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Shi Q, Liu L, Duan H, Jiang Y, Luo W, Sun G, Ge Y, Liang L, Liu W, Shi H, Hu J. Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State. Molecules 2023; 28:7139. [PMID: 37894619 PMCID: PMC10609312 DOI: 10.3390/molecules28207139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/14/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Amino acid binding proteins (AABPs) undergo significant conformational closure in the periplasmic space of Gram-negative bacteria, tightly binding specific amino acid substrates and then initiating transmembrane transport of nutrients. Nevertheless, the possible closure mechanisms after substrate binding, especially long-range signaling, remain unknown. Taking three typical AABPs-glutamine binding protein (GlnBP), histidine binding protein (HisJ) and lysine/arginine/ornithine binding protein (LAOBP) in Escherichia coli (E. coli)-as research subjects, a series of theoretical studies including sequence alignment, Gaussian network model (GNM), anisotropic network model (ANM), conventional molecular dynamics (cMD) and neural relational inference molecular dynamics (NRI-MD) simulations were carried out. Sequence alignment showed that GlnBP, HisJ and LAOBP have high structural similarity. According to the results of the GNM and ANM, AABPs' Index Finger and Thumb domains exhibit closed motion tendencies that contribute to substrate capture and stable binding. Based on cMD trajectories, the Index Finger domain, especially the I-Loop region, exhibits high molecular flexibility, with residues 11 and 117 both being potentially key residues for receptor-ligand recognition and initiation of receptor allostery. Finally, the signaling pathway of AABPs' conformational closure was revealed by NRI-MD training and trajectory reconstruction. This work not only provides a complete picture of AABPs' recognition mechanism and possible conformational closure, but also aids subsequent structure-based design of small-molecule oncology drugs.
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Affiliation(s)
- Quanshan Shi
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Ling Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Huaichuan Duan
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
| | - Yu Jiang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Wenqin Luo
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Guangzhou Sun
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Yutong Ge
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China; (Q.S.); (L.L.); (Y.J.); (W.L.); (G.S.); (Y.G.); (L.L.); (W.L.)
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Liu L, Cheng Y, Zhang Z, Li J, Geng Y, Li Q, Luo D, Liang L, Liu W, Hu J, Ouyang W. Study on the allosteric activation mechanism of SHP2 via elastic network models and neural relational inference molecular dynamics simulation. Phys Chem Chem Phys 2023; 25:23588-23601. [PMID: 37621251 DOI: 10.1039/d3cp02795c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
As a ubiquitous protein tyrosine phosphatase, SHP2 is involved in PD-1/PD-L1 mediated tumor immune escape and undergoes substantial conformational changes. Therefore, it is considered an ideal target for tumor intervention. However, the allosteric mechanisms of SHP2 binding PD-1 intracellular ITIM/ITSM phosphopeptides remain unclear, which greatly hinders the development of novel structure-based anticancer allosteric inhibitors. In this work, the open and closed structural models of SHP2 are first constructed based on this knowledge; next their motion modes are investigated via elastic network models such as the Gaussian network model (GNM), anisotropic network model (ANM) and adaptive anisotropic network model (aANM); and finally, a possible allosteric signaling pathway is proposed using a neural relational inference molecular dynamics (NRI-MD) simulation embedded with an artificial intelligence (AI) strategy. In GNM and ANM, the N-SH2, C-SH2 and PTP domains all exhibit distinct dynamics partitions, and the N-SH2/C-SH2 regions show a rigid rotation relative to PTP. According to a series of intermediate snapshots given by aANM, N-SH2 is first identified with pY223 specifically, inducing a D'E-loop to change from β-sheets to random coils, and then, C-SH2 serves as a fulcrum to drive N-SH2 to rotate 110° completely away from the original active sites of PTP. Finally, a possible allosteric signaling-transfer path for SHP2, namely R220-R138-T108-R32, is proposed based on NRI-MD sampling. This work provides a possible allosteric mechanism of SHP2, which is helpful for the following design of novel allosteric inhibitors and is expected to be used in clinical synergies with PD-1 monoclonal antibody.
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Affiliation(s)
- Ling Liu
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yan Cheng
- Breast Disease Center, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Zhigang Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jing Li
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yichao Geng
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Qingsong Li
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Daxian Luo
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Weiwei Ouyang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
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Duan H, Hu K, Zheng D, Cheng Y, Zhang Z, Wang Y, Liang L, Hu J, Luo T. Recognition and release of uridine and hCNT3: From multivariate interactions to molecular design. Int J Biol Macromol 2022; 223:1562-1577. [PMID: 36402394 DOI: 10.1016/j.ijbiomac.2022.11.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
As a vital target for the development of novel anti-cancer drugs, human concentrative nucleoside transporter 3 (hCNT3) has been widely concerned. Nevertheless, the lack of a comprehensive understanding of molecular interactions and motion mechanism has greatly hindered the development of novel inhibitors against hCNT3. In this paper, molecular recognition of hCNT3 with uridine was investigated with molecular docking, conventional molecular dynamics (CMD) simulations and adaptive steered molecular dynamics (ASMD) simulations; and then, the uridine derivatives with possibly highly inhibitory activity were designed. The result of CMD showed that more water-mediated H-bonds and lower binding free energy both explained higher recognition ability and transported efficiency of hCNT3. While during the ASMD simulation, nucleoside transport process involved the significant side-chain flip of residues F321 and Q142, a typical substrate-induced conformational change. By considering electronegativity, atomic radius, functional group and key H-bonds factors, 25 novel uridine derivatives were constructed. Subsequently, the receptor-ligand binding free energy was predicted by solvated interaction energy (SIE) method to determine the inhibitor c8 with the best potential performance. This work not only revealed molecular recognition and release mechanism of uridine with hCNT3, but also designed a series of uridine derivatives to obtain lead compounds with potential high activity.
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Affiliation(s)
- Huaichuan Duan
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Kaixuan Hu
- School of Pharmaceutical Sciences, Jishou University, Jishou, China
| | - Dan Zheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Cheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Zelan Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China.
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Wu Z, Han Z, Zhou W, Sun X, Chen L, Yang S, Hu J, Li C. Insight into the Nucleoside Transport and Inhibition of Human ENT1. Curr Res Struct Biol 2022; 4:192-205. [PMID: 35677775 PMCID: PMC9168172 DOI: 10.1016/j.crstbi.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/02/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
The human equilibrative nucleoside transporter 1 (hENT1) is an effective controller of adenosine signaling by regulating its extracellular and intracellular concentration, and has become a solid drug target of clinical used adenosine reuptake inhibitors (AdoRIs). Currently, the mechanisms of adenosine transport and inhibition for hENT1 remain unclear, which greatly limits the in-depth understanding of its inner workings as well as the development of novel inhibitors. In this work, the dynamic details of hENT1 underlie adenosine transport and the inhibition mechanism of the non-nucleoside AdoRIs dilazep both were investigated by comparative long-time unbiased molecular dynamics simulations. The calculation results show that the conformational transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. One of the trimethoxyphenyl rings in dilazep serves as the adenosyl moiety of the endogenous adenosine substrate to competitively occupy the orthosteric site of hENT1. Due to extensive and various VDW interactions with N30, M33, M84, P308 and F334, the other trimethoxyphenyl ring is stuck in the opportunistic site near the extracellular side preventing the complete occlusion of thin gate simultaneously. Obviously, dilazep shows significant inhibitory activity by disrupting the local induce-fit action in substrate binding cavity and blocking the transport cycle of whole protein. This study not only reveals the nucleoside transport mechanism by hENT1 at atomic level, but also provides structural guidance for the subsequent design of novel non-nucleoside AdoRIs with enhanced pharmacologic properties. The transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. The induce-fit action by adenosine recognition precedes. inward contraction of the extracellular side. Dilazep exerts its special hENT1 inhibitory function through competitive binding and allosteric regulation. A gating strategy of extracellular loop is revealed to ensure adenosine is firmly located in the transport cavity.
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Affiliation(s)
- Zhixiang Wu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Wenxue Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Lei Chen
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Shuang Yang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
- Corresponding author. Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Corresponding author. Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China.
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