Reserach

(1) Bio-detector modeling

(a) Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force:

Transport of molecules through macromolecular pores is of considerable importance in many biological systems and nanoscale biosensors. In recent years, engineered carbon nanotubes (CNTs) have been developed to function as protein toxin transporters. We present molecular dynamics simulation of the small mastoparan-X peptide transporting through the single-walled CNT (SWCNT) under application of an external electric field force. The molecules studied include a small mastoparan-X peptide, a finite segment of carbon nanotube, and TIP3 water molecules. The external electric field vectors are 1.0, 2.0, 3.0, 4.0, and 10.0 kcal/(mol Å e), respectively. We show that under the external electric field vector of 1.0 kcal/(mol Å e), the transportation of mastoparan-X peptide through SWCNT was accomplished within 12 ns. Our results also show more external electric field vectors would speed up the transportation process.

(b) Bio-detector modeling related papers(*):

1. Yeng-Tseng Wang,* Wen-Jay Lee, Zhi-Yuan Su* and Cheng-Lung Chen* (2011) “Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force.” Journal of the Taiwan Institute of Chemical Engineers, 42, 724-726 (SCI) (Citation: 1) (ISI 2013 IF: 2.637; ranking: 33/133, ENGINEERING, CHEMICAL)

(2) Disease antibodies designing modeling

(a) Potential of mean force of the hepatitis C virus core protein–monoclonal 19D9D6 antibody interaction:

Antigen-antibody interactions are critical for understanding antigen-antibody associations in immunology. To shed further light on this question, we studied a dissociation of the 19D9D6-HCV core protein antibody complex structure. However, forced separations in single molecule experiments are difficult, and therefore molecular simulation techniques were applied in our study. The stretching, that is, the distance between the centre of mass of the HCV core protein and the 19D9D6 antibody, has been studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. Our simulations indicate that the 7 residues Gly70, Gly72, Gly134, Gly158, Glu219, Gln221 and Tyr314, the interaction region (antibody), and the 14 interprotein molecular hydrogen bonds might play important roles in the antigen-antibody interaction, and this finding may be useful for protein engineering of this antigen-antibody structure. In addition, the 3 residues Gly134, Gly158 and Tyr314 might be more important in the development of bioactive antibody analogues.

(b) Modelling and predicting the binding mechanics of HIV P1053-0.5b antibody complex:

Simulating antigen–antibody interactions is crucial in understanding the mechanics of antigen–antibody binding in medical science. In this study, molecular dynamics simulations are performed to analyse the dissociation of the P1053-0.5b antibody complex structure. The two-dimensional free energy profiles of the complex structure are extracted using the weighted histogram analysis method, and the binding pathway is then predicted using a modified form of the MaxFlux-PRM method. The simulation results suggest that 10 amino residues (i.e. Leu11, Val13, Asp34, Arg112, Thr101, Gly127, Val229, Ser231, Ile235 and Arg236) play a key role in relaxing the antibody structure, thereby facilitating the binding of the 0.5b antibody-P1053 peptide system.

(c) Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach

Antibody drugs are very useful tools for the treatment of many chronic diseases. Recently, however, patients and doctors have encountered the problem of drug resistance. How to improve the affinity of antibody drugs has therefore become a pressing issue. Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1. This study investigates the mutation residues of the complementarity determining regions of Ibalizumab. We propose using the wild and mutations of Ibalizumab-human CD4 receptor complex structures, molecular dynamics techniques, alanine-scanning mutagenesis calculations and solvated interaction energies methods to predict the binding free energy of the Ibalizumab-human CD4 receptor complex structures. This work found that revealed three key positions (31th, 32th and 33th in HCDR-1) of the residues may play an important role in Ibalizumab-human CD4 receptor complex interactions. Therefore, bioengineering substitutions of the three key positions and increasing number of intermolecular interactions (HCDR-1 of Ibalizumab/human CD4 receptor) might improve the binding affinities of this complex structure

(d) disease antibodies designing modeling related papers.

1. Yeng-Tseng Wang, Wen-Jay Lee (2012). Binding hot-spots in an antibody-ssDNA interface: a molecular dynamics study. Molecular BioSystems, 8, 3274-3280. (SCI) (Citation:0) (ISI 2013 IF: 3.183, ranking: 119/291, BIOCHEMISTRY & MOLECULAR BIOLOGY)

2. Yeng-Tseng Wang*, Zhi-Yuan Su, (2011) “Modeling and predicting the binding mechanics of HIV P1053-0.5β antibody complex.” Molecular Simulation, 2:37, 164-171 (SCI) (Citation:0) (ISI 2013 IF: 1.119 ranking: 28/33, PHYSICS, ATOMIC, MOLECULAR & CHEMICAL)

3. Yeng-Tseng Wang*, Lea-Yea Chuang (2014) “Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach.” Journal of Computer-Aided Molecular Design (In press). (SCI) (Citation:0) (ISI 2013 IF: 2.782 ranking: 13/102, COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)

(3) Disease receptor protein drug designing modeling

(a) Insights from QM/MM Modeling the 3D Structure of the 2009 H1N1 Influenza A Virus Neuraminidase and Its Binding Interactions with Antiviral Drugs:

binding mode of neuraminidase is not yet completely understood. In this work, we propose a model for a neuraminidase-1 complex based on four known X-ray structures of drug/neuraminidase-1 complexes. Specifically, H1N1 neuraminidase-1 complexed with 4 drugs (zanamivir, laninamivir, laninamivir octanoate and oseltamivir) was first investigated using a combined quantum mechanical and molecular mechanical (QM/MM) approach. Based on these structures, a model for the H1N1 neuraminidase-1 complex was proposed and simulated using the same computational protocol. Implications to drug/H1N1 neuraminidase-1 binding modes are discussed. From our simulations, the predicted binding free energies of the four drugs are in good agreement with the experimental results, with the correlation coefficient being 0.84.

(b) Combining homology modeling, docking, and molecular dynamics to predict the binding modes of oseltamivir, zanamivir, and Chinese natural herb products with the neuramindase of the H1N1 influenza A virus

The neuraminidase of the influenza virus is the target of the anti-flu drugs oseltamivir and zanamivir. Clinical practices show that zanamivir and oseltamivir are effective to treat the 2009 H1N1 influenza virus. Herein, we report the findings of molecular simulations for zanamivir, oseltamivir, and Chinese natural herb products with the neuramindase of the 2009 H1N1 influenza. Our approach theoretically suggests that the Glu278 residue is responsible for the neuramindase of the 2009 influenza drug selectivity.

(c) Theoretical Investigation on Reaction of Sulbactam with Wild-type SHV-1 β-lactamase: Acylation, Tautomerization and Deacylation.:

Molecular dynamics (MD) simulation and quantum mechanical (QM) calculations were used to investigate the reaction mechanism of sulbactam with class A wild-type SHV-1 β-lactamase including acylation, tautomerization, and deacylation. Five different sulbactam-enzyme configurations were investigated by MD simulations. In the acylation step, we found that Glu166 cannot activate Ser70 directly for attacking on the carbonyl carbon, and Lys73 would participate in the reaction acting as a relay. Additionally, we found that sulbactam carboxyl can also act as a general base. QM calculations were performed on the formation mechanism of linear intermediates. We suggest that both imine and trans-enamine intermediates can be obtained in the opening of a five-membered thiazolidine ring. By MD simulation, we found that imine intermediate can exist in two conformations, which can generate subsequent trans- and cis-enamine intermediates, respectively. The QM calculations revealed that trans-enamine intermediate is much more stable than other intermediates. The deacylation mechanism of three linear intermediates (imine, trans-enamine, cis-enamine) was investigated separately. It is remarkably noted that, in cis-enamine intermediate, Glu166 cannot activate water for attacking on the carbonyl carbon directly. This leads to a decreasing of the deacylation rate of cis-enamine. These findings will be potentially useful in the development of new inhibitors.

(d) Insights from modelling the 3D structure of the 2013 H7N9 influenza A virus neuraminidase and its binding interactions with drugs:

Neuraminidase of the influenza virus is the target of the antibiotic drugs peramivir, oseltamivir and zanamivir. The WHO Collaborating Centre in China announced these drugs (peramivir, oseltamivir and zanamivir) to be effective to treat the 2013 H7N9 influenza virus. Herein, we report the findings of molecular simulations and computational alanine-scanning mutagenesis for peramivir, oseltamivir and zanamivir with the neuraminidase of 2013 H7N9 influenza. Our simulation results theoretically suggest that peramivir might be the best potential antiviral agent for treatment of avian influenza A (H7N9); the Asp147 and Arg367 residues are responsible for the H7N9 neuraminidase of the 2013 influenza drug selectivity.

(e) Inhibitor and Substrate Binding by New Delhi metallo-beta-lactamase-1: A Molecular Dynamics Studies:

The control of beta-lactam antibiotics released through the inhibition of the New Delhi metallo-beta-lactamase 1 (NDM-1) has been identified as a potential target for the treatment of the muti-drugs resistance (MDR) bacteria disease. We have employed molecular dynamics (MD), alanine-scanning mutagenesis and molecular docking techniques to optimize the x-ray NDM-1 structure with 11 drugs (Tigecycline, BAL30072, D-captopril, Penicillin G, Ampicillin, Carbenicillin, Cephalexin, Cefaclor, Nitrocefin, Meropenem, and Imipenem). From our simulations, we found that the 5 residues Asp223, His120, His122, His162 and His189 are responsible for the selectivity of NDM-1 associated drugs.

(f) Disease receptor protein drug designing modeling related papers(*)

1. Yeng-Tseng Wang,* Yu-Ching Chen (2014) “Insights from QM/MM Modeling the 3D Structure of the 2009 H1N1 Influenza A Virus Neuraminidase and Its Binding Interactions with Antiviral Drugs” Molecular Informatics , 33(3), 240–249. (SCI) (Citation:0) (ISI 2013 IF: 2.013, ranking: 17/52, MATHEMATICAL & COMPUTATIONAL BIOLOGY)

2. Yeng-Tseng Wang*, Chen-hsiung Chan,* Zhi-Yuan Su,* Cheng-Lung Chen* (2010) “Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A (H1N1) influenza neuraminidase,” BIOPHYSICAL CHEMISTRY, 147:74-80 (SCI) (Citation:7) (ISI 2013 IF: 2.319, ranking: 60/136, CHEMISTRY, PHYSICAL )

3. Rui Li, Jun-Min Liao, Chi-Ruei Gu, Yeng-Tseng Wang and Cheng-Lung Chen* (2011) “Theoretical Investigation on Reaction of Sulbactam with Wild-type SHV-1 β-lactamase: Acylation, Tautomerization and Deacylation.” Journal of Physical Chemistry B, 115, 10298-10310 (SCI) (Citation:2) (ISI 2013 IF: 3.377, ranking: 39/136, CHEMISTRY, PHYSICAL)

4. Yeng-Tseng Wang* (2013) ” Insights from modelling the 3D structure of the 2013 H7N9 influenza A virus neuraminidase and its binding interactions with drugs”, MedChemComm 4, 1370-1375. (SCI) (Citation:0) (ISI 2013 IF: 2.626, ranking: 26/58, CHEMISTRY, MEDICINAL)

5. Yeng-Tseng Wang*, Chi-Yu Lu, Tzyh-Chyuan Hour and Tian-Lu Cheng (2014) “Inhibitor and Substrate Binding by New Delhi metallo-beta-lactamase-1: Molecular Mechanical Molecular Dynamics Studies. Current Computer-Aided Drug Design” (accepted) (SCI) (Citation:0) (ISI 2013 IF =1.942, ranking: 25/102, Computer Science, Interdisciplinary Applications)

(4) Biophysics simulations

(a) Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes:

Cobra cytotoxins, which are small three-looped proteins composed of approximately 60 amino acid residues, primarily act by destroying the bilayer membranes of cells and artificial vesicles. However, the molecular mechanism governing this process is not yet completely understood. We used coarse-grained molecular dynamics (CGMD) simulations to study the mechanism underlying the penetra-tion of cardiotoxin A3 (CTX A3), the major toxic component of Naja atra (Chinese cobra) venom, into a hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer. We performed CGMD simulations for three different conformations of the cobra cytotoxin; the tail, lying, and harrow conformations. The results of our simulations indicate that two of these, the tail and lying conformations, did not penetrate the bilayer system. Further, for the harrow conformation, loops 2 and 3 played important roles in penetration of CTX A3 into the bilayer system.

(b) Computer simulation to investigate the FRET application in DNA hybridization systems:

Molecular dynamics (MD) and quantum mechanics (QM) were used to investigate fluorescence resonance energy transfer (FRET) between coumarin and ethidium in two Mergny's DNA hybridization systems. By combining the transition dipoles calculated by the quantum semi-empirical method and the conformations of the FRET probes collected by MD, FRET efficiencies were derived from the Förster equation at five temperatures from 273 K to 313 K. The plotted efficiencies were compared with Mergny's experiments, and showed good agreement. The simulated orientation factor and isotropically averaged orientation factor were compared, and the results demonstrated that the assumption of isotropic orientations is invalid when FRET probes are close to each other. The first order kinetic assumptions were also used to calculate the transfer efficiencies, and the results show that this D–A FRET process approximates the first order kinetic reactions.

(c) Free energies and folding mechanics between human prion fragment α-2 domain and β-2 domain under steered molecular dynamics simulations:

Prion proteins are associated with a group of transmissible neurodegenerative disorders such as scrapie in sheep and Creutzfeldt–Jakob disease in humans. Previous studies have shown that the C-terminal side of α-helix 2 of the prion protein undergoes a conformational change to the β-sheet form, which is the infectious isoform causing scrapie. However, information about the three-dimensional structure of the prion β-sheet is still lacking. As the α-helix 2 displays “chameleon” conformational behavior, gathering several disease-associated point mutations, it can be toxic to neuronal cells. This makes it a very important focus for research into the folding mechanics of PrPC. The purpose of this study was to investigate the differences in folding mechanics between prion fragment α-helix 2 and prion fragment β-sheet 2, and to use a steered molecular dynamics approach to infer which events are important to achieve a normal α-helix 2 peptide. Based on our simulations, we suggest that 2 conformational barriers, comprising 4 intramolecular hydrogen bonds (the 8th, 9th, 10th, and 11th) and 6 residues (Thr183, Ile184, Lys185, His187, Thr188, and Val189), might play important roles in the folding mechanics of α-helix 2 and that a lack of these events might cause its misfolding. Steered molecular dynamics simulations were carried out on the folding mechanics of protein α-helix 2. The hypothesis we propose is that 6 residues (Thr183, Ile184, Lys185, His187, Thr188, and Val189) are important in the correct folding of prion α-helix 2.

(d) Target Molecular Simulations of RecA Family Protein Filaments:

Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism.

(e) Biophysics simulations related papers(*)

1. Zhi-Yuan Su, Yeng-Tseng Wang* (2011) “Coarse-grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes” Journal of Physical Chemistry B, 5:115, 796–802 (SCI) (Citation:6) (ISI 2013 IF: 3.377, ranking: 39/136, CHEMISTRY, PHYSICAL)

2. Jun-Min Liao, Yeng-Tseng Wang and Cheng-Lung Chen (2011) “Computer simulation to investigate the FRET application in DNA hybridization systems.” Physical Chemistry Chemical Physics, 13, 10364-10371 (SCI) (Citation:1) (ISI 2013 IF: 4.198, ranking: 5/33, PHYSICS, ATOMIC, MOLECULAR & CHEMICA)

3. Yeng-Tseng Wang* and Zhi-Yuan Su (2011) “Free energies and folding mechanics between human prion fragment α-2 domain and β-2 domain under steered molecular dynamics simulations.” Journal of the Taiwan Institute of Chemical Engineers, 42, 719-723 (SCI) (Citation:0) (ISI 2013 IF: 2.637; ranking: 23/133, ENGINEERING, CHEMICAL)

4. Zhi-Yuan Su, Wen-Jay Lee, Wan-Sheng Su and Yeng-Tseng Wang* (2012, Jun). Target Molecular Simulations of RecA Family Protein Filaments. International Journal of Molecular Sciences, 13, 7138-7148. (SCI) (Citation:1) (ISI 2013 IF: 2.339, ranking: 52/148, CHEMISTRY, MULTIDISCIPLINARY)

(5) Combining experimental and theoretical studies

(a) Serendipitous Discovery of Short Peptides from Natural Products as Tyrosinase Inhibitors

Tyrosinase, which is the crucial copper-containing enzyme involved in melanin synthesis, is strongly associated with hyperpigmentation disorders, cancer, and neurodegenerative disease; thus, it has attracted considerable interest in the fields of medicine and cosmetics. The known tyrosinase inhibitors show numerous adverse side effects, and there is a lack of safety regulations governing their use. As a result, there is a need to develop novel inhibitors with no toxicity and long-term stability. In this study, we use molecular docking and pharmacophore modeling to construct a reasonable and reliable pharmacophore model, called Hypo 1, that could be used for identifying potent natural products with crucial complementary functional groups for mushroom tyrosinase inhibition. It was observed that, out of 47?263 natural compounds, A5 structurally resembles a dipeptide (WY) and natural compound B16 is the equivalent of a tripeptide (KFY), revealing that the C-terminus tyrosine residues play a key role in tyrosinase inhibition. Tripeptides RCY and CRY, which show high tyrosinase inhibitory potency, revealed a positional and functional preference for the cysteine residue at the N-terminus of the tripeptides, essentially determining the capacity of tyrosinase inhibition. CRY and RCY used the thiol group of cysteine residues to coordinate with the Cu ions in the active site of tyrosinase and showed reduced tyrosinase activity. We discovered the novel tripeptide CRY that shows the most striking inhibitory potency against mushroom tyrosinase (IC50 = 6.16 μM); this tripeptide is more potent than the known oligopeptides and comparable with kojic acid-tripeptides. Our study provides an insight into the structural and functional roles of key amino acids of tripeptides derived from the natural compound B16, and the results are expected to be useful for the development of tyrosinase inhibitors.

(b)Development of an Anti-Methoxy Poly(ethylene glycol) (α-mPEG) Cell-Based Capture System to Measure mPEG and mPEGylated Molecules

Quantitative pharmacokinetic analysis of methoxy-poly(ethylene glycol) (mPEG) and mPEGylated molecules is important for clinical drug development. Here we developed sensitive sandwich and competitive ELISAs by expressing an anti-mPEG antibody on the surface of fibroblasts for effective capture of mPEG molecules in biological samples. α-mPEG sandwich ELISA could quantify the higher-molecular-weight of mPEG (2, 5, and 20 kDa) and mPEGylated molecules. α-mPEG cell-based competitive ELISA was developed to measure the lower-molecular-weight of mPEG molecules (559, 750, and 1000 Da) at nanomolar levels. In addition, α-mPEG cell-based ELISA was unaffected by the presence of 10% human serum or murine serum. We further demonstrate that the α-mPEG cell-based ELISA determined similar pharmacokinetics of mPEG5K as traditional gamma counting of 131I-mPEG5K. The α-mPEG cell-based ELISA may provide an accurate, high sensitivity and easy-to-use tool for directly measuring mPEG and mPEGylated molecules in complex biological samples to accelerate the clinical development of mPEG drugs.

(c)High-Throughput Sorting of the Highest Producing Cell via a Transiently Protein-Anchored System

Developing a high-throughput method for the effecient selection of the highest producing cell is very important for the production of recombinant protein drugs. Here, we developed a novel transiently protein-anchored system coupled with fluorescence activated cell sorting (FACS) for the efficient selection of the highest producing cell. A furin cleavage peptide (RAKR) was used to join a human anti-epithelial growth factor antibody (αEGFR Ab) and the extracellular-transmembrane-cytosolic domains of the mouse B7-1 antigen (B7). The furin inhibitor can transiently switch secreted αEGFR Ab into a membrane-anchored form. After cell sorting, the level of membrane αEGFR Ab-RAKR-B7 is proportional to the amount of secreted αEGFR Ab in the medium. We further selected 23 αEGFR Ab expressing cells and demonstrated a high correlation (R2 = 0.9165) between the secretion level and surface expression levels of αEGFR Ab. These results suggested that the novel transiently protein-anchored system can easily and efficiently select the highest producing cells, reducing the cost for the production of biopharmaceuticals.

(d) related papers(*)

1. Nai-Wan Hsiao, Tien-Sheng Tseng, Yu-Ching Lee, Wang-Chuan Chen, Hui-Hsiung Lin, Yun-Ru Chen ,Yeng-Tseng Wang, Hung-Ju Hsu and Keng-Chang Tsai* (2014) “Serendipitous Discovery of Short Peptides from Natural Products as Tyrosinase Inhibitors” Journal of Chemical Information and Modeling, 54:11, 3099–3111 (SCI) (Citation:0) (ISI 2013 IF: 4.068, ranking: 6/135, COMPUTER SCIENCE, INFORMATION SYSTEMS)

2. Kuo-Hsiang Chuang, Chien-Han Kao, Steve R. Roffler, Ssu-Jung Lu, Ta-Chun Cheng, Yun-Ming Wang, Chih-Hung Chuang, Yuan-Chin Hsieh, Yeng-Tseng Wang, Jaw-Yuan Wang, Kuo-Yi Weng and Tian-Lu Cheng* (2014)” Development of an Anti-Methoxy Poly(ethylene glycol) (α-mPEG) Cell-Based Capture System to Measure mPEG and mPEGylated Molecules” Macromolecules 47:19, 6880-6888. (SCI) (Citation:0) (ISI 2013 IF=5.927, ranking: 3/82, POLYMER SCIENCE).

3. Kuo-Hsiang Chuang, Yuan-Chin Hsieh, I-Shiuan Chiang, Chih-Hung Chuang, Chien-Han Kao, Ta-Chun Cheng, Yeng-Tseng Wang, Wen-Wei Lin, Bing-Mae Chen, Steve R. Roffler, Ming-Yii Huang, Tian-Lu Cheng* (2014) “High-Throughput Sorting of the Highest Producing Cell via a Transiently Protein-Anchored System.” PLoS One 18;9(7):e102569. (SCI) (Citation:0) (ISI 2013 I.F.=3.534, ranking: 8/55, MULTIDISCIPLINARY SCIENCES).