Fazri, Achmad Tri Sugiarto Kharisul Islam and dr. Dewi Santosaningsih, ,MKes, SpMK, PhD and Prof. Dr. Apt. Roihatul Mutiah, M.Kes (2022) Aktivitas Senyawa Etil P-Metoksi Sinamat Dan Galangin Pada Non-structural protein 3 dan Non-structural protein 5 Covid-19. Magister thesis, Universitas Brawijaya.
Abstract
Coronavirus Disease 2019 atau Covid-19 merupakan infeksi saluran pernapasan akut akibat virus Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) yang menyebabkan pandemi di berbagai belahan dunia. Kecepatan penularan virus SARS-CoV- 2 dan minimnya keterbatasan pilihan obat untuk terapi Covid-19 menyebabkan angka kematian penderita yang tinggi dengan lebih dari 2 juta angka kematian dari 40 juta jiwa terinfeksi di seluruh dunia. Pengobatan pasien Covid-19 pada umumnya menggunakan regimen remdesivir yang bekerja dengan menghambat replikasi virus melalui blokade fungsi RNA dependent RNA polymerase (RdRp) virus sehingga menyebabkan produksi RNA prematur yang menurunkan viral load dari pasien. Namun, penggunaan remdesivir sebagai pilihan obat yang masih dalam fase uji coba klinis membawa efek samping berupa kerusakan jaringan ginjal, hati dan paru yang berujung pada kerusakan multiorgan pada pasien Covid-19. Studi in silico yang merupakan metode pengkajian prediksi kinerja suatu senyawa obat pada target patogen maupun sel tubuh melalui simulasi komputer dapat menjadi solusi dalam pengujian obat alternatif tersebut. Hal ini dikarenakan kemudahan dan kecepatan proses pengujian terhadap target obat melalui pemodelan komputer. Senyawa EPMS dan Galangin yang banyak terkandung dalam tanaman rempah mudah diperoleh di Indonesia seperti lengkuas (Alpinia galanga), jahe (Zingiber officinale), dan kencur (Kaempferia galanga). diduga kuat berikatan dengan NSP3 dan NSP5 virus SARSCOV- 2 yang diharapakan mampu menghambat infeksi dan replikasi virus dalam tubuh manusia. Pengujian secara in silico senyawa EPMS, senyawa Galangin dan senyawa Remdesivir sebagai obat pembanding dilakukan melalui pengunduhan disitus PubChem untuk senyawa uji (EPMS = CID 5281783, Galangin = CID 5281616, Remdesivir = CID 121304016) dan situs PDB untuk protein reseptor (NSP3 = PDB 6W6Y, NSP5 = PDB 6M2N ) dilakukan prediksi fisikokimia melaui program swissADME dan uji toksisitas melalui server Protox Online Tool dan pkCSM Online Tool. Didapatkan hasil senyawa Galangin tidak menembus sawar darah-otak, bukan merupakan subtrat P-gp, tidak terdapat pelanggaran pada hukum lima lipinski. Senyawa EPMS memiliki hasil serupa yakni tidak menembus sawar darah-otak, bukan merupakan subtrat P-gp, tidak terdapat pelanggaran pada hukum lima lipinski. Hal tersebut sedikit berbeda dari senyawa Remdesivir dimana senyawa tersebut tidak menembus sawar darah otak namun merupakan substrat P-gp dan memiliki 2 pelanggaran pada hukum lima lipinski (Torsi ≥ 10 dan Berat Molekul ≥ 500 g/mol). Hal tersebut menyebabkan senyawa Galangin dan EPMS memiliki bioavaibilitas oral lebih baik dibandingkan senyawa Remdesivir. Pada pengujian prediksi toksisitas didapatkan hasil bahwa senyawa EPMS termasuk dalam kelas 6 dengan LD50 sebesar 7900 mg/kg, senyawa Galangin termasuk dalam kelas 5 dengan LD50 sebesar 3919 mg/kg, senyawa Remdesivir termasuk dalam kelas 4 dengan LD50 sebesar 1190 mg/kg. Hasil tersebut memberi gambaran bahwa ketiga senyawa tidak bersifat toksik pada tubuh. Uji mutagenik AMES pada ketiga senyawa menunjukkan hasil negatif sehingga ketiga senyawa tersebut tidak memicu mutasi dan karsinogenik. Uji hepatotoksisitas melaporkan hanya senyawa Remdesivir yang memicu toksisitas pada hepar sedangkan uji sensitisasi kulit melaporkan hanya senyawa EPMS yang memicu sensitisasi kulit. Pada uji Docking melalui software Molegro Virtual Docker 6.0 didapatkan hasil senyawa EPMS berafinitas paling baik dan memiliki ikatan paling stabil pada NSP3 (Rerank score -130.11 kkal/mol) dan NSP5 (Rerank score -113.87 kkal/mol). Senyawa Galangin berafinitas lebih rendah yakni pada NSP3 (Rerank score -107.02 kkal/mol) dan NSP5 (Rerank score -84.40 kkal/mol). Nilai Docking dari kedua senyawa tersebut lebih baik bila dibandingkan dengan senyawa Remdesivir pada NSP3 (Rerank score -83.55 kkal/mol) dan NSP5 (Rerank score -83.55 kkal/mol). Pada uji Docking dengan NSP3 didapatkan ligand native berikatan sterik dengan protein NSP3 melalui asam amino Gly 130 (B), Phe 132 (B), Ser 128 (B), Asn 40 (B), dan Ala 38 (B). Terdapat beberapa ikatan identik dengan ikatan tersebut diantaranya pada x senyawa EPMS melalui asam amino 130 (B) dan Ser 128 (B), Galangin melalui asam amino Gly 130 (B), Ser 128 (B), Phe 132 (B) dan Ala 38 (B), serta Remdesivir melalui asam amino Ser 128 (B), Gly 130 (B), Phe 132 (B), dan Ala 38 (B). NSP3 berikatan hidrogen dengan Ligand Native melalui asam amino Gly 130 (B), Phe 132 (B), Ser 128 (B), Asn 40 (B). Ikatan hidrogen melalui asam amino serupa terbentuk dari senyawa EPMS melalui asam amino Gly 130 (B) dan Ser 128 (B), pada senyawa Galangin melalui asam amino Gly 130 (B), pada senyawa Remdesivir Gly 130 (B) dan Phe 132 (B). Pada uji Docking dengan NSP5 didapatkan interaksi sterik dengan ligand native melalui Cys 145 (B) dan Glu 166 (B). Terdapat beberapa ikatan identik dengan ikatan tersebut diantaranya pada senyawa EPMS melalui Glu 166 (B), senyawa Galangin diperantarai oleh asam amino Cys 145 (B) Gly 143 (B) Ser 144 (B) Leu 141 (B) Glu 166 (B), senyawa Remdesivir diperantarai oleh Leu 141 (B) Ser 144 (B) Cys 146 (B) Glu 166 (B). Tidak ditemukan adanya ikatan elektrostatik pada pengujian dengan reseptor NSP3 dengan senyawa uji maupun reseptor NSP5 dengan senyawa uji. Hasil penelitian tersebut menunjukkan bahwa senyawa EPMS dan senyawa Galangin memiliki sifat fisikokimiawi dan afinitas lebih baik daripada senyawa Remdesivir.
English Abstract
Coronavirus Disease 2019 or Covid-19 is an acute respiratory infection caused by the Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) which causes a pandemic in various parts of the world. The speed of transmission of the SARS-CoV-2 virus and the lack of limited drug options for the treatment of Covid-19 caused a high patient mortality rate with more than 2 million deaths out of 40 million people infected worldwide. Treatment of COVID-19 patients generally uses a regimen of remdesivir, which works by inhibiting viral replication by blocking the viral RNA dependent RNA polymerase (RdRp) function, causing premature RNA production which reduces the viral load of the patient. However, the use of remdesivir as a drug of choice, which is still in the clinical trial phase, has side effects in the form of kidney, liver and lung tissue damage, which can lead to multiorgan damage in Covid-19 patients. An in silico study which is a method of assessing the predictive performance of a drug compound on target pathogens and body cells through computer simulations can be a solution in testing these alternative drugs. This is due to the ease and speed of the testing process for drug targets through computer modeling. EPMS and Galangin compounds which are widely contained in spice plants are easily obtained in Indonesia such as galangal (Alpinia galanga), ginger (Zingiber officinale), and kencur (Kaempferia galanga). strongly suspected to bind to the NSP3 and NSP5 of the SARSCOV- 2 virus which is expected to be able to inhibit infection and viral replication in the human body.testing In silico of EPMS compounds, Galangin compounds and Remdesivir compounds as comparison drugs was carried out by downloading the PubChem site for the test compound (EPMS = CID 5281783, Galangin = CID 5281616, Remdesivir = CID 121304016) and the PDB site for the receptor protein (NSP3 = PDB 6W6Y , NSP5 = GDP 6M2N ) physicochemical predictions were carried out through the swissADME program and toxicity tests through the Protox Online Tool and pkCSM Online Tool servers. It was found that the Galangin compound did not penetrate the blood-brain barrier, was not a P-gp substrate, there was no violation of Lipinski's Five Laws. The EPMS compound had similar results, namely that it did not penetrate the blood-brain barrier, was not a P-gp substrate, and there was no violation of Lipinski's Five Laws. It is slightly different from the compound Remdesivir in that the compound does not cross the Blood Brain Barrier but is a P-gp substrate and has 2 violations of Lipinski's law of five (Torque 10 and Molecular Weight 500 g/mol). This causes Galangin and EPMS compounds to have better oral bioavailability than Remdesivir compounds. In the toxicity prediction test, the results showed that the EPMS compound was included in class 6 with an LD50 of 7900 mg/kg, Galangin compound was included in class 5 with an LD50 of 3919 mg/kg, Remdesivir compound was included in class 4 with an LD50 of 1190 mg/kg. kg. These results illustrate that the three compounds are not toxic to the body. AMES mutagenic test on the three compounds showed negative results so that the three compounds did not trigger mutations and were carcinogenic. Hepatotoxicity test reported that only Remdesivir compound triggered liver toxicity while skin sensitization test reported only EPMS compound that triggered skin sensitization. In the Docking using Molegro Virtual Docker 6.0 software, the results showed that the EPMS compound had the best affinity and had the most stable binding on NSP3 (Rerank score -130.11 kcal/mol) and NSP5 (Rerank score -113.87 kcal/mol). Galangin compounds have lower affinity for NSP3 (Rerank score -107.02 kcal/mol) and NSP5 (Rerank score -84.40 kcal/mol). The Docking of these two compounds were better when compared to Remdesivir in NSP3 (Rerank score -83.55 kcal/mol) and NSP5 (Rerank score -83.55 kcal/mol). In the Docking test with NSP3, it was found that the native ligand binds sterically to the NSP3 protein through the amino acids Gly 130 (B), Phe 132 (B), Ser 128 (B), Asn 40 (B), and Ala 38 (B). There are several identical bonds with these bonds, including in EPMS compounds through amino acids 130 (B) and Ser 128 (B), Galangin through amino acids Gly 130 (B), Ser 128 (B), Phe 132 (B) and Ala 38 ( B), and Remdesivir through the amino acids Ser 128 (B), Gly 130 (B), Phe 132 (B), and Ala 38 (B). NSP3 is hydrogen bonded to the Native xi i Ligand via the amino acids Gly 130 (B), Phe 132 (B), Ser 128 (B), Asn 40 (B). Hydrogen bonds through similar amino acids are formed from EPMS compounds through amino acids Gly 130 (B) and Ser 128 (B), in Galangin compounds through amino acids Gly 130 (B), in Remdesivir compounds Gly 130 (B) and Phe 132 (B). ). In the Docking test with NSP5, steric interactions with native ligands were found through Cys 145 (B) and Glu 166 (B). There are several identical bonds with these bonds, including in EPMS compounds through Glu 166 (B), Galangin compounds mediated by the amino acid Cys 145 (B) Gly 143 (B) Ser 144 (B) Leu 141 (B) Glu 166 (B), Remdesivir compounds are mediated by Leu 141 (B) Ser 144 (B) Cys 146 (B) Glu 166 (B). No electrostatic bond was found in the test with the NSP3 receptor with the test compound and the NSP5 receptor with the test compound. The results showed that EPMS compounds and Galangin compounds had better physicochemical properties and affinity than Remdesivir compounds.
| Item Type: | Thesis (Magister) |
|---|---|
| Identification Number: | 0423060014 |
| Subjects: | 600 Technology (Applied sciences) > 616 Diseases > 616.02 Special topics of disease > 616.025 Medical emergencies / Emergency medicine / Emergency nursing / Triage (Medicine) |
| Divisions: | S2/S3 > Magister Ilmu Biomedis, Fakultas Kedokteran |
| Depositing User: | Endang Susworini |
| Date Deposited: | 01 Nov 2023 08:13 |
| Last Modified: | 01 Nov 2023 08:13 |
| URI: | http://repository.ub.ac.id/id/eprint/204198 |
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