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In Silico Drug Design of Sembukan (Paederia scandenz) As Anti-Breast Cancer Agents

Journal of Science and Technology Research for Pharmacy · Vol. 5 No. 1 (2025) · hlm. 1–13

DOI
10.15294/jstrp.v5i1.27527
ISSN
2776-0685
Terbit
2025-07-25
Penerbit
Universitas Negeri Semarang
Bahasa
eng

Abstrak

cancer is a disease of excessive cell growth and is one of the cases of disease that has increased every year. cancer treatment therapy in the form of chemotherapy drugs has various side effects so that safer long-term treatment is needed, namely using herbal medicines such as sembukan plants (Paederia scandens). This research was conducted using experimental methods computationally through in silico methods as a potential prediction test as a reference for further studies. isolate compounds are carried out molecular tethering against progesterone, estrogen, HER2, and NfkB receptors using PyRx 0.8 software. Then the isolated compounds were tested for the feasibility of chemical and pharmacokinetic properties and toxicity using the Lipinski Rules of Five data base and ADMETLab 3.0. Furthermore, visualization was carried out to see the bonding interaction between ligand and receptor protein using Biovia Discovery Studio 2024 software. Based on the results of molecular tethering compounds Kaempferol 3-rutinoside-7-glucoside, Cosmetin, Quercetin 3-o-rutinoside-7-o-glucoside, Daidzein and Linarin have the potential as inhibitors respectively against progesterone, HER2, Nf-kB, estrogen and overall average receptors with each binding affinity value of -9. 6 kcal/mol, -9.8 kcal/mol, -9.8 kcal/mol, -10.8 kcal/mol, -8.9 kcal/mol and -9.0 kcal/mol respectively. The best physico-chemical properties were obtained for Daidzein and Linarin compounds. Visualization data generated that Kaempferol 3-rutinoside-7-glucoside, Cosmetin, Quercetin 3-o-rutinoside-7-o-glucoside, Daidzein and Linarin compounds have similar interactions and amino acid residues with control drugs so that they are predicted to have similar pharmacological effects as breast anticancer.

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  • State University of Semarang
  • National University of Singapore
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Rekan penulisOrganisasiArtikel bersama
Ari YuniastutiAfiliasi tidak diketahui4
Retno Sri IswariState University of Semarang3
Priyantini WidiyaningrumAfiliasi tidak diketahui2
Ani RusilowatiState University of Semarang2
Prima Gita IslamiAfiliasi tidak diketahui1
Prima Gita Islami IslamiState University of Semarang1
Nana Kariada MartutiAfiliasi tidak diketahui1
Retno PurwantiAfiliasi tidak diketahui1
- UmarudinAfiliasi tidak diketahui1
Wiwi IsnaeniState University of Semarang1
Rheza Alfy YuliantoAfiliasi tidak diketahui1
Yuliana AstrianaAfiliasi tidak diketahui1
Ning SetiatiAfiliasi tidak diketahui1
Muhammad Rofiq NezarAfiliasi tidak diketahui1
Margareta RahayuningsihAfiliasi tidak diketahui1
Denny Herbianto BahtiarAfiliasi tidak diketahui1
Aditya MariantiState University of Semarang1
Fatchun NaimAfiliasi tidak diketahui1
Siti Rofiatus Sa’adahAfiliasi tidak diketahui1
Siti Harnina BintariAfiliasi tidak diketahui1
Sri UtamiAfiliasi tidak diketahui1
Masrukan MasrukanState University of Semarang1
Heru SetyantoAfiliasi tidak diketahui1
Triastuti SulistyaningsihAfiliasi tidak diketahui1
Tri Sri NoorAsihAfiliasi tidak diketahui1
Fitri Arum SasiAfiliasi tidak diketahui1
Wulan ChristijantiState University of Semarang1
Senda Kartika RakainsaState University of Semarang1
Kartika WidyaningrumState University of Semarang1
Mohd Salim Bin MohamedNational University of Singapore1
Enni Suwarsi RahayuState University of Semarang1
Prapti DyahwatiAfiliasi tidak diketahui1
Dian LestariAfiliasi tidak diketahui1
Sri Mulyani E.S.Afiliasi tidak diketahui1
Aisa Nikmah RahmatihAfiliasi tidak diketahui1
Andreas Priyono Budi PrasetyoState University of Semarang1
1Yohanes Nong BungaAfiliasi tidak diketahui1
Lili Astuti IsnaeniAfiliasi tidak diketahui1

Afiliasi berasal dari OpenAlex; metadata OAI-PMH jurnal tidak memuatnya. Penulis tanpa ID OpenAlex dicocokkan berdasarkan nama, sehingga dua orang bisa tergabung atau satu orang bisa terpisah.

Sumber metadata: OAI-PMH (metadata jurnal) https://journal.unnes.ac.id/journals/JSTRP/oai, pertama di-harvest 5 Nov 2026, terakhir terlihat 8 Nov 2026.
Metadata asli (oai_dc) 
<oai_dc:dc xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/  http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
	<dc:title xml:lang="en">In Silico Drug Design of Sembukan (Paederia scandenz) As Anti-Breast Cancer Agents</dc:title>
	<dc:creator xml:lang="en">Eva Ulfiatus Shofia</dc:creator>
	<dc:creator xml:lang="en">R. Susanti</dc:creator>
	<dc:subject xml:lang="en">in silico</dc:subject>
	<dc:subject xml:lang="en">paederia scandens</dc:subject>
	<dc:subject xml:lang="en">breast cancer</dc:subject>
	<dc:description xml:lang="en">cancer is a disease of excessive cell growth and is one of the cases of disease that has increased every year. cancer treatment therapy in the form of chemotherapy drugs has various side effects so that safer long-term treatment is needed, namely using herbal medicines such as sembukan plants (Paederia scandens). This research was conducted using experimental methods computationally through in silico methods as a potential prediction test as a reference for further studies. isolate compounds are carried out molecular tethering against progesterone, estrogen, HER2, and NfkB receptors using PyRx 0.8 software. Then the isolated compounds were tested for the feasibility of chemical and pharmacokinetic properties and toxicity using the Lipinski Rules of Five data base and ADMETLab 3.0. Furthermore, visualization was carried out to see the bonding interaction between ligand and receptor protein using Biovia Discovery Studio 2024 software. Based on the results of molecular tethering compounds Kaempferol 3-rutinoside-7-glucoside, Cosmetin, Quercetin 3-o-rutinoside-7-o-glucoside, Daidzein and Linarin have the potential as inhibitors respectively against progesterone, HER2, Nf-kB, estrogen and overall average receptors with each binding affinity value of -9. 6 kcal/mol, -9.8 kcal/mol, -9.8 kcal/mol, -10.8 kcal/mol, -8.9 kcal/mol and -9.0 kcal/mol respectively. The best physico-chemical properties were obtained for Daidzein and Linarin compounds. Visualization data generated that Kaempferol 3-rutinoside-7-glucoside, Cosmetin, Quercetin 3-o-rutinoside-7-o-glucoside, Daidzein and Linarin compounds have similar interactions and amino acid residues with control drugs so that they are predicted to have similar pharmacological effects as breast anticancer.</dc:description>
	<dc:publisher xml:lang="en">Universitas Negeri Semarang</dc:publisher>
	<dc:date>2025-07-25</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:type xml:lang="en">Peer-reviewed Article</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.unnes.ac.id/journals/JSTRP/article/view/27527</dc:identifier>
	<dc:identifier>10.15294/jstrp.v5i1.27527</dc:identifier>
	<dc:source xml:lang="en">Journal of Science and Technology Research for Pharmacy; Vol. 5 No. 1 (2025): Journal of Science and Technology Research for Pharmacy; 1-13</dc:source>
	<dc:source>2776-0685</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journal.unnes.ac.id/journals/JSTRP/article/view/27527/5143</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2025 Journal of Science and Technology Research for Pharmacy</dc:rights>
</oai_dc:dc>