Wan Mardhiyana Wan AyubNurul Amirah MarjohanMohamed Haneif KhalidEnoch Kumar PerimalMuhamad Arif Mohamad Jamali2025-12-022025-12-022025Wan Mardhiyana Wan Ayub, Nurul Amirah Marjohan, Mohamed Haneif Khalid, Enoch Kumar Perimal & Muhamad Arif Mohamad Jamali (2025) Elucidating zerumbone’s low-efficacy agonism at the μ-opioid receptor via molecular dynamics simulation and Markov state modeling. J Comput Aided Mol Des 39, 94 . https://doi.org/10.1007/s10822-025-00677-21573-495110.007/s10822-025-00677-2https://link.springer.com/article/10.1007/s10822-025-00677-2https://oarep.usim.edu.my/handle/123456789/28108IndexedZerumbone is a natural sesquiterpene compound from Zingiber zerumbet plant. While it significantly exhibits analgesic properties through the μ-opioid receptor (μOR) found in animal models, its precise molecular mechanism at the receptor level remains poorly investigated. The present work involves 1-µs molecular dynamics (MD) simulations, MM/PBSA binding-free energy analyses, principal component analysis (PCA) as well as Markov state modeling (MSM) to address how the dynamic basis of zerumbone-μOR interactions compared to morphine, which is a known full agonist. MD trajectories reported greater receptor backbone fluctuations, improved loop mobility, reduced stable hydrogen bonds, and moderate receptor compaction in the zerumbone-bound state in contrast to morphine. MM/PBSA calculations indicated similar total binding affinity and the driven for zerumbone affinity was primarily hydrophobic interaction. PCA recognized notable intermediate conformational substates that were stabilized by zerumbone. In the interim, highly stabilized intermediate-activation macrostate with high-kinetic barriers (~ 8–16 k_BT) and millisecond-scale residency was also revealed through MSM analysis. In agreement with analgesic activities reported previously, these computational insights identify zerumbone as a low-efficacy partial agonist, providing comprehensive molecular explanation to its analgesic profile to serve as a source of safer and more opioid-like drugs.en-USμ-opioid receptor (μOR) · Analgesia · Docking simulations · Molecular dynamics (MD) simulations · MMPBSA analysis · Safer opioid alternativestext::journal::journal article1113994