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Li WY, Ma Y, Li HX, Lu XH, Du S, Ma YC, Zhou L, Wang RL. Scaffold-based selective SHP2 inhibitors design using core hopping, molecular docking, biological evaluation and molecular simulation. Bioorg Chem 2020; 105:104391. [PMID: 33113413 DOI: 10.1016/j.bioorg.2020.104391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/07/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
PTPN11 (coding the gene of SHP2), a classic non-receptor protein tyrosine phosphatase, is implicated in multiple cell signaling pathway. Abnormal activation of SHP2 has been shown to contribute to a variety of human diseases, including Juvenile myelomonocytic leukemia (JMML), Noonan syndrome and tumors. Thus, the SHP2 inhibitors have important therapeutic value. Here, based on the compound PubChem CID 8,478,960 (IC50 = 45.01 μM), a series of thiophene [2,3-d] pyrimidine derivatives (IC50 = 0.4-37.87 μM) were discovered as novel and efficient inhibitors of SHP2 through powerful "core hopping" and CDOCKER technology. Furthermore, the SHP2-PTP phosphatase activity assay indicated that Comp#5 (IC50 = 0.4 μM) was the most active SHP2 inhibitor. Subsequently, the effects of Comp#5 on the structure and function of SHP2 were investigated through molecular dynamics (MD) simulation and post-kinetic analysis. The result indicated that Comp#5 enhanced the interaction of residues THR357, ARG362, LYS366, PRO424, CYS459, SER460, ALA461, ILE463, ARG465, THR507 and GLN510 with the surrounding residues, improving the stability of the catalytic active region and the entrance of catalytic active region. In particular, the Comp#5 conjugated with residue ARG362, elevating the efficient and selectivity of SHP2 protein. The study here may pave the way for discovering the novel SHP2 inhibitors for suffering cancer patients.
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Affiliation(s)
- Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Hao-Xin Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang 050015, Hebei, China
| | - Shan Du
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yang-Chun Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Liang Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
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Machado LDA, Guimarães ACR. Evidence for Disruption of Mg 2+ Pair as a Resistance Mechanism Against HIV-1 Integrase Strand Transfer Inhibitors. Front Mol Biosci 2020; 7:170. [PMID: 32974383 PMCID: PMC7468422 DOI: 10.3389/fmolb.2020.00170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/02/2020] [Indexed: 11/28/2022] Open
Abstract
HIV-1 integrase is the enzyme responsible for integrating the viral DNA into the host genome and is one of the main targets for antiretroviral therapy; however, there are documented cases of resistance against all the currently used integrase strand transfer inhibitors (INSTIs). While some resistance-related mutations occur near the inhibitor’s binding site, the mutation N155H occurs on the opposite side of the drug-interacting Mg2+ ions, thus, not interacting directly with the drug molecules and currently lacking an explanation for its resistance mechanism. Moreover, mutation N155H and the resistance-related mutation Q148H are mutually exclusive for unknown reasons. In the present study, we use molecular dynamics simulations to understand the impact of the N155H mutation in the HIV-1 integrase structure and dynamics, when alone or in combination with Q148H. Our findings suggest that the Mg2+ ions of the active site adopt different orientations in each of the mutants, causing the catalytic triad residues involved in the ion coordination to adapt their side-chain configurations, completely changing the INSTIs binding site. The change in the ion coordination also seems to affect the flexibility of the terminal viral DNA nucleotide near the active site, potentially impairing the induced-fit mechanism of the drugs. The explanations obtained from our simulations corroborate previous hypotheses drawn from crystallographic studies. The proposed resistance mechanism can also explain the resistance caused by other mutations that take place in the same region of the integrase and help uncover the structural details of other HIV-1 resistance mechanisms.
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Affiliation(s)
- Lucas de Almeida Machado
- Laboratory for Functional Genomics and Bioinformatics, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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3
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Chen Q, Cheng X, Wei D, Xu Q. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase. Interdiscip Sci 2014; 7:36-42. [PMID: 25519157 DOI: 10.1007/s12539-014-0235-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/16/2013] [Accepted: 03/24/2014] [Indexed: 10/24/2022]
Abstract
Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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4
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Chen Q, Cheng X, Wei D, Xu Q. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase. Interdiscip Sci 2014. [PMID: 25373632 DOI: 10.1007/s12539-013-0215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/16/2013] [Accepted: 03/24/2014] [Indexed: 06/04/2023]
Abstract
Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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5
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Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, Wei D. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. J Chem Inf Model 2013; 53:3297-307. [PMID: 24205814 DOI: 10.1021/ci400537n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) is essential for HIV-1 replication, catalyzing two key reaction steps termed 3' processing and strand transfer. Therefore, IN has become an important target for antiviral drug discovery. However, mutants have emerged, such as E92Q/N155H and G140S/Q148H, which confer resistance to raltegravir (RAL), the first IN strand transfer inhibitor (INSTI) approved by the FDA, and to the recently approved elvitegravir (EVG). To gain insights into the molecular mechanisms of ligand binding and drug resistance, we performed molecular dynamics (MD) simulations of homology models of the HIV-1 IN and four relevant mutants complexed with viral DNA and RAL. The results show that the structure and dynamics of the 140s' loop, comprising residues 140 to 149, are strongly influenced by the IN mutations. In the simulation of the G140S/Q148H double mutant, we observe spontaneous dissociation of RAL from the active site, followed by an intrahelical swing-back of the 3'-OH group of nucleotide A17, consistent with the experimental observation that the G140S/Q148H mutant exhibits the highest resistance to RAL compared to other IN mutants. An important hydrogen bond between residues 145 and 148 is present in the wild-type IN but not in the G140S/Q148H mutant, accounting for the structural and dynamical differences of the 140s' loop and ultimately impairing RAL binding in the double mutant. End-point free energy calculations that broadly capture the experimentally known RAL binding profiles elucidate the contributions of the 140s' loop to RAL binding free energies and suggest possible approaches to overcoming drug resistance.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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Xue W, Jin X, Ning L, Wang M, Liu H, Yao X. Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. J Chem Inf Model 2012; 53:210-22. [DOI: 10.1021/ci300541c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Weiwei Xue
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojie Jin
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Lulu Ning
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Meixia Wang
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
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Sgobba M, Olubiyi O, Ke S, Haider S. Molecular dynamics of HIV1-integrase in complex with 93del - a structural perspective on the mechanism of inhibition. J Biomol Struct Dyn 2012; 29:863-77. [PMID: 22292948 DOI: 10.1080/07391102.2012.10507418] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.
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Affiliation(s)
- Miriam Sgobba
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, 97 Lisburn Road, BT9 7BL, Belfast, UK.
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Hu JP, He HQ, Tang DY, Sun GF, Zhang YQ, Fan J, Chang S. Study on the interactions between diketo-acid inhibitors and prototype foamy virus integrase-DNA complex via molecular docking and comparative molecular dynamics simulation methods. J Biomol Struct Dyn 2012; 31:734-47. [PMID: 22913375 DOI: 10.1080/07391102.2012.709458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an important drug target for anti-acquired immune deficiency disease (AIDS) treatment and diketo-acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN. Due to lack of three-dimensional structures including detail interactions between HIV-1 IN and its substrate viral DNA, the drug design and screening platform remains incompleteness and deficient. In addition, the action mechanism of DKA inhibitors with HIV-1 IN is not well understood. In view of the high homology between the structure of prototype foamy virus (PFV) IN and that of HIV-1 IN, we used PFV IN as a surrogate model for HIV-1 IN to investigate the inhibitory mechanism of raltegravir (RLV) and the binding modes with a series of DKA inhibitors. Firstly, molecular dynamics simulations of PFV IN, IN-RLV, IN-DNA, and IN-DNA-RLV systems were performed for 10 ns each. The interactions and inhibitory mechanism of RLV to PFV IN were explored through overall dynamics behaviors, catalytic loop conformation distribution, and hydrogen bond network analysis. The results show that the coordinated interactions of RLV with IN and viral DNA slightly reduce the flexibility of catalytic loop region of IN, and remarkably restrict the mobility of the CA end of viral DNA, which may lead to the partial loss of the inhibitory activity of IN. Then, we docked a series of DKA inhibitors into PFV IN-DNA receptor and obtained the IN-DNA-inhibitor complexes. The docking results between PFV IN-DNA and DKA inhibitors agree well with the corresponding complex of HIV-1 IN, which proves the dependability of PFV IN-DNA used for the anti-AIDS drug screening. Our study may help to make clear some theoretical questions and to design anti-AIDS drug based on the structure of IN.
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Affiliation(s)
- Jian-Ping Hu
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China.
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Xue W, Qi J, Yang Y, Jin X, Liu H, Yao X. Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study. MOLECULAR BIOSYSTEMS 2012; 8:2135-44. [DOI: 10.1039/c2mb25114k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Xue W, Liu H, Yao X. Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. J Comput Chem 2011; 33:527-36. [DOI: 10.1002/jcc.22887] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/25/2011] [Accepted: 10/20/2011] [Indexed: 01/03/2023]
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Havukainen H, Halskau Ø, Skjaerven L, Smedal B, Amdam GV. Deconstructing honeybee vitellogenin: novel 40 kDa fragment assigned to its N terminus. ACTA ACUST UNITED AC 2011; 214:582-92. [PMID: 21270306 DOI: 10.1242/jeb.048314] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Vitellogenin, an egg-yolk protein precursor common to oviparous animals, is found abundantly in honeybee workers - a caste of helpers that do not usually lay eggs. Instead, honeybee vitellogenin (180 kDa) participates in processes other than reproduction: it influences hormone signaling, food-related behavior, immunity, stress resistance and longevity. The molecular basis of these functions is largely unknown. Here, we establish and compare the molecular properties of vitellogenin from honeybee hemolymph (blood) and abdominal fat body, two compartments that are linked to vitellogenin functions. Our results reveal a novel 40 kDa vitellogenin fragment in abdominal fat body tissue, the main site for vitellogenin synthesis and storage. Using MALDI-TOF combined with MS/MS mass-spectroscopy, we assign the 40 kDa fragment to the N terminus of vitellogenin, whereas a previously observed 150 kDa fragment corresponded to the remainder of the protein. We show that both protein units are N glycosylated and phosphorylated. Focusing on the novel 40 kDa fragment, we present a homology model based on the structure of lamprey lipovitellin that includes a conserved β-barrel-like shape, with a lipophilic cavity in the interior and two insect-specific loops that have not been described before. Our data indicate that the honeybee fat body vitellogenin experiences cleavage unlike hemolymph vitellogenin, a pattern that can suggest a tissue-specific role. Our experiments advance the molecular understanding of vitellogenin, of which the multiple physiological and behavioral effects in honeybees are well established.
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Affiliation(s)
- Heli Havukainen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
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12
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Wang YT, Su ZY, Hsieh CH, Chen CL. Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method. J Chem Inf Model 2009; 49:2369-75. [DOI: 10.1021/ci9002238] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yeng-Tseng Wang
- National Center for High-performance Computing, Hsin-Shi, Tainan County 741, Taiwan, and The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan, and The Department of Information Management, Chia Nan University of Pharmacy & Science, Tainan 717, Taiwan
| | - Zhi-Yuan Su
- National Center for High-performance Computing, Hsin-Shi, Tainan County 741, Taiwan, and The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan, and The Department of Information Management, Chia Nan University of Pharmacy & Science, Tainan 717, Taiwan
| | - Chang-Huain Hsieh
- National Center for High-performance Computing, Hsin-Shi, Tainan County 741, Taiwan, and The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan, and The Department of Information Management, Chia Nan University of Pharmacy & Science, Tainan 717, Taiwan
| | - Cheng-Lung Chen
- National Center for High-performance Computing, Hsin-Shi, Tainan County 741, Taiwan, and The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan, and The Department of Information Management, Chia Nan University of Pharmacy & Science, Tainan 717, Taiwan
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Williams SL, Andrew McCammon J. Conformational dynamics of the flexible catalytic loop in Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase. Chem Biol Drug Des 2009; 73:26-38. [PMID: 19152632 DOI: 10.1111/j.1747-0285.2008.00749.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In mycobacteria, the biosynthesis of the precursors to the essential isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate is carried out by the methylerythritol phosphate pathway. This route of synthesis is absent in humans, who utilize the alternative mevalonate acid route, thus making the enzymes of the methylerythritol phosphate pathway of chemotherapeutic interest. One such identified target is the second enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase. Only limited information is currently available concerning the catalytic mechanism and structural dynamics of this enzyme, and only recently has a crystal structure of Mycobacterium tuberculosis species of this enzyme been resolved including all factors required for binding. Here, the dynamics of the enzyme is studied in complex with NADPH, Mn2+, in the presence and absence of the fosmidomycin inhibitor using conventional molecular dynamics and an enhanced sampling technique, reversible digitally filtered molecular dynamics. The simulations reveal significant differences in the conformational dynamics of the vital catalytic loop between the inhibitor-free and inhibitor-bound enzyme complexes and highlight the contributions of conserved residues in this region. The substantial fluctuations observed suggest that 1-deoxy-D-xylulose 5-phosphate reductoisomerase may be a promising target for computer-aided drug discovery through the relaxed complex method.
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Affiliation(s)
- Sarah L Williams
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0365, USA
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