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Molecular modeling on the identification of potential Janus Kinase 3 (JAK3) inhibitor based on the Indonesian Medicinal Plant Database

Journal of Mathematical and Fundamental Sciences · Vol. 52 No. 3 (2020) · hlm. 276–285

DOI
10.5614/j.math.fund.sci.2020.52.3.2
ISSN
2338-5510, 2337-5760
Terbit
2020-12-31
Penerbit
Directorate for Research and Innovation (DRI) ITB
Bahasa
eng

Abstrak

The Janus tyrosine kinases (JAKs) have shown great promise as therapeutic protein targets in the treatment of cancer and inflammation diseases. This study used pharmacophore modeling to identify potential inhibitors of Janus kinase 3 (JAK3). A pharmacophore model was developed based on a known JAK3 inhibitor (1NX) and was employed to search for potential JAK3 inhibitors against Indonesian herbal compounds. Among 28 hit molecules that were identified and subjected to a molecular docking protocol against JAK3, the three compounds that had the highest affinities toward JAK3 were camelliaside B, 3-O-galloylepicatechin-(4beta-6)-epicatechin-3-O-gallate, and mesuaferrone B. These were then each subjected to a 50-ns molecular dynamics (MD) simulation. Analysis of RMSD and RMSF values indicated that the three compounds reached stability during the MD simulation. Interestingly, all three compounds had lower binding energies than 1NX against JAK3, as predicted by the MM-PBSA binding energy calculation.

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  • Universitas Halu Oleo
  • National Nuclear Energy Agency of Indonesia
  • Bandung Institute of Technology
  • University of Indonesia
  • Tadulako University
  • Muhammadiyah University Purwokerto
  • Indonesian Institute of Sciences
  • Afiliasi tidak diketahui
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Rekan penulisOrganisasiArtikel bersama
Ruslin RuslinUniversitas Halu Oleo6
L.B.S. KardonoIndonesian Institute of Sciences3
Rahmana Emran KartasasmitaBandung Institute of Technology3
Ari SartinahUniversitas Halu Oleo2
Yamin YaminUniversitas Halu Oleo2
Wening LestariNational Nuclear Energy Agency of Indonesia2
Sri SetiyowatiNational Nuclear Energy Agency of Indonesia2
Agus AriyantoNational Nuclear Energy Agency of Indonesia2
Puji WidayatiNational Nuclear Energy Agency of Indonesia2
Gusti Ayu Made CandrayantiUniversitas Halu Oleo1
NUR ILLIYYIN AKIBUniversitas Halu Oleo1
Andi Nafisah Tendri AdjengUniversitas Halu Oleo1
Nurhasana NurhasanaAfiliasi tidak diketahui1
Asniar PascayantriUniversitas Halu Oleo1
Muhammad Jefriyanto BudikafaUniversitas Halu Oleo1
R RuslinUniversitas Halu Oleo1
Suci Rahmawati PutriUniversitas Halu Oleo1
La Ode Muhammad FitrawanUniversitas Halu Oleo1
Sunandar IhsanUniversitas Halu Oleo1
S SabarudinUniversitas Halu Oleo1
Nuralifah NuralifahUniversitas Halu Oleo1
Wa Ode Sitti NurrokhmadhaniAfiliasi tidak diketahui1
Y. SusiloAfiliasi tidak diketahui1
C.N. ArdiyatnoNational Nuclear Energy Agency of Indonesia1
Sutari SutariNational Nuclear Energy Agency of Indonesia1
Gina MondridaNational Nuclear Energy Agency of Indonesia1
Triningsih TriningsihNational Nuclear Energy Agency of Indonesia1
S. DarwatiNational Nuclear Energy Agency of Indonesia1
Setiawan SetiawanAfiliasi tidak diketahui1
Anung PujiyantoNational Nuclear Energy Agency of Indonesia1
Rien RitawidyaNational Nuclear Energy Agency of Indonesia1
Mujinah MujinahNational Nuclear Energy Agency of Indonesia1
Witarti WitartiNational Nuclear Energy Agency of Indonesia1

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Sumber metadata: OAI-PMH (metadata jurnal) https://journals.itb.ac.id/index.php/jmfs/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">Molecular modeling on the identification of potential Janus Kinase 3 (JAK3) inhibitor based on the Indonesian Medicinal Plant Database</dc:title>
	<dc:creator>Arba, Muhammad</dc:creator>
	<dc:creator>Safitri, Sanang Nur</dc:creator>
	<dc:creator>Hidayat, Andry Nur</dc:creator>
	<dc:creator>Yanuar, Arry</dc:creator>
	<dc:creator>Zubair, Muhammad Sulaiman</dc:creator>
	<dc:creator>Djalil, Asmiyenti Djaliasrin</dc:creator>
	<dc:creator>Tjahjono, Daryono Hadi</dc:creator>
	<dc:subject xml:lang="en-US">Janus kinase</dc:subject>
	<dc:subject xml:lang="en-US">MM-PBSA</dc:subject>
	<dc:subject xml:lang="en-US">molecular dynamics simulation</dc:subject>
	<dc:subject xml:lang="en-US">pharmacophore modeling</dc:subject>
	<dc:subject xml:lang="en-US">virtual screening</dc:subject>
	<dc:description xml:lang="en-US">The Janus tyrosine kinases (JAKs) have shown great promise as therapeutic protein targets in the treatment of cancer and inflammation diseases. This study used pharmacophore modeling to identify potential inhibitors of Janus kinase 3 (JAK3). A pharmacophore model was developed based on a known JAK3 inhibitor (1NX) and was employed to search for potential JAK3 inhibitors against Indonesian herbal compounds. Among 28 hit molecules that were identified and subjected to a molecular docking protocol against JAK3, the three compounds that had the highest affinities toward JAK3 were camelliaside B, 3-O-galloylepicatechin-(4beta-6)-epicatechin-3-O-gallate, and mesuaferrone B. These were then each subjected to a 50-ns molecular dynamics (MD) simulation. Analysis of RMSD and RMSF values indicated that the three compounds reached stability during the MD simulation. Interestingly, all three compounds had lower binding energies than 1NX against JAK3, as predicted by the MM-PBSA binding energy calculation.</dc:description>
	<dc:publisher xml:lang="en-US">Directorate for Research and Innovation (DRI) ITB</dc:publisher>
	<dc:date>2020-12-31</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journals.itb.ac.id/index.php/jmfs/article/view/12588</dc:identifier>
	<dc:identifier>10.5614/j.math.fund.sci.2020.52.3.2</dc:identifier>
	<dc:source xml:lang="en-US">Journal of Mathematical and Fundamental Sciences; Vol. 52 No. 3 (2020); 276-285</dc:source>
	<dc:source>2338-5510</dc:source>
	<dc:source>2337-5760</dc:source>
	<dc:source>10.5614/j.math.fund.sci.2020.52.3</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journals.itb.ac.id/index.php/jmfs/article/view/12588/5045</dc:relation>
</oai_dc:dc>