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Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chem Sci 2024; 15:12861-12878. [PMID: 39148808 PMCID: PMC11322960 DOI: 10.1039/d4sc00690a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
The development of reliable and extensible molecular mechanics (MM) force fields-fast, empirical models characterizing the potential energy surface of molecular systems-is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1 M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides and folded proteins, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.
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Affiliation(s)
- Kenichiro Takaba
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - Chapin E Cavender
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA
| | - Iván Pulido
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Michael M Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | | | - Christopher R Iacovella
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Arnav M Nagle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA
| | - Alexander Matthew Payne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
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2
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Patel R, Onyema A, Tang PK, Loverde SM. Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:4709-4726. [PMID: 38865599 PMCID: PMC11200259 DOI: 10.1021/acs.jcim.4c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
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Affiliation(s)
- Rutika Patel
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Augustine Onyema
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Phu K. Tang
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Sharon M. Loverde
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Physics, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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3
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Ngueanngam N, Jityuti B, Patnin S, Boonsri P, Makarasen A, Buranaprapuk A. Multiple spectroscopic and computational studies on binding interaction of 2-phenylamino-4-phenoxyquinoline derivatives with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123948. [PMID: 38309006 DOI: 10.1016/j.saa.2024.123948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Binding characteristics of potent non-nucleoside HIV-1 reverse transcriptase inhibitors, 4-(2',6'-dimethyl-4'-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (1) and 4-(2',6'-dimethyl-4'-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (2), to bovine serum albumin (BSA) under simulative physiological conditions were investigated by multiple spectroscopic and computational methods. The experimental results demonstrated that (1) and (2) bound to BSA at site III (subdomain IB), and quenched BSA fluorescence through a static quenching process. The binding interaction of (1) or (2) to BSA forms stable complexes with the binding constants (Kb) at the level of 104 L/mol and the number of binding site was determined to be 1 for both systems, indicating that new synthesized compounds occupied one site in BSA with moderate binding affinities. Based on the analysis of the thermodynamic parameters, it can be indicated that the main binding forces for interaction between BSA and both compounds were hydrogen bonding and van der Waals force. Synchronous fluorescence results revealed that the interaction of two compounds with BSA led to modifications in the microenvironment surrounding tryptophan residue of BSA. Circular dichroism spectra demonstrated alterations in the secondary structure of BSA induced by (1) and (2). Moreover, the experimental data of molecular docking and molecular dynamics (MD) simulations supported the results obtained from multiple spectroscopic techniques, confirming the binding interactions between both compounds and BSA.
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Affiliation(s)
- Natchaphon Ngueanngam
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Benchawan Jityuti
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Suwicha Patnin
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Pornthip Boonsri
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Arthit Makarasen
- Department of Chemistry, Laboratory of Organic Synthesis, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
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4
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Ratre P, Nazeer N, Soni N, Kaur P, Tiwari R, Mishra PK. Smart carbon-based sensors for the detection of non-coding RNAs associated with exposure to micro(nano)plastics: an artificial intelligence perspective. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:8429-8452. [PMID: 38182954 DOI: 10.1007/s11356-023-31779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
Micro(nano)plastics (MNPs) are pervasive environmental pollutants that individuals eventually consume. Despite this, little is known about MNP's impact on public health. In this article, we assess the evidence for potentially harmful consequences of MNPs in the human body, concentrating on molecular toxicity and exposure routes. Since MNPs are present in various consumer products, foodstuffs, and the air we breathe, exposure can occur through ingestion, inhalation, and skin contact. MNPs exposure can cause mitochondrial oxidative stress, inflammatory lesions, and epigenetic modifications, releasing specific non-coding RNAs in circulation, which can be detected to diagnose non-communicable diseases. This article examines the most fascinating smart carbon-based nanobiosensors for detecting circulating non-coding RNAs (lncRNAs and microRNAs). Carbon-based smart nanomaterials offer many advantages over traditional methods, such as ease of use, sensitivity, specificity, and efficiency, for capturing non-coding RNAs. In particular, the synthetic methods, conjugation chemistries, doping, and in silico approach for the characterization of synthesized carbon nanodots and their adaptability to identify and measure non-coding RNAs associated with MNPs exposure is discussed. Furthermore, the article provides insights into the use of artificial intelligence tools for designing smart carbon nanomaterials.
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Affiliation(s)
- Pooja Ratre
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Nazim Nazeer
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Nikita Soni
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Prasan Kaur
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajnarayan Tiwari
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pradyumna Kumar Mishra
- Department of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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5
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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [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: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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6
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Kumar R. Structural dynamics and mechanistic action guided engineering of lipolytic enzymes. J Cell Biochem 2023. [PMID: 37087743 DOI: 10.1002/jcb.30410] [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: 02/16/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
Lipases have been established as important biocatalysts in several industrial applications, owing to their diverse substrate specificity. The availability of data on three-dimensional crystal structures for various lipases offers an opportunity for modulating their structural and functional aspects to design and engineer better versions of lipases. With the aim of investigating the structural components governing the extremophilic behavior of lipases, structural analysis of microbial lipases was performed using advanced bioinformatics and molecular dynamics simulation approaches. In sequences and functionally distinct alkaliphilic and thermophilic lipases were investigated for their functional properties to understand the distinguishing features of their structures. The alkaliphilic lipase from Bacillus subtilis (LipA) showed conformational changes in the loop region Ala132-Met137, subsequently, the active site residue His156 shows two conformations, toward the active site nucleophilic residues Ser77 and away from the Ser77. Interestingly, the active site of LipA is more solvent-exposed and can be correlated with the adoption of an open conformation which might extend and expose the active site region to solvents during the catalysis process. Furthermore, the MD simulation of thermophilic lipase from marine Streptomyces (MAS1) revealed the role of N- and C-terminal regions with disulfide bridges and identified a metal ion binding site that facilitates the enzyme stability. The novel thermo-alkaliphilic lipase can be designed to integrate the stability features of MAS1 into the alkaliphilic LipA. These structural-level intrinsic characteristics can be used for lipase engineering to amend the lipase activity and stability as per the requirements of the industrial processes.
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Affiliation(s)
- Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
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7
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Somai S, Yue K, Acevedo O, Ellis HR. Shorter Alkanesulfonate Carbon Chains Destabilize the Active Site Architecture of SsuD for Desulfonation. Biochemistry 2023; 62:85-94. [PMID: 36534405 DOI: 10.1021/acs.biochem.2c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacteria have evolved to utilize alternative organosulfur sources when sulfur is limiting. The SsuE/SsuD and MsuE/MsuD enzymes expressed when sulfur sources are restricted, are responsible for providing specific bacteria with sulfur in the form of alkanesulfonates. In this study, we evaluated why two structurally and functionally similar FMNH2-dependent monooxygenase enzymes (MsuD and SsuD) are needed for the acquisition of alkanesulfonates in some bacteria. In desulfonation assays, MsuD was able to utilize the entire range of alkanesulfonates (C1-C10). However, SsuD was not able to utilize smaller alkanesulfonate substrates. Interestingly, SsuD had a similar binding affinity for methanesulfonate (MES) (15 ± 1 μM) as MsuD (12 ± 1 μM) even though SsuD was not able to catalyze the desulfonation of the MES substrate. SsuD and MsuD showed decreased proteolytic susceptibility in the presence of FMNH2 with MES and octanesulfonate (OCS). Tighter loop closure was observed for the MsuD/FMNH2 complex with MES and OCS compared to SsuD under comparable conditions. Analysis of the SsuD/FMNH2/MES structure using accelerated molecular dynamics simulations found three different conformations for MES, demonstrating the instability of the bound structure. Even when MES was bound in a similar fashion to OCS within the active site, the smaller alkane chain resulted in a shift of FMNH2 so that it was no longer in a position to catalyze the desulfonation of MES. The active site of SsuD requires a longer alkane chain to maintain the appropriate architecture for desulfonation.
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Affiliation(s)
- Shruti Somai
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
| | - Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
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8
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Kolocouris A, Arkin I, Glykos NM. A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent. Phys Chem Chem Phys 2022; 24:25391-25402. [PMID: 36239696 DOI: 10.1039/d2cp02881f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here, we have carried out a proof-of-concept molecular dynamics (MD) simulation with adaptive tempering in a membrane mimetic environment to study the folding of single-pass membrane peptides. We tested the influenza A M2 viroporin, influenza B M2 viroporin, and protein E from coronaviruses MERS-Cov-2 and SARS-CoV-2 peptides with known experimental secondary structures in membrane bilayers. The two influenza-derived peptides are significantly different in the peptide sequence and secondary structure and more polar than the two coronavirus-derived peptides. Through a total of more than 50 μs of simulation time that could be accomplished in trifluoroethanol (TFE), as a membrane model, we characterized comparatively the folding behavior, helical stability, and helical propensity of these transmembrane peptides that match perfectly their experimental secondary structures, and we identified common motifs that reflect their quaternary organization and known (or not) biochemical function. We showed that BM2 is organized into two structurally distinct parts: a significantly more stable N-terminal half, and a fast-converting C-terminal half that continuously folds and unfolds between α-helical structures and non-canonical structures, which are mostly turns. In AM2, both the N-terminal half and C-terminal half are very flexible. In contrast, the two coronavirus-derived transmembrane peptides are much more stable and fast helix-formers when compared with the influenza ones. In particular, the SARS-derived peptide E appears to be the fastest and most stable helix-former of all the four viral peptides studied, with a helical structure that persists almost without disruption for the whole of its 10 μs simulation. By comparing the results with experimental observations, we benchmarked TFE in studying the conformation of membrane and hydrophobic peptides. This work provided accurate results suggesting a methodology to run long MD simulations and predict structural properties of biologically important membrane peptides.
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Affiliation(s)
- Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Greece.
| | - Isaiah Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, 91904, Israel
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
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9
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Zhang W, Zhang Y, Lu Y, Herman RA, Zhang S, Hu Y, Zhao W, Wang J, You S. More efficient barley malting under catalyst: thermostability improvement of a β-1,3-1,4-glucanase through surface charge engineering with higher activity. Enzyme Microb Technol 2022; 162:110151. [DOI: 10.1016/j.enzmictec.2022.110151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/25/2022]
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10
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Wang J, Zhou Y, Tang X, Yu X, Wang Y, Chan S, Song X, Tu Z, Zhang Z, Lu X, Zhang Z, Ding K. JND4135, a New Type II TRK Inhibitor, Overcomes TRK xDFG and Other Mutation Resistance In Vitro and In Vivo. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196500. [PMID: 36235036 PMCID: PMC9570838 DOI: 10.3390/molecules27196500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
The tropomyosin receptor kinases (TRKs) have been validated as effective targets in anticancer drug discovery. Two first-generation TRK inhibitors have been approved into market and displayed an encouraging therapeutic response in cancer patients harboring TRK fusion proteins. However, acquired resistance mediated by secondary TRK mutations especially in the xDFG motif remains an unsolved challenge in the clinic. Herein, we report the preclinical pharmacological results of JND4135, a new type II pan-TRK inhibitor, in overcoming TRK mutant resistance, including the xDFG mutations in vitro and in vivo. At a low nanomolar level, JND4135 displays a strong activity against wild-type TRKA/B/C and secondary mutations involving xDFG motif substitutions in kinase assays and cellular models; occupies the TRK proteins for an extended time; and has a slower dissociation rate than other TRK inhibitors. Moreover, by intraperitoneal injection, JND4135 exhibits tumor growth inhibition (TGI) of 81.0% at a dose of 40 mg/kg in BaF3-CD74-TRKA-G667C mice xenograft model. Therefore, JND4135 can be considered as a lead compound for drug discovery overcoming the resistance of TRK inhibitor drugs mediated by xDFG mutations.
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Affiliation(s)
- Jie Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xia Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiuwen Yu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shingpan Chan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaojuan Song
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhengchao Tu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhimin Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People’s Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
- Correspondence: (X.L.); (Z.Z.); (K.D.); Tel.: +86-020-8522-3764 (Z.Z.)
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11
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Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2. Cells 2022; 11:cells11081274. [PMID: 35455955 PMCID: PMC9032924 DOI: 10.3390/cells11081274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022] Open
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (RBDCoV2) has a higher binding affinity to the human receptor angiotensin-converting enzyme 2 (ACE2) than the SARS-CoV RBD (RBDCoV). Here, we performed molecular dynamics (MD) simulations, binding free energy (BFE) calculations, and interface residue contact network (IRCN) analysis to explore the mechanistic origin of different ACE2-binding affinities of the two RBDs. The results demonstrate that, when compared to the RBDCoV2-ACE2 complex, RBDCoV-ACE2 features enhanced dynamicsand inter-protein positional movements and increased conformational entropy and conformational diversity. Although the inter-protein electrostatic attractive interactions are the primary determinant for the high ACE2-binding affinities of both RBDs, the significantly enhanced electrostatic attractive interactions between ACE2 and RBDCoV2 determine the higher ACE2-binding affinity of RBDCoV2 than of RBDCoV. Comprehensive comparative analyses of the residue BFE components and IRCNs between the two complexes reveal that it is the residue changes at the RBD interface that lead to the overall stronger inter-protein electrostatic attractive force in RBDCoV2-ACE2, which not only tightens the interface packing and suppresses the dynamics of RBDCoV2-ACE2, but also enhances the ACE2-binding affinity of RBDCoV2. Since the RBD residue changes involving gain/loss of the positively/negatively charged residues can greatly enhance the binding affinity, special attention should be paid to the SARS-CoV-2 variants carrying such mutations, particularly those near or at the binding interfaces with the potential to form hydrogen bonds and/or salt bridges with ACE2.
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12
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Andrews B, Guerra J, Schweitzer-Stenner R, Urbanc B. Do molecular dynamics force fields accurately model Ramachandran distributions of amino acid residues in water? Phys Chem Chem Phys 2022; 24:3259-3279. [PMID: 35048087 DOI: 10.1039/d1cp05069a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular dynamics (MD) is a powerful tool for studying intrinsically disordered proteins, however, its reliability depends on the accuracy of the force field. We assess Amber ff19SB, Amber ff14SB, OPLS-AA/M, and CHARMM36m with respect to their capacity to capture intrinsic conformational dynamics of 14 guest residues x (=G, A, L, V, I, F, Y, DP, EP, R, C, N, S, T) in GxG peptides in water. The MD-derived Ramachandran distribution of each guest residue is used to calculate 5 J-coupling constants and amide I' band profiles to facilitate a comparison to spectroscopic data through reduced χ2 functions. We show that the Gaussian model, optimized to best fit the experimental data, outperforms all MD force fields by an order of magnitude. The weaknesses of the MD force fields are: (i) insufficient variability of the polyproline II (pPII) population among the guest residues; (ii) oversampling of antiparallel at the expense of transitional β-strand region; (iii) inadequate sampling of turn-forming conformations for ionizable and polar residues; and (iv) insufficient guest residue-specificity of the Ramachandran distributions. Whereas Amber ff19SB performs worse than the other three force fields with respect to χ2 values, it accounts for residue-specific pPII content better than the other three force fields. Additional testing of residue-specific RSFF1 and Amber ff14SB combined with TIP4P/2005 on six guest residues x (=A, I, F, DP, R, S) reveals that residue specificity derived from protein coil libraries or an improved water model alone do not result in significantly lower χ2 values.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Jose Guerra
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | | | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
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13
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You S, Zhang YX, Shi F, Zhang WX, Li J, Zhang S, Chen ZL, Zhao WG, Wang J. Lowering energy consumption for fermentable sugar production from Ramulus mori: Engineered xylanase synergy and improved pretreatment strategy. BIORESOURCE TECHNOLOGY 2022; 344:126368. [PMID: 34808317 DOI: 10.1016/j.biortech.2021.126368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Biorefinery of Ramulus mori with lower energy consumption through improved enzyme and pretreatment strategies was reported. Directed evolution and saturation mutagenesis were used for the modification of xylanase, the yield of fermentable sugars and the degree of synergy (DS) were determined for different pretreatment (seawater/non-seawater) and enzyme treatment groups (xylanase/cellulase/co-treatment). The dominant mutant I133A/Q143Y of Bispora sp. xylanase XYL10C_ΔN was obtained with improved specific activity (1860 U/mg), catalytic efficiency (1150 mL/s∙mg) at 40 °C, and thermostability (T50 increased by 7 °C). With the pretreatment of seawater immersion, the highest yield of fermentable sugars for Ramulus mori at 40 °C reached 199 μmol/g when hydrolyzed with cellulase and I133A/Q143Y, with the highest DS of 2.6; this was 4.5-fold that of the group hydrolyzed by cellulase alone with non-seawater pretreatment. Thus, bioconversion of reducing sugar from Ramulus mori was improved significantly at lower temperatures, which provides an efficient and energy-saving wayfor biofuel production.
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Affiliation(s)
- Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Yi-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Fan Shi
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Jing Li
- Department of Nephrology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, PR China
| | - Sheng Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Zhong-Li Chen
- Xinyuan Cocoon Silk Group Co., Ltd., Nantong 226600, PR China
| | - Wei-Guo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China.
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14
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King KM, Sharp AK, Davidson DS, Brown AM, Lemkul JA. Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021; 21:449-460. [PMID: 35756548 DOI: 10.1142/s2737416521420059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amyloids are a subset of intrinsically disordered proteins (IDPs) that self-assemble into cross-[Formula: see text] oligomers and fibrils. The structural plasticity of amyloids leads to sampling of metastable, low-molecular-weight oligomers that contribute to cytotoxicity. Of interest are amyloid-[Formula: see text] (A[Formula: see text] and islet amyloid polypeptide (IAPP), which are involved in the pathology of Alzheimer’s disease and Type 2 diabetes mellitus, respectively. In addition to forming homogenous oligomers and fibrils, these species have been found to cross-aggregate in heterogeneous structures. Biophysical properties, including electronic effects, that are unique or conserved between homogenous and heterogeneous amyloids oligomers are thus far unexplored. Here, we simulated homogenous and heterogeneous amyloid oligomers of A[Formula: see text] and IAPP[Formula: see text] fragments using the Drude oscillator model to investigate the impact of electronic polarization on the structural morphology and stability of preformed hexamers. Upon simulation of preformed, [Formula: see text]-strand rich oligomers with Drude, structural rearrangement occurred causing some loss of [Formula: see text]-strand structure in favor of random coil content for all oligomers. Homogenous A[Formula: see text] was the most stable system, deriving stability from low polarization in hydrophobic residues and through salt bridge formation. Changes in polarization were observed primarily for A[Formula: see text] residues in heterogeneous cross-amyloid systems, displaying a decrease in charged residue dipole moments and an increase in hydrophobic sidechain dipole moments. This work is the first study utilizing the Drude-2019 force field with amyloid oligomers, providing insight into the impact of electronic effects on oligomer structure and highlighting the importance of different microenvironments on amyloid oligomer stability.
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Affiliation(s)
- Kelsie M. King
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
| | - Amanda K. Sharp
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
| | - Darcy S. Davidson
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
| | - Anne M. Brown
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
- University Libraries, Virginia Tech, 560 Drillfield, Dr Blacksburg, VA 24061, USA
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
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15
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You S, Li J, Zhang F, Bai ZY, Shittu S, Herman RA, Zhang WX, Wang J. Loop engineering of a thermostable GH10 xylanase to improve low-temperature catalytic performance for better synergistic biomass-degrading abilities. BIORESOURCE TECHNOLOGY 2021; 342:125962. [PMID: 34563821 DOI: 10.1016/j.biortech.2021.125962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Lignocellulosic biorefining for producing biofuels poses technical challenges. It is usually conducted over a long time using heat, making it energy intensive. In this study, we lowered the energy consumption of this process through an optimized enzyme and pretreatment strategy. First, the dominant mutant M137E/N269G of Bispora sp. MEY-1XYL10C_ΔN was obtained by directed evolution with highcatalytic efficiency (970 mL/s∙mg)and specific activity (2090 U/mg)at 37 °C, and thermostability was improved (T50 increased by5 °C). After pretreatment with seawater immersionfollowing steam explosion,bagasse was co-treated with cellulase and M137E/N269G under mild conditions (37 °C), the resulting highest yield of fermentable sugars reached 219 µmol/g of bagasse,46% higher than that of the non-seawater treatment group, with the highest degree of synergy of 2.0. Pretreatment with seawater following steam explosion and synergistic hydrolysis through high activity xylanase and cellulase helped to achieve low energy degradation of lignocellulosic biomass.
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Affiliation(s)
- Shuai You
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Jing Li
- Department of Nephrology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, PR China
| | - Fang Zhang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Zhi-Yuan Bai
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Saidi Shittu
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Richard-Ansah Herman
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China.
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16
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Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. J Chem Theory Comput 2021; 17:6491-6508. [PMID: 34506133 DOI: 10.1021/acs.jctc.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarse-grained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein-membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and cross-linking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.
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Affiliation(s)
- Lily Wang
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
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17
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Wang X, Li X, He X, Zhang JZH. A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions. Phys Chem Chem Phys 2021; 23:21001-21012. [PMID: 34522933 DOI: 10.1039/d1cp02776j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fixed multi-site interaction charge (FMIC) model was proposed for the accurate prediction of intermolecular electrostatic interactions based on the quantum mechanical linear response of a molecule to an external electric field. In such a model, some additional off-center interaction sites were added for capturing multipole interactions for a given molecule. By multivariate least-square fitting analysis of the calculated QM/MM interactions of a given molecule with the electrostatic environment and the electrostatic potentials of the environment at the pre-defined distributed interaction sites, the FMIC of the molecule was obtained. The model system of CO in myoglobin (Mb) was utilized to demonstrate the derivation of the FMIC. The accuracy of FMIC in predicting the electrostatic interactions between CO and the Mb environment was investigated using 10 000 different Mb-CO configurations generated from the 400 ps QM/MM MD simulation. In comparison to the QM/MM calculations at the B3LYP/aug-cc-pVTZ/ff99SB level, the mean unsigned error (MUE) of the results based on the FMIC model was merely 0.10 kcal mol-1, and the root mean square error (RMSE) was only 0.13 kcal mol-1, which are significantly lower than the results predicted by the ESP charge model (MUE = 1.45 kcal mol-1, and RMSE = 1.7 kcal mol-1, respectively). The transferability of FMIC was tested by applying the obtained FMIC in the wild type Mb-CO system to the mutants of V68F and H64L Mb-CO systems. The MUEs of the obtained results for 10 000 different configurations are both smaller than 0.2 kcal mol-1 for the V68F and H64L Mb-CO systems in comparison to the B3LYP/aug-cc-pVTZ/ff99SB calculations, and the RMSEs are also lower than 0.2 kcal mol-1 for both mutants. The applications of FMIC were extended to model the electrostatic interactions between a hydrogen fluoride molecule and 492 waters in a truncated octahedron box; our study showed that the FMIC could give satisfactory results with a MUE of 0.12 kcal mol-1 and a RMSE of 0.16 kcal mol-1 in comparison to the B3LYP/aug-cc-pVDZ/TIP3P calculations for 10 000 different configurations generated using the 10 ns classical MD simulation. Therefore, the FMIC method provides an accurate and efficient tool for predicting intermolecular electrostatic interactions, which can be utilized in the future development of molecular force fields.
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Affiliation(s)
- Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China. .,Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Xilong Li
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Xiao He
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China. .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China. .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China. .,Department of Chemistry, New York University, New York, New York 10003, USA
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18
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Caciolla J, Martini S, Spinello A, Pavlin M, Turrini E, Simonelli F, Belluti F, Rampa A, Bisi A, Fimognari C, Zaffaroni N, Gobbi S, Magistrato A. Balanced dual acting compounds targeting aromatase and estrogen receptor α as an emerging therapeutic opportunity to counteract estrogen responsive breast cancer. Eur J Med Chem 2021; 224:113733. [PMID: 34364162 DOI: 10.1016/j.ejmech.2021.113733] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/05/2023]
Abstract
Breast Cancer (BC) is a leading cause of death in women, currently affecting 13% of female population worldwide. First-line clinical treatments against Estrogen Receptor positive (ER+) BC rely on suppressing estrogen production, by inhibiting the aromatase (AR) enzyme, or on blocking estrogen-dependent pro-oncogenic signaling, by targeting Estrogen Receptor (ER) α with selective Modulators/Degraders (SERMs/SERDs). The development of dual acting molecules targeting AR and ERα represents a tantalizing alternative strategy to fight ER + BC, reducing the incidence of adverse effects and resistance onset that limit the effectiveness of these gold-standard therapies. Here, in silico design, synthesis, biological evaluation and an atomic-level characterization of the binding and inhibition mechanism of twelve structurally related drug-candidates enable the discovery of multiple compounds active on both AR and ERα in the sub-μM range. The best drug-candidate 3a displayed a balanced low-nanomolar IC50 towards the two targets, SERM activity and moderate selectivity towards a BC cell line. Moreover, most of the studied compounds reduced ERα levels, suggesting a potential SERD activity. This study dissects the key structural traits needed to obtain optimal dual acting drug-candidates, showing that multitarget compounds may be a viable therapeutic option to counteract ER + BC.
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Affiliation(s)
- Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Silvia Martini
- Fondazione IRCSS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20113, Milano, Italy
| | - Angelo Spinello
- National Research Council of Italy Institute of Materials (CNR-IOM) C/o SISSA, Via Bonomea 265, 34136, Trieste, Italy
| | - Matic Pavlin
- National Research Council of Italy Institute of Materials (CNR-IOM) C/o SISSA, Via Bonomea 265, 34136, Trieste, Italy; Laboratory of Microsensor Structures and Electronics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, SI-1000 Ljubljana, Slovenia
| | - Eleonora Turrini
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D'Augusto 237, 47921, Rimini, Italy
| | - Federica Simonelli
- National Research Council of Italy Institute of Materials (CNR-IOM) C/o SISSA, Via Bonomea 265, 34136, Trieste, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Carmela Fimognari
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D'Augusto 237, 47921, Rimini, Italy
| | - Nadia Zaffaroni
- Fondazione IRCSS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20113, Milano, Italy
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.
| | - Alessandra Magistrato
- National Research Council of Italy Institute of Materials (CNR-IOM) C/o SISSA, Via Bonomea 265, 34136, Trieste, Italy.
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Liu M, Das AK, Lincoff J, Sasmal S, Cheng SY, Vernon RM, Forman-Kay JD, Head-Gordon T. Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins. Int J Mol Sci 2021; 22:ijms22073420. [PMID: 33810353 PMCID: PMC8037987 DOI: 10.3390/ijms22073420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/02/2023] Open
Abstract
Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experiments for the disordered states. This work considers a new direction-the connection to configurational entropy-and how it might change the nature of our understanding of protein force field development to equally well encompass globular proteins, IDRs/IDPs, and disorder-to-order transitions. We have evaluated representative pairwise and many-body protein and water force fields against experimental data on representative IDPs and IDRs, a peptide that undergoes a disorder-to-order transition, for seven globular proteins ranging in size from 130 to 266 amino acids. We find that force fields with the largest statistical fluctuations consistent with the radius of gyration and universal Lindemann values for folded states simultaneously better describe IDPs and IDRs and disorder-to-order transitions. Hence, the crux of what a force field should exhibit to well describe IDRs/IDPs is not just the balance between protein and water energetics but the balance between energetic effects and configurational entropy of folded states of globular proteins.
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Affiliation(s)
- Meili Liu
- Department of Chemistry, Beijing Normal University, Beijing 100875, China;
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Akshaya K. Das
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - James Lincoff
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Sukanya Sasmal
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Sara Y. Cheng
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Robert M. Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (R.M.V.); (J.D.F.-K.)
| | - Julie D. Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (R.M.V.); (J.D.F.-K.)
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA 94720, USA; (A.K.D.); (J.L.); (S.S.); (S.Y.C.)
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Correspondence:
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20
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Role of water in the determination of protonation states of titratable residues. J Mol Model 2021; 27:61. [PMID: 33517493 DOI: 10.1007/s00894-021-04677-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Water is the fundamental unit for living being, and its contribution in variety of crucial cellular functions is widely accepted. The presence of water molecules in protein's environment also accounts for structural optimization, in which highly conserved water molecules ensure structural stability of the biomolecule by providing protein-water (solute-solvent) hydrogen-bond interaction networks. Similarly, protonation states and pKa values of individual amino acid residues are also influenced by neighboring water molecules present in the protein's vicinity. In the present study, we have highlighted the role of water molecules in hydrogen-bond optimization, in determining pKa values and protonation states of titratable residues in JH2 domain of JAK2 apo protein. We found that inclusion or exclusion of water molecules while calculating pKa and assigning protonation states to amino acid residues during the molecular system build-up step resulted in slight differences in pKa values of few titratable residues and alternative protonation states of a certain residue. Accordingly, different protonation states of ionizable residues offer differing interaction patterns. Thus, we inferred that the presence of water optimizes the hydrogen-bond interactions by forming direct protein-water interactions and by linking via protein-protein bridging interactions. However, in the absence of water, the interaction pattern is somewhat disrupted. We assume that water molecules could modulate the plausibility of a particular protonation state of titratable residues on the basis of its fit with the local environment, by utilizing some particular hydrogen-bond contacts that would remain unexploited in the absence of water.
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21
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Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020; 153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023] Open
Abstract
Knowledge of protein structure is paramount to the understanding of biological function, developing new therapeutics, and making detailed mechanistic hypotheses. Therefore, methods to accurately elucidate three-dimensional structures of proteins are in high demand. While there are a few experimental techniques that can routinely provide high-resolution structures, such as x-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, which have been developed to determine the structures of proteins, these techniques each have shortcomings and thus cannot be used in all cases. However, additionally, a large number of experimental techniques that provide some structural information, but not enough to assign atomic positions with high certainty have been developed. These methods offer sparse experimental data, which can also be noisy and inaccurate in some instances. In cases where it is not possible to determine the structure of a protein experimentally, computational structure prediction methods can be used as an alternative. Although computational methods can be performed without any experimental data in a large number of studies, inclusion of sparse experimental data into these prediction methods has yielded significant improvement. In this Perspective, we cover many of the successes of integrative modeling, computational modeling with experimental data, specifically for protein folding, protein-protein docking, and molecular dynamics simulations. We describe methods that incorporate sparse data from cryo-EM, NMR, mass spectrometry, electron paramagnetic resonance, small-angle x-ray scattering, Förster resonance energy transfer, and genetic sequence covariation. Finally, we highlight some of the major challenges in the field as well as possible future directions.
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Affiliation(s)
- Justin T. Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
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22
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Mitsikas DA, Glykos NM. A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations. PLoS One 2020; 15:e0243429. [PMID: 33270807 PMCID: PMC7714341 DOI: 10.1371/journal.pone.0243429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/23/2020] [Indexed: 11/19/2022] Open
Abstract
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.
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Affiliation(s)
- Dimitrios A. Mitsikas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, Alexandroupolis, Greece
- * E-mail:
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23
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [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: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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24
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Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17165664. [PMID: 32764486 PMCID: PMC7459580 DOI: 10.3390/ijerph17165664] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 12/22/2022]
Abstract
The intensive use of pesticides has led to their increasing presence in water, soil, and agricultural products. Mounting evidence indicates that some pesticides may be endocrine disrupting chemicals (EDCs), being therefore harmful for the human health and the environment. In this study, three pesticides, glyphosate, thiacloprid, and imidacloprid, were tested for their ability to interfere with estrogen biosynthesis and/or signaling, to evaluate their potential action as EDCs. Among the tested compounds, only glyphosate inhibited aromatase activity (up to 30%) via a non-competitive inhibition or a mixed inhibition mechanism depending on the concentration applied. Then, the ability of the three pesticides to induce an estrogenic activity was tested in MELN cells. When compared to 17β-estradiol, thiacloprid and imidacloprid induced an estrogenic activity at the highest concentrations tested with a relative potency of 5.4 × 10−10 and 3.7 × 10−9, respectively. Molecular dynamics and docking simulations predicted the potential binding sites and the binding mode of the three pesticides on the structure of the two key targets, providing a rational for their mechanism as EDCs. The results demonstrate that the three pesticides are potential EDCs as glyphosate acts as an aromatase inhibitor, whereas imidacloprid and thiacloprid can interfere with estrogen induced signaling.
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25
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Mohanty P, Bhatnagar S. In Silico Screening to Identify Inhibitors of Growth Factor Receptor 2-Focal Adhesion Kinase Interaction for Therapeutic Treatment of Pathological Cardiac Hypertrophy. Assay Drug Dev Technol 2020; 17:58-67. [PMID: 30869527 DOI: 10.1089/adt.2018.887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The focal adhesion kinase-growth factor receptor 2 (FAK-Grb2) protein-protein interaction is implicated in pathogenesis of stress-induced cardiac hypertrophy. The focal adhesion targeting (FAT) domain of FAK unfolds to form a structural intermediate that interacts with a multibinding hot spot in the SH2 domain of Grb2. Disruption of the Grb2-FAT interaction is a therapeutic strategy for prevention of pathological cardiac hypertrophy. A pharmacophore was generated on the basis of structural and electrostatic properties of FAT bound to FAK using the Forge tool (Cresset). This pharmacophore was used as a query for Blaze server (Cresset) to screen a selectively enriched chemical library of 4,32,508 small molecules. The compounds selected were further filtered by hierarchical flexible docking approach using AutoDock v4. From the favorably docked compounds, five were selected on the basis of good adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties using SwissADME, MedChem Designer v.3, and MOLINSPIRATION. Stability of the binding mode of the inhibitors was further confirmed by molecular dynamic simulation study with AMBER v15 for a simulation time of 50 ns in aqueous environment. PM2307 was identified as the best inhibitor in terms of pharmacophoric features, dock score, and in silico ADMET analysis. The calculated binding affinity of PM2307 was better than that of the FAT-Grb2 complex as well as a previously reported small molecule inhibitor. PM2307 is also a quinolyl derivative sharing a similar scaffold with ofloxacin drugs, asserting its drug-like properties. Thus, it was proposed as a lead compound for development of drugs for pathological cardiac hypertrophy.
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Affiliation(s)
- Pallavi Mohanty
- Computational and Structural Biology Laboratory, Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, India
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26
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Lee J, Kang M, Kim S, Chang I. Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity. PLoS Comput Biol 2020; 16:e1007405. [PMID: 32315300 PMCID: PMC7173763 DOI: 10.1371/journal.pcbi.1007405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/13/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding the gating mechanism of ion channel proteins is key to understanding the regulation of cell signaling through these channels. Channel opening and closing are regulated by diverse environmental factors that include temperature, electrical voltage across the channel, and proton concentration. Low permeability in voltage-gated potassium ion channels (Kv) is intimately correlated with the prolonged action potential duration observed in many acidosis diseases. The Kv channels consist of voltage-sensing domains (S1-S4 helices) and central pore domains (S5-S6 helices) that include a selectivity filter and water-filled cavity. The voltage-sensing domain is responsible for the voltage-gating of Kv channels. While the low permeability of Kv channels to potassium ion is highly correlated with the cellular proton concentration, it is unclear how an intracellular acidic condition drives their closure, which may indicate an additional pH-dependent gating mechanism of the Kv family. Here, we show that two residues E327 and H418 in the proximity of the water cavity of Kv1.2 play crucial roles as a pH switch. In addition, we present a structural and molecular concept of the pH-dependent gating of Kv1.2 in atomic detail, showing that the protonation of E327 and H418 disrupts the electrostatic balance around the S6 helices, which leads to a straightening transition in the shape of their axes and causes dewetting of the water-filled cavity and closure of the channel. Our work offers a conceptual advancement to the regulation of the pH-dependent gating of various voltage-gated ion channels and their related biological functions.
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Affiliation(s)
- Juhwan Lee
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Department of Emerging Material Sciences, DGIST, Daegu, Korea
- Core Protein Resources Center, DGIST, Daegu, Korea
| | - Mooseok Kang
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, Korea
| | - Sangyeol Kim
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
- * E-mail: (SK); (IC)
| | - Iksoo Chang
- Center for Proteome Biophysics, DGIST, Daegu, Korea
- Core Protein Resources Center, DGIST, Daegu, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
- * E-mail: (SK); (IC)
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27
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Esmaeilpour D, Hussein A, Almalki F, Shityakov S, Bordbar A. Probing inclusion complexes of 2-hydroxypropyl-β-cyclodextrin with mono-amino mono-carboxylic acids: physicochemical specification, characterization and molecular modeling. Heliyon 2020; 6:e03360. [PMID: 32322699 PMCID: PMC7160434 DOI: 10.1016/j.heliyon.2020.e03360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/20/2019] [Accepted: 01/31/2020] [Indexed: 01/28/2023] Open
Abstract
Density (ρ), viscosity (η) and surface tension (γ) of three amino acids (valine, alanine, and glycine) have been measured at a different mass fraction (0.002 - 0.009) of aqueous hydroxypropyl-β-cyclodextrin (HPβCD) mixtures and different temperatures (278.15 - 295.15 K). The formation of inclusion complexes has been analyzed via evaluating the amounts of apparent and limiting apparent molar volumes, limiting apparent molar expansibilities, activation energy, kinematic, relative, intrinsic, spatial, and dynamic viscosities. The surface tension studies indicated that the inclusion complexes have been formed with 1:1 stoichiometry and mediated by hydrophobic effects and electrostatic forces. Additionally, the ρ and η parameters were evaluated by molecular modeling experiments to provide more details on the mechanisms of the complexation.
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Affiliation(s)
| | - A.A. Hussein
- College of Dentistry, University of Al-Ameed, Karbala, Iraq
- Department of Chemistry, University of Southampton, Southampton, Hampshire, UK
| | - F.A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - S. Shityakov
- Department of Bioinformatics, University of Würzburg, Germany
- Corresponding author.
| | - A.K. Bordbar
- Department of Chemistry, University of Isfahan, Iran
- California Institute of Quantitative Biosciences, University of California, Berkeley, California, USA
- Corresponding author.
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28
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Gupta S, Gupta V. Homology modeling, structural insights and in-silico screening for selective inhibitors of mycobacterial CysE. J Biomol Struct Dyn 2020; 39:1547-1560. [PMID: 32093568 DOI: 10.1080/07391102.2020.1734089] [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] [Indexed: 01/27/2023]
Abstract
Tuberculosis posses a major threat for health practitioners due to lengthy treatment regimen, increase in the drug-resistant strains of Mycobacterium tuberculosis (M. tb) and unavailability of drugs for its persistent form. Therefore, there is an urgent need for discovery of new and improved anti-tubercular drugs. In M. tb, the two step de novo biosynthesis of L-cysteine, an essential metabolic pathway is reported to be up-regulated in the persistent phase of the organism, involves two enzymes CysE and CysK. Although, structural insights for rational drug discovery are available for the later, not much information is known for the former. This study proposes a 3-dimensional model of M. tb CysE followed by in-silico screening of 67,030 anti-tuberculosis bioactive compounds. Subsequently, post-processing of 1000 best hits was carried out and top 200 compounds thus obtained were docked into the active site cleft of E. coli homologue as a control, but revealed unexpected results. Differences in the active site architectures and comparative analysis of molecular electrostatic potentials between the two CysEs provide molecular basis for the compounds C1, C3, C4 and C7 exhibiting preferential binding for M. tb CysE. In addition, shorter N-terminus along with positive and irregular trimeric base of M. tb CysE indicates its biological assembly as trimer. Based on mapping of residues involved in cysteine sensitivity on to the model structure of M. tb CysE, it is hypothesized that feedback inhibition of this homologue by cysteine may be affected.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunita Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Vibha Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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29
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Diem M, Oostenbrink C. Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. J Chem Inf Model 2020; 60:279-288. [PMID: 31873012 DOI: 10.1021/acs.jcim.9b01034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations of proteins depend critically on the underlying force field, which may be parameterized against experimental data or high-quality quantum calculations. Here, we develop search algorithms based on Monte Carlo and steepest descent calculations to optimize the backbone dihedral angle parameters from a single reference simulation. We apply these tools to improve the agreement between simulations of single, capped amino acids and experimentally determined J values and secondary structure propensities of these molecules. The parameters are further refined based on simulations of a set of seven proteins and finally validated in simulations on a large set of 52 protein structures. Improvements in the dihedral angle distributions are observed, and structural propensities of the proteins are reproduced very well. Overall, the GROMOS 54A8_bb parameter set forms an improvement to previous parameter sets, both for small molecules and for protein simulations.
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Affiliation(s)
- Matthias Diem
- Institute for Molecular Modeling and Simulation , University of Natural Resources and Life Sciences , Muthgasse 18 , 1190 Vienna , Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation , University of Natural Resources and Life Sciences , Muthgasse 18 , 1190 Vienna , Austria
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30
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Qu F, ElOmari K, Wagner A, De Simone A, Beis K. Desolvation of the substrate-binding protein TauA dictates ligand specificity for the alkanesulfonate ABC importer TauABC. Biochem J 2019; 476:3649-3660. [PMID: 31802112 PMCID: PMC6906117 DOI: 10.1042/bcj20190779] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/02/2022]
Abstract
Under limiting sulfur availability, bacteria can assimilate sulfur from alkanesulfonates. Bacteria utilize ATP-binding cassette (ABC) transporters to internalise them for further processing to release sulfur. In gram-negative bacteria the TauABC and SsuABC ensure internalization, although, these two systems have common substrates, the former has been characterized as a taurine specific system. TauA and SsuA are substrate-binding proteins (SBPs) that bind and bring the alkanesulfonates to the ABC importer for transport. Here, we have determined the crystal structure of TauA and have characterized its thermodynamic binding parameters by isothermal titration calorimetry in complex with taurine and different alkanesulfonates. Our structures revealed that the coordination of the alkanesulfonates is conserved, with the exception of Asp205 that is absent from SsuA, but the thermodynamic parameters revealed a very high enthalpic penalty cost for binding of the other alkanesulfonates relative to taurine. Our molecular dynamic simulations indicated that the different levels of hydration of the binding site contributed to the selectivity for taurine over the other alkanesulfonates. Such selectivity mechanism is very likely to be employed by other SBPs of ABC transporters.
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Affiliation(s)
- Feng Qu
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
| | - Kamel ElOmari
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Armin Wagner
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
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31
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Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J Chem Theory Comput 2019; 16:528-552. [PMID: 31714766 DOI: 10.1021/acs.jctc.9b00591] [Citation(s) in RCA: 868] [Impact Index Per Article: 173.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.
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Affiliation(s)
- Chuan Tian
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Koushik Kasavajhala
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Kellon A A Belfon
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Lauren Raguette
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Angela N Migues
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - John Bickel
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Yuzhang Wang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jorge Pincay
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Qin Wu
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Carlos Simmerling
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
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32
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Altan I, Khan AR, James S, Quinn MK, McManus JJ, Charbonneau P. Using Schematic Models to Understand the Microscopic Basis for Inverted Solubility in γD-Crystallin. J Phys Chem B 2019; 123:10061-10072. [PMID: 31557434 DOI: 10.1021/acs.jpcb.9b07774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inverted solubility-melting a crystal by cooling-is observed in a handful of proteins, such as carbomonoxy hemoglobin C and γD-crystallin. In human γD-crystallin, the phenomenon is associated with the mutation of the 23rd residue, a proline, to a threonine, serine, or valine. One proposed microscopic mechanism entails an increase in surface hydrophobicity upon mutagenesis. Recent crystal structures of a double mutant that includes the P23T mutation allow for a more careful investigation of this proposal. Here, we first measure the surface hydrophobicity of various mutant structures of γD-crystallin and discern no notable increase in hydrophobicity upon mutating the 23rd residue. We then investigate the solubility inversion regime with a schematic patchy particle model that includes one of three variants of temperature-dependent patch energies: two of the hydrophobic effect, and one of a more generic nature. We conclude that, while solubility inversion due to the hydrophobic effect may be possible, microscopic evidence to support it in γD-crystallin is weak. More generally, we find that solubility inversion requires a fine balance between patch strengths and their temperature-dependent component, which may explain why inverted solubility is not commonly observed in proteins. We also find that the temperature-dependent interaction has only a negligible impact on liquid-liquid phase boundaries of γD-crystallin, in line with previous experimental observations.
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Affiliation(s)
| | - Amir R Khan
- School of Biochemistry and Immunology , Trinity College Dublin , Dublin , Ireland
| | - Susan James
- Department of Chemistry , Maynooth University , Maynooth , Ireland
| | - Michelle K Quinn
- Department of Chemistry , Maynooth University , Maynooth , Ireland
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33
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Zhang D, Lazim R. Exploring indole channeling in tryptophan synthase using steered molecular dynamics simulation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Pavlin M, Gelsomino L, Barone I, Spinello A, Catalano S, Andò S, Magistrato A. Structural, Thermodynamic, and Kinetic Traits of Antiestrogen-Compounds Selectively Targeting the Y537S Mutant Estrogen Receptor α Transcriptional Activity in Breast Cancer Cell Lines. Front Chem 2019; 7:602. [PMID: 31552220 PMCID: PMC6737084 DOI: 10.3389/fchem.2019.00602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/15/2019] [Indexed: 12/14/2022] Open
Abstract
The most frequently diagnosed cancers in women are the estrogen receptor (ER)-positive breast cancer subtypes, which are characterized by estrogen dependency for their growth. The mainstay of clinical treatment for this tumor relies on the modulation of ERα action or on the suppression of estrogen biosynthesis via the administration of Selective ERα Modulators/Down-regulators (SERMs/SERDs) or aromatase inhibitors, respectively. Nevertheless, de novo and acquired resistance to these therapies frequently occurs and represents a major clinical concern for patient survival. Recently, somatic mutations affecting the hormone-binding domain of ERα (i.e., Y537S, Y537N, D538G) have been associated with endocrine resistance, disease relapse and increased mortality rates. Hence, devising novel therapies against these ERα isoforms represents a daunting challenge. Here, we identified five molecules active on recurrent Y537S ERα polymorphism by employing in silico virtual screening on commercial databases of molecules, complemented by ER-transactivation and MTT assays in MCF7 and MDA-MB-231 breast cancer cells expressing wild type or mutated ERα. Among them, one molecule selectively targets Y537S ERα without inducing any cytotoxicity in breast cell lines. Multi-microseconds (4.5 μs) of biased and unbiased molecular dynamics provided an atomic-level picture of the structural, thermodynamics (i.e., binding free energies) and the kinetic (i.e., dissociation free energy barriers) of these active ligands as compared to clinically used SERM/SERDs upon binding to wild type and distinct ERα variants (Y537S, Y537N, D538G). This study contributes to a dissection of the key molecular traits needed by drug-candidates to hamper the agonist (active)-like conformation of ERα, normally selected by those polymorphic variants. This information can be useful to discover mutant specific drug-candidates, enabling to move a step forward toward tailored approaches for breast cancer treatment.
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Affiliation(s)
- Matic Pavlin
- National Research Council - Institute of Materials (IOM) at International School for Advanced Studies (ISAS), Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutrition Sciences, Centro Sanitario, University of Calabria, Rende, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutrition Sciences, Centro Sanitario, University of Calabria, Rende, Italy
| | - Angelo Spinello
- National Research Council - Institute of Materials (IOM) at International School for Advanced Studies (ISAS), Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutrition Sciences, Centro Sanitario, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutrition Sciences, Centro Sanitario, University of Calabria, Rende, Italy
| | - Alessandra Magistrato
- National Research Council - Institute of Materials (IOM) at International School for Advanced Studies (ISAS), Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
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35
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Lenarčič T, Pirc K, Hodnik V, Albert I, Borišek J, Magistrato A, Nürnberger T, Podobnik M, Anderluh G. Molecular basis for functional diversity among microbial Nep1-like proteins. PLoS Pathog 2019; 15:e1007951. [PMID: 31479498 PMCID: PMC6743777 DOI: 10.1371/journal.ppat.1007951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/13/2019] [Accepted: 06/29/2019] [Indexed: 11/18/2022] Open
Abstract
Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by several phytopathogenic microorganisms. They trigger necrosis in various eudicot plants upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Interestingly, HaNLP3 from the obligate biotroph oomycete Hyaloperonospora arabidopsidis does not induce necrosis. We determined the crystal structure of HaNLP3 and showed that it adopts the NLP fold. However, the conformations of the loops surrounding the GIPC headgroup-binding cavity differ from those of cytotoxic Pythium aphanidermatum NLPPya. Essential dynamics extracted from μs-long molecular dynamics (MD) simulations reveals a limited conformational plasticity of the GIPC-binding cavity in HaNLP3 relative to toxic NLPs. This likely precludes HaNLP3 binding to GIPCs, which is the underlying reason for the lack of toxicity. This study reveals that mutations at key protein regions cause a switch between non-toxic and toxic phenotypes within the same protein scaffold. Altogether, these data provide evidence that protein flexibility is a distinguishing trait of toxic NLPs and highlight structural determinants for a potential functional diversification of non-toxic NLPs utilized by biotrophic plant pathogens.
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Affiliation(s)
- Tea Lenarčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
| | - Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva, Ljubljana, Slovenia
| | - Isabell Albert
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle, Tübingen, Germany
| | - Jure Borišek
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle, Tübingen, Germany
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- * E-mail: (MP); (GA)
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- * E-mail: (MP); (GA)
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36
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Zhou Y, Zou R, Kuang G, Långström B, Halldin C, Ågren H, Tu Y. Enhanced Sampling Simulations of Ligand Unbinding Kinetics Controlled by Protein Conformational Changes. J Chem Inf Model 2019; 59:3910-3918. [DOI: 10.1021/acs.jcim.9b00523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yang Zhou
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Rongfeng Zou
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Bengt Långström
- Department of Chemistry, Uppsala University, Uppsala 75123, Sweden
| | - Christer Halldin
- Department of Clinical Neuroscience, Center for Psychiatric Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
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37
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Structure and dynamics of Trichoderma harzianum Cel7B suggest molecular architecture adaptations required for a wide spectrum of activities on plant cell wall polysaccharides. Biochim Biophys Acta Gen Subj 2019; 1863:1015-1026. [DOI: 10.1016/j.bbagen.2019.03.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 11/19/2022]
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38
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Ritacco I, Spinello A, Ippoliti E, Magistrato A. Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme. J Chem Inf Model 2019; 59:2930-2940. [PMID: 31033287 DOI: 10.1021/acs.jcim.9b00157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Phosphorylation by kinases enzymes is a widespread regulatory mechanism able of rapidly altering the function of target proteins. Among these are cytochrome P450s (CYP450), a superfamily of enzymes performing the oxidation of endogenous and exogenous substrates thanks to the electron supply of a redox partner. In spite of its pivotal role, the molecular mechanism by which phosphorylation modulates CYP450s metabolism remains elusive. Here by performing microsecond-long all-atom molecular dynamics simulations, we disclose how phosphorylation regulates estrogen biosynthesis, catalyzed by the Human Aromatase (HA) enzyme. Namely, we unprecedentedly propose that HA phosphorylation at Y361 markedly stabilizes its adduct with the flavin mononucleotide domain of CYP450s reductase (CPR), the redox partner of microsomal CYP450s, and a variety of other proteins. With CPR present at physiological conditions in a limiting ratio with respect to its multiple oxidative partners, the enhanced stability of the CPR/HA adduct may favor HA in the competition with the other proteins requiring CPR's electron supply, ultimately facilitating the electron transfer and estrogen biosynthesis. As a result, our work elucidates at atomic-level the post-translational regulation of CYP450s catalysis. Given the potential for rational clinical management of diseases associated with steroid metabolism disorders, unraveling this mechanism is of utmost importance, and raises the intriguing perspective of exploiting this knowledge to devise novel therapies.
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Affiliation(s)
- Ida Ritacco
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
| | - Angelo Spinello
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
| | - Emiliano Ippoliti
- IAS-5/INM-9 Computational Biomedicine Institute and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Straße , 52425 Jülich , Germany
| | - Alessandra Magistrato
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
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39
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Abstract
One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here, I derive equations for the equilibrium distributions generated by restrained ensemble simulations and the corresponding expected values of observables. My results suggest a method to restrain simulations so that they generate distributions that are minimally perturbed from the unbiased distributions while reproducing the experimental values of the observables within their measurement uncertainties.
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Affiliation(s)
- Huafeng Xu
- Silicon Therapeutics LLC, Boston, Massachusetts 02210, USA
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40
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Spinello A, Martini S, Berti F, Pennati M, Pavlin M, Sgrignani J, Grazioso G, Colombo G, Zaffaroni N, Magistrato A. Rational design of allosteric modulators of the aromatase enzyme: An unprecedented therapeutic strategy to fight breast cancer. Eur J Med Chem 2019; 168:253-262. [DOI: 10.1016/j.ejmech.2019.02.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022]
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41
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Qi HW, Kulik HJ. Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. J Chem Inf Model 2019; 59:2199-2211. [DOI: 10.1021/acs.jcim.9b00144] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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42
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Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures. Arch Biochem Biophys 2019; 664:76-88. [DOI: 10.1016/j.abb.2019.01.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/24/2022]
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43
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Wang J, Cieplak P, Luo R, Duan Y. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy. J Chem Theory Comput 2019; 15:1146-1158. [PMID: 30645118 PMCID: PMC7197406 DOI: 10.1021/acs.jctc.8b00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A set of atomic polarizability parameters for a new polarizable Gaussian model (pGM) has been developed with the goal to accurately reproduce the polarizability anisotropy, taking advantage of its ability to attenuate all short-range electrostatic interactions, by fitting the ab initio molecular polarizability tensors ( A pq) calculated at the B3LYP/aug-cc-pVTZ level. For comparison, we also rederived the parameters for three Thole models in which the 1-2 (bonded), 1-3 (separated by two bonds), and 1-4 (separated by three bonds) interactions are fully included. The average percent errors (APEs) of molecular polarizability tensors for 4842 molecules or dimers are 2.98, 3.76, 3.28, and 3.82% for the pGM, Thole linear, Thole exponential, and Thole Amoeba models, respectively, with atom-type independent, universal screening factors (USF). The APEs are reduced further to 2.30, 2.69, 2.25, and 2.48% for the four corresponding polarizable models with atom-type dependent, variable screening factors (VSF). It is encouraging that the pGM with variable screening factors achieved APEs of 1.83 for 1155 amino acid analogs, dipeptides, and tetrapeptides, 1.39 for 28 nucleic acid bases, 0.708 for 1464 water clusters, and 1.99 for 85 dimers of water and biological building blocks. Compared to the new set of models, the APEs of the old Thole models that were fitted to isotropic molecular polarizabilities are 8.7% for set A (without the 1-2 and 1-3 interactions) and 6.3% for set D (with the 1-2 and 1-3 interactions) models, respectively. MPAD, a metric of molecular polarization anisotropy difference based on the diagonal terms of molecular polarizability tensors was defined and applied to assess the polarizable models in reproducing the ab initio molecular polarization anisotropy. The MPADs are 3.71, 4.70, 4.11, and 4.77% for the pGM, Thole linear, Thole exponential, and Thole Amoeba USF models, respectively. The APEs are reduced further to 2.85, 3.58, 2.90, and 3.15% for the four corresponding VSF models. Thus, the new pGM and Thole models notably improve molecular polarization anisotropy. Since pGM attenuates all short-range electrostatic interactions, its application is expected to improve stability in charge fitting, energy, and force calculations and the accuracy of multibody polarization.
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Affiliation(s)
- Junmei Wang
- Department of Pharmaceutical Sciences , University of Pittsburgh , 3501 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering , University of California, Irvine , Irvine , California 92697 , United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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44
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Zhou S, Zhu Y, Yao X, Liu H. Carbon Nanoparticles Inhibit the Aggregation of Prion Protein as Revealed by Experiments and Atomistic Simulations. J Chem Inf Model 2018; 59:1909-1918. [DOI: 10.1021/acs.jcim.8b00725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shuangyan Zhou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yongchang Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
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45
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Anandakrishnan R, Izadi S, Onufriev AV. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model. J Chem Theory Comput 2018; 15:625-636. [DOI: 10.1021/acs.jctc.8b00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramu Anandakrishnan
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia 24060, United States
| | - Saeed Izadi
- Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, California 94080, United States
| | - Alexey V. Onufriev
- Department of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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46
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Huang H, Simmerling C. Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs. J Chem Theory Comput 2018; 14:5797-5814. [PMID: 30303377 DOI: 10.1021/acs.jctc.8b00413] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a pairwise and readily parallelizable SASA-based nonpolar solvation approach for protein simulations, inspired by our previous pairwise GB polar solvation model development. In this work, we developed a novel function to estimate the atomic and molecular SASAs of proteins, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values. Implemented in Amber software and tested on consumer GPUs, our pwSASA method reasonably reproduces LCPO simulation results, but accelerates MD simulations up to 30 times compared to the LCPO implementation, which is greatly desirable for protein simulations facing sampling challenges. The value of incorporating the nonpolar term in implicit solvent simulations is explored on a peptide fragment containing the hydrophobic core of HP36 and evaluating thermal stability profiles of four small proteins.
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Affiliation(s)
- He Huang
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
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47
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Collins AP, Anderson PC. Complete Coupled Binding-Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling. Biochemistry 2018; 57:4404-4420. [PMID: 29990433 DOI: 10.1021/acs.biochem.8b00441] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intrinsically disordered proteins (IDPs) make up a large class of proteins that lack stable structures in solution, existing instead as dynamic conformational ensembles. To perform their biological functions, many IDPs bind to other proteins or nucleic acids. Although IDPs are unstructured in solution, when they interact with binding partners, they fold into defined three-dimensional structures via coupled binding-folding processes. Because they frequently underlie IDP function, the mechanisms of this coupled binding-folding process are of great interest. However, given the flexibility inherent to IDPs and the sparse populations of intermediate states, it is difficult to reveal binding-folding pathways at atomic resolution using experimental methods. Computer simulations are another tool for studying these pathways at high resolution. Accordingly, we have applied 40 μs of unbiased molecular dynamics simulations and Markov state modeling to map the complete binding-folding pathway of a model IDP, the 59-residue C-terminal portion of the DNA binding domain of Drosophila melanogaster transcription factor Brinker (BrkDBD). Our modeling indicates that BrkDBD binds to its cognate DNA and folds in ∼50 μs by an induced fit mechanism, acquiring most of its stable secondary and tertiary structure only after it reaches the final binding site on the DNA. The protein follows numerous pathways en route to its bound and folded conformation, occasionally becoming stuck in kinetic traps. Each binding-folding pathway involves weakly bound, increasingly folded intermediate states located at different sites on the DNA surface. These findings agree with experimental data and provide additional insight into the BrkDBD folding mechanism and kinetics.
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Affiliation(s)
- Andrew P Collins
- Physical Sciences Division , University of Washington Bothell , Bothell , Washington 98011-8246 , United States
| | - Peter C Anderson
- Physical Sciences Division , University of Washington Bothell , Bothell , Washington 98011-8246 , United States
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48
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Reiter S, Keefer D, de Vivie-Riedle R. RNA Environment Is Responsible for Decreased Photostability of Uracil. J Am Chem Soc 2018; 140:8714-8720. [DOI: 10.1021/jacs.8b02962] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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49
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Spinello A, Pavlin M, Casalino L, Magistrato A. A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme? Chemistry 2018; 24:10840-10849. [DOI: 10.1002/chem.201802025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Matic Pavlin
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Lorenzo Casalino
- International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
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50
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Zhao X, Li R, Zhou Y, Xiao M, Ma C, Yang Z, Zeng S, Du Q, Yang C, Jiang H, Hu Y, Wang K, Mok CKP, Sun P, Dong J, Cui W, Wang J, Tu Y, Yang Z, Hu W. Discovery of Highly Potent Pinanamine-Based Inhibitors against Amantadine- and Oseltamivir-Resistant Influenza A Viruses. J Med Chem 2018; 61:5187-5198. [PMID: 29799746 DOI: 10.1021/acs.jmedchem.8b00042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Influenza pandemic is a constant major threat to public health caused by influenza A viruses (IAVs). IAVs are subcategorized by the surface proteins hemagglutinin (HA) and neuraminidase (NA), in which they are both essential targets for drug discovery. While it is of great concern that NA inhibitor oseltamivir resistant strains are frequently identified from human or avian influenza virus, structural and functional characterization of influenza HA has raised hopes for new antiviral therapies. In this study, we explored a structure-activity relationship (SAR) of pinanamine-based antivirals and discovered a potent inhibitor M090 against amantadine-resistant viruses, including the 2009 H1N1 pandemic strains, and oseltamivir-resistant viruses. Mechanism of action studies, particularly hemolysis inhibition, indicated that M090 targets influenza HA and it occupied a highly conserved pocket of the HA2 domain and inhibited virus-mediated membrane fusion by "locking" the bending state of HA2 during the conformational rearrangement process. This work provides new binding sites within the HA protein and indicates that this pocket may be a promising target for broad-spectrum anti-influenza A drug design and development.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China.,Department of Pharmacology and Toxicology, College of Pharmacy , The University of Arizona , Tucson , Arizona 85721 , United States
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China
| | - Yang Zhou
- Division of Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology (KTH), AlbaNova University Center , Stockholm SE-100 44 , Sweden
| | - Mengjie Xiao
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy , The University of Arizona , Tucson , Arizona 85721 , United States.,BIO5 Institute , The University of Arizona , Tucson , Arizona 85721 , United States
| | - Zhongjin Yang
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China
| | - Shaogao Zeng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China
| | - Qiuling Du
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China
| | - Chunguang Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy , The University of Arizona , Tucson , Arizona 85721 , United States.,BIO5 Institute , The University of Arizona , Tucson , Arizona 85721 , United States
| | - Kefeng Wang
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China.,HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine , The University of Hong Kong , 5 Sassoon Road , Pokfulam , Hong Kong
| | - Ping Sun
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China
| | - Jianghong Dong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China
| | - Wei Cui
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy , The University of Arizona , Tucson , Arizona 85721 , United States.,BIO5 Institute , The University of Arizona , Tucson , Arizona 85721 , United States
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology , Royal Institute of Technology (KTH), AlbaNova University Center , Stockholm SE-100 44 , Sweden
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital , Guangzhou Medical University , Guangzhou 510120 , P. R. China
| | - Wenhui Hu
- State Key Laboratory of Respiratory Disease, Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , P. R. China.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , P. R. China
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