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Rahman, Awalil RK.
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Biochemistry, Genetics & Molecular Biology Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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In silico analysis of Arbacia lixula-derived peptides and plasmid construction for recombinant anti-aging therapies Yenny, Satya W.; Jamsari, Jamsari; Hazmi, Auliya A.; Cuandra, Kevin N.; Hanifah, Wafiq; Yahono, Angela S.; Wahyudi, Dhyani P.; Buana, Gherriandi R.; Rahman, Awalil RK.; Maharani, Annisa D.; Firjatullah, Muhammad F.; Maulana, Rafi; Prayogi, Norbertus M.; Tristan, Christopher D.
Narra J Vol. 4 No. 3 (2024): December 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i3.1283

Abstract

Skin aging is one of the degenerative processes influenced by tyrosinase, elastase, collagenase, hyaluronidase, and matrix metalloproteinase-9 (MMP9) activity. One promising avenue for discovering antiaging therapeutics is the peptides from the Arbacia lixula spine. The aim of this study was to explore the potential of peptides from A. lixula spine as a multitarget inhibitor for recombinant antiaging therapies through in silico approaches. The crystal structure of peptides previously identified in A. lixula spine was visualized using the UCSF Chimera. The protein data bank (PDB) database was used to obtain the crystal structures of protein targets. The webservers Innovagen, AllerTop, and ToxinPred were utilized to predict the peptide's water solubility, toxicity, and allergenicity. MOE application was used to prepare all ligands and proteins, molecular docking, and visualization. Molecular dynamics simulations were carried out on the protein-ligand complexes on Yasara Dynamics application. The Benchling website was used to perform virtual electrophoresis and reconstruct the recombinant plasmid (Psb1c3). Based on the molecular docking results, peptide REGSPDLLE has the potential as a multitarget inhibitor of tyrosinase (-9.07 kcal/mol), hyaluronidase (-10.57 kcal/mol), elastase (-9.32 kcal/mol), collagenase (-10.57 kcal/mol), and MMP9 (-10.43 kcal/mol). Peptide REGSPDLLE was selected due to its strong binding affinity on the active site of each target protein and exhibits non-toxic, non-allergenic, and good water-soluble as indicated by Support Vector Machine score <0. Molecular dynamics simulations confirmed stable interactions with receptor proteins. Peptide REGSPDLLE was successfully inserted into the recombinant pSB1C3 plasmid, confirmed by virtual electrophoresis with bands at ~2000 bp and ~150 bp. Further in vitro and in vivo studies are necessary to verify the anti-aging efficacy of peptide REGSPDLLE.
Peptide-based drug as atherosclerosis multitarget therapy from Lytechinus variegatus spine: An in silico study Arisanty, Dessy; Khairani, Salsabila P.; Nathaniel, Kevin; Wahyudi, Dhyani P.; Kamila, Isna C.; Maharani, Malya CS.; Theodora, Eillen; Budianto, Raymond E.; Shofiy, Alifya R.; Nugraha, Ikwandi C.; Aaliyya, Zaki S.; Rahman, Awalil RK.; Ariouso, Al H.
Narra J Vol. 5 No. 2 (2025): August 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i2.1152

Abstract

Atherosclerosis is a leading cardiovascular disease characterized by the buildup of plaques within arterial walls. The aim of this study was to investigate the potential of peptides derived from Lytechinus variegatus spines as novel therapeutic agents for atherosclerosis using an in silico approach. Key proteins involved in atherosclerosis were selected as target proteins: vascular endothelial growth factor receptor (VEGFR), protein kinase B (AKT1), epidermal growth factor receptor (EGFR), mitogen-activated protein kinase 8 (MAPK8), and endothelin-1 (ET-1). Comprehensive analysis involving ligand and protein preparation, toxicity, and allergenicity assessments, absorption, distribution, metabolism and excretion (ADME) predictions, and molecular docking were conducted to evaluate the safety, pharmacokinetic properties, binding affinity (kcal/mol), root mean square deviation (RMSD) (Å), as well as a 2D and 3D visualization. Toxicity predictions revealed that peptide 9 was non-toxic and non-allergenic, with a lethal dose 50 (LD50) of 3,000 mg/kg, indicating its safety. Peptide 9 demonstrated the most promising results, effectively inhibiting VEGFR2 (-10,90 kcal/mol), AKT1 (-10,56 kcal/mol), EGFR (-9,82 kcal/mol), MAPK8 (-9,64 kcal/mol), and ET-1 (-11,41 kcal/mol) with strong binding affinities and specificity. These interactions suggested that peptide 9 from Lytechinus variegatus spines may serve as a competitive multitarget inhibitor, offering potential multitarget therapeutic activity against atherosclerosis. Peptide 9 also had high water solubility and did not affect the concentration or excretion of other drugs or compounds, minimizing the risk of drug-drug interactions.
Co-Authors Aaliyya, Zaki S. Ariouso, Al H. Buana, Gherriandi R. Budianto, Raymond E. Cuandra, Kevin N. Dessy Arisanty Firjatullah, Muhammad F. Hanifah, Wafiq Hazmi, Auliya A. Jamsari Jamsari Kamila, Isna C. Khairani, Salsabila P. Maharani, Annisa D. Maharani, Malya CS. Maulana, Rafi Nathaniel, Kevin Nugraha, Ikwandi C. Prayogi, Norbertus M. Shofiy, Alifya R. Theodora, Eillen Tristan, Christopher D. Wahyudi, Dhyani P. Yahono, Angela S. Yenny, Satya W.