13-Acetoxysarcocrassolide induces apoptosis in human hepatocellular carcinoma cells through mitochondrial dysfunction and suppression of the PI3K/AKT/mTOR/p70S6K signalling pathway.

CONTEXT: 13-Acetoxysarcocrasside, isolated from the Taiwanese soft coral Sarcophyton crassocaule Moser (Alcyoniidae), has biological activity and induces apoptosis in hepatocellular carcinoma cells. OBJECTIVE: To elucidate the mechanisms underlying apoptosis induced by 13-acetoxysarcocrasside in HA22T and HepG2 hepatocellular carcinoma cells. MATERIAL AND METHODS: MTT and morphology assays were employed to assess the anti-proliferative effects of 13-acetoxysarcocrasside (1-5 µM). TUNEL/DAPI staining and annexin V-fluorescein isothiocyanate/propidium iodide staining were used to detect apoptosis. Cells were treated with13-acetoxysarcocrassolide (0, 1, 2, and 4 µM) for 24 h, and the mechanism of cells apoptotic was detected by western blotting. Cells treated with DMSO were the control. RESULTS: Survival of the cells decreased with the addition of 13-acetoxysarcocrassolide, and at 4 µM cell survival was inhibited by approximately 40%. After treatment of cells with 13-acetoxysarcocrassolide, the incidence of early/late apoptosis to be 0.3%/0.5%∼5.4%/22.7% for HA22T cells, in the HePG2 cells were 0.6%/0.2%∼14.4%/23.7%. Western blotting analysis showed that the expression of Bax, Bad, cleaved caspase 3, cleaved caspase 9, cleaved-PARP-1, cytochrome c, and p-4EBP1 increased with an increasing concentration of 13-acetoxysarcocrasside (0, 1, 2, and 4 µM), whereas that of Bcl-2, Bcl-xL, Mcl-1, p-Bad, p-PI3K, p-AKT, p-mTOR, p-70S6K, p-S6, p-eIF4E, and p-eIF4B decreased. DISCUSSION AND CONCLUSIONS: Apoptosis induced by 13-acetoxysarcocrassolide in HA22T and HepG2 cells is mediated by mitochondrial dysfunction and inactivation of the PI3K/AKT/mTOR/p70S6K pathway. The potential of 13-acetoxysarcocrassolide as a chemotherapeutic agent should be further assessed for use in human hepatocellular carcinoma treatment.

Sinulariolide Inhibits Gastric Cancer Cell Migration and Invasion through Downregulation of the EMT Process and Suppression of FAK/PI3K/AKT/mTOR and MAPKs Signaling Pathways.

Cancer metastasis is the main cause of death in cancer patients; however, there is currently no effective method to predict and prevent metastasis of gastric cancer. Therefore, gaining an understanding of the molecular mechanism of tumor metastasis is important for the development of new drugs and improving the survival rate of patients who suffer from gastric cancer. Sinulariolide is an active compound isolated from the cultured soft coral Sinularia flexibilis. We employed sinulariolide and gastric cancer cells in experiments such as MTT, cell migration assays, cell invasion assays, and Western blotting analysis. Analysis of cell migration and invasion capabilities showed that the inhibition effects on cell metastasis and invasion increased with sinulariolide concentration in AGS and NCI-N87 cells. Immunostaining analysis showed that sinulariolide significantly reduced the protein expressions of MMP-2, MMP-9, and uPA, but the expressions of TIMP-1 and TIMP-2 were increased, while FAK, phosphorylated PI3K, phosphorylated AKT, phosphorylated mTOR, phosphorylated JNK, phosphorylated p38MAPK, and phosphorylated ERK decreased in expression with increasing sinulariolide concentration. From the results, we inferred that sinulariolide treatment in AGS and NCI-N87 cells reduced the activities of MMP-2 and MMP-9 via the FAK/PI3K/AKT/mTOR and MAPKs signaling pathways, further inhibiting the invasion and migration of these cells. Moreover, sinulariolide altered the protein expressions of E-cadherin and N-cadherin in the cytosol and Snail in the nuclei of AGS and NCI-N87 cells, which indicated that sinulariolide can avert the EMT process. These findings suggested that sinulariolide is a potential chemotherapeutic agent for development as a new drug for the treatment of gastric cancer.

Flaccidoxide-13-Acetate-Induced Apoptosis in Human Bladder Cancer Cells is through Activation of p38/JNK, Mitochondrial Dysfunction, and Endoplasmic Reticulum Stress Regulated Pathway.

Flaccidoxide-13-acetate, an active compound isolated from cultured-type soft coral Sinularia gibberosa, has been shown to have inhibitory effects against invasion and cell migration of RT4 and T24 human bladder cancer cells. In our study, we used an 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT), colony formation assay, and flow cytometry to determine the mechanisms of the anti-tumor effect of flaccidoxide-13-acetate. The MTT and colony formation assays showed that the cytotoxic effect of flaccidoxide-13-acetate on T24 and RT4 cells was dose-dependent, and the number of colonies formed in the culture was reduced with increasing flaccidoxide-13-acetate concentration. Flow cytometry analysis revealed that flaccidoxide-13-acetate induced late apoptotic events in both cell lines. Additionally, we found that flaccidoxide-13-acetate treatment upregulated the expressions of cleaved caspase 3, cleaved caspase 9, Bax, and Bad, and down-regulated the expressions of Bcl-2, p-Bad, Bcl-x1, and Mcl-1. The results indicated that apoptotic events were mediated by mitochondrial dysfunction via the caspase-dependent pathway. Flaccidoxide-13-acetate also provoked endoplasmic reticulum (ER) stress and led to activation of the PERK-eIF2α-ATF6-CHOP pathway. Moreover, we examined the PI3K/AKT signal pathway, and found that the expressions of phosphorylated PI3K (p-PI3K) and AKT (p-AKT) were decreased with flaccidoxide-13-acetate concentrations. On the other hand, our results showed that the phosphorylated JNK and p38 were obviously activated. The results support the idea that flaccidoxide-13-acetate-induced apoptosis is mediated by mitochondrial dysfunction, ER stress, and activation of both the p38 and JNK pathways, and also relies on inhibition of PI3K/AKT signaling. These findings imply that flaccidoxide-13-acetate has potential in the development of chemotherapeutic agents for human bladder cancer.

Involvement of Mitochondrial Dysfunction, Endoplasmic Reticulum Stress, and the PI3K/AKT/mTOR Pathway in Nobiletin-Induced Apoptosis of Human Bladder Cancer Cells.

Nobiletin (NOB) is a polymethoxylated flavonoid isolated from citrus fruit peel that has been shown to possess anti-tumor, antithrombotic, antifungal, anti-inflammatory and anti-atherosclerotic activities. The main purpose of this study was to explore the potential of using NOB to induce apoptosis in human bladder cancer cells and study the underlying mechanism. Using an MTT assay, agarose gel electrophoresis, a wound-healing assay, flow cytometry, and western blot analysis, this study investigated the signaling pathways involved in NOB-induced apoptosis in BFTC human bladder cancer cells. Our results showed that NOB at concentrations of 60, 80, and 100 µM inhibited cell growth by 42%, 62%, and 80%, respectively. Cells treated with 60 µM NOB demonstrated increased DNA fragmentation, and flow cytometry analysis confirmed that the treatment caused late apoptotic cell death. Western blot analysis showed that mitochondrial dysfunction occurred in NOB-treated BFTC cells, leading to cytochrome C release into cytosol, activation of pro-apoptotic proteins (caspase-3, caspase-9, Bad, and Bax), and inhibition of anti-apoptotic proteins (Mcl-1, Bcl-xl, and Bcl-2). NOB-induced apoptosis was also mediated by regulating endoplasmic reticulum stress via the PERK/elF2α/ATF4/CHOP pathway, and downregulating the PI3K/AKT/mTOR pathway. Our results suggested that the cytotoxic and apoptotic effects of NOB on bladder cancer cells are associated with endoplasmic reticulum stress and mitochondrial dysfunction.

Bornyl cis-4-Hydroxycinnamate Suppresses Cell Metastasis of Melanoma through FAK/PI3K/Akt/mTOR and MAPK Signaling Pathways and Inhibition of the Epithelial-to-Mesenchymal Transition.

Bornyl cis-4-hydroxycinnamate, a bioactive compound isolated from Piper betle stems, has the potential for use as an anti-cancer agent. This study investigated the effects of bornyl cis-4-hydroxycinnamate on cell migration and invasion in melanoma cells. Cell migration and invasion were compared in A2058 and A375 melanoma cell lines treated with/without bornyl cis-4-hydroxycinnamate (1⁻6 µM). To examine whether bornyl cis-4-hydroxycinnamate has a potential anti-metastatic effect on melanoma cells, cell migration and invasion assays were performed using a Boyden chamber assay and a transwell chamber in A2058 and A375 cells. Gelatin zymography was employed to determine the enzyme activities of MMP-2 and MMP-9. Cell lysates were collected for Western blotting analysis of matrix metalloproteinase (MMP)-2, MMP-9 and tissue inhibitors of metalloproteinase-1/2 (TIMP-1/2), as well as key molecules in the mitogen-activated protein kinase (MAPK), focal adhesion kinase (FAK)/ phosphatidylinositide-3 kinases (PI3K)/Akt/ mammalian target of rapamycin (mTOR), growth factor receptor-bound protein 2 (GRB2) signaling pathways. Our results demonstrated that bornyl cis-4-hydroxycinnamate is a potentially useful agent that inhibits melanoma cell migration and invasion, and altered melanoma cell metastasis by reducing MMP-2 and MMP-9 expression through inhibition of the FAK/PI3K/Akt/mTOR, MAPK, and GRB2 signaling pathways. Moreover, bornyl cis-4-hydroxycinnamate inhibited the process of the epithelial-to-mesenchymal transition in A2058 and A375 melanoma cells. These findings suggested that bornyl cis-4-hydroxycinnamate has potential as a chemotherapeutic agent, and warrants further investigation for its use in the management of human melanoma.

Secoiridoids from the Seed of Gonocaryum calleryanum and Their Inhibitory Potential on LPS-Induced Tumor Necrosis Factor and Nitric Oxide Production.

Three new secoiridoid constituents, goncarin A−C (1⁻3), and a new derivative, goncarin A monoacetate (4), along with two known lignins, pinoresinol (5) and paulownin (6), were isolated from the seed of Gonocaryum calleryanum (Baill.) Becc. The structures of the new metabolites were determined on the basis of extensive spectroscopic analysis, particularly mass spectroscopy and 2D NMR (¹H⁻¹H COSY, HMQC, HMBC, and NOESY) spectroscopy. The aim of this study was to identify the anti-inflammatory effects of compounds 1⁻6 on lipopolysaccharide (LPS)-stimulated murine macrophage cell lines (RAW 264.7). Following stimulation with LPS, elevated levels of nitric oxide (NO) production were detected in RAW 264.7 cells; however, pretreatment with compounds 1⁻6 significantly inhibited the production of NO (around 40⁻80%, p < 0.01⁻0.05), by suppressing the expression of inducible NO synthase (iNOS). In addition, LPS-stimulated tumor necrosis factor-α (TNF-α) production was significantly reduced by compounds 1⁻3 (25⁻40%, p < 0.01⁻0.05). These results suggested that compounds 1⁻3 may exert anti-inflammatory activity, and that compounds 1⁻3 may be considered a potential therapeutic for the treatment of inflammatory diseases associated with macrophage activation.

Sinulariolide Suppresses Cell Migration and Invasion by Inhibiting Matrix Metalloproteinase-2/-9 and Urokinase through the PI3K/AKT/mTOR Signaling Pathway in Human Bladder Cancer Cells.

Sinulariolide is a natural product extracted from the cultured-type soft coral Sinularia flexibilis, and possesses bioactivity against the movement of several types of cancer cells. However, the molecular pathway behind its effects on human bladder cancer remain poorly understood. Using a human bladder cancer cell line as an in vitro model, this study investigated the underlying mechanism of sinulariolide against cell migration/invasion in TSGH-8301 cells. We found that sinulariolide inhibited TSGH-8301 cell migration/invasion, and the effect was concentration-dependent. Furthermore, the protein expressions of matrix metalloproteinases (MMPs) MMP-2 and MMP-9, as well as urokinase, were significantly decreased after 24-h sinulariolide treatment. Meanwhile, the increased expression of tissue inhibitors of metalloproteinases (TIMPs) TIMP-1 and TIMP-2 were in parallel with an increased concentration of sinulariolide. Finally, the expressions of several key phosphorylated proteins in the mTOR signaling pathway were also downregulated by sinulariolide treatment. Our results demonstrated that sinulariolide has significant effects against TSGH-8301 cell migration/invasion, and its effects were associated with decreased levels of MMP-2/-9 and urokinase expression, as well as increased TIMP-1/TIMP-2 expression. The inhibitory effects were mediated by reducing phosphorylation proteins of the PI3K, AKT, and mTOR signaling pathway. The findings suggested that sinulariolide is a good candidate for advanced investigation with the aim of developing a new drug for the treatment of human bladder cancer.

Flaccidoxide-13-Acetate Extracted from the Soft Coral Cladiella kashmani Reduces Human Bladder Cancer Cell Migration and Invasion through Reducing Activation of the FAK/PI3K/AKT/mTOR Signaling Pathway.

Metastasis of cancer is the cause of the majority of cancer deaths. Active compound flaccidoxide-13-acetate, isolated from the soft coral Cladiella kashmani, has been found to exhibit anti-tumor activity. In this study, Boyden chamber analysis, Western blotting and gelatin zymography assays indicated that flaccidoxide-13-acetate exerted inhibitory effects on the migration and invasion of RT4 and T24 human bladder cancer cells. The results demonstrated that flaccidoxide-13-acetate, in a concentration-dependent manner, reduced the levels of matrix metalloproteinase-2 (MMP-2), MMP-9, urokinase-type plasminogen activator receptor (uPAR), focal adhesion kinase (FAK), phosphatidylinositide-3 kinases (PI3K), p-PI3K, AKT, p-AKT, mammalian target of rapamycin (mTOR), p-mTOR, Ras homolog gene family, member A (Rho A), Ras, mitogen-activated protein kinase kinase 7 (MKK7) and mitogen-activated protein kinase kinase kinase 3 (MEKK3), and increased the expressions of tissue inhibitor of metalloproteinase-1 (TIMP-1) and TIMP-2 in RT4 and T24 cells. This study revealed that flaccidoxide-13-acetate suppressed cell migration and invasion by reducing the expressions of MMP-2 and MMP-9, regulated by the FAK/PI3K/AKT/mTOR pathway. In conclusion, our study was the first to demonstrate that flaccidoxide-13-acetate could be a potent medical agent for use in controlling the migration and invasion of bladder cancer.

Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces.

The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.

Novel Aporphine- and Proaporphine-Clerodane Hybrids Identified from the Barks of Taiwanese Polyalthia longifolia (Sonn.) Thwaites var. pendula with Strong Anti-DENV2 Activity.

Hybrid natural products produced via mixed biosynthetic pathways are unique and often surprise one with unexpected medicinal properties in addition to their fascinating structural complexity/diversity. In view of chemical structures, hybridization is a way of diversifying natural products usually through dimerization of two similar or dissimilar subcomponents through a C-C or N-C covalent linkage. Here, we report four structurally attractive diterpene-alkaloid conjugates polyalongarins A-D (1-4), clerodane-containing aporphine and proaporphine alkaloids, the first of its kind from the barks of Taiwanese Polyalthia longifolia (Sonn.) Thwaites var. pendula. In addition to conventional spectroscopic analysis, single crystal X-ray crystallography was employed to determine the chemical structures and stereo-configurations of 1. Compounds 1-4 were subsequently subjected to in vitro antiviral examination against DENV2 by evaluating the expression level of the NS2B protein in DENV2-infected Huh-7 cells. These compounds display encouraging anti-DENV2 activity with superb EC50 (2.8-6.4 µM) and CC50 values (50.4-200 µM). The inhibitory mechanism of 1-4 on NS2B was further explored drawing on in-silico molecular docking analysis. Based on calculated binding affinities and predicted interactions between the functional groups of 1-4 and the allosteric-site residues of the DENV2 NS2B-NS3 protease, our analysis concludes that the clerodane-aporphine/proaporphine-type hybrids are novel and effective DENV NS2B-NS3 protease inhibitors.

Proteomic analysis of anti-tumor effects of 11-dehydrosinulariolide on CAL-27 cells.

The anti-tumor effects of 11-dehydrosinulariolide, an active ingredient isolated from soft coral Sinularia leptoclados, on CAL-27 cells were investigated in this study. In the MTT assay for cell proliferation, increasing concentrations of 11-dehydrosinulariolide decreased CAL-27 cell viability. When a concentration of 1.5 µg/mL of 11-dehydrosinulariolide was applied, the CAL-27 cells viability was reduced to a level of 70% of the control sample. The wound healing function decreased as the concentration of 11-dehydrosinulariolide increased. The results in this study indicated that treatment with 11-dehydrosinulariolide for 6 h significantly induced both early and late apoptosis of CAL-27 cells, observed by flow cytometric measurement and microscopic fluorescent observation. A comparative proteomic analysis was conducted to investigate the effects of 11-dehydrosinulariolide on CAL-27 cells at the molecular level by comparison between the protein profiling (revealed on a 2-DE map) of CAL-27 cells treated with 11-dehydrosinulariolide and that of CAL-27 cells without the treatment. A total of 28 differential proteins (12 up-regulated and 16 down-regulated) in CAL-27 cells treated with 11-dehydrosinulariolide have been identified by LC-MS/MS analysis. Some of the differential proteins are associated with cell proliferation, apoptosis, protein synthesis, protein folding, and energy metabolism. The results of this study provided clues for the investigation of biochemical mechanisms of the anti-tumor effects of 11-dehydrosinulariolide on CAL-27 cells and could be valuable information for drug development and progression monitoring of oral squamous cell carcinoma (OSCC).

New secondary metabolite with cytotoxicity from spawning soft coral Asterospicularia laurae in Taiwan.

We have conducted a long-term research on the Taiwanese soft coral Asterospicularia laurae, which resulted in many xenicane-type diterpenoids such as asterolaurins A-M from A. laurae coral tissues during the non-spawning period were isolated. Here, we report a new xenicane diterpenoid, asterolaurin N (1), along with three known xenicane-type monocarbocyclic diterpenes [13-epi-9-desacetylxenicin (2), xeniolide-B 9-acetate (3) and asterolaurin I (4)] from A. laurae during the spawning period. The structures of the new secondary metabolite were established with an extensive spectroscopic analysis. The 1D and 2D nuclear magnetic resonance (NMR) data of the compounds were discussed. We discovered that the C-15 of 1 contains two methyl groups on a carbon bearing an acetyl group, which has not been reported previously. In addition, Compounds 1, 3, and 4 showed selective cytotoxic activity against Molt 4, while 2 exhibited significant cytotoxicity against Molt 4, K562, Sup-T1 and U937 cell lines.

Hydrophobic contribution of amino acids in peptides measured by hydrophobic interaction chromatography.

The adsorption behaviors of amino acids in short chain peptides were examined. Each amino acid, aliphatic or charged, was inserted between the two tryptophans of a peptide, GWWG. The capacity factors of these peptides on an Ocytl-Sepharose column were measured. The adsorption enthalpies, entropies, and the number of repelled water molecules after adsorption were estimated to analyze the contribution of each different amino acid to its hydrophobic adsorption. The peptides inserted with aliphatic amino acids owned the highest capacity factors but released the least amount of adsorption heat among all the peptides under examination. It was found that the hydrophobic contribution of aliphatic amino acids was derived from the entropy gain by repelling the ordered water surrounding them. The insertion of negatively charged amino acids greatly reduced the capacity factors but still repelled a significant number of water molecules after adsorption. This indicated that the water molecules surrounding ionic amino acids were not orderly aligned. The dehydration cost energy but the water repelling did not offer enough entropy to drive the adsorption. Subsequently, lower retention was obtained from the peptides inserted with negatively charged ionic amino acids. The insertion of lysine increased the adsorption enthalpy but repelled no water molecules after adsorption. It was speculated that the inserted lysine still interacted with hydrophobic ligands but disturbed the interaction between ligands and adjacent tryptophans. Therefore, the adsorption enthalpy increased and the capacity factors decreased. Different amino acids contributed to hydrophobic interaction in different ways. The simultaneous analysis of capacity factor, adsorption enthalpy, adsorption entropy, and the number of repelled water molecules facilitated the understanding of the adsorption processes.

The consideration of indolicidin modification to balance its hemocompatibility and delivery efficiency.

Indolicidin (IL) is an antimicrobial peptide (AMP), which has been utilized as a cell penetrating peptide (CPP) for drug delivery. However, the hemolysis restricts its clinical application. Therefore, we investigated the delivery efficiency and hemocompatibility of IL and its derivatives. The transportation of fluorophore to NIH/3T3 cells could be improved either by in accompany with these peptides or in the form of peptide-conjugates. The hydrophobicity scales of these peptides were calculated according to their residues, which were compared to their effects on hemolysis as well as cell uptake efficiency. The results suggested that the cell penetrability of IL and its derivatives was related to their hydrophobicity scales based on the octanol-interface scale (ΔGoct-if), whereas their hemolysis levels depended on the hydrophobicity scales based on interface (ΔGwif). Consequently, we designed two peptides, IL-R57F89 and SAP10, to validate the correlation. These two peptides had similar ΔGwif; however, the ΔGoct-if of SAP10 was much higher than that of IL-K7F89. Both IL-R57F89 and SAP10 demonstrated extremely low hemolysis. Compared to the limit cell uptake of SAP10, IL-R57F89 greatly promoted the delivery efficiency. These results were consistent to our prediction, suggesting that hydrophobicity scales should be a useful preliminary guidance for AMP-derived CPP design.

Proteomic profiling of the 11-dehydrosinulariolide-treated oral carcinoma cells Ca9-22: effects on the cell apoptosis through mitochondrial-related and ER stress pathway.

An oral squamous cell carcinoma Ca9-22 cell line was treated with 11-dehydrosinulariolide, an active compound isolated from the soft coral Sinularia leptoclados, in order to evaluate the effect of this compound on cell growth and protein expression. Cell proliferation was strongly inhibited by 11-dehydrosinulariolide treatment. The 2-DE master maps of control and treated Ca9-22 cells were generated by analysis with the PDQuest software. The comparison between such maps showed up- and down-regulation of 23 proteins, of which 14 were upregulated and 9 were downregulated. The proteomic studies described here have identified some proteins, which are involved in the mitochondrial dysfunction and ER-stress pathway and imply that 11-dehydrosinulariolide induces cell apoptosis through either mitochondrial dysfunction-related or ER stress pathway. Based on this observation, several proteins related to apoptosis pathway were explored for the potential roles involved in this drug-induced cytotoxicity. Furthermore, Salubrinal, an ER stress inhibitor, is able to protect the cell from 11-dehydrosinulariolide-induced apoptosis in a physiological dosage. The significance of these studies illustrates the potential development of anticancer drugs from the natural derivatives of soft coral.

Study of conformation effects on the retention of small peptides in reversed-phase chromatography by thermodynamic analysis and molecular dynamics simulation.

Chromatographic behavior of a small peptide in RP-HPLC can generally be correlated with the summation of the hydrophobic contribution from its composed amino acid residues. But this approach fails to predict the retention deviation between two sequence shuffled peptides. One set of 11-residue peptides was designed to study the conformation effect. The two sequence shuffled peptides had different conformations and showed different retention behaviors in a C18 column. The retention factors of the relatively helical peptide GELELKLKLEG (GELE) were consistently lower than those of the peptide GELKLELKLEG (GELK) at all conditions under investigation. All atom molecular dynamics (MD) simulation was performed to study the origin of the deviation in column retention. Circular dichroism spectra and MD simulation confirmed that the structure of GELE is more helical and the energy of GELE in solution is lower than that of GELK. The deformation energies calculated from MD described well the concentration effect on DeltaC(P) obtained from column retention data. After analyzing the desolvation, deformation, and interaction energies after the adsorption of these two sequence shuffled peptides on C18 self assembly monolayer (SAM), it was found that the longer retention of GELK in the column was not due to its higher accessibility toward the hydrophobic stationary phase. The structurally rigid peptide, i.e., the low potential energy one, owned a lower retention time because its ability to minimize the overall adsorption energy was limited. This result suggested that the overall potential energy of peptide in solution calculated from MD simulation may be used to quantify the conformation effect.