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Issahaku AR, Wilhelm A, Schutte-Smith M, Erasmus E, Visser H. Elucidating the binding mechanisms of GABA and Muscimol as an avenue to discover novel GABA-mimetic small molecules. J Biomol Struct Dyn 2024:1-16. [PMID: 38520326 DOI: 10.1080/07391102.2024.2331088] [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: 01/04/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Gamma-aminobutyric acid (GABA) signaling is the principal inhibitory pathway in the central nervous system. It is critical in neuronal cell proliferation and fate determination. Any aberration in GABA inhibition results in psychiatric and neurological diseases. Thus, modulating GABAergic neurotransmission has become the basis of drug therapy for psychiatric and several neurological diseases. Though GABA and muscimol are classical inhibitors of GABA receptors, the search for novel inhibitors continues unabated. In this study, the binding mechanism of GABA and muscimol was elucidated and applied in the search for small molecule GABAergic inhibitors using comprehensive computational techniques. It was revealed that a high-affinity binding of GABA and muscimol was mediated by a water molecule involving α1Thr129 and then stabilized by strong interactions including salt bridges with β2Glu155 and α1Arg66 amidst hydrogen bonds, π-π stacking, and π -cation interactions with other residues. The binding of GABA and muscimol was also characterized by stability and deeper penetration into the hydrophobic core of the protein which resulted in conformational changes of the binding pocket and domain, by inducing correlated motions of the residues. Thermodynamics analysis showed GABA and muscimol exhibited total binding free energies of -19.85 ± 8.83 Kcal/mol and -26.55 ± 3.42 Kcal/mol, respectively. A pharmacophore model search, based on the energy contributions of implicating binding residues, resulted in the identification of ZINC68604167, ZINC19735138, ZINC04202466, ZINC00901626, and ZINC01532854 as potential GABA-mimetic compounds from metabolites and natural products libraries. This study has elucidated the binding mechanisms of GABA and muscimol and successfully applied in the identification of GABA-mimetic compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anke Wilhelm
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | | | - Elizabeth Erasmus
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - Hendrik Visser
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
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Opoku F, Govender P, Shonhai A, Simelane MB. Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway. BMC Chem 2024; 18:55. [PMID: 38500145 PMCID: PMC10949600 DOI: 10.1186/s13065-024-01159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.
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Affiliation(s)
- Francis Opoku
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Penny Govender
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Addmore Shonhai
- Department of Biochemistry & Microbiology, University of Venda, Thohoyandou, South Africa
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Oyeneyin OE, Ibrahim A, Ipinloju N, Ademoyegun AJ, Ojo ND. Insight into the corrosion inhibiting potential and anticancer activity of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide via computational approaches. J Biomol Struct Dyn 2023:1-18. [PMID: 37747068 DOI: 10.1080/07391102.2023.2260491] [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: 06/26/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Cancer is a major health concern globally. Orthodox and traditional medicine have actively been explored to manage this disease. Also, corrosion is a natural catastrophe that weakens and deteriorates metallic structures and their alloys causing major structural failures and severe economic implications. Designing and exploring multi-functional materials are beneficial since they are adaptive to different fields including engineering and pharmaceutics. In this study, we examined the anti-corrosion and anti-cancer potentials of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide (MAC) using computational approaches. The molecular reactivity descriptors and charge distribution parameters of MAC were studied in gas and water at density functional theory (DFT) at B3LYP/6-311++G(d,p) theory level. The binding and mechanism of interaction between MAC and iron surface was studied using Monte Carlo (MC) and molecular dynamics (MD) simulation in hydrochloric acid medium. From the DFT, MC, and MD simulations, it was observed that MAC interacted spontaneously with iron surface essentially via van der Waal and electrostatic interactions. The near-parallel alignment of the corrosion inhibitor on iron plane facilitates its adsorption and isolation of the metal surface from the acidic solution. Further, the compound was docked in the binding pocket of anaplastic lymphoma kinase (ALK: 4FNZ) protein to assess its anti-cancer potential. The binding score, pharmacokinetics, and drug-likeness of MAC were compared with the reference drug (Crizotinib). The MAC displayed binding scores of -5.729 kcal/mol while Crizotinib has -3.904 kcal/mol. MD simulation of the complexes revealed that MAC is more stable and exhibits more favourable hydrogen bonding with the ALK receptor's active site than Crizotinib.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- School of Chemistry and Physics, University of Kwazulu-Natal, Durban, South Africa
| | - Abdulwasiu Ibrahim
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto Nigeria
| | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Adeniyi John Ademoyegun
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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Issahaku AR, Mncube SM, Agoni C, Kwofie SK, Alahmdi MI, Abo-Dya NE, Sidhom PA, Tawfeek AM, Ibrahim MAA, Mukelabai N, Soremekun O, Soliman MES. Multi-dimensional structural footprint identification for the design of potential scaffolds targeting METTL3 in cancer treatment from natural compounds. J Mol Model 2023; 29:122. [PMID: 36995499 DOI: 10.1007/s00894-023-05516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
CONTEXT [Formula: see text]-adenosine-methyltransferase (METTL3) is the catalytic domain of the 'writer' proteins which is involved in the post modifications of [Formula: see text]-methyladinosine ([Formula: see text]). Though its activities are essential in many biological processes, it has been implicated in several types of cancer. Thus, drug developers and researchers are relentlessly in search of small molecule inhibitors that can ameliorate the oncogenic activities of METTL3. Currently, STM2457 is a potent, highly selective inhibitor of METTL3 but is yet to be approved. METHODS In this study, we employed structure-based virtual screening through consensus docking by using AutoDock Vina in PyRx interface and Glide virtual screening workflow of Schrodinger Glide. Thermodynamics via MM-PBSA calculations was further used to rank the compounds based on their total free binding energies. All atom molecular dynamics simulations were performed using AMBER 18 package. FF14SB force fields and Antechamber were used to parameterize the protein and compounds respectively. Post analysis of generated trajectories was analyzed with CPPTRAJ and PTRAJ modules incorporated in the AMBER package while Discovery studio and UCSF Chimera were used for visualization, and origin data tool used to plot all graphs. RESULTS Three compounds with total free binding energies higher than STM2457 were selected for extended molecular dynamics simulations. The compounds, SANCDB0370, SANCDB0867, and SANCDB1033, exhibited stability and deeper penetration into the hydrophobic core of the protein. They engaged in relatively stronger intermolecular interactions involving hydrogen bonds with resultant increase in stability, reduced flexibility, and decrease in the surface area of the protein available for solvent interactions suggesting an induced folding of the catalytic domain. Furthermore, in silico pharmacokinetics and physicochemical analysis of the compounds revealed good properties suggesting these compounds could serve as promising MEETL3 entry inhibitors upon modifications and optimizations as presented by natural compounds. Further biochemical testing and experimentations would aid in the discovery of effective inhibitors against the berserk activities of METTL3.
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Cui Y, Tan Z, Liu S, Cao Z, Shao B, Guo M, Jiang N, Zhai X. Fragment-based discovery of novel phenyltriazolyl derivatives as allosteric type-I 1/2 ALK inhibitors with promising antitumor effects. Bioorg Med Chem Lett 2022; 75:128990. [PMID: 36113668 DOI: 10.1016/j.bmcl.2022.128990] [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: 07/21/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Based on the high-throughput screening hit BY-1, a series of phenyltriazolyl derivatives were developed. Satisfyingly, most compounds were detected moderate to excellent antitumor effects against Karpas299 and H2228 cells. Among them, 12k bearing 4‑hydroxypiperidinyl group exhibited the optimal activities against tested cells with IC50 values of 51 nM and 175 nM, as well as promising inhibitory effects on ALKWT (3.7 nM) and ALKL1196M (6.8 nM). Unlike the conventional type-I ALK inhibitors, molecular models identified 12k as an allosteric type-I1/2 inhibitor by forming key interactions in both the ATP binding region and the hydrophobic back pocket of ALK. Intriguingly, 12k could dose-dependently induce apoptosis on H2228 cell and inhibit colony formation and tumor cell migration. Taken together, the rationalization of 12k may shed new light on the identification of novel allosteric type-I1/2 ALK inhibitors.
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Affiliation(s)
- Youbao Cui
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zehui Tan
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuyu Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhi Cao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bin Shao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengrao Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Nan Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Chandak T, Wong CF. EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery. Protein Sci 2021; 30:1087-1097. [PMID: 33733530 DOI: 10.1002/pro.4065] [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: 12/23/2020] [Revised: 03/07/2021] [Accepted: 03/15/2021] [Indexed: 01/08/2023]
Abstract
EDock-ML is a web server that facilitates the use of ensemble docking with machine learning to help decide whether a compound is worthwhile to be considered further in a drug discovery process. Ensemble docking provides an economical way to account for receptor flexibility in molecular docking. Machine learning improves the use of the resulting docking scores to evaluate whether a compound is likely to be useful. EDock-ML takes a bottom-up approach in which machine-learning models are developed one protein at a time to improve predictions for the proteins included in its database. Because the machine-learning models are intended to be used without changing the docking and model parameters with which the models were trained, novice users can use it directly without worrying about what parameters to choose. A user simply submits a compound specified by an ID from the ZINC database (Sterling, T.; Irwin, J. J., J Chem Inf Model 2015, 55[11], 2,324-2,337.) or upload a file prepared by a chemical drawing program and receives an output helping the user decide the likelihood of the compound to be active or inactive for a drug target. EDock-ML can be accessed freely at edock-ml.umsl.edu.
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Affiliation(s)
- Tanay Chandak
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Chung F Wong
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
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Shang J, Zhu Z, Chen Y, Song J, Huang Y, Song K, Zhong J, Xu X, Wei J, Wang C, Cui L, Liu CY, Zhang J. Small-molecule activating SIRT6 elicits therapeutic effects and synergistically promotes anti-tumor activity of vitamin D 3 in colorectal cancer. Theranostics 2020; 10:5845-5864. [PMID: 32483423 PMCID: PMC7255010 DOI: 10.7150/thno.44043] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the leading cause of cancer death; however, targets with broad anti-CRC effects are limited. Sirtuin6 (SIRT6) is a conserved nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase that is widely pathologically downregulated in CRC, but its pharmacological effect in CRC remains undefined due to the lack of small-molecule SIRT6 activators. We searched for a compound activating SIRT6 and investigated its anti-CRC effect in various models. Methods: We identified an allosteric SIRT6 activator, MDL-811. Its ability to enhance SIRT6 deacetylation at protein and cellular levels was evaluated by Fluor de Lys (FDL) and western blots. We assessed the proliferation of 26 CRC cell lines and patient-derived organoids (PDOs) treated with MDL-811. In vivo efficacy of MDL-811 was evaluated in HCT116 cell line- and patient-derived xenografts as well as a spontaneous CRC model. RNA sequencing and real-time quantitative PCR assays were performed to analyze gene expression changes in MDL-811-treated HCT116 cells. Along with controls in SIRT6-overexpressing HCT116 cells, the SIRT6-mediated histone H3 deacetylation at the Cytochrome P450 family 24 subfamily A member 1 (CYP24A1) gene locus was assessed by chromatin immunoprecipitation (ChIP) in MDL-811-treated HCT116 cells. A combination therapy against CRC based on the downstream gene of SIRT6 activation was evaluated in cells and mouse models. Results: MDL-811 significantly activated SIRT6 histone H3 deacetylation (H3K9Ac, H3K18Ac, and H3K56Ac) in vitro and had broad antiproliferative effects on diverse CRC cell lines and PDOs. More importantly, the in vivo anti-tumor efficacy of MDL-811 was demonstrated across cell line- and patient-derived xenografts and in the APCmin/+ spontaneous CRC model. Mechanically, we identified a new downstream target gene of SIRT6 in CRC, CYP24A1. Based on these findings, a combination drug strategy with MDL-811 to synergistically enhance the anti-CRC effect of vitamin D3 was validated in vitro and in vivo. Conclusions: Our data provide proof of concept that targeting SIRT6 using a small-molecule activator is an attractive therapeutic strategy for CRC and that MDL-811 could be a promising lead compound for further preclinical and clinical studies of treatments for CRC.
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Li S, Zhao H, Li J, Hao J, Yu H. A series of molecular modeling techniques to reveal selective mechanisms of inhibitors to β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) and β-site amyloid precursor protein cleaving enzyme 2 (BACE2). J Biomol Struct Dyn 2020; 39:2824-2837. [PMID: 32276567 DOI: 10.1080/07391102.2020.1754917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inhibition of β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) has been shown to be an effective treatment for Alzheimer's disease. A wealth of research has focused on finding highly selective small-molecule inhibitors targeting the BACE1 over its close homologue BACE2 to avoid potential side effects. However, given the highly structural similarities of BACE1 and BACE2, designing highly selective BACE1 inhibitors remains a huge challenge. Recently, it has been reported that a potential BACE1 inhibitor named C28 (∼52-fold selectivity) exhibited greater selectivity to BACE1 over BACE2 than the previously reported inhibitors AZD3293 and AZD3839 (∼1.5-fold and 14-fold selectivity). However, few computational studies have been performed to reveal its underlying mechanisms. In this study, a series of molecular modeling techniques were performed to reveal the selective mechanisms. Classical molecular dynamics (cMD) simulations indicated that the major variations appeared to be controlled by overall protein dynamics. Free energy calculations further suggested that the binding affinities of AZD3293 to BACE1 and BACE2 are similar, but the binding affinity of AZD3839 and C28 to BACE1 is much higher than to BACE2, and that the major variations are electrostatic interactions. The protein dynamics and energy differences were further observed in accelerated molecular dynamics (aMD) simulations. In addition, the umbrella sampling simulations revealed the inhibitors' different patterns of dissociation from the binding pockets of BACE1 and BACE2, and that different energy barriers were responsible for the selectivity. The physical principles revealed by this study may facilitate the rational design of more potent BACE1 selective inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shipeng Li
- Department of Neurosurgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Hexiang Zhao
- Department of Neurosurgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Jinghui Li
- Department of Neurosurgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Jiajia Hao
- Kunming Medical University Haiyuan College, Kunming, Yunnan Province, China
| | - Hualin Yu
- Department of Neurosurgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
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Mou L, Ma Z, Meng X, Li W, Liang S, Chen X. Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02514-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Li J, Wu G, Fu Q, Ge H, Liu S, Li X, Cheng B. Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations. Comput Biol Chem 2019; 83:107098. [DOI: 10.1016/j.compbiolchem.2019.107098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 12/29/2022]
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Ji M, Ding Y, Li X, Mao N, Chen J. Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex. Comput Biol Chem 2019; 83:107159. [PMID: 31743832 DOI: 10.1016/j.compbiolchem.2019.107159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 12/18/2022]
Abstract
The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 to form a ternary SnoN-SMAD3-SMAD4 complex in the TGFβ signaling pathway. However, how the interaction of SnoN with the SMAD3 and SMAD4 remains unclear. Here, molecular dynamics (MD) simulations and molecular modeling methods were performed to figure out this issue. The simulations reveal that SnoNopen exists in two, open and semi-closed, conformations. Molecular modeling and MD simulation studies suggest that the SnoNclosed form interferes with the SMAD3-SMAD4 protein; in contract, the SnoNopen can form a stable SnoN-SMAD3-SMAD4 complex. These mechanistic mechanisms may help elucidate the detailed engagement of SnoN with two SMAD3 and SMAD4 transcriptional factors in the regulation of TGFβ signaling pathway.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Yelei Ding
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Jie Chen
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China.
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Liu S, Jiang Y, Yan R, Li Z, Wan S, Zhang T, Wu X, Hou J, Zhu Z, Tian Y, Zhang J. Design, synthesis and biological evaluations of 2-amino-4-(1-piperidine) pyridine derivatives as novel anti crizotinib-resistant ALK/ROS1 dual inhibitors. Eur J Med Chem 2019; 179:358-375. [PMID: 31260890 DOI: 10.1016/j.ejmech.2019.06.043] [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] [Received: 04/09/2019] [Revised: 05/29/2019] [Accepted: 06/15/2019] [Indexed: 12/11/2022]
Abstract
ALK and ROS1 kinases have become promising therapeutic targets since Crizotinib was used to treat non-small-cell lung cancer clinically. Aiming to explore new potent inhibitors, a series of 2-amino-4-(1-piperidine) pyridine derivatives that stabilized a novel DFG-shifted conformation in the kinase domain of ALK were designed and synthesized on the base of lead compound A. Biological evaluation highlighted that most of these new compounds could also potently inhibit ROS1 kinase, leading to the promising inhibitors against both ROS1 and ALK. Among them, the representative compound 2e stood out potent anti-proliferative activity against ALK-addicted H3122 and ROS1-addicted HCC78 cell lines (IC50 = 6.27 μM and 10.71 μM, respectively), which were comparable to that of Crizotinib. Moreover, 2e showed impressive enzyme activity against clinically Crizotinib-resistant ALKL1196M with an IC50 value of 41.3 nM, which was about 2-fold more potent than that of Crizotinib. 2e also showed potent inhibitory activity in about 6-fold superior to Crizotinib (IC50: 104.7 nM vs. 643.5 nM) in Ba/F3 cell line harboring ROS1G2032R. Furthermore, molecular modeling disclosed that all the representative inhibitors could dock into the active site of ALK and ROS1, which gave a probable explanation of anti Crizotinib-resistant mutants. These results indicated that our work has established a path forward for the generation of anti Crizotinib-resistant ALK/ROS1 dual inhibitors.
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Affiliation(s)
- Siming Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ying Jiang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ruohong Yan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaoyun Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ju Hou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhengguang Zhu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
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Yu E, Xu Y, Shi Y, Yu Q, Liu J, Xu L. Discovery of novel natural compound inhibitors targeting estrogen receptor α by an integrated virtual screening strategy. J Mol Model 2019; 25:278. [PMID: 31463793 DOI: 10.1007/s00894-019-4156-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
Abstract
Estrogen receptor (ER) is a nuclear hormone receptor and plays an important role in mediating the cellular effects of estrogen. ER can be classified into two receptors: estrogen receptor alpha (ERα) and beta (ERβ), and the former is expressed in 50~80% of breast tumors and has been extensively investigated in breast cancer for decades. Excessive exposure to estrogen can obviously stimulate the growth of breast cancers primarily mediated by ERα, and thus anti-estrogen therapies by small molecules are of concern to clinicians and pharmaceutical industry in the treatment of ERα-positive breast cancers. Although a series of estrogen receptor modulators have been developed, these drugs can lead to resistance and side effects. Therefore, the development of small molecule inhibitors with high target specificity has been intensified. In this pursuit, an integrated computer-aided virtual screening technique, including molecular docking and pharmacophore model screening, was used to screen traditional Chinese medicine (TCM) databases. The compounds with high docking scores and fit values were subjected to ADME (adsorption, distribution, metabolism, excretion) and toxicity prediction, and ten hits were identified as potential inhibitors targeting ERα. Molecular docking was used to investigate the binding modes between ERα and three most potent hits, and molecular dynamic simulations were chosen to explore the stability of these complexes. The rank of the predicted binding free energies evaluated by MM/GBSA is consistent with the docking score. These novel scaffolds discovered in the present study can be used as critical starting point in the drug discovery process for treating ERα-positive breast cancer. Graphical abstract .
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Affiliation(s)
- Enguang Yu
- Department of Chinese Surgery, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Yueping Xu
- Department of Nursing, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Yanbo Shi
- Central Laboratory of Molecular Medicine Research Center, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Qiuyan Yu
- Department of Breast Surgery, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Jie Liu
- Department of Traditional Chinese Medicine Oncology, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, Jiangsu, China.
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14
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Kong X, Pan P, Sun H, Xia H, Wang X, Li Y, Hou T. Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK). J Med Chem 2019; 62:10927-10954. [PMID: 31419130 DOI: 10.1021/acs.jmedchem.9b00446] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaotian Kong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China.,Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Peichen Pan
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital , Zhejiang University , Hangzhou 310058 , China
| | - Xuwen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
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15
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Mou L, Dou W, Meng G, Sun K, Chen X. The structural basis of the autoinhibition mechanism of glycogen synthase kinase 3β (GSK3β): molecular modeling and molecular dynamics simulation studies. J Biomol Struct Dyn 2019; 38:1741-1750. [PMID: 31057052 DOI: 10.1080/07391102.2019.1615988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The autoinhibition phenomenon has been frequently observed in enzymes and represents an important regulatory strategy to fine-tune enzyme activity. Evolution has exploited this mechanism to reduce enzymatic activity. Glycogen synthase kinase 3β (GSK3β) undergoes autoinhibition via the phosphorylation of Ser9 at the N-terminus of the kinase, which, acting as a pseudosubstrate, occupies the catalytic domain of GSK3β and subsequently blocks primed substrates from having access to the catalytic domain. The detailed structural basis of the autoinhibition mechanism of GSK3β by the pseudosubstrate, however, has not yet been fully resolved. Here, a three-dimensional model of the binary GSK3β-pseudosubstrate complex was built via the molecular modeling method. Based on the constructed model, extensive molecular dynamics (MD) simulations and subsequent molecular mechanics generalized Born/surface area (MM_GBSA) calculations were performed on the wild-type GSK3β-pseudosubstrate complex and three mutated systems (R4A, R6A, and S9A). Analyses of MD simulations and binding free energies revealed that the phosphorylation of Ser9 is the prerequisite for the autoinhibition of GSK3β, and both mutations of Arg4 and Arg6 to alanine markedly reduced the binding affinities of the mutated pseudosubstrate to the GSK3β catalytic domain, thereby disrupting the autoinhibition of the kinase. This study highlights the importance of Ser9, Arg6, and Arg4 in modulating the autoinhibition mechanism of GSK3β, contributing to a deeper understanding of GSK3β biology.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medicinal University, Weifang, Shandong, China
| | - Wenwen Dou
- Department of Infectious Diseases, Affiliated Hospital of Weifang Medicinal University, Weifang, Shandong, China
| | - Gang Meng
- Department of Urology, Affiliated Hospital of Weifang Medicinal University, Weifang, Shandong, China
| | - Ke Sun
- Department of Urology, Affiliated Hospital of Weifang Medicinal University, Weifang, Shandong, China
| | - Xiangyu Chen
- Department of Laboratory Medicine, Weifang Medicinal University, Weifang, Shandong, China
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16
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Niu Y, Yao X, Ji H. Importance of protein flexibility in ranking ERK2 Type I 1/2 inhibitor affinities: a computational study. RSC Adv 2019; 9:12441-12454. [PMID: 35515820 PMCID: PMC9063686 DOI: 10.1039/c9ra01657k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular-regulated kinase (ERK2) has been regarded as an essential target for various cancers, especially melanoma. Recently, pyrrolidine piperidine derivatives were reported as Type I1/2 inhibitors of ERK2, which occupy both the ATP binding pocket and the allosteric pocket. Due to the dynamic behavior of ERK2 upon the binding of Type I1/2 inhibitors, it is difficult to predict the binding structures and relative binding potencies of these inhibitors with ERK2 accurately. In this work, the binding mechanism of pyrrolidine piperidines was discussed by using different simulation techniques, including molecular docking, ensemble docking based on multiple receptor conformation, molecular dynamics simulations and free energy calculations. Our computational results show that the traditional docking method cannot predict the relative binding ability of the studied inhibitors with high accuracy, but incorporating ERK2 protein flexibility into docking is an effective method to improve the prediction accuracy. It is worth noting that the binding free energies predicted by MM/GBSA or MM/PBSA based on the MD simulations for the docked poses have the highest correlation with the experimental data, which highlights the importance of protein flexibility for accurately predicting the binding ability of Type I1/2 inhibitors of ERK2. In addition, the comprehensive analysis of several representative inhibitors indicates that hydrogen bonds and hydrophobic interactions are of significance for improving the binding affinities of the inhibitors. We hope this work will provide valuable information for further design of novel and efficient Type I1/2 ERK2 inhibitors.
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Affiliation(s)
- Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, College of Life Sciences, Shandong University of Technology Zibo 255049 China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University Lanzhou 730000 China
| | - Hongfang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, College of Life Sciences, Shandong University of Technology Zibo 255049 China
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17
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Shen C, Liu H, Wang X, Lei T, Wang E, Xu L, Yu H, Li D, Yao X. Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I 1/2 NIK Inhibitors. Front Pharmacol 2019; 10:345. [PMID: 31024312 PMCID: PMC6465739 DOI: 10.3389/fphar.2019.00345] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
NF-κB inducing kinase (NIK), which is considered as the central component of the non-canonical NF-κB pathway, has been proved to be an important target for the regulation of the immune system. In the past few years, NIK inhibitors with various scaffolds have been successively reported, among which type I1/2 inhibitors that can not only bind in the ATP-binding pocket at the DFG-in state but also extend into an additional back pocket, make up the largest proportion of the NIK inhibitors, and are worthy of more attention. In this study, an integration protocol that combines molecule docking, MD simulations, ensemble docking, MM/GB(PB)SA binding free energy calculations, and decomposition was employed to understand the binding mechanism of 21 tricyclic type I1/2 NIK inhibitors. It is found that the docking accuracy is largely dependent on the selection of docking protocols as well as the crystal structures. The predictions given by the ensemble docking based on multiple receptor conformations (MRCs) and the MM/GB(PB)SA calculations based on MD simulations showed higher linear correlations with the experimental data than those given by conventional rigid receptor docking (RRD) methods (Glide, GOLD, and Autodock Vina), highlighting the importance of incorporating protein flexibility in predicting protein–ligand interactions. Further analysis based on MM/GBSA demonstrates that the hydrophobic interactions play the most essential role in the ligand binding to NIK, and the polar interactions also make an important contribution to the NIK-ligand recognition. A deeper comparison of several pairs of representative derivatives reveals that the hydrophobic interactions are vitally important in the structural optimization of analogs as well. Besides, the H-bond interactions with some key residues and the large desolvation effect in the back pocket devote to the affinity distinction. It is expected that our study could provide valuable insights into the design of novel and potent type I1/2 NIK inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Huidong Yu
- Rongene Pharma Co., Ltd., Shenzhen, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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18
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Hu S, Dong Y, Zhao X, Zhang L. Insights into the structure-affinity relationships and solvation effects between OfHex1 and inhibitors using molecular dynamics simulations. J Mol Graph Model 2019; 90:1-8. [PMID: 30939332 DOI: 10.1016/j.jmgm.2019.03.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 11/19/2022]
Abstract
OfHex1 is a potential target for the rational design of pesticides. TMG-chitotriomycin is one of the most highly specific known inhibitors of chitinolytic β-GlcNAcases from bacteria, fungi and insects. TMG-chitotriomycin and its analogues show different activities to OfHex1, dependent on the number of GlcNAc units. Subsequently, it is essential to explore how these GlcNAc unit number changes cause alterations in activity. In this study, we examined the free energy patterns and per residue decomposition of binding within the complexes of OfHex1 and a series of inhibitors, utilizing restricted molecular dynamics (MD) and water-mediated MM/GBSA calculations. The results indicated Glu328 could form a stronger polar interaction with OfHex1 inhibitors, while Trp448 and Trp490 had important non-polar contributions. Interestingly, the conformation of Trp448 was different in the open or closed state, when OfHex1 bound different inhibitors. Moreover, the water molecule that mediates the GlcNAc Ⅱ and Trp490 may be critical to stabilizing the hydrophobic interaction. Further study showed that isomerization of TMG-chitotriomycin analogs did not decrease binding affinity, however, there was a highly positive correlation between the calculated binding affinities and the experimental activity data (r2 = 0.92) when water molecules were explicitly taken into account. Moreover, the water molecules that mediated GlcNAc II and Trp490 might be critical to the stabilization of the hydrophobic interaction and cause the activity difference between TMG-(GlcNAc)2 and TMG-(GlcNAc).
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Affiliation(s)
- Song Hu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Yawen Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Xiao Zhao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Li Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China.
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19
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Wang Y, Peng C, Wang G, Xu Z, Luo Y, Wang J, Zhu W. Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation. Chem Biol Drug Des 2019; 93:934-948. [DOI: 10.1111/cbdd.13493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/31/2018] [Accepted: 01/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Yu Wang
- Hunan Province Key Laboratory of Materials Surface & Interface Science and TechnologyCollege of ScienceCentral South University of Forestry and Technology Changsha Hunan China
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Cheng Peng
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Guimin Wang
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Yongfeng Luo
- Hunan Province Key Laboratory of Materials Surface & Interface Science and TechnologyCollege of ScienceCentral South University of Forestry and Technology Changsha Hunan China
| | - Jinan Wang
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
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20
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He MY, Li WK, Meiler J, Zheng QC, Zhang HX. Insight on mutation-induced resistance to anaplastic lymphoma kinase inhibitor ceritinib from molecular dynamics simulations. Biopolymers 2019; 110:e23257. [PMID: 30664251 DOI: 10.1002/bip.23257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 11/09/2022]
Abstract
Ceritinib, an advanced anaplastic lymphoma kinase (ALK) next-generation inhibitor, has been proved excellent antitumor activity in the treatment of ALK-associated cancers. However, the accumulation of acquired resistance mutations compromise the therapeutic efficacy of ceritinib. Despite abundant mutagenesis data, the structural determinants for reduced ceritinib binding in mutants remains elusive. Focusing on the G1123S and F1174C mutations, we applied molecular dynamics (MD) simulations to study possible reasons for drug resistance caused by these mutations. The MD simulations predict that the studied mutations allosterically impact the configurations of the ATP-binding pocket. An important hydrophobic cluster is identified that connects P-loop and the αC-helix, which has effects on stabilizing the conformation of ATP-binding pocket. It is suggested, in this study, that the G1123S and F1174C mutations can induce the conformational change of P-loop thereby causing the reduced ceritinib affinity and causing drug resistance.
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Affiliation(s)
- Mu-Yang He
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
| | - Wei-Kang Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
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21
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Chen H, Fu W, Wang Z, Wang X, Lei T, Zhu F, Li D, Chang S, Xu L, Hou T. Reliability of Docking-Based Virtual Screening for GPCR Ligands with Homology Modeled Structures: A Case Study of the Angiotensin II Type I Receptor. ACS Chem Neurosci 2019; 10:677-689. [PMID: 30265513 DOI: 10.1021/acschemneuro.8b00489] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The number of solved G-protein-coupled receptor (GPCR) crystal structures has expanded rapidly, but most GPCR structures remain unsolved. Therefore, computational techniques, such as homology modeling, have been widely used to produce the theoretical structures of various GPCRs for structure-based drug design (SBDD). Due to the low sequence similarity shared by the transmembrane domains of GPCRs, accurate prediction of GPCR structures by homology modeling is quite challenging. In this study, angiotensin II type I receptor (AT1R) was taken as a typical case to assess the reliability of class A GPCR homology models for SBDD. Four homology models of angiotensin II type I receptor (AT1R) at the inactive state were built based on the crystal structures of CXCR4 chemokine receptor, CCR5 chemokine receptor, and δ-opioid receptor, and refined through molecular dynamics (MD) simulations and induced-fit docking, to allow for backbone and side-chain flexibility. Then, the quality of the homology models was assessed relative to the crystal structures in terms of two criteria commonly used in SBDD: prediction accuracy of ligand-binding poses and screening power of docking-based virtual screening. It was found that the crystal structures outperformed the homology models prior to any refinement in both assessments. MD simulations could generally improve the docking results for both the crystal structures and homology models. Moreover, the optimized homology model refined by MD simulations and induced-fit docking even shows a similar performance of the docking assessment to the crystal structures. Our results indicate that it is possible to establish a reliable class A GPCR homology model for SBDD through the refinement by integrating multiple molecular modeling techniques.
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Affiliation(s)
| | | | | | | | | | | | | | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, P. R. China
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22
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Shen C, Wang Z, Yao X, Li Y, Lei T, Wang E, Xu L, Zhu F, Li D, Hou T. Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Brief Bioinform 2018; 21:282-297. [PMID: 30379986 DOI: 10.1093/bib/bby103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/08/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022] Open
Abstract
Protein kinases have been regarded as important therapeutic targets for many diseases. Currently, a total of 41 kinase inhibitors have been approved by the Food and Drug Administration, along with a large number of kinase inhibitors being evaluated in clinical and preclinical trials. Among all, allosteric inhibitors, such as type II kinase inhibitors, have attracted extensive attention owing to their potential high selectivity. Nowadays, molecular docking has become a powerful tool to search for novel kinase inhibitors. However, as for type II kinase inhibitors, their allosteric characteristics may exert a deep influence on docking accuracy. In this study, a comprehensive assessment was conducted to evaluate the effectiveness of nine docking algorithms towards type II kinase inhibitors. The calculation results showed that most tested docking programs, especially Glide with XP scoring, LeDock and Surflex-Dock, succeeded in the accurate identification of near-native binding poses, with the success rates ranging from 0.80 to 0.90, and the scoring functions in GOLD and LeDock outperformed the others in the prediction of relative binding affinities. In terms of the P-values, areas under the curve and enrichment factors, Glide with XP scoring, Surflex-Dock, GOLD with Astex Statistical Potential scoring and LeDock had better screening power to discriminate between active compounds and decoys. However, the screening power is sensitive to different initial conformations of the same target. It is expected that our study can provide some guidance for docking-based virtual screening to discover novel type II kinase inhibitors, as well as other allosteric inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health,Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau (SAR), P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu, P. R. China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, P. R. China
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23
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Niu Y, Zhang Y, Yao X. Resistance mechanism of the oncogenic β3-αC deletion mutation in BRAF kinase to dabrafenib and vemurafenib revealed by molecular dynamics simulations and binding free energy calculations. Chem Biol Drug Des 2018; 93:177-187. [PMID: 30225883 DOI: 10.1111/cbdd.13399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/10/2018] [Accepted: 09/02/2018] [Indexed: 12/15/2022]
Abstract
BRAF kinase is an essential target for anti-cancer drug development. Emergence of the β3-αC loop deletion mutation (ΔNVTAP) in BRAF kinase frequently occurred in human cancers seriously compromises the therapeutic efficacy of some BRAF kinase inhibitors, such as dabrafenib and vemurafenib. However, the mechanism of this resistance is still not well understood. In this study, the influence of the β3-αC deletion mutation on the binding profiles of three BRAF kinase inhibitors (AZ628, dabrafenib, and vemurafenib) with BRAFV600E or BRAFΔNVTAP was explored by conventional molecular dynamics (MD) simulations and binding free energy calculations. The simulation results indicated that the β3-αC deletion mutation enhances the flexibility of the αC helix and alters their conformations, which amplify the conformational entropy change (-TΔS) and weaken the interactions between the inhibitors and BRAF. The further per-residue binding free energy decomposition analysis revealed that the ΔNVTAP mutation changed the contributions of a few key residues to the bindings of dabrafenib or vemurafenib, such as L57, L66, W83, C84, F135, G145, and F147, but did not have obvious impact on the contributions of these residues to AZ628. Our results provide valuable clues to understand the mechanisms of drug resistance conferred by the β3-αC deletion mutation.
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Affiliation(s)
- Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Yan Zhang
- Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Xiaojun Yao
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, China
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24
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Tu J, Song LT, Liu RR, Zhai HL, Wang J, Zhang XY. Molecular inhibitory mechanism study on the potent inhibitor brigatinib against four crizotinib‐resistant ALK mutations. J Cell Biochem 2018; 120:562-574. [DOI: 10.1002/jcb.27412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/10/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Jing Tu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Rui Rui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Juan Wang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Xiao Yun Zhang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
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25
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Huang X, Xu P, Cao Y, Liu L, Song G, Xu L. Exploring the binding mechanisms of PDE5 with chromeno[2,3- c]pyrrol-9(2 H)-one by theoretical approaches. RSC Adv 2018; 8:30481-30490. [PMID: 35546827 PMCID: PMC9085377 DOI: 10.1039/c8ra06405a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/17/2018] [Indexed: 01/10/2023] Open
Abstract
Cyclic nucleotide phosphodiesterase type 5 (PDE5), exclusively specific for the cyclic guanosine monophosphate (cGMP), is an important drug target for the treatment of erectile dysfunction and pulmonary arterial hypertension (PAH). Although many PDE5 inhibitors have been approved, such as sildenafil, vardenafil, tadalafil and so on, extensive studies have reported some side effects, such as vision disturbance and hearing loss as a result of the amino acid sequence and the secondary structural similarity of other PDEs to the catalytic domain of PDE5. In this study, multiple docking strategies, molecular dynamics (MD) simulations, free energy calculations and decomposition were employed to explore the structural determinants of PDE5 with a series of chromeno[2,3-c]pyrrol-9(2H)-one derivatives. First, reliable docking results were obtained using quantum mechanics/molecular mechanics (QM/MM) docking. Then, MD simulations and MM/GBSA free energy calculations were used to explore the dynamic binding process and characterize the binding modes of the inhibitors with different activities. The predicted binding free energies are in good agreement with the experimental data, and the MM/GBSA free energy decomposition analysis sheds light on the importance of hydrogen bonds with Gln817, π-π stacks against Phe820 and hydrophobic residues for the PDE5 binding of the studied inhibitors. The structural and energetic insights obtained here are useful for understanding the molecular mechanism of ligand binding and designing novel potent and selective PDE5 inhibitors with new scaffolds.
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Affiliation(s)
- Xianfeng Huang
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University Changzhou Jiangsu 213164 PR China +86-519-86334598 +86-519-86330600
| | - Peng Xu
- Department of Orthopedics, Second Military Medical University Affiliated Changzheng Hospital Shanghai 200003 China
| | - Yijing Cao
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University Changzhou Jiangsu 213164 PR China +86-519-86334598 +86-519-86330600
| | - Li Liu
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University Changzhou Jiangsu 213164 PR China +86-519-86334598 +86-519-86330600
| | - Guoqiang Song
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University Changzhou Jiangsu 213164 PR China +86-519-86334598 +86-519-86330600
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou 213001 China +86-519-86953223 +86-519-86953220
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26
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He MY, Li WK, Zheng QC, Zhang HX. Conformational Transition of Key Structural Features Involved in Activation of ALK Induced by Two Neuroblastoma Mutations and ATP Binding: Insight from Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2018; 9:1783-1792. [PMID: 29638111 DOI: 10.1021/acschemneuro.8b00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Deregulated kinase activity of anaplastic lymphoma kinase (ALK) has been observed to be implicated in the development of tumor progression. The activation mechanism of ALK is proposed to be similar to other receptor tyrosine kinases (RTKs), but the distinct static X-ray crystal conformation of ALK suggests its unique conformational transition. Herein, we have illustrated the dynamic conformational property of wild-type ALK as well as the kinase activation equilibrium variation induced by two neuroblastoma mutations (R1275Q and Y1278S) and ATP binding by performing enhanced sampling accelerated Molecular Dynamics (aMD) simulations. The results suggest that the wild-type ALK is mostly favored in the inactive state, whereas the mutations and ATP binding promote a clear shift toward the active-like conformation. The R1275Q mutant stabilizes the active conformation by rigidifying the αC-in conformation. The Y1278S mutant promotes activation at the expense of a π-stacking hydrophobic cluster, which plays a critical role in the stabilization of the inactive conformation of native ALK. ATP produces a more compact active site and thereby facilitates the activation of ALK. Taken together, these findings not only elucidate the diverse conformations in different ALKs but can also shed light on new strategies for protein engineering and structural-based drug design for ALK.
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Affiliation(s)
- Mu-Yang He
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Wei-Kang Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, People’s Republic of China
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
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27
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Discovery of potent and novel smoothened antagonists via structure-based virtual screening and biological assays. Eur J Med Chem 2018; 155:34-48. [DOI: 10.1016/j.ejmech.2018.05.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/19/2018] [Accepted: 05/22/2018] [Indexed: 12/29/2022]
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Insights into Resistance Mechanisms of Inhibitors to Mps1 C604Y Mutation via a Comprehensive Molecular Modeling Study. Molecules 2018; 23:molecules23061488. [PMID: 29925769 PMCID: PMC6100145 DOI: 10.3390/molecules23061488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 11/17/2022] Open
Abstract
Mono-polar spindle 1 (Mps1/TTK) represents a protein kinase reported to be vital for cell division processes and is generally regarded as an attractive target for the treatment of hepatocellular carcinoma, breast carcinoma, and colon cancer. However, the C604Y mutation has been linked to acquired resistance. Recently, three potential small-molecule inhibitors of Mps1 (i.e., reversine, NMS-P715, and its derivative Cpd-5) were reported for the C604Y mutation that exhibit significant resistance to NMS-P715 and Cpd-5, but retain affinity for reversine. In this study, classical molecular dynamic (MD) simulations, accelerated MD (aMD) simulations, and umbrella sampling (US) simulations were performed to illustrate the resistance mechanisms of inhibitors to Mps1. The classical MD simulations combined with free energy calculations revealed that reversine features similar binding affinity characteristics to both Mps1WT and Mps1C604Y, but both NMS-P715 and Cpd-5 feature much higher binding affinities to Mps1WT than to Mps1C604Y. The major variations were shown to be controlled by electrostatic energy and the conformational change of A-loop-induced entropy increased. The large conformational changes of Mps1C604Y bound to NMS-P715 and Cpd-5 were also observed in aMD simulations. The US simulation results further suggest that reversine and Cpd-5 both exhibit similar dissociation processes from both Mps1WT and Mps1C604Y, but Cpd-5 and NMS-P715 were found to dissociate more easily from Mps1C604Y than from Mps1WT, thus a reduced residence time was responsible for the inhibitors resistance to the C604Y mutation. The physical principles provided by the present study may provide important clues for the discovery and rational design of novel inhibitors to combat the C604Y mutation of Mps1.
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Xu L, Li D, Ding J, Pan L, Ding X. Insight into tetrodotoxin blockade and resistance mechanisms of Na v 1.2 sodium channel by theoretical approaches. Chem Biol Drug Des 2018; 92:1445-1457. [PMID: 29673065 DOI: 10.1111/cbdd.13310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/08/2018] [Accepted: 03/17/2018] [Indexed: 11/30/2022]
Abstract
Nav 1.2, a member of voltage-gated sodium channels (Nav s) that are responsible for the generation and propagation of action potentials along the cell membrane, and play a vital role in the process of information transmission within the nervous system and muscle contraction, is preferentially expressed in the central nervous system. As a potent and selective blocker of Nav s, tetrodotoxin (TTX) has been extensively studied in biological and chemical sciences, whereas the detailed mechanism by which it blocks nine Nav 1 channel subtypes remain elusive. Despite the high structural similarity, the TTX metabolite 4,9-anhydro-TTX is 161 times less effective toward the mammalian Nav 1.2, which puzzled us to ask a question why such a subtle structural variation results in the largely binding affinity difference. In the current work, an integrated computational strategy, including homology modeling, induced fit docking, explicit-solvent MD simulations, and free energy calculations, was employed to investigate the binding mechanism and conformational determinants of TTX analogs. Based on the computational results, the H-bond interactions between C4-OH and C9-OH of TTX and the outer ring carboxylates of the selectivity-filter residues, and the cation-π interaction between the primary amine of guanidinium of TTX and Phe385 determine the difference of their binding affinities. Moreover, the computationally simulations were carried out for the D384N and E945K mutants of hNav 1.2-TTX, and the rank of the predicted binding free energies is in accordance with the experimental data. These observations provide a valuable model to design potent and selective neurotoxins of Nav 1.2 and shed light on the blocking mechanism of TTX to sodium channels.
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Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Dayu Li
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Junjie Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Li Pan
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Xiaoqin Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
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30
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Tang X, Wang Z, Lei T, Zhou W, Chang S, Li D. Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2. Phys Chem Chem Phys 2018; 20:5591-5605. [PMID: 29270587 DOI: 10.1039/c7cp07588j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
NIMA-related kinase 2 (Nek2) plays a significant role in cell cycle regulation, and overexpression of Nek2 has been observed in several types of carcinoma, suggesting it is a potential target for cancer therapy. In this study, we attempted to gain more insight into the binding mechanisms of a series of aminopyrazine inhibitors of Nek2 through multiple molecular modeling techniques, including molecular docking, molecular dynamics (MD) simulations and free energy calculations. The simulation results showed that the induced fit docking and ensemble docking based on multiple protein structures yield better predictions than conventional rigid receptor docking, highlighting the importance of incorporating receptor flexibility into the accurate predictions of the binding poses and binding affinities of Nek2 inhibitors. Additionally, we observed that the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations did not show better performance than the docking scoring to rank the binding affinities of the studied inhibitors, suggesting that MM/GBSA is system-dependent and may not be the best choice for the Nek2 systems. Moreover, the detailed information on protein-ligand binding was characterized by the MM/GBSA free energy decomposition, and a number of derivatives with improved docking scores were designed. It is expected that our study can provide valuable information for the future rational design of novel and potent inhibitors of Nek2.
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Affiliation(s)
- Xinyi Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China.
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31
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Behmard E, Najafi A, Ahmadi A. Understanding the resistance mechanism of penicillin binding protein 1a mutant against cefotaxime using molecular dynamic simulation. J Biomol Struct Dyn 2018; 37:741-749. [PMID: 29429394 DOI: 10.1080/07391102.2018.1439404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antibiotic resistance is a threatening challenge for global health, as the expansion of resistance to current antibiotics has made serious therapeutic problems. Genome mutations are key evolutionary mechanisms conferring antibiotic resistance in bacterial pathogens. For example, penicillin and cephalosporins resistance is mostly mediated by mutations in penicillin binding proteins to change the affinity of the drug. Accordingly, threonine point mutations were reported to develop antibiotic resistance in various bacterial infections including pneumococcal infections. In this study, conventional molecular dynamics simulations, umbrella sampling simulations and MM/GBSA free energy calculations were applied to figure out how the Threonine to Alanine mutation (T to A) at STMK motif affects the binding of cefotaxime to Penicillin Binding Protein 1a and to reveal the resistance mechanism induced by the T to A mutation. The results obtained from the computational methods demonstrate that the T to A mutation increases the flexibility of the binding pocket and changes its conformation, which leads to increased conformational entropy change (-TΔS) and attenuates the bonds between the ligand and the receptor. In brief, our findings indicate that both of the alterations of the conformational enthalpy and entropy contribute to the T to A-induced resistance in the binding of cefotaxime into penicillin binding protein 1a.
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Affiliation(s)
- Esmaeil Behmard
- a Molecular Biology Research Center, Systems Biology and Poisonings Institute , Baqiyatallah University of Medical Sciences , Tehran , Iran
| | - Ali Najafi
- a Molecular Biology Research Center, Systems Biology and Poisonings Institute , Baqiyatallah University of Medical Sciences , Tehran , Iran
| | - Ali Ahmadi
- a Molecular Biology Research Center, Systems Biology and Poisonings Institute , Baqiyatallah University of Medical Sciences , Tehran , Iran
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32
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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33
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Pan P, Yu H, Liu Q, Kong X, Chen H, Chen J, Liu Q, Li D, Kang Y, Sun H, Zhou W, Tian S, Cui S, Zhu F, Li Y, Huang Y, Hou T. Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I 1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation. ACS CENTRAL SCIENCE 2017; 3:1208-1220. [PMID: 29202023 PMCID: PMC5704298 DOI: 10.1021/acscentsci.7b00419] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Indexed: 05/07/2023]
Abstract
Targeted inhibition of anaplastic lymphoma kinase (ALK) dramatically improved therapeutic outcomes in the treatment of ALK-positive cancers, but unfortunately patients invariably progressed due to acquired resistance mutations in ALK. Currently available drugs are all type-I inhibitors bound to the ATP-binding pocket and are most likely to be resistant in patients harboring genetic mutations surrounding the ATP pocket. To overcome drug resistance, we rationally designed a novel kind of "bridge" inhibitor, which specially bind into an extended hydrophobic back pocket adjacent to the ATP-binding site of ALK. The novel type-I1/2 inhibitors display excellent antiproliferation activity against ALK-positive cancer cells and appear superior to two clinically used drugs, crizotinib and ceritinib. Structural and molecular modeling analyses indicate that the inhibitor induces dramatic conformational transition and stabilizes unique DFG-shifted loop conformation, enabling persistent sensitivity to different genetic mutations in ALK. These data highlight a rationale for further development of next-generation ALK inhibitors to combat drug resistance.
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Affiliation(s)
- Peichen Pan
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huidong Yu
- Rongene
Pharma Co., Ltd., Shenzhen, Guandong 518054, China
| | - Qinglan Liu
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
- Innovative
Drug R & D Center, Shenzhen Salubris
Pharmaceuticals Co., Ltd., Huabao Industrial Zone, Shenzhen 518102, China
| | - Xiaotian Kong
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hu Chen
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Jiean Chen
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Qi Liu
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Dan Li
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenfang Zhou
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng Tian
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sunliang Cui
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youyong Li
- Institute of Functional Nano and
Soft Materials (FUNSOM) and Jiangsu Key Laboratory
of Translational Research and Therapy for Neuropsychiatric Diseases
and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yong Huang
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology,
Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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35
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How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study. Sci Rep 2017; 7:9088. [PMID: 28831147 PMCID: PMC5567357 DOI: 10.1038/s41598-017-09586-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/26/2017] [Indexed: 01/17/2023] Open
Abstract
Janus kinase 2 (JAK2) has been regarded as an essential target for the treatment of myeloproliferative neoplasms (MPNs). BBT594 and CHZ868, Type-II inhibitors of JAK2, illustrate satisfactory efficacy in preclinical MPNs and acute lymphoblastic leukemia (ALL) models. However, the L884P mutation of JAK2 abrogates the suppressive effects of BBT594 and CHZ868. In this study, conventional molecular dynamics (MD) simulations, umbrella sampling (US) simulations and MM/GBSA free energy calculations were employed to explore how the L884P mutation affects the binding of BBT594 and CHZ868 to JAK2 and uncover the resistance mechanism induced by the L884P mutation. The results provided by the US and MD simulations illustrate that the L884P mutation enhances the flexibility of the allosteric pocket and alters their conformations, which amplify the conformational entropy change (−TΔS) and weaken the interactions between the inhibitors and target. Additionally, the structural analyses of BBT594 and CHZ868 in complex with the WT JAK2 illustrate that the drug tail with strong electronegativity and small size located in the allosteric pocket of JAK2 may enhance anti-resistance capability. In summary, our results highlight that both of the changes of the conformational entropies and enthalpies contribute to the L884P-induced resistance in the binding of two Type-II inhibitors into JAK2 kinase.
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36
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Cao H, Sun Y, Wang L, Zhao C, Fu J, Zhang A. Understanding the microscopic binding mechanism of hydroxylated and sulfated polybrominated diphenyl ethers with transthyretin by molecular docking, molecular dynamics simulations and binding free energy calculations. MOLECULAR BIOSYSTEMS 2017; 13:736-749. [PMID: 28217795 DOI: 10.1039/c6mb00638h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites. However, experimentally determined data for the TTR binding potential of the sulfated PBDEs are still not available. Therefore, molecular docking and molecular dynamics (MD) simulations were employed in the present study to probe the molecular basis of TTR interacting with hydroxylated and sulfated PBDEs at the atomic level. The docking scores of LeDock were used to construct the structure-based predictive model. The calculated results showed that the sulfated PBDEs have stronger affinity for TTR than the corresponding OH-PBDEs. Further analysis of structural characteristics based on MD simulations indicated that upon the binding of PBDE metabolites, the stability of TTR was enhanced and the dissociation rate of the tetrameric protein structure was potentially decreased. Subsequent binding free energy calculations implied that van der Waals interactions are the dominant forces for the binding of these metabolites of PBDEs at the T4 site of TTR. The residues Ser117/Ser117' and Lys15/Lys15' were identified, by both residue energy decomposition and computational alanine-scanning mutagenesis methods, as key residues which play an important role in determining the binding orientations of the -OSO3- group of sulfated PBDEs by formation of either hydrogen bonds or electrostatic interactions, respectively. In general, the combination of docking calculations with MD simulations provided a theoretically toxicological assessment for the metabolites of PBDEs, deep insight into the recognition mechanism of TTR for these compounds, and thus more comprehensive understanding of the thyroid-related toxic effects of PBDEs as well.
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Affiliation(s)
- Huiming Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yuzhen Sun
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Ling Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China and Institute of Environment and Health, Jianghan University, Wuhan 430056, China
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Ji M, Zheng G, Li X, Zhang Z, Jv G, Wang X, Wang J. Computational dissection of allosteric inhibition of the SH2 domain of Bcr-Abl kinase by the monobody inhibitor AS25. J Mol Model 2017; 23:183. [DOI: 10.1007/s00894-017-3353-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/19/2017] [Indexed: 11/30/2022]
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38
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Dong CL, Guo FC, Xue J. Computational insights into HER3 gatekeeper T768I resistance mutation to bosutinib in HER3-related breast cancer. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1901-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Zhao S, Zhu J, Xu L, Jin J. Theoretical studies on the selective mechanisms of GSK3β and CDK2 by molecular dynamics simulations and free energy calculations. Chem Biol Drug Des 2016; 89:846-855. [PMID: 27863047 DOI: 10.1111/cbdd.12907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 10/30/2016] [Accepted: 10/31/2016] [Indexed: 01/09/2023]
Abstract
Glycogen synthase kinase 3 (GSK3) is a serine/threonine protein kinase which is widely involved in cell signaling and controls a broad number of cellular functions. GSK3 contains α and β isoforms, and GSK3β has received more attention and becomes an attractive drug target for the treatment of several diseases. The binding pocket of cyclin-dependent kinase 2 (CDK2) shares high sequence identity to that of GSK3β, and therefore, the design of highly selective inhibitors toward GSK3β remains a big challenge. In this study, a computational strategy, which combines molecular docking, molecular dynamics simulations, free energy calculations, and umbrella sampling simulations, was employed to explore the binding mechanisms of two selective inhibitors to GSK3β and CDK2. The simulation results highlighted the key residues critical for GSK3β selectivity. It was observed that although GSK3β and CDK2 share the conserved ATP-binding pockets, some different residues have significant contributions to protein selectivity. This study provides valuable information for understanding the GSK3β-selective binding mechanisms and the rational design of selective GSK3β inhibitors.
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Affiliation(s)
- Sufang Zhao
- Department of Gastroenterology, The 2nd Hospital of Shenzhen (The First Affiliated Hospital of Shenzhen University), ShenZhen, Guangdong, China
| | - Jingyu Zhu
- School of Medicine and Pharmaceutics, Jiangnan University, Wuxi, Jiangsu, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Jian Jin
- School of Medicine and Pharmaceutics, Jiangnan University, Wuxi, Jiangsu, China
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40
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Molecular dynamics simulations reveal the allosteric effect of F1174C resistance mutation to ceritinib in ALK-associated lung cancer. Comput Biol Chem 2016; 65:54-60. [DOI: 10.1016/j.compbiolchem.2016.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/13/2016] [Accepted: 10/05/2016] [Indexed: 01/14/2023]
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Combined 3D-QSAR modeling and molecular docking study on spiro-derivatives as inhibitors of acetyl-CoA carboxylase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1743-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sun H, Pan P, Tian S, Xu L, Kong X, Li Y, Dan Li, Hou T. Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery. Sci Rep 2016; 6:24817. [PMID: 27102549 PMCID: PMC4840416 DOI: 10.1038/srep24817] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/06/2016] [Indexed: 01/23/2023] Open
Abstract
The MIEC-SVM approach, which combines molecular interaction energy components (MIEC) derived from free energy decomposition and support vector machine (SVM), has been found effective in capturing the energetic patterns of protein-peptide recognition. However, the performance of this approach in identifying small molecule inhibitors of drug targets has not been well assessed and validated by experiments. Thereafter, by combining different model construction protocols, the issues related to developing best MIEC-SVM models were firstly discussed upon three kinase targets (ABL, ALK, and BRAF). As for the investigated targets, the optimized MIEC-SVM models performed much better than the models based on the default SVM parameters and Autodock for the tested datasets. Then, the proposed strategy was utilized to screen the Specs database for discovering potential inhibitors of the ALK kinase. The experimental results showed that the optimized MIEC-SVM model, which identified 7 actives with IC50 < 10 μM from 50 purchased compounds (namely hit rate of 14%, and 4 in nM level) and performed much better than Autodock (3 actives with IC50 < 10 μM from 50 purchased compounds, namely hit rate of 6%, and 2 in nM level), suggesting that the proposed strategy is a powerful tool in structure-based virtual screening.
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Affiliation(s)
- Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Lei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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Abstract
INTRODUCTION Molecular docking has become a popular method for virtual screening. Docking small molecules to a rigid biological receptor is fast but could produce many false negatives and identify less diverse compounds. Flexible receptor docking has alleviated this problem. AREAS COVERED This article focuses on reviewing ensemble docking as an approximate but inexpensive method to incorporate receptor flexibility in molecular docking. It outlines key features and recent advances of this method and points out problem areas that need to be addressed to make it even more useful in drug discovery. EXPERT OPINION Among the different methods introduced for flexible receptor docking, ensemble docking represents one of the most popular approaches, especially for high-throughput virtual screening. One can generate structural ensembles by using experimental structures, by structural modeling and by various types of molecular simulations. In building a structural ensemble, a judicious choice of the structures to be included can improve performance. Furthermore, reducing the size of the structural ensemble can cut computational costs, and removing the structures that can bind few ligands well could enrich the number of true actives identified by ensemble docking. The ability of ensemble docking to identify more true positives at the top of a rank-ordered list also depends on the choice of the methods to score and rank compounds, an area that needs further research.
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Affiliation(s)
- Chung F Wong
- a University of Missouri-St. Louis, Department of Chemistry and Biochemistry , 1 University Boulevard, St. Louis, MO 63121, USA +1 31 4516 5318 ;
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Maršavelski A, Močibob M, Gruić-Sovulj I, Vianello R. The origin of specificity and insight into recognition between an aminoacyl carrier protein and its partner ligase. Phys Chem Chem Phys 2015; 17:19030-8. [PMID: 26129823 DOI: 10.1039/c5cp03066h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Acyl carrier proteins (ACPs) are among the most promiscuous proteins in terms of protein-protein interactions and it is quite puzzling how ACPs select the correct partner between many possible upstream and downstream binding proteins. To address this question, we performed molecular dynamics simulations on dimeric Bradyrhizobium japonicum Gly:CP ligase 1 to inspect the origin of its selectivity towards the three types of carrier proteins, namely holoCP, apoCP, and holoCP-Gly, which only differ in the attached prosthetic group. In line with experiments, MM-GBSA analysis revealed that the ligase preferentially binds the holoCP form to both subunits with the binding free energies of -20.7 and -19.1 kcal mol(-1), while the apoCP form, without the prosthetic group, is also recognized, but the binding values of -9.2 and -3.6 kcal mol(-1) suggest that there is no competition for the ligase binding as long as the holoCP is present. After the prosthetic group becomes glycylated, the holoCP-Gly dissociates from the ligase, as supported by its endergonic binding free energies of 2.9 and 20.9 kcal mol(-1). Our results indicate that these affinity differences are influenced by three aspects: the form of the prosthetic group and the specific non-polar hydrophobic interactions, as well as charge complementarity dominantly manifested through Arg220-Glu53 ion pair within the binding region among proteins. A careful examination of the bonding patterns within the ligase active site elucidated the interactions with Arg258, Asp215 and Tyr132 as being predominant in stabilizing the prosthetic group, which are significantly diminished upon glycation, thus promoting complex dissociation.
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Affiliation(s)
- Aleksandra Maršavelski
- Quantum Organic Chemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
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Ni Z, Zhang TC. Computationally unraveling how ceritinib overcomes drug-resistance mutations in ALK-rearranged lung cancer. J Mol Model 2015; 21:175. [DOI: 10.1007/s00894-015-2716-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023]
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Yao K, Tan P, Luo Y, Feng L, Xu L, Liu Z, Li Y, Peng R. Graphene Oxide Selectively Enhances Thermostability of Trypsin. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12270-12277. [PMID: 25985836 DOI: 10.1021/acsami.5b03118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the past few years, graphene and its derivative, graphene oxide (GO), have been extensively studied for their applications in biotechnology. In our previous work, we reported certain PEGylated GOs (GO-PEGs) can selectively promote trypsin activity and enhance its thermostability. To further explore this, here we synthesized a series of GO-PEGs with varying PEGylation degrees. Enzymatic activity assay shows that both GO and GO-PEGs can protect trypsin, but not chymotrypsin, from thermal denaturation at high temperature. Surprisingly, the lower the PEGylation degree, the better the protection, and GO as well as the GO-PEG with the lowest PEGylation degree show the highest protection efficiency (∼70% retained activity at 70 °C). Fluorescence spectroscopy analysis shows that GO/GO-PEGs have strong interactions with trypsin. Molecular Dynamics (MD) simulation results reveal that trypsin is adsorbed onto the surface of GO through its cationic residues and hydrophilic residues. Different from chymotrypsin adsorbed on GO, the active site of trypsin is covered by GO. MD simulation at high temperature shows that, through such interaction with GO, trypsin's active site is therefore stabilized and protected by GO. Our work not only illustrates the promising potential of GO/GO-PEGs as efficient, selective modulators for trypsin, but also provides the interaction mechanism of GO with specific proteins at the nano-bio interface.
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