambiloto (Andrographis paniculata) Based on Molecular Docking and ADMET Prediction Approach Ahsana, Dina; Pratama, Rizki Rahmadi; Meily, Alfisyahriatunnida; Andika, Andika
Pharmaceutical Sciences and Research Vol. 9, No. 2
Publisher : UI Scholars Hub

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The rapid spread of the coronavirus disease 2019 (COVID-19) has led to the development of therapeutic inhibitor drug of SARS-CoV-2, which can inhibit the viral enzyme RNA-dependent-RNA-polymerase (RdRp), thereby preventing the replication, transcription, and synthesis of RNA virus in the host cells. Previous in-vitro studies revealed that Andrographis paniculata has the potential to inhibit the virus. Therefore, this study aims to isolate the specific compounds of Andrographis paniculata, which play a role in inhibiting SARS-CoV-2 RdRp using molecular docking. A total of 19 compounds were identified in previous literature studies, while remdesivir and favipiravir were used as the positive control. All compounds and proteins were applied to minimize and optimize energy. Furthermore, the docking method was carried out using Autodock 4.2.6 software with a specific grid box containing the active site of RdRp (ID: 6M71), and the Lamarckian Genetic Algorithm was used to determine the conformation. The best docking was screened on ADMET prediction and the binding energy was evaluated. There are 18 compounds of Andrographis paniculata including the top three, namely andrographolactone (∆G = -8.86 kcal/mol), andrographolide (∆G = -7.74 kcal/mol), and andrographidine-A (∆G = -7.68 kcal/mol), which showed the strongest binding affinity to the SARS-CoV-2 RdRp protein compared to other compounds and the positive control remdesivir (∆G = -5.73 kcal/mol) and favipiravir (∆G = -5.20 kcal/mol). Furthermore, active amino acids play a role in this interaction by forming strong hydrogen bonds, such as TYR 619, LYS 621, ASP 760, and ASP 623. Andrographolactone has the highest potential as SARS-CoV-2 RdRp inhibitor, hence, it can be used as a novel therapeutic candidate.

SENYAWA FITOESTROGEN UNTUK POTENSI TERAPI PENYAKIT NEURODEGENERATIF TERHADAP RESEPTOR TLR2: PENDEKATAN IN SILICO Faisal Akhmal Muslikh; Rizki Rahmadi Pratama; Marisca Evalina Gondokesumo
Jurnal Kesehatan Islam : Islamic Health Journal Vol. 12 No. 1 (2023): Jurnal Kesehatan Islam : Islamic Health Journal
Publisher : Publikasi oleh Fakultas Kedokteran Universitas Islam Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33474/jki.v12i1.19860

ABSTRAK Latar belakang: Toll-like receptor (TLRs) secara umum diekspresikan dalam sistem saraf pusat (SSP) dan memainkan peran penting dalam keberlangsungan hidup sel baik sel neuron, mikroglia, astrosit, dan oligodendrosit. TLR2 merupakan salah satu kelompok TLR yang banyak diteliti dan dikaitkan dengan penyakit neurodegenerative karena dapat menimbulkan kondisi pro-inflamasi dalam SSP. Senyawa fitoestrogen mampu menggantikan peran estrogen dalam menjaga homeostasis tubuh termasuk pada SSP. Penelitian ini bertujuan untuk mengetahui peran senyawa fitoestrogen dalam menghambat aktivasi TLR2 (6NIG) yang dapat menyebabkan penyakit neurodegenerative. Metode: Metode yang digunakan adalah molecular docking dengan AutoDockTools 1.5.6 program. Prediksi sifat farmakokinetik dan farmakodinamik dilakukan menggunakan SwissADME, sedangkan toksisitas menggunakan pkCSM dan ProTox II. Hasil dan Pembahasan: Hasil docking menggunakan protein 6NIG menunjukkan bahwa senyawa Î±-amyrin dan Î²-amyrin memiliki potensi terbaik dalam pengikatan dibandingkan dengan 17Î²-estradiol yang merupakan kontrol positif. Secara uji farmakokinetik dan farmakodinamik menunjukkan bahwa kedua senyawa tersebut memiliki permeabilitas yang baik, lipofilitas yang kuat sehingga mampu menembus membrane sel, dan tidak bersifat toksik. Kesimpulan: senyawa memiliki potensi untuk terapi penyakit neurodegenerative terhadap reseptor TLR2 (6NIG). Kata Kunci: ADMET; in silico; neurodegenerative; senyawa fitoestrogen; TLR2.

Studi In Silico Senyawa Flavonoid dalam Mengambat RNA-dependent RNA polymerase (RdRp) sebagai Antivirus COVID-19 Faisal Akhmal Muslikh; Rizki Rahmadi Pratama; Burhan Ma'arif; Neny Purwitasari
Journal of Islamic Pharmacy Vol 8, No 1 (2023): J. Islamic Pharm.
Publisher : Universitas Islam Negeri Maulana Malik Ibrahim Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18860/jip.v8i1.21722

Pada akhir tahun 2019, muncul coronavirus disease 2019 (COVID-19) yang disebabkan oleh severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yang menjadi ancaman serius bagi kesehatan masyarakat global sampai saat ini. Seiring berjalannya waktu, pengembangan obat repurposing telah menjadi metode yang efektif. Flavonoid, sejenis senyawa, telah dikenal memiliki sifat antivirus. Oleh karena itu, tujuan dari penelitian ini adalah untuk mengidentifikasi lima senyawa flavonoid (Genistein, Daidzein, Glycitein, Formonoetin, dan Biochanin A) yang sudah dikenal memiliki berbagai manfaat farmakologi dalam menghambat aktivitas RdRp SARS-CoV-2. Untuk melakukan analisis, metode molecular docking digunakan dengan menggunakan software AutoDockTools 1.5.6. Prediksi sifat farmakokinetik dan farmakodinamik dilakukan dengan menggunakan SwissADME, sedangkan untuk mengevaluasi toksisitas, digunakan ProTox II. Hasil molecular docking menunjukkan bahwa kelima senyawa flavonoid memiliki hasil yang lebih baik dibandingkan dengan senyawa kontrol positif remdesivir. Selain itu, hasil prediksi sifat farmakokinetik, farmakodinamik, dan toksisitas menunjukkan bahwa Biochanin A, Glycitein, Genistein, dan Formonoetin memiliki potensi terbaik untuk dikembangkan sebagai obat antivirus COVID-19 dengan kemampuan mengikat reseptor RdRp dengan PDB id. 6M71.

IDENTIFICATION OF COMPOUNDS IN SOURSOP LEAVES (Annona muricata L) AS BREAST ANTICANCER AGAINST ALFA ESTROGEN RECEPTORS BY MOLECULAR DOCKING Muhammad Fauzi; Nur Aini; Auliana Auliana; Syarifah Rugayah; Ciara Fitri Pribadi; Rizki Rahmadi Pratama
AL ULUM: JURNAL SAINS DAN TEKNOLOGI Vol 10, No 2 (2024)
Publisher : UPT Publication and Journal Management, Islamic University of Kalimantan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31602/jst.v10i2.15784

The incidence of breast cancer in Indonesia is steadily rising. Women have the highest incidence of breast cancer. Acetogenins are highly effective inhibitors of mitochondrial complex I or NADH dehydrogenase, making them a promising option for therapeutic creation against breast cancer. The plant known as Annona muricata, also referred to as the soursop leaf plant, is purported to possess the ability to suppress the activity of breast cancer. Hence, it is imperative to assess the chemical composition of soursop leaves on receptors by docking experiments. Research utilizing the active site on the alpha estrogen receptor has determined that the reticulin molecule, with a free energy of -8.14 kcal/mol, is a potential contender for breast cancer therapeutic medications. Reticulin exhibits the highest affinity for binding to the active site of estrogen receptor alpha. This chemical exhibits the capacity to impede the growth of breast cancer.

Studi In Silico Senyawa Flavonoid dalam Mengambat RNA-dependent RNA polymerase (RdRp) sebagai Antivirus COVID-19 Muslikh, Faisal Akhmal; Pratama, Rizki Rahmadi; Ma'arif, Burhan; Purwitasari, Neny
Journal of Islamic Pharmacy Vol 8, No 1 (2023): J. Islamic Pharm.
Publisher : Universitas Islam Negeri Maulana Malik Ibrahim Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18860/jip.v8i1.21722

Pada akhir tahun 2019, muncul coronavirus disease 2019 (COVID-19) yang disebabkan oleh severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yang menjadi ancaman serius bagi kesehatan masyarakat global sampai saat ini. Seiring berjalannya waktu, pengembangan obat repurposing telah menjadi metode yang efektif. Flavonoid, sejenis senyawa, telah dikenal memiliki sifat antivirus. Oleh karena itu, tujuan dari penelitian ini adalah untuk mengidentifikasi lima senyawa flavonoid (Genistein, Daidzein, Glycitein, Formonoetin, dan Biochanin A) yang sudah dikenal memiliki berbagai manfaat farmakologi dalam menghambat aktivitas RdRp SARS-CoV-2. Untuk melakukan analisis, metode molecular docking digunakan dengan menggunakan software AutoDockTools 1.5.6. Prediksi sifat farmakokinetik dan farmakodinamik dilakukan dengan menggunakan SwissADME, sedangkan untuk mengevaluasi toksisitas, digunakan ProTox II. Hasil molecular docking menunjukkan bahwa kelima senyawa flavonoid memiliki hasil yang lebih baik dibandingkan dengan senyawa kontrol positif remdesivir. Selain itu, hasil prediksi sifat farmakokinetik, farmakodinamik, dan toksisitas menunjukkan bahwa Biochanin A, Glycitein, Genistein, dan Formonoetin memiliki potensi terbaik untuk dikembangkan sebagai obat antivirus COVID-19 dengan kemampuan mengikat reseptor RdRp dengan PDB id. 6M71.

In Silico Analysis of Phytoestrogens' Neuroprotective Effect on N-methyl-D-aspartate (NMDA) Receptors Muslikh, Faisal Akhmal; Pratama, Rizki Rahmadi; Ma'arif, Burhan; Gondokesumo, Marisca Evalina
Journal of Islamic Medicine Vol 7, No 2 (2023): JOURNAL OF ISLAMIC MEDICINE EDISI SEPTEMBER 2023
Publisher : Faculty of Medicine and Health Science, Universitas Islam Negeri Maulana Malik Ibrahim

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18860/jim.v7i2.21381

cause of death and disability globally. One of the causes is associated with cell signaling disorders, neuronal apoptosis, inflammation, and the deposition of aggregate proteins. The N-methyl-D-aspartate (NMDA) receptor is a glutamate receptor that, when activated, causes synaptic dysfunction and leads to neuronal death. Phytoestrogen compounds are able to replace the role of estrogen in maintaining body homeostasis, including in the CNS. Objectif: This study aims to determine the role of phytoestrogen compounds in inhibiting NMDA activation (1PBQ), which causes neurodegenerative diseases. Methods: The method used is molecular docking with the AutoDockTools 1.5.6 program. The prediction of pharmacokinetic and pharmacodynamic properties used SwissADME, while the toxicity used pkCSM and ProTox II. Results: The results of docking using the 1PBQ protein showed that the compounds α-amyrin, β-amyrin and eudesmin had the best binding potential compared to 17β-estradiol which was the positive control. Pharmacokinetic and pharmacodynamic tests showed that the three compounds had good permeability and strong lipophilicity, so they could penetrate cell membranes, and were not toxic, except for eudesmin, which was included in class IV in the toxicity test using ProTox II. Conclusion : α-amyrin and β-amyrin compounds have the potential to treat neurodegenerative diseases against NMDA receptors (1PBQ).

Ekplorasi Senyawa Ekstrak Etanol Rumput Belulang (Eleusine indica (L.) Gaertn) Menggunakan LC-MS/MS-QTOF Serta Uji Aktivitas Anti-Diare: In-Vivo Pratama, Rizki Rahmadi; Septianto, Andre; Al-Hasyimi, Said Muhammad; Herliana, Herliana; Hasniah, Hasniah; Muslikh, Faisal Akhmal
Bioscientist : Jurnal Ilmiah Biologi Vol 12, No 2 (2024): December
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v12i2.14192

Diarrhea is one of the diseases caused by symptoms of intestinal tract infections due to various microorganisms. Goosegrass (Eleusine indica (L.) Gaertn) is a wild weed that has long been used as a traditional medicine, attributed to its phytochemical compounds such as tannins, alkaloids, flavonoids. This study aims to evaluate the antidiarrheal effects of Eleusine indica extract by comparing six treatment groups: a healthy group, a negative control group (Na-CMC), a positive control group (Loperamide 2 mg), and three variations of the extract dosage. Observations were made over 360 minutes at 30-minute intervals, using a fecal consistency scale from 1 (solid) to 5 (liquid). LC-MS/QToF analysis identified 25 secondary metabolites in the extract, including flavonoids (Schaftoside, Orientin, Vitexin, Tricin), phenolic compounds, and terpenoids. In vivo testing showed that the third dose of Eleusine indica grass extract had the most optimal antidiarrheal effect among the three doses, as evidenced by its ability to reduce diarrhea frequency, decrease fecal weight, shorten diarrhea duration, and improve fecal consistency, approaching the effectiveness of Loperamide 2 mg as a positive control. These findings suggest the potential of Eleusine indica extract as a promising natural antidiarrheal agent.

IDENTIFICATION OF COMPOUNDS IN SOURSOP LEAVES (Annona muricata L) AS BREAST ANTICANCER AGAINST ALFA ESTROGEN RECEPTORS BY MOLECULAR DOCKING Muhammad Fauzi; Nur Aini; Auliana Auliana; Syarifah Rugayah; Ciara Fitri Pribadi; Rizki Rahmadi Pratama
AL ULUM: JURNAL SAINS DAN TEKNOLOGI Vol 10, No 2 (2024)
Publisher : UPT Publication and Journal Management, Islamic University of Kalimantan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31602/jst.v10i2.15784

The incidence of breast cancer in Indonesia is steadily rising. Women have the highest incidence of breast cancer. Acetogenins are highly effective inhibitors of mitochondrial complex I or NADH dehydrogenase, making them a promising option for therapeutic creation against breast cancer. The plant known as Annona muricata, also referred to as the soursop leaf plant, is purported to possess the ability to suppress the activity of breast cancer. Hence, it is imperative to assess the chemical composition of soursop leaves on receptors by docking experiments. Research utilizing the active site on the alpha estrogen receptor has determined that the reticulin molecule, with a free energy of -8.14 kcal/mol, is a potential contender for breast cancer therapeutic medications. Reticulin exhibits the highest affinity for binding to the active site of estrogen receptor alpha. This chemical exhibits the capacity to impede the growth of breast cancer.

Characterization of Lactococcus garvieae Isolated from Wadi Papuyu (Anabas testudineus Bloch) Fermentation of Indonesian Origin as a Probiotic Candidate Soemarie, Yulistia Budianti; Pratama, Rizki Rahmadi; Milanda, Tiana; Barliana, Melisa Intan
Sciences of Pharmacy Volume 4 Issue 2
Publisher : ETFLIN Publishing House

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.58920/sciphar0402317

Lactococcus garvieae was isolated from the traditional fermented food Wadi Papuyu (Anabas testudineus Bloch) and characterized for its potential as a probiotic candidate. Growth assays demonstrated that L. garvieae could proliferate in MRS medium, reaching cell counts exceeding 107 CFU/mL after 72 h of anaerobic incubation. The isolate exhibited optimal growth at both 30 °C and 37 °C, as indicated by significant increases in absorbance at these temperatures. However, in the bile salt tolerance test using 0.5% (w/v) bile salts, L. garvieae showed a marked decline in growth, with absorbance values decreasing substantially after 24 and 48 h, indicating insufficient bile tolerance. The autoaggregation assay revealed values below 10%, suggesting limited autoaggregation capability and reduced potential for colonization in the gastrointestinal tract. In contrast, the co-aggregation assay showed that L. garvieae was able to coaggregate with pathogenic bacteria such as Escherichia coli, Salmonella spp., and Shigella spp., with co-aggregation percentages exceeding 40% after 5 h. Antimicrobial activity tests demonstrated that L. garvieae produced strong inhibition zones (diameters >10–20 mm and >20 mm) against Gram-positive and Gram-negative pathogenic bacteria. These findings indicate that while L. garvieae exhibits promising antimicrobial activity and co-aggregation ability, its limited bile salt tolerance and autoaggregation capacity are significant constraints in its development as a probiotic candidate.

POTENSI SENYAWA BIOAKTIF PHALERIA MACROCARPA TERHADAP RESEPTOR ESTROGEN ALFA SEBAGAI TERAPI KANKER PAYUDARA SECARA MOLECULAR DOCKING Rahmadi Pratama, Rizki; Amelia Putri, Irena; Indah Fajarwati, Jelita; Puji Rahmawati, Dwi; Fauzi, Muhammad
JURNAL FARMASI, SAINS, dan KESEHATAN Vol. 5 No. 1 (2025): FARMASAINKES: JURNAL FARMASI, SAINS dan KESEHATAN
Publisher : Fakultas Farmasi Universitas Muslim Nusantara Al Washliyah

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32696/farmasainkes.v5i1.5217

Kanker payudara menjadi penyebab utama kematian perempuan di seluruh dunia, oleh karena itu dibutuhkan pencarian agen antikanker yang lebih efektif dan lebih aman. Penelitian ini bertujuan mengevaluasi metabolit sekunder dan mikrobia endofit dari Phaleria macrocarpa sebagai sumber senyawa antikanker payudara menggunakan pendekatan in silico. Lima senyawa aktif apigenin, cafestol, fraxetin, mangiferin, dan sesamin docking terhadap reseptor estrogen alfa manusia (PDB: 3ERT) dengan AutoDock 4.0. Hasil docking menunjukkan semua senyawa menunjukkan afinitas ikatan yang baik, ditunjukkan oleh nilai energi bebas (ΔG) negatif; cafestol memiliki energi terbaik (-10,75 kkal/mol), diikuti sesamin (-8,69), apigenin (-8,42), mangiferin (-7,82), dan fraxetin (-5,78), serta nilai konstanta inhibisi (Ki) menunjukan potensi sebagai inhibitor. Visualisasi interaksi molekuler memperlihatkan kelima senyawa membentuk ikatan hidrogen dan hidrofobik dengan residu asam amino kunci di kantong aktif reseptor estrogen alfa, yaitu Glu353, Arg394, dan His524, yang diketahui penting untuk pengikatan ligan dan aktivitas inhibisi. Semua senyawa memenuhi kriteria Lipinski, dan sebagian besar memiliki profil farmakokinetik serta toksisitas (ADMET) yang baik, meskipun beberapa menunjukkan potensi mutagenisitas. Temuan ini mendukung metabolit sekunder dan endofit Phaleria macrocarpa sebagai kandidat untuk pengembangan agen antikanker payudara, namun validasi lebih lanjut secara in vitro dan in vivo masih diperlukan untuk memastikan efektivitas dan keamanannya.

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