Jonathan Suciono Purnomo1, Richelle Clarence Saptura1, Dikson1, Dela Rosa2, Ariela Samantha1,
Reinhard Pinontoan1*
1Department of Biology, Faculty of Health Science, Universitas Pelita Harapan, Jl. Jendral Sudirman 20, Lippo Karawaci, Tangerang 15810, Banten, Indonesia
2Department of Pharmacy, Faculty of Health Science, Universitas Pelita Harapan. Jl. Jendral Sudirman 20, Lippo Karawaci, Tangerang 15810, Banten, Indonesia
*Corresponding author’s email: reinhard.pinontoan@uph.edu
Received: 15 November 2025 / Revised: 25 March 2026 / Accepted: 30 March 2026 / Published Online: 09 April 2026
Abstract
Thrombosis is a major cause of cardiovascular diseases, contributing significantly to global mortality rates. It has become necessary to develop more cost-effective and safer treatments for thrombosis, such as those derived from plants, due to prohibitively high costs and severe side effects of existing medications. Ginger (Zingiber officinale) has been reported to have thrombolytic abilities via fibrinolysis in vitro. Subsequently, the in silico studies described herein aimed to further understand the fibrinolytic mechanisms of zingibain-2 at the molecular level through molecular docking and dynamics simulations. AlphaFold3 accurately predicted the zingibain-2 structure and stably predicted the fibrin peptide-zingibain interactions. A preference for proline at the P2 position, typical of cysteine proteases, was found in 18, 8-residue peptides screened from human fibrin chains (PDB: 2HLO). Protein superimposition between the AlphaFold3 prediction and X-ray crystallography structures showed a minimum root mean square deviation value of 0.33 Å and 97.72% favorable residue orientation on a Ramachandran plot. Initial docking identified 13 out of 18, 8-residue human fibrin peptides with short catalytic distances. However, GROMACS molecular dynamics simulations of these AlphaFold3-docked complexes over 100 ns further narrowed this down to 11 out of 18, 8-residue human fibrin peptides with stable interactions, as demonstrated by their reliably short catalytic distances and negative binding energy. These stable models showed close, stable interactions with zingibain-2, and thus, support its potential as a plant-based thrombolytic agent. However, this must be experimentally validated.
Keywords: Fibrinolytic mechanism, Molecular docking, Molecular dynamics, Thrombolytic, Zingibain
