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Zhang X, Tong X, Tang X, Yang Y, Zhang L, Zhan X, Zhang X. Behavioral toxicity of TDCPP in marine zooplankton: Evidence from feeding and swimming responses, molecular dynamics and metabolomics of rotifers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170864. [PMID: 38401740 DOI: 10.1016/j.scitotenv.2024.170864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 02/26/2024]
Abstract
As new organic flame retardants, chlorinated organophosphate esters (Cl-OPEs) have high water solubility and structural similarity to organophosphate pesticides, posing risks to aquatic organisms. The potential neurotoxicity of Cl-OPEs has attracted attention, especially in marine invertebrates with a relatively simple nervous system. In this study, a marine rotifer with a cerebral ganglion, Brachionus plicatilis, was exposed to tris (1,3-dichloro-2-propyl) phosphate (TDCPP) (two environmental concentrations and one extreme level), and the changes in feeding and swimming behaviors and internal mechanism were explored. Exposure to 1.05 nM TDCPP did not change the filtration and ingestion rates of rotifers and average linear velocity. But 0.42 and 4.20 μM TDCPP inhibited these three parameters and reduced unsaturated fatty acid content, reproduction and population growth. All TDCPP test concentrations suppressed AChE activity, causing excessive accumulation of acetylcholine within rotifers, thereby disturbing the neural innervation of corona cilia. Molecular docking and molecular dynamics revealed that this inhibition was because TDCPP can bind to the catalytic active site of rotifer AChE through van der Waals forces and electrostatic interactions. TRP420 was the leading amino residue in the binding, and GLY207 contributed to a hydrogen bond. Nontargeted metabolomics using LC-MS and GC-MS identified differentially expressed metabolites in TDCPP treatments, mainly from lipid and lipid-like molecules, especially sphingolipids. TDCPP decreased ganglioside content but stimulated ceramide generation and the expression levels of 3 genes related to ceramide de novo synthesis. The mitochondrial membrane potential (MMP) and ATP content decreased, and the electron respiratory chain complex and TCA cycle were deactivated. An inhibitor of ceramide synthase, fumonisin, alleviated MMP and ATP, implying a critical role of ceramide in mitochondrial dysfunction. Thus, TDCPP exposure caused an energy supply deficit affecting ciliary movement and ultimately inhibiting rotifer behaviors. Overall, this study promotes the understanding of the neurotoxicity of Cl-OPEs in marine invertebrates.
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Affiliation(s)
- Xin Zhang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Xin Tong
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Xuexi Tang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yixin Yang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Luyuchen Zhang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Xiaotong Zhan
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Xinxin Zhang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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2
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Cabezudo I, Lobertti CA, Véscovi EG, Furlan RLE. Effect-Directed Synthesis of PhoP/PhoQ Inhibitors to Regulate Salmonella Virulence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6755-6763. [PMID: 35607919 DOI: 10.1021/acs.jafc.2c01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Salmonella spp. are among the leading bacterial causes of foodborne infections. The PhoP/PhoQ two-component regulatory system serves as a master virulence regulator in Salmonella. Although PhoP/PhoQ represents an ideal target for disarming Salmonella virulence, it has very few inhibitors reported so far. We describe a novel platform by which an inhibitor was selected out of around 185 compounds directly from reaction media containing thiosemicarbazones and mono-, di-, and trihydrazones. To achieve this, tandem library preparation, thin-layer chromatography (TLC) bioautography, and effect-directed deconvolution were applied. We illustrate the potential of this effect-directed synthesis for the identification of new useful bioactive compounds for the food field.
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Affiliation(s)
- Ignacio Cabezudo
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario 2000 Argentina
| | - Carlos A Lobertti
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET), Rosario S2000EZP Argentina
- Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario 2000 Argentina
| | - Eleonora García Véscovi
- Instituto de Biología Molecular y Celular de Rosario (IBR CONICET), Rosario S2000EZP Argentina
| | - Ricardo L E Furlan
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario 2000 Argentina
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3
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Purushothaman M, Dhar SK, Natesh R. Role of unique loops in oligomerization and ATPase function of Plasmodium falciparum gyrase B. Protein Sci 2022; 31:323-332. [PMID: 34716632 PMCID: PMC8820116 DOI: 10.1002/pro.4217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
DNA gyrase is an ATP dependent Type IIA topoisomerase that is unique to prokaryotes. Interestingly DNA gyrase has also been found in the apicoplasts of apicomplexan parasites like Plasmodium falciparum (Pf) the causative agent of Malaria. Gyrase B (GyrB), a subunit of gyrase A2 B2 complex has an N-terminal domain (GyrBN) which is endowed with ATPase activity. We reported earlier that PfGyrB exhibits ATP-independent dimerization unlike its bacterial counterparts. Here we report the role of two unique regions (L1 and L2) identified in PfGyrBN. Deletions of L1 alone (PfGyrBNΔL1), or L1 and L2 together (PfGyrBNΔL1ΔL2) have indicated that these regions may play an important role in ATPase activity and the oligomeric state of PfGyrBN. Our experiments show that the deletion of L1 region disrupts the dimer interface of PfGyrBN and reduces its ATPase activity. Further through ITC experiments we show that the binding affinity of ATP to PfGyrBN is reduced upon the deletion of L1 region. We have observed a reduction in ATPase activity for of all three proteins PfGyrBN, PfGyrBNΔL1, and PfGyrBNΔL1ΔL2 in presence of coumermycin. Our results suggests that L1 region of PfGyrBN is likely to be functionally important and may provide a unique dimer interface that affects its enzymatic activity. Since deletion of L1 region decreases the affinity of ATP to the protein, this region can be targeted toward designing novel inhibitors of ATP hydrolysis.
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Affiliation(s)
- Monica Purushothaman
- School of BiologyIndian Institute of Science Education and Research ThiruvananthapuramThiruvananthapuramKeralaIndia
| | - Suman Kumar Dhar
- Special Centre of Molecular MedicineJawaharlal Nehru UniversityNew DelhiIndia
| | - Ramanathan Natesh
- School of BiologyIndian Institute of Science Education and Research ThiruvananthapuramThiruvananthapuramKeralaIndia
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4
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Chen F, Wang Q, Mu Y, Sun S, Yuan X, Shang P, Ji B. Systematic profiling and identification of the peptide-mediated interactions between human Yes-associated protein and its partners in esophageal cancer. J Mol Recognit 2021; 35:e2947. [PMID: 34964176 DOI: 10.1002/jmr.2947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
Human Yes-associated protein (YAP) is involved in the Hippo signaling pathway and serves as a coactivator to modulate gene expression, which contains a transactivation domain (TD) responsible for binding to the downstream TEA domain family (TEAD) of transcription factors and two WW1/2 domains that recognize the proline-rich motifs (PRMs) present in a variety of upstream protein partners through peptide-mediated interactions (PMIs). The downstream YAP TD-TEAD interactions are closely associated with gastric cancer, and a number of therapeutic agents have been developed to target the interactions. In contrast, the upstream YAP WW1/2-partner interactions are thought to be involved in esophageal cancer but still remain largely unexplored. Here, we attempted to elucidate the complicated PMIs between the YAP WW1/2 domains and various PRMs of YAP-interacting proteins. A total of 106 peptide segments carrying the class I WW-binding motif [P/L]Px[Y/P] were extracted from 22 partner candidates, which are potential recognition sites of YAP WW1/2 domains. Structural and energetic analyses of the intermolecular interactions between the domains and peptides created a systematic domain-peptide binding profile, from which a number of biologically functional PMIs were identified and then substantiated in vitro using fluorescence spectroscopy assays. It is revealed that: (a) The sequence requirement for the partner recognition site binding to YAP WW1/2 domains is a decapeptide segment that contains a core PRM motif as well as two three-residue extensions from each side of the motif; the core motif and extended sections are responsible for the binding stability and recognition specificity of domain-peptide interaction, respectively. (b) There is an exquisite difference in the recognition specificity of the two domains; the LPxP and PPxP appear to more prefer WW1 than WW2, whereas the WW2 can bind more effectively to LPxY and PPxY than WW1. (c) WW2 generally exhibits a higher affinity to the panel of recognition site candidates than WW1. In addition, a number of partner peptides were found as promising recognition sites of the two domains and/or to have a good selectivity between the two domains. For example, the DVL1 peptide was determined to have moderate affinity to WW2 and strong selectivity for WW2 over WW1. Hydrogen bonds play a central role in selectivity.
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Affiliation(s)
- Fei Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Qifei Wang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Yushu Mu
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Shibin Sun
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Xulong Yuan
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Pan Shang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Bo Ji
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
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5
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Zhang D, Wu H, Zhao J. Computational design and experimental substantiation of conformationally constrained peptides from the complex interfaces of transcriptional enhanced associate domains with their cofactors in gastric cancer. Comput Biol Chem 2021; 94:107569. [PMID: 34500324 DOI: 10.1016/j.compbiolchem.2021.107569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 08/08/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Transcriptional enhanced associate domains (Teads) are the downstream effectors of the hippo signaling pathway and have been recognized as attractive druggable targets of gastric cancer. The biological function of Teads is regulated by diverse cofactors. In this study, the intermolecular interactions of Teads with their cognate cofactors were systematically characterized at structural, thermodynamic and dynamic levels. The Teads possess a double-stranded helical hairpin that is surrounded by three independent structural elements β-sheet, α-helix and Ω-loop of cofactor proteins and plays a central role in recognition and association with cofactors. A number of functional peptides were split from the hairpin region at Tead-cofactor complex interfaces, which, however, cannot maintain in native conformation without the support of protein context and would therefore incur a considerable entropy penalty upon competitively rebinding to the interfaces. Here, we further used disulfide and hydrocarbon bridges to cyclize and staple the hairpin and helical peptides, respectively. The chemical modification strategies were demonstrated to effectively constrain peptide conformation into active state and to largely reduce peptide flexibility in free state, thus considerably improving their affinity. Since the cyclization and stapling only minimize the indirect entropy cost but do not influence the direct enthalpy effect upon peptide binding, the designed conformationally constrained peptides can retain in their native selectivity over different cofactors. This is particularly interesting because it means that the cyclized/stapled, affinity-improved peptides can specifically compete with their parent Teads for the cofactor arrays as they share consistent target specificity.
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Affiliation(s)
- Donglei Zhang
- Department of Pharmacy, Cangzhou Central Hospital, Hebei Medical University, Cangzhou 061014, China
| | - Hongna Wu
- Cangzhou Institute for Food and Drug Control, Cangzhou 061003, China
| | - Jing Zhao
- Department of Pharmacy, Cangzhou Central Hospital, Hebei Medical University, Cangzhou 061014, China.
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6
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Xu C, Liu X, Shen J, Sun Q, Guo X, Yang M, Leng J. Integrative identification of human serpin PAI-1 inhibitors from Dracaena dragon blood and molecular implications for inhibitor-induced PAI-1 allosterism. Biotechnol Appl Biochem 2021; 69:221-229. [PMID: 33433923 DOI: 10.1002/bab.2100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/06/2021] [Indexed: 11/08/2022]
Abstract
Human plasminogen activator inhibitor-1 (PAI-1) is an important component of the coagulation system and has been recognized as a potential therapeutic target of diverse cardiovascular disorders. Previously, it was found that the extracts from the Chinese medicine Dracaena dragon blood have potent inhibitory activity against PAI-1, but it is unclear which constituents directly participate in the inhibition and how do they regulate PAI-1 at molecular level. Here, we describe an integrated strategy to identify the dragon blood's chemical constituents that can directly target PAI-1. With the strategy, five compounds 1-5 are hit as promising PAI-1 inhibitor candidates, from which three are measured to have high or moderate activity against PAI-1. In particular, the compound 3 is determined to exhibit the highest potency; this value is roughly comparable with the widely used PAI-1 inhibitor Tiplaxtinin. We further examine the molecular effect of compound 3 on PAI-1 conformation at structural level. It is supposed that small-molecule inhibitor regulates the reactive center loop (RCL) of PAI-1 through an allosterism, that is, binding of compound 3 to PAI-1 can allosterically stabilize RCL in latent form, thus promoting PAI-1 conformational conversion from metastable active form to the inactive latent form. Long-term atomistic simulations also demonstrate that removal of compound 3 can destabilize the structured β-stranded conformation of RCL in latent form, although the current simulations are still not sufficient to characterize the full conversion dynamics trajectory.
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Affiliation(s)
- Chong Xu
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Xia Liu
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Jie Shen
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Quan Sun
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Xiaohong Guo
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Min Yang
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
| | - Jing Leng
- Chongqing Academy of Traditional Chinese Medicine, Chongqing, People's Republic of China.,Chongqing Traditional Chinese Medicine Hospital, Chongqing, People's Republic of China
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7
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Zhou P, Wang H, Chen Z, Liu Q. Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specificity by optimizing indirect readout. Mol Omics 2020; 17:86-94. [PMID: 33174576 DOI: 10.1039/d0mo00103a] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an etiological agent of the current rapidly growing outbreak of coronavirus disease (COVID-19), which is straining health systems around the world. Disrupting the intermolecular association of SARS-CoV-2 spike glycoprotein (S protein) with its cell surface receptor human angiotensin-converting enzyme 2 (hACE2) has been recognized as a promising therapeutic strategy against COVID-19. The association is a typical peptide-mediated interaction, where the hACE adopts an α1-helix, which can form a two-helix bundle with the α2-helix, to pack against a flat pocket on the S protein surface. Here, we demonstrate that the protein context of full-length hACE plays an essential role in supporting the hACE2 α1-helix recognition by viral S protein. Energetic analysis reveals that the α1-helical peptide (αHP) and also the two-helix bundle peptide (tBP) cannot bind effectively to S protein when they are split from the hACE protein. The context contributes moderately and considerably to the direct readout (DR) and indirect readout (IR) of peptide recognition, respectively. Dynamics simulation suggests that the two free peptides exhibit a large intrinsic disorder without the support of protein context, which would incur a considerable entropy penalty upon binding to S protein. To restore the IR effect lost by splitting peptides from hACE, we herein propose employing hydrocarbon stapling and cyclization strategies to constrain the free αHP and tBP peptides into their native ordered conformations, respectively. The stapling and cyclization are carefully designed in order to avoid influencing the peptide DR effect, which has been demonstrated to improve the peptide binding affinity (but not specificity) to S protein. The stapling/cyclization-imposed conformational constraint can effectively minimize the unfavorable IR effect (i) by reducing the peptide flexibility and entropy cost upon their binding to S protein, and (ii) by helping peptide pre-folding into their native state to facilitate the conformational selection by S protein.
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Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, No. 2006 Xiyuan Ave West Hi-Tech Zone, Chengdu 611731, China.
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8
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Zhang D, He D, Pan X, Liu L. Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface. Protein Pept Lett 2020; 27:999-1006. [DOI: 10.2174/0929866527666200414160723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
Background:
The Yes-Associated Protein (YAP) is a central regulator of Hippo pathway
involved in carcinogenesis, which functions through interaction with TEA Domain (TEAD)
transcription factors. Pharmacological disruption of YAP–TEAD4 complexes has been recognized
as a potential therapeutic strategy against diverse cancers by suppressing the oncogenic activity of
YAP.
Objective:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Methods:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Result:
The native conformation of PS-2 peptide is a cyclic loop, which is supposed to be constrained
by adding a disulfide bond across the spatially vicinal residue pair Arg87-Phe96 or Met86-
Phe95 at the peptide’s two ends, consequently resulting in two intramolecular cyclized counterparts
of linear PS-2 peptide, namely PS-2(cyc87,96) and PS-2(cyc86,95). The linear PS-2 peptide
is determined as a weak binder of TEAD4 (Kd = 190 μM), while the two cyclic PS-2(cyc87,96) and
PS-2(cyc86,95) peptides are measured to have moderate or high affinity towards TEAD4 (Kd = 21
and 45 μM, respectively).
Conclusion:
PS-1 and PS-2 peptides are highly flexible and cannot maintain in native active conformation
when splitting from the interfacial context, and thus would incur a considerable entropy
penalty upon rebinding to the interface. Cyclization does not influence the direct interaction between
PS-2 peptide and TEAD4 protein, but can largely reduce the intrinsic disorder of PS-2 peptide
in free state and considerably minimize indirect entropy effect upon the peptide binding.
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Affiliation(s)
- Dingwa Zhang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Deyong He
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Xiaoliang Pan
- School of Mechanical and Electrical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Lijun Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
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Studying Calcium Ion-Dependent Effect on the Inter-subunit Interaction Between the cTnC N-terminal Domain and cTnI C-terminal Switch Peptide of Human Cardiac Troponin via Chou’s 5-Steps Rule. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09875-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Cai W, Wu J, Sun Y, Liu A, Wang R, Ma Y, Shuqing Wang, Dong W. Synthesis, evaluation, molecular dynamics simulation and targets identification of novel pyrazole-containing imide derivatives. J Biomol Struct Dyn 2020; 39:2176-2188. [PMID: 32189577 DOI: 10.1080/07391102.2020.1745284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A new series of novel pyrazole-containing imide derivatives were synthesized and evaluated for their anticancer activities against A-549, Bel7402, and HCT-8 cell lines. Among these compounds A2, A4, A11 and A14 possessed high inhibition activity against A-549 cell lines with IC50 values at 4.91, 3.22, 27.43 and 18.14 μM, respectively, better than that of 5-fluorouracil (IC50=59.27 μM). A2, A4, and A11 also exhibited significant inhibitory activity towards HCT-8 and Bel7402 cell lines. Interestingly, the Heat Shock Protein 90α (Hsp90α, PDB ID: 1UYK) was found to be the potential drug target of these synthesized compounds with the aid of PharmMapper server (http://lilab.ecust.edu.cn/pharmmapper/) and docking module of Schrödinger (Maestro 10.2). Additionally, molecular dynamics simulation was performed out to explore the most likely binding mode of compound A2 with Hsp90α.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wenxi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.,Department of Pharmacy, Characteristic Medical Center of PAP, Tianjin, China
| | - Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yingzhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ailin Liu
- National Center for Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shuqing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Weili Dong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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11
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Wu J, Li W, Zheng Z, Lu X, Zhang H, Ma Y, Wang R. Design, synthesis, biological evaluation, common feature pharmacophore model and molecular dynamics simulation studies of ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate as Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors. J Biomol Struct Dyn 2020; 39:1174-1188. [PMID: 32036779 DOI: 10.1080/07391102.2020.1726817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell death pathway (PD-1/PD-L1) and cell growth and differentiation pathway (MAPK). Moreover, mutations in SHP2 have been implicated in Leopard syndrome (LS), Noonan syndrome (NS), juvenile myelomonocytic leukemia (JMML) and several types of cancer and solid tumors. Thus, SHP2 inhibitors are much needed reagents for evaluation of SHP2 as a therapeutic target. A series of novel ethyl 4-(phenoxymethyl)-2-phenylthiazole-5-carboxylate derivatives were designed and synthesized, and their SHP2 inhibitory activities (IC50) were determined. Among the desired compounds, 1d shares the highest inhibitory activity (IC50 = 0.99 μM) against SHP2. Additionally, a common feature pharmacophore model was established to explain the structure activity relationship of the desired compounds. Finally, molecular dynamics simulation was carried out to explore the most likely binding mode of compound 1d with SHP2. In brief, the findings reported here may at least provide a new strategy or useful insights in discovering novel effective SHP2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Weiya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhihui Zheng
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Xinhua Lu
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering &Technology Research Center, Key Laboratory for New Drug, Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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12
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Zhou P, Yan F, Miao Q, Chen Z, Wang H. Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode? J Biomol Struct Dyn 2020; 39:310-318. [DOI: 10.1080/07391102.2019.1709547] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
- Center for Information in BioMedicine, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
| | - Fugang Yan
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Qingqing Miao
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Zheng Chen
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Heyi Wang
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
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13
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Zhou K, Lu J, Yin X, Xu H, Li L, Ma B. Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy. Biophys Chem 2019; 253:106213. [DOI: 10.1016/j.bpc.2019.106213] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022]
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14
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Bo G, Cao F, Li M, Xing J, Su X, Zhu Y, Wu D. Exploring calcium ion-dependent effect on the intermolecular interaction between human secreted phospholipase A2 and its peptide inhibitors in coronary artery disease. J Mol Graph Model 2019; 93:107449. [PMID: 31536875 DOI: 10.1016/j.jmgm.2019.107449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/31/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022]
Abstract
Human secreted phospholipase A2 (hsPLA2) is a small calcium ion (Ca2+)-regulatory protein secreting from platelets, eosinophils and T-lymphocytes, which has been established as an important biomarker and potential target for the diagnosis and therapy of coronary artery disease. Short peptide inhibitors are used to competitively suppress the enzymatic activity of hsPLA2. Here, Ca2+ effect on the intermolecular recognition and interaction between hsPLA2 and its peptide inhibitors is investigated systematically by using molecular modeling and bioinformatics analysis. Dynamics simulations reveal that the hsPLA2 structure bound with Ca2+ is rather stable and has low thermal motion; removal of Ca2+ considerably increases structural flexibility and intrinsic disorder of the protein. Energetics calculations suggest that presence of Ca2+ can effectively promote the interaction of hsPLA2 with peptide inhibitors. In particular, the local substructures of hsPLA2 such as helix H1, loop L2 and double-stranded β-sheet DS that participate in peptide recognition are involved in or nearby Ca2+-coordinating site and can be directly stabilized by the Ca2+. In addition, a significant concentration-dependent effect of Ca2+ on peptide-hsPLA2 binding is observed in vitro, that is, a little of Ca2+ can largely improve peptide binding affinity, but high Ca2+ concentration does not increase the affinity substantially. The correlation between calculated free energy and experimental binding affinity over different peptide inhibitors is improved considerably by adding Ca2+ to hsPLA2. Specifically, the FLSYK peptide can generally bind to Ca2+-bound hsPLA2 with a moderate or high affinity (Kd ranges between 56 and 210 μM), but have only a modest affinity or even nonbinding to Ca2+-free hsPLA2 (Kd > 400 μM or = n.d.).
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Affiliation(s)
- Guanggan Bo
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China.
| | - Fang Cao
- Department of Respiration, Anhui Provincial Children's Hospital, Hefei, 230051, China
| | - Min Li
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Junwu Xing
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Xiaoye Su
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Yunxian Zhu
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Dingkun Wu
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
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15
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Wei-Ya L, Yu-Qing D, Yang-Chun M, Xin-Hua L, Ying M, Wang RL. Exploring the cause of the inhibitor 4AX attaching to binding site disrupting protein tyrosine phosphatase 4A1 trimerization by molecular dynamic simulation. J Biomol Struct Dyn 2019; 37:4840-4851. [PMID: 30661451 DOI: 10.1080/07391102.2019.1567392] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ectopic overexpression of protein tyrosine phosphatase of liver regeneration-1 (PTP4A1, also called PRL-1) markedly enhanced hepatocellular carcinoma (HCC) cells migration and invasion. The PTP4A1 trimerization played a vital role in mediating cell proliferation and motility. Biochemical and structural studies have proved that the compound 4AX, a well-known inhibitor for PRL1, directly binds to the PTP4A1 trimer interface and obstructs trimer formation of PTP4A1. However, the molecular basis of the ligand-4AX inhibition on PTP4A1 trimer conformations remains unclear. In this study, the docking analysis and the molecular dynamics simulation (MD simulation) study were performed to investigate how the molecule binding at each interface disrupted the trimer formation. The results suggested that the ligand-4AX attaching to the binding site changed the conformation of A:Q131, A:Q135 in the AC interface, C:R18, C:P96 in the CA interface and B:Q131 in the BA interface, leading to the weak interactions between subunits and thus resulting in the disruption of the PTP4A1 trimerization.
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Affiliation(s)
- Li Wei-Ya
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin , China
| | - Duan Yu-Qing
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College , Tianjin , China
| | - Ma Yang-Chun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin , China
| | - Lu Xin-Hua
- National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, New Drug Research & Development Center of North China Pharmaceutical Group Corporation , Shijiazhuang , China
| | - Ma Ying
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin , China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University , Tianjin , China
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16
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Zhou P, Miao Q, Yan F, Li Z, Jiang Q, Wen L, Meng Y. Is protein context responsible for peptide-mediated interactions? Mol Omics 2019; 15:280-295. [DOI: 10.1039/c9mo00041k] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many cell signaling pathways are orchestrated by the weak, transient, and reversible peptide-mediated interactions (PMIs). Here, the role of protein context in contributing to the stability and specificity of PMIs is investigated systematically.
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Affiliation(s)
- Peng Zhou
- Center for Informational Biology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 611731
- China
- School of Life Science and Technology
| | - Qingqing Miao
- Center for Informational Biology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 611731
- China
- School of Life Science and Technology
| | - Fugang Yan
- Center for Informational Biology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 611731
- China
- School of Life Science and Technology
| | - Zhongyan Li
- Center for Informational Biology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 611731
- China
- School of Life Science and Technology
| | - Qianhu Jiang
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Li Wen
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Yang Meng
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
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17
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Beheshti A, Hashemi F, Behavndi F, Zahedi M, Kolahi M, Motamedi H, Mayer P. Synthesis, structural characterization, QSAR and docking studies of a new binuclear nickel (II) complex based on the flexible tetradentate N-donor ligand as a potent antibacterial and anticancer agent. Int J Biol Macromol 2017; 104:1107-1123. [PMID: 28663150 DOI: 10.1016/j.ijbiomac.2017.06.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 10/19/2022]
Abstract
A new nickel (II)complex namely [Ni2(Lt)Cl4] derived from the NiCl2.6H2O and 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl)propane (Lt) has been synthesized and fully characterized by the single crystal X-ray diffraction, elemental analysis, FT-IR, UV-vis, density functional theory (DFT) calculations, antibacterial and anticancer activities. In the title complex, each of the Ni(II) atoms is tetrahedrally coordinated by two N atoms from one of the chelating bidentate bis(3,5-dimethylpyrazolyl)methane units of the Lt ligand and two Cl as terminal ligands. The neighboring [Ni2(Lt)Cl4] molecules are linked together by the intermolecular CH⋯Cl hydrogen bonds to generate a 1D chain structure. The chains are further stabilized by the intermolecular CH⋯π interactions to form a two-dimensional non-covalent bonded structure. The antibacterial activity of the free Lt ligand and its Ni (II) complex shows that the ability of these compounds to inhibit growth of the tested bacteria increase from the Lt to binuclear nickel (II) complex. Scanning probe microscopy (SPM) study of the treated B. subtilis and E. coli bacteria was implemented to understand the structural changes caused by the interactions between the nickel (II) complex and the target bacteria. The cytotoxicity test of the Lt ligand and its complex was evaluated against the human carcinoma cell line (Caco-2) using the MTT assay. The results indicate that the Lt ligand and its complex display cytotoxicity against Caco-2 with the IC50 values of 36.29μM and 12.97μM, respectively. Therefore, the complex can be nominated as a potential anticancer agent. Molecular docking investigations on the five standard antibiotic, five standard anticancer drugs, free Lt ligand, title complex and twelve receptors were performed by Autodock vina function. The results of docking and DFT calculations are in line with the in vitro data obtained via the antibacterial and anticancer activity of Lt ligand and its made-complex.
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Affiliation(s)
- Azizolla Beheshti
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Faezeh Hashemi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Fatemeh Behavndi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Chemistry, Shahid Beheshti University, G. C. Tehran, 19839, Evin, P.O. Box 19395-4716, Iran
| | - Maryam Kolahi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hossein Motamedi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran; Biotechnology and Biological Science Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Peter Mayer
- Department Chemie Butenandtstr, LMU München University, München, Germany
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Azam MA, Thathan J. Pharmacophore generation, atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:275-296. [PMID: 28399673 DOI: 10.1080/1062936x.2017.1310131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.
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Affiliation(s)
- M A Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
| | - J Thathan
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Tamil Nadu , India
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19
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Synthesis, structural characterization, antibacterial activity, DNA binding and computational studies of bis(2-methyl-1H-imidazole κN3)silver(I)dichromate(VI). J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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20
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Synthesis, structural characterization, antibacterial activity and computational studies of new cobalt (II) complexes with 1,1,3,3-tetrakis (3,5-dimethyl-1-pyrazolyl)propane ligand. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Dong K, Wang X, Yang X, Zhu X. Binding mechanism of CDK5 with roscovitine derivatives based on molecular dynamics simulations and MM/PBSA methods. J Mol Graph Model 2016; 68:57-67. [PMID: 27371933 DOI: 10.1016/j.jmgm.2016.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/21/2016] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
Roscovitine derivatives are potent inhibitors of cyclin-dependent kinase 5 (CDK5), but they exhibit different activities, which has not been understood clearly up to now. On the other hand, the task of drug design is difficult because of the fuzzy binding mechanism. In this context, the methods of molecular docking, molecular dynamics (MD) simulation, and binding free energy analysis are applied to investigate and reveal the detailed binding mechanism of four roscovitine derivatives with CDK5. The electrostatic and van der Waals interactions of the four inhibitors with CDK5 are analyzed and discussed. The calculated binding free energies in terms of MM-PBSA method are consistent with experimental ranking of inhibitor effectiveness for the four inhibitors. The hydrogen bonds of the inhibitors with Cys83 and Lys33 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the pivotal contacts with Ile10 and Leu133 have larger contributions to the binding free energy and play critical roles in distinguishing the variant bioactivity of four inhibitors. In terms of binding mechanism of the four inhibitors with CDK5 and energy contribution of fragments of each inhibitor, two new CDK5 inhibitors are designed and have stronger inhibitory potency.
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Affiliation(s)
- Keke Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xuan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xueyu Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Xiaolei Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
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22
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Wang A, Song T, Wang Z, Liu Y, Fan Y, Zhang Y, Zhang Z. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation. Chem Biol Drug Des 2016; 87:551-61. [DOI: 10.1111/cbdd.12679] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Anhui Wang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; Dalian 116024 China
- School of Innovation Experiment; Dalian University of Technology; Dalian 116024 China
| | - Ting Song
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; Dalian 116024 China
| | - Ziqian Wang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; Dalian 116024 China
| | - Yubo Liu
- School of Life Science and Medicine; Dalian University of Technology; Panjin 124221 China
| | - Yudan Fan
- School of Life Science and Technology; Dalian University of Technology; Dalian 116024 China
| | - Yahui Zhang
- Department of Engineering Mechanics; Dalian University of Technology; Dalian 116024 China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals; School of Chemistry; Dalian University of Technology; Dalian 116024 China
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23
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Moonrin N, Songtawee N, Rattanabunyong S, Chunsrivirot S, Mokmak W, Tongsima S, Choowongkomon K. Understanding the molecular basis of EGFR kinase domain/MIG-6 peptide recognition complex using computational analyses. BMC Bioinformatics 2015; 16:103. [PMID: 25885222 PMCID: PMC4383062 DOI: 10.1186/s12859-015-0528-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 03/06/2015] [Indexed: 11/22/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) signalling plays a major role in biological processes, including cell proliferation, differentiation and survival. Since the over-expression of EGFR causes human cancers, EGFR is an attractive drug target. A tumor suppressor endogenous protein, MIG-6, is known to suppress EGFR over-expression by binding to the C-lobe of EGFR kinase. Thus, this C-lobe of the EGFR kinase is a potential new target for EGFR kinase activity inhibition. In this study, molecular dynamics (MD) simulations and binding free energy calculations were used to investigate the protein-peptide interactions between EGFR kinase and a 27-residue peptide derived from MIG-6_s1 segment (residues 336–362). Results These 27 residues of MIG-6_s1 were modeled from the published MIG-6 X-ray structure. The binding dynamics were detailed by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method to predict the binding free energy. Both van der Waals interactions and non-polar solvation were favorable driving forces for binding process. Six residues of EGFR kinase and eight residues of MIG-6_s1 residues were shown to be responsible for interface binding in which we investigated per residue free energy decomposition and the results from the computational alanine scanning approach. These residues also had higher hydrogen bond occupancies than other residues at the binding interface. The results from the aforementioned calculations reasonably agreed with the previous experimental mutagenesis studies. Conclusions Molecular dynamics simulations were used to investigate the interactions of MIG-6_s1 to EGFR kinase domain. Our study provides an insight into such interactions that is useful in guiding the design of novel anticancer therapeutics. The information on our modelled peptide interface with EGFR kinase could be a possible candidate for an EGFR dimerization inhibitor.
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Affiliation(s)
- Ninnutt Moonrin
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam, Wong Wan Rd, Bangkok, Chatuchak, 10900, Thailand.
| | - Napat Songtawee
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
| | - Siriluk Rattanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam, Wong Wan Rd, Bangkok, Chatuchak, 10900, Thailand.
| | - Surasuk Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Pathum Wan, 10330, Thailand.
| | - Wanwimon Mokmak
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, 50 Ngam Wong Wan Rd, Bangkok, Chatuchak, 10900, Thailand. .,Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Pathum Thani, Khlong Luang, 12120, Thailand.
| | - Sissades Tongsima
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Pathum Thani, Khlong Luang, 12120, Thailand.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam, Wong Wan Rd, Bangkok, Chatuchak, 10900, Thailand. .,Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Pathum Thani, Khlong Luang, 12120, Thailand. .,Center for Advanced Studies in Tropical Natural Resources, National Research, University-Kasetsart University, Kasetsart University, Bangkok, Chatuchak, 10900, Thailand.
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24
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Computational determination of binding structures and free energies of glucose 6-phosphate dehydrogenase with novel steroid inhibitors. J Mol Graph Model 2014; 51:168-72. [PMID: 24929815 DOI: 10.1016/j.jmgm.2014.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 05/09/2014] [Accepted: 05/23/2014] [Indexed: 11/21/2022]
Abstract
Glucose 6-phosphate dehydrogenase (G6PD), the first and the rate-limiting enzyme in the pentose phosphate pathway (PPP), catalyzes the oxidation of G6P to 6-phosphogluconolactone and the reduction of NADP(+) to NADPH. Its key role in cancer promotes the development of a potent and selective inhibitor that might increase cancer cell death when combined with radiotherapy. In the present study, we investigated the detailed binding modes and binding free energies for G6PD interacting with a promising series of recently developed inhibitors, i.e., the steroid derivatives, by performing molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations. The docking indicates that the inhibitors occupy the binding sites of both G6P and NADP(+). The calculated binding free energies on the basis of the MD-simulated enzyme-inhibitor complexes are in good agreement with the experimental activity data for all of the examined inhibitors. The valuable insights into the detailed enzyme-inhibitor binding including the important intermolecular interactions, e.g., the hydrogen bond interaction and the hydrophobic interaction, have been provided. The computational results provide new insights into future rational design of more potent inhibitors of G6PD as a treatment for cancer.
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25
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Determinants of protein–ligand complex formation in the thyroid hormone receptor α: A molecular dynamics simulation study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Gu Y, Wang W, Zhu X, Dong K. Molecular dynamic simulations reveal the mechanism of binding between xanthine inhibitors and DPP-4. J Mol Model 2014; 20:2075. [PMID: 24481594 DOI: 10.1007/s00894-014-2075-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022]
Abstract
We apply molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation to investigate and reveal the binding mechanism between five xanthine inhibitors and DPP-4. The electrostatic and van der Waals interactions of the five inhibitors with DPP-4 are analyzed and discussed. The computed binding free energies using MM-PBSA method are in qualitatively agreement with experimental inhibitory potency of five inhibitors. The hydrogen bonds of inhibitors with Ser630 and Asp663 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the key contacts with His740, Asn710, Trp629, and Tyr666 have larger contributions to the binding free energy and play important roles in distinguishing the variant bioactivity of five inhibitors.
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Affiliation(s)
- Yongliang Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing, 210009, China
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27
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Improved scFv anti-HIV-1 p17 binding affinity guided from the theoretical calculation of pairwise decomposition energies and computational alanine scanning. BIOMED RESEARCH INTERNATIONAL 2013; 2013:713585. [PMID: 24308004 PMCID: PMC3838816 DOI: 10.1155/2013/713585] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 09/03/2013] [Accepted: 09/10/2013] [Indexed: 11/23/2022]
Abstract
Computational approaches have been used to evaluate and define important residues for protein-protein interactions, especially antigen-antibody complexes. In our previous study, pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants has indicated the key specific residues in the complementary determining regions (CDRs) of scFv anti-p17. In this present investigation in order to determine whether a specific side chain group of residue in CDRs plays an important role in bioactivity, computational alanine scanning has been applied. Molecular dynamics simulations were done with several complexes of original scFv anti-p17 and scFv anti-p17mutants with HIV-1 p17 epitope variants with a production run up to 10 ns. With the combination of pairwise decomposition residue interaction and alanine scanning calculations, the point mutation has been initially selected at the position MET100 to improve the residue binding affinity. The calculated docking interaction energy between a single mutation from methionine to either arginine or glycine has shown the improved binding affinity, contributed from the electrostatic interaction with the negative favorably interaction energy, compared to the wild type. Theoretical calculations agreed well with the results from the peptide ELISA results.
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Saíz-Urra L, Pérez MÁC, Froeyen M. Thermodynamic computational approach to capture molecular recognition in the binding of different inhibitors to the DNA gyrase B subunit from Escherichia coli. J Mol Model 2013; 19:3187-200. [PMID: 23625033 DOI: 10.1007/s00894-013-1849-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 04/04/2013] [Indexed: 11/29/2022]
Abstract
DNA gyrase subunit B, that catalyzes the hydrolysis of ATP, is an attractive target for the development of antibacterial drugs. This work is intended to rationalize molecular recognition at DNA gyrase B enzyme - inhibitor binding interface through the evaluation of different scoring functions in finding the correct pose and scoring properly 50 Escherichia coli DNA Gyrase B inhibitors belonging to five different classes. Improving the binding free energy calculation accuracy is further attempted by using rescoring schemes after short molecular dynamic simulations of the obtained docked complexes. These data are then compared with the corresponding experimental enzyme activity data. The results are analyzed from a structural point of view emphasizing the strengths and limitations of the techniques applied in the study.
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Affiliation(s)
- Liane Saíz-Urra
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Wang W, Cao X, Zhu X, Gu Y. Molecular dynamic simulations give insight into the mechanism of binding between 2-aminothiazole inhibitors and CDK5. J Mol Model 2013; 19:2635-45. [PMID: 23525963 DOI: 10.1007/s00894-013-1815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 03/04/2013] [Indexed: 12/20/2022]
Abstract
Molecular docking, molecular dynamics (MD) simulations, and binding free energy analysis were performed to reveal differences in the binding affinities between five 2-aminothiazole inhibitors and CDK5. The hydrogen bonding and hydrophobic interactions between inhibitors and adjacent residues are analyzed and discussed. The rank of calculated binding free energies using the MM-PBSA method is consistent with experimental result. The results illustrate that hydrogen bonds with Cys83 favor inhibitor binding. The van der Waals interactions, especially the important contact with Ile10, dominate in the binding free energy and play a crucial role in distinguishing the different bioactivity of the five inhibitors.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009, China
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30
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Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T. Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem 2012; 55:6413-26. [PMID: 22731783 DOI: 10.1021/jm300395d] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4'-methyl-N(2)-phenyl-[4,5'-bithiazole]-2,2'-diamine inhibitors of gyrase B with a low micromolar inhibitory activity by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques (differential scanning fluorimetry, surface plasmon resonance, and microscale thermophoresis). The binding mode of the potent inhibitor 18 was revealed by X-ray crystallography, confirming our initial in silico binding model. Furthermore, the high resolution of the complex structure allowed for the placement of the Gly97-Ser108 flexible loop, thus revealing its role in binding of this class of compounds. The crystal structure of the complex protein G24 and inhibitor 18 provides valuable information for further optimization of this novel class of DNA gyrase B inhibitors.
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Affiliation(s)
- Matjaž Brvar
- National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
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31
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Ling B, Sun M, Bi S, Jing Z, Liu Y. Molecular dynamics simulations of the coenzyme induced conformational changes of Mycobacterium tuberculosis L-alanine dehydrogenase. J Mol Graph Model 2012; 35:1-10. [PMID: 22459692 DOI: 10.1016/j.jmgm.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/31/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
Abstract
Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) catalyzes the NADH-dependent reversible oxidative deamination of L-alanine to pyruvate and ammonia. L-MtAlaDH has been proposed to be a potential target in the treatment of tuberculosis. Based on the crystal structures of this enzyme, molecular dynamics simulations were performed to investigate the conformational changes of L-MtAlaDH induced by coenzyme NADH. The results show that the presence of NADH in the binding domain restricts the motions and conformational distributions of L-MtAlaDH. There are two loops (residues 94-99 and 238-251) playing important roles for the binding of NADH, while another loop (residues 267-293) is responsible for the binding of substrate. The opening/closing and twisting motions of two domains are closely related to the conformational changes of L-MtAlaDH induced by NADH.
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Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
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32
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Lu SY, Jiang YJ, Zou JW, Wu TX. Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based α-helix mimetic as dual inhibitors of MDM2 and MDMX. J Mol Graph Model 2011; 30:167-78. [PMID: 21820342 DOI: 10.1016/j.jmgm.2011.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 01/09/2023]
Abstract
Inhibition of the interactions between the tumor suppressor protein p53 and its negative regulators, the MDM2 and MDMX oncogenic proteins, is increasingly gaining interest in cancer therapy and drug design. In this study, we carry out molecular docking, molecular dynamics (MD) simulations, and molecular mechanics Poisson-Boltzmann and generalized Born/surface area (MM-PB/GBSA) binding free energy calculations on an active compound 3a and an inactive compound NC-1, which share a common pyrrolopyrimidine-based scaffold. MD simulations and MM-PB/GBSA calculations show that the compound NC-1 may not bind to MDM2 and MDMX, in agreement with the experimental results. Detailed MM-PB/GBSA calculations on the MDM2-3a and MDMX-3a complexes unravel that the binding free energies are similar for the two complexes. Furthermore, the van der Waals energy is the largest component of the binding free energy for both complexes, which indicates that the interactions between the compound 3a and MDM2 and MDMX are dominated by shape complementarity. In addition, the analysis of individual residue contribution and protein-ligand binding mode show that the three functional groups on R₁, R₂, and R₃ of the compound 3a can mimic the spatial orientation of the side chains of Phe19, Trp23, and Leu26 of p53, respectively. The obtained computational results suggest that the compound 3a can act as a dual inhibitor of MDM2-p53 and MDMX-p53 interactions, consistent with the experimental results.
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Affiliation(s)
- Shao-Yong Lu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, PR China
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Saíz-Urra L, Cabrera Pérez MÁ, Helguera AM, Froeyen M. Combining molecular docking and QSAR studies for modelling the antigyrase activity of cyclothialidine derivatives. Eur J Med Chem 2011; 46:2736-47. [PMID: 21530019 DOI: 10.1016/j.ejmech.2011.03.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/21/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022]
Abstract
DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2), where GyrB catalyzes the hydrolysis of ATP. Cyclothialidine (Ro 09-1437) has been considered as a promising inhibitor whose modifications might lead to more potent compounds against the enzyme. We report here for the first time, QSAR studies regarding to ATPase inhibitors of DNA Gyrase. 1D, 2D and 3D descriptors from DRAGON software were used on a set of 42 cyclothialidine derivatives. Based on the core of the cyclothialidine GR122222X, different conformations were created by using OMEGA. FRED was used to dock these conformers in the cavity of the GyrB subunit to select the best conformations, paying special attention to the 12-membered ring. Three QSAR models were developed considering the dimension of the descriptors. The models were robust, predictive and good in statistical significance, over 70% of the experimental variance was explained. Interpretability of the models was possible by extracting the SAR(s) encoded by these predictive models. Analyzing the compound-enzyme interactions of the complexes obtained by docking allowed us to increase the reliability of the information obtained for the QSAR models.
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Affiliation(s)
- Liane Saíz-Urra
- Centro de Bioactivos Quimicos, Universidad Central "Marta Abreu" de las Villas, Carretera a Camajuani Km 5.5, Santa Clara (54830), Villa Clara, Cuba.
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