1
|
Machine Learning for the Prediction of Antiviral Compounds Targeting Avian Influenza A/H9N2 Viral Proteins. Symmetry (Basel) 2022. [DOI: 10.3390/sym14061114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Avian influenza subtype A/H9N2—which infects chickens, reducing egg production by up to 80%—may be transmissible to humans. In humans, this virus is very harmful since it attacks the respiratory system and reproductive tract, replicating in both. Previous attempts to find antiviral candidates capable of inhibiting influenza A/H9N2 transmission were unsuccessful. This study aims to better characterize A/H9N2 to facilitate the discovery of antiviral compounds capable of inhibiting its transmission. The Symmetry of this study is to apply several machine learning methods to perform virtual screening to identify H9N2 antivirus candidates. The parameters used to measure the machine learning model’s quality included accuracy, sensitivity, specificity, balanced accuracy, and receiver operating characteristic score. We found that the extreme gradient boosting method yielded better results in classifying compounds predicted to be suitable antiviral compounds than six other machine learning methods, including logistic regression, k-nearest neighbor analysis, support vector machine, multilayer perceptron, random forest, and gradient boosting. Using this algorithm, we identified 10 candidate synthetic compounds with the highest scores. These high scores predicted that the molecular fingerprint may involve strong bonding characteristics. Thus, we were able to find significant candidates for synthetic H9N2 antivirus compounds and identify the best machine learning method to perform virtual screenings.
Collapse
|
2
|
Devaurs D, Antunes DA, Hall-Swan S, Mitchell N, Moll M, Lizée G, Kavraki LE. Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins. BMC Mol Cell Biol 2019; 20:42. [PMID: 31488048 PMCID: PMC6729087 DOI: 10.1186/s12860-019-0218-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/08/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Docking large ligands, and especially peptides, to protein receptors is still considered a challenge in computational structural biology. Besides the issue of accurately scoring the binding modes of a protein-ligand complex produced by a molecular docking tool, the conformational sampling of a large ligand is also often considered a challenge because of its underlying combinatorial complexity. In this study, we evaluate the impact of using parallelized and incremental paradigms on the accuracy and performance of conformational sampling when docking large ligands. We use five datasets of protein-ligand complexes involving ligands that could not be accurately docked by classical protein-ligand docking tools in previous similar studies. RESULTS Our computational evaluation shows that simply increasing the amount of conformational sampling performed by a protein-ligand docking tool, such as Vina, by running it for longer is rarely beneficial. Instead, it is more efficient and advantageous to run several short instances of this docking tool in parallel and group their results together, in a straightforward parallelized docking protocol. Even greater accuracy and efficiency are achieved by our parallelized incremental meta-docking tool, DINC, showing the additional benefits of its incremental paradigm. Using DINC, we could accurately reproduce the vast majority of the protein-ligand complexes we considered. CONCLUSIONS Our study suggests that, even when trying to dock large ligands to proteins, the conformational sampling of the ligand should no longer be considered an issue, as simple docking protocols using existing tools can solve it. Therefore, scoring should currently be regarded as the biggest unmet challenge in molecular docking.
Collapse
Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| | - Dinler A Antunes
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| | - Sarah Hall-Swan
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| | - Nicole Mitchell
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| | - Mark Moll
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| | - Gregory Lizée
- Department of Melanoma Medical Oncology - Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030 USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005 USA
| |
Collapse
|
3
|
Zwitterionic structures: from physicochemical properties toward computer-aided drug designs. Future Med Chem 2016; 8:2245-2262. [DOI: 10.4155/fmc-2016-0176] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.
Collapse
|
4
|
Yang Z, Wu F, Yuan X, Zhang L, Zhang S. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies. J Mol Graph Model 2016; 65:27-34. [PMID: 26905206 DOI: 10.1016/j.jmgm.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/09/2023]
Abstract
Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.
Collapse
Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China.
| | - Fei Wu
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, PR China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China.
| |
Collapse
|
5
|
Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
6
|
Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review. BIOMED RESEARCH INTERNATIONAL 2015; 2015:183918. [PMID: 25785262 PMCID: PMC4345249 DOI: 10.1155/2015/183918] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/05/2014] [Indexed: 01/08/2023]
Abstract
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.
Collapse
|
7
|
YANG ZHIWEI, WU FEI, LIU JUNXING, WANG SHUQIU, YUAN XIAOHUI. SUSCEPTIBILITY OF COMMERCIAL NEURAMINIDASE INHIBITORS AGAINST 2013 A/H7N9 INFLUENZA VIRUS: A DOCKING AND MOLECULAR DYNAMICS STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The latest influenza A ( H 7 N 9) virus attracted a worldwide attention due to the first report of human infections and the continuing reported cases in China. In this work, homology modeling, docking and molecular dynamics simulations were combined to study the interactions between neuraminidase ( N 9_2013, from novel A/ H 7 N 9 virus) and agents zanamivir, oseltamivir, peramivir. It was found that N 9_2013 protein is structurally close to the template (PDB code: 1F8B), especially the active site. The binding properties of N 9_2013 protein were nearly identical to those of template. As a result, the three available drugs should be still efficacious for the new emerging A ( H 7 N 9) virus. However, the stabilities of docked complexes and binding affinities (Eint) were slightly reduced, in contrast to the corresponding inhibitor-template complexes, with the values of -82.27 (-84.30), -78.84 (-80.28) and -77.52 (-81.94) kcal mol-1, respectively. Besides, R292K mutation might induce the resistance of the novel virus to the commercial inhibitors. Thus, it arouses the need for continuous monitoring of antiviral drug susceptibilities.
Collapse
Affiliation(s)
- ZHIWEI YANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - FEI WU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - JUNXING LIU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - SHUQIU WANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - XIAOHUI YUAN
- Institute of Biomedicine, Jinan University, Guangzhou 510632, P. R. China
| |
Collapse
|
8
|
Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. J Comput Aided Mol Des 2013; 27:935-50. [DOI: 10.1007/s10822-013-9691-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/05/2013] [Indexed: 01/15/2023]
|
9
|
Linobiflavonoid inhibits human lung adenocarcinoma A549 cells: effect on tubulin protein. Mol Biol Rep 2013; 40:6019-25. [PMID: 24057268 DOI: 10.1007/s11033-013-2711-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
The antitumor bioactivities of linobiflavonoid were studied through evaluating its in vitro cytotoxicity against several cell lines (A549, H1975, SMMC-7721, HEP-2 and Vero cells), with the aid of 3-(4,5)-dimethylthiazoly1)-3,5-diphenytetrazolium bromide (MTT) assay. It was found that linobiflavonoid shows more notable inhibiting activity against A549 cells, with IC50 value of 4.67 μM. Furthermore, western blot analysis revealed that linobiflavonoid is able to increase the expression of β-tubulin, whereas not α-tubulin. In virtuale simulations indicated that linobiflavonoid specifically interacts with the binding pocket which is located at the top of β-tubulin, due to the presence of strong hydrophobic effects between the core templates and the hydrophobic surface of the tubulin protein (TB) binding site. The binding energy (E inter ) was calculated to be -140.47 kcal/mol. Results above suggest that linobiflavonoid possesses anti-A549 properties relating to β-tubulin depolymerization inhibition.
Collapse
|
10
|
Yang Z, Yang Y, Wu F, Feng X. Computational investigation of interaction mechanisms between juglone and influenza virus surface glycoproteins. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.769683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
11
|
Zhao Y, Wu F, Wang Y, Chen S, Han G, Liu M, Jin D. Inhibitory action of chamaejasmin A against human HEP-2 epithelial cells: effect on tubulin protein. Mol Biol Rep 2012; 39:11105-12. [DOI: 10.1007/s11033-012-2016-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
|
12
|
Berlinck RGS, Trindade-Silva AE, Santos MFC. The chemistry and biology of organic guanidine derivatives. Nat Prod Rep 2012; 29:1382-406. [PMID: 22991131 DOI: 10.1039/c2np20071f] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The chemistry and biology of organic natural guanidines are reviewed, including the isolation, structure determination, synthesis, biosynthesis and biological activities of alkaloids, non-ribosomal peptides, guanidine-bearing terpenes, polyketides and shikimic acid derivatives from natural sources.
Collapse
Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brasil.
| | | | | |
Collapse
|
13
|
Liu CC, Liu BG, Yang ZW, Li CM, Wang BC, Yang CP. Genome-wide identification and in silico analysis of poplar peptide deformylases. Int J Mol Sci 2012; 13:5112-5124. [PMID: 22606033 PMCID: PMC3344269 DOI: 10.3390/ijms13045112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/12/2012] [Accepted: 04/18/2012] [Indexed: 01/07/2023] Open
Abstract
Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them.
Collapse
Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; E-Mail:
- Laboratory for Chemical Defense and Microscale Analysis, P.O. Box 3, Zhijiang 443200, China; E-Mail:
| | - Bao-Guang Liu
- Forestry College, Beihua University, Jilin 132013, China; E-Mail:
| | - Zhi-Wei Yang
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154000, China; E-Mail:
| | - Chun-Ming Li
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China; E-Mail:
| | - Bai-Chen Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; E-Mail:
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-0451-8219-0006; Fax: +86-0451-8219-0006
| |
Collapse
|
14
|
LIU JUNXING, YANG ZHIWEI, WANG SHUQIU, LIU LEI, CHEN GUANG, WANG LIN. EXPLORING THE MOLECULAR BASIS OF H5N1 HEMAGGLUTININ BINDING WITH CATECHINS IN GREEN TEA: A FLEXIBLE DOCKING AND MOLECULAR DYNAMICS STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The influenza A (H5N1) virus attracts a worldwide attention and calls for the urgent development of novel antiviral drugs. In this study, explicitly solvated flexible docking and molecular dynamics (MD) simulations were used to study the interactions between the H5N1 sub-type hemagglutinin (HA) and various catechin compounds, including EC ([–]-epicatechin), EGC ([–]-epigallocatechin), ECG ([–]-epicatechin gallate) and EGCG ([–]-epigallocatechin gallate). The four compounds have respective binding specificities and their interaction energies with HA decrease in the order of EGCG (-133.52) > ECG (-111.11) > EGC (-97.94) > EC (-83.39). Units in kcal mol-1. Residues IleA267, LysA269, ArgB68 and GluB78 play important roles during all the binding processes. EGCG has the best bioactivity and shows potential as a lead compound. Besides, the importance was clarified for the functional groups it was revealed that the C5′ hydroxyl and trihydroxybenzoic acid groups are crucial for the catechin inhibitory activities, especially the latter. Combined with the structural and property analyses, this work also proposed the way to effectively modify the functional groups of EGCG. The experimental efforts are expected in order to actualize the catechin derivatives as novel anti-influenza agents in the near future.
Collapse
Affiliation(s)
- JUNXING LIU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 15400, P. R. China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University Harbin 150040, P. R. China
- The First Affiliated Hospital of Jiamusi University, Jiamusi 154003, P. R. China
| | - ZHIWEI YANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 15400, P. R. China
| | - SHUQIU WANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 15400, P. R. China
| | - LEI LIU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 15400, P. R. China
| | - GUANG CHEN
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 15400, P. R. China
| | - LIN WANG
- The First Affiliated Hospital of Jiamusi University, Jiamusi 154003, P. R. China
| |
Collapse
|
15
|
Inhibitory effect and possible mechanism of action of patchouli alcohol against influenza A (H2N2) virus. Molecules 2011; 16:6489-501. [PMID: 21814161 PMCID: PMC6264369 DOI: 10.3390/molecules16086489] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/25/2011] [Accepted: 07/28/2011] [Indexed: 12/13/2022] Open
Abstract
In the present study, the anti-influenza A (H2N2) virus activity of patchouli alcohol was studied in vitro, in vivo and in silico. The CC50 of patchouli alcohol was above 20 µM. Patchouli alcohol could inhibit influenza virus with an IC50 of 4.03 ± 0.23 µM. MTT assay showed that the inhibition by patchouli alcohol appears strongly after penetration of the virus into the cell. In the influenza mouse model, patchouli alcohol showed obvious protection against the viral infection at a dose of 5 mg/kg/day. Flexible docking and molecular dynamic simulations indicated that patchouli alcohol was bound to the neuraminidase protein of influenza virus, with an interaction energy of –40.38 kcal mol–1. The invariant key active-site residues Asp151, Arg152, Glu119, Glu276 and Tyr406 played important roles during the binding process. Based on spatial and energetic criteria, patchouli alcohol interfered with the NA functions. Results presented here suggest that patchouli alcohol possesses anti-influenza A (H2N2) virus properties, and therefore is a potential source of anti-influenza agents for the pharmaceutical industry.
Collapse
|
16
|
Fang W, Liu S, Nie Y. Anticancer activity of chamaejasmine: effect on tubulin protein. Molecules 2011; 16:6243-54. [PMID: 21788932 PMCID: PMC6264762 DOI: 10.3390/molecules16086243] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 07/15/2011] [Accepted: 07/18/2011] [Indexed: 11/16/2022] Open
Abstract
In this work, the anticancer activity of chamaejasmine was studied by evaluating its in vitro cytotoxicity against several human cancer cell lines (MCF-7, A549, SGC-7901, HCT-8, HO-4980, Hela, HepG2, PC-3, LNCap, Vero and MDCK) using the MTT assay. Results indicated chamaejasmine showed more notable anticancer activity than taxol against PC-3 cells, with IC50 values of 2.28 and 3.98 µM, respectively. Furthermore, Western blot analysis showed that chamaejasmine was able to increase the expression of β-tubulin, but not α-tubulin. In silico simulations indicated that chamaejasmine specifically interacts with the active site which is located at the top of β-tubulin, thanks to the presence of strong hydrophobic effects between the core templates and the hydrophobic surface of the TB active site. The binding energy (Einter) was calculated to be −164.77 kcal·mol−1. Results presented here suggest that chamaejasmine possesses anti-cancer properties relating to β-tubulin depolymerization inhibition, and therefore is a potential source of anticancer leads for the pharmaceutical industry.
Collapse
Affiliation(s)
- Wenlong Fang
- Department of Rheumatology, The Second Hospital Affiliated Harbin Medical University, Harbin 150086, China; (W.F.)
| | - Songtao Liu
- Hei longjiang Disabled Federation for Human Care Clinic, Harbin 150020, China; (S.L.)
| | - Yingkun Nie
- Department of Rheumatology, The Second Hospital Affiliated Harbin Medical University, Harbin 150086, China; (W.F.)
- Author to whom correspondence should be addressed; ; Tel.: +86-0451-89877490; Fax: +86-0451-86605060
| |
Collapse
|
17
|
Comparative anti-infectious bronchitis virus (IBV) activity of (-)-pinene: effect on nucleocapsid (N) protein. Molecules 2011; 16:1044-54. [PMID: 21350392 PMCID: PMC6259611 DOI: 10.3390/molecules16021044] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 12/23/2010] [Accepted: 01/17/2011] [Indexed: 01/25/2023] Open
Abstract
In the present study, anti-IBV (infectious bronchitis virus) activities of (-)-pinenes were studied by MTT assay, as well as docking and molecular dynamic (MD) simulations. The CC₅₀ values of (-)-α-pinene and (-)-β-pinene were above 10 mM. And the maximum noncytotoxic concentrations (TD₀) of (-)-α-pinene and (-)-β-pinene were determined as 7.88 ± 0.06 and 6.09 ± 0.31 mM, respectively. The two compounds were found to inhibit IBV with an IC₅₀ of 0.98 ± 0.25 and 1.32 ± 0.11 mM. The MTT assay showed that the inhibitions of (-)-pinenes against IBV appear to occur moderately before entering the cell but are much stronger occur after penetration of the virus into the cell. Molecular simulations indicated that (-)-α-pinene and (-)-β-pinene specifically interact with the active site which is located at the N terminus of phosphorylated nucleocapsid (N) protein, with the former being more potent than the latter. The binding energies of them are -36.83 and -35.59 kcal mol-1, respectively. Results presented here may suggest that (-)-α-pinene and (-)-β-pinene possess anti-IBV properties, and therefore are a potential source of anti-IBV ingredients for the pharmaceutical industry.
Collapse
|
18
|
Yang Z, Yang G, Zu Y, Fu Y, Zhou L. Computer-based de novo designs of tripeptides as novel neuraminidase inhibitors. Int J Mol Sci 2010; 11:4932-51. [PMID: 21614183 PMCID: PMC3100827 DOI: 10.3390/ijms11124932] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/12/2010] [Accepted: 11/18/2010] [Indexed: 12/22/2022] Open
Abstract
The latest influenza A (H1N1) pandemic attracted worldwide attention and called for the urgent development of novel antiviral drugs. Here, seven tripeptides are designed and explored as neuraminidase (NA) inhibitors on the structural basis of known inhibitors. Their interactions with NA are studied and compared with each other, using flexible docking and molecular dynamics simulations. The various composed tripeptides have respective binding specificities and their interaction energies with NA decrease in the order of FRI > FRV > FRT > FHV > FRS > FRG > YRV (letters corresponding to amino acid code). The Arg and Phe portions of the tripeptides play important roles during the binding process: Arg has strong electrostatic interactions with the key residues Asp151, Glu119, Glu227 and Glu277, whereas Phe fits well in the hydrophobic cave within the NA active site. Owing to the introduction of hydrophobic property, the interaction energies of FRV and FRI are larger; in particular, FRI demonstrates the best binding quality and shows potential as a lead compound. In addition, the influence of the chemical states of the terminal amino acids are clarified: it is revealed that the charged states of the N-terminus (NH(3) (+)) and C-terminus (COO(-)) are crucial for the tripeptide inhibitory activities and longer peptides may not be appropriate. In addition, the medium inhibiting activity by acetylation of the N-terminus indicates the possible chemical modifications of FRI. Experimental efforts are expected in order to actualize the tripeptides as potent NA inhibitors in the near future.
Collapse
Affiliation(s)
- Zhiwei Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
| | - Gang Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Authors to whom correspondence should be addressed; E-Mails: (G.Y.); (Y.Z.); Tel.: +86-451-82192223; Fax: +86-451-82102082
| | - Yuangang Zu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
- Authors to whom correspondence should be addressed; E-Mails: (G.Y.); (Y.Z.); Tel.: +86-451-82192223; Fax: +86-451-82102082
| | - Yujie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
| | - Lijun Zhou
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
| |
Collapse
|