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Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O. Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM. J Am Chem Soc 2023; 145:8583-8592. [PMID: 37023263 PMCID: PMC10119980 DOI: 10.1021/jacs.3c01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/08/2023]
Abstract
Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.
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Affiliation(s)
- Yun Huang
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Krishna D. Reddy
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Clay Bracken
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Biao Qiu
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Wenhu Zhan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - David Eliezer
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Olga Boudker
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
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2
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Chen Y, Luo Z, Lin J, Qi B, Sun Y, Li F, Guo C, Lin W, Kang X, He X, Wang Q, Chen S, Chen J. Exploring the Potential Mechanisms of Melilotus officinalis (L.) Pall. in Chronic Muscle Repair Patterns Using Single Cell Receptor-Ligand Marker Analysis and Molecular Dynamics Simulations. DISEASE MARKERS 2022; 2022:9082576. [PMID: 35692879 PMCID: PMC9177293 DOI: 10.1155/2022/9082576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/28/2022] [Accepted: 04/26/2022] [Indexed: 02/07/2023]
Abstract
Information regarding the function of Melilotus officinalis (L.) Pall. in skeletal muscles is still unknown. In this study, we explored the possible regulatory targets of M. (L.) Pall. that affects the repair patterns in chronic muscle injury. We analyzed the potential target genes and chemical composition of M. (L.) Pall. and constructed a "drug-component-disease target genes" network analysis. Five active ingredients and 87 corresponding targets were obtained. Muscle-tendon junction (MTJ) cells were used to perform receptor-ligand marker analysis using the CellphoneDB algorithm. Targets of M. (L.) Pall. were screened further for the cellular ligand-receptor protein action on MTJs. Enrichment analysis suggests that those protein-associated ligand receptors may be associated with a range of intercellular signaling pathways. Molecular docking validation was then performed. Five proteins (CCL2, VEGFA, MMP2, MET, and EGFR) may be regulated by the active ingredient luteolin and scoparone. Finally, molecular dynamics simulations revealed that luteolin can stably target binding to MMP2. M. (L.) Pall. influences skeletal muscle repair patterns by affecting the fibroblast interactions in the muscle-tendon junctions through the active ingredients luteolin and scoparone.
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Affiliation(s)
- Yisheng Chen
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhiwen Luo
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Beijie Qi
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangqi Li
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Chenyang Guo
- 2Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Weiwei Lin
- 3Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou, 310009 Zhejiang, China
| | - Xueran Kang
- 4Shanghai Jiao Tong University, Shanghai 200080, China
| | - Xinyi He
- 5State Key Laboratory of Genetics Engineering, Collaborative Innovation Center for Genetics and Development, School Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Qian Wang
- 6Postdoctoral Workstation, Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian 271000, China
| | - Shiyi Chen
- 1Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiwu Chen
- 2Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
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3
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Goldstein M, Goodey NM. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2253:185-219. [PMID: 33315225 DOI: 10.1007/978-1-0716-1154-8_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein motions play a fundamental role in enzyme catalysis and ligand binding. The relationship between protein motion and function has been extensively investigated in the model enzyme dihydrofolate reductase (DHFR). DHFR is an essential enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. Numerous experimental and computational methods have been used to probe the motions of DHFR through the catalytic cycle and to investigate the effect of distal mutations on DHFR motions and ligand binding. These experimental investigations have pushed forward the study of protein motions and their role in protein-ligand interactions. The introduction of mutations distal to the active site has been shown to have profound effects on ligand binding, hydride transfer rates and catalytic efficacy and these changes are captured by enzyme kinetics measurements. Distal mutations have been shown to exert their effects through a network of correlated amino acids and these effects have been investigated by NMR, protein dynamics, and analysis of coupled amino acids. The experimental methods and the findings that are reviewed here have broad implications for our understanding of enzyme mechanisms, ligand binding and for the future design and discovery of enzyme inhibitors.
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Affiliation(s)
- Melanie Goldstein
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA
| | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
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4
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Helliwell JR. What is the structural chemistry of the living organism at its temperature and pressure? Acta Crystallogr D Struct Biol 2020; 76:87-93. [PMID: 32038039 PMCID: PMC7008516 DOI: 10.1107/s2059798320000546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/02/2022] Open
Abstract
The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature will never be performed at room temperature, crystallization often requires nonphysiological chemical conditions, and X-rays and electrons cause beam damage. However, integrated structural biology techniques and functional assays provide a package towards physiological relevance of any given study. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are, as discussed in detail in this feature article.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, England
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5
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Pinpointing dynamic coupling in enzymes for efficient drug design. Future Sci OA 2016; 2:FSO95. [PMID: 28031945 PMCID: PMC5137909 DOI: 10.4155/fsoa.2015.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 11/17/2022] Open
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6
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Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res 2015; 48:482-9. [PMID: 25565178 PMCID: PMC4334233 DOI: 10.1021/ar500390e] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes
are essential for all living organisms, and their effectiveness as
chemical catalysts has driven more than a half century of research
seeking to understand the enormous rate enhancements they provide.
Nevertheless, a complete understanding of the factors that govern
the rate enhancements and selectivities of enzymes remains elusive,
due to the extraordinary complexity and cooperativity that are the
hallmarks of these biomolecules. We have used a combination of site-directed
mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear
magnetic resonance (NMR), vibrational and fluorescence spectroscopies,
resonance energy transfer, and computer simulations to study the implications
of conformational motions and electrostatic interactions on enzyme
catalysis in the enzyme dihydrofolate reductase (DHFR). We have
demonstrated that modest equilibrium conformational changes are functionally
related to the hydride transfer reaction. Results obtained for mutant
DHFRs illustrated that reductions in hydride transfer rates are correlated
with altered conformational motions, and analysis of the evolutionary
history of DHFR indicated that mutations appear to have occurred to
preserve both the hydride transfer rate and the associated conformational
changes. More recent results suggested that differences in local electrostatic
environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination
of primary and solvent kinetic isotope effects, we demonstrated that
the reaction mechanism is consistent across a broad pH range, and
computer simulations suggested that deprotonation of the active site
Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into
the ecDHFR active site provided an experimental tool
for interrogating these microenvironments and for investigating changes
in electrostatics along the DHFR catalytic cycle. Complementary molecular
dynamics simulations in conjunction with mixed quantum mechanical/molecular
mechanical calculations accurately reproduced the vibrational frequency
shifts in these probes and provided atomic-level insight into the
residues influencing these changes. Our findings indicate that conformational
and electrostatic changes are intimately related and functionally
essential. This approach can be readily extended to the study of other
enzyme systems to identify more general trends in the relationship
between conformational fluctuations and electrostatic interactions.
These results are relevant to researchers seeking to design novel
enzymes as well as those seeking to develop therapeutic agents that
function as enzyme inhibitors.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - C. Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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7
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Godwin RC, Melvin R, Salsbury FR. Molecular Dynamics Simulations and Computer-Aided Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2015. [DOI: 10.1007/7653_2015_41] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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9
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Lukman S, Verma CS, Fuentes G. Exploiting Protein Intrinsic Flexibility in Drug Design. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:245-69. [DOI: 10.1007/978-3-319-02970-2_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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10
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LaPlante SR, Bös M, Brochu C, Chabot C, Coulombe R, Gillard JR, Jakalian A, Poirier M, Rancourt J, Stammers T, Thavonekham B, Beaulieu PL, Kukolj G, Tsantrizos YS. Conformation-based restrictions and scaffold replacements in the design of hepatitis C virus polymerase inhibitors: discovery of deleobuvir (BI 207127). J Med Chem 2013; 57:1845-54. [PMID: 24159919 DOI: 10.1021/jm4011862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational restrictions of flexible torsion angles were used to guide the identification of new chemotypes of HCV NS5B inhibitors. Sites for rigidification were based on an acquired conformational understanding of compound binding requirements and the roles of substituents in the free and bound states. Chemical bioisosteres of amide bonds were explored to improve cell-based potency. Examples are shown, including the design concept that led to the discovery of the phase III clinical candidate deleobuvir (BI 207127). The structure-based strategies employed have general utility in drug design.
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Affiliation(s)
- Steven R LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5
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11
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LaPlante SR, Nar H, Lemke CT, Jakalian A, Aubry N, Kawai SH. Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. J Med Chem 2013; 57:1777-89. [PMID: 24144444 DOI: 10.1021/jm401338c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds. All adopt similar bioactive conformations for the common core derived from the hit peptide DDIVPC. A carefully designed SAR analysis, based on the advanced inhibitor 1 in which the P1 to P3 side chains and the N-terminal Boc were sequentially truncated, revealed a correlation between affinity and the relative predominance of the bioactive conformation in the free state. Interestingly, synergistic conformation effects on potency were also noted. Comparisons with clinical and recently marketed drugs from the pharmaceutical industry showed that all have the same core and similar bioactive conformations. This suggested that the variety of appendages discovered for these compounds also properly satisfy the bioactive conformation requirements and allowed for a large variety of HCV protease drug candidates to be designed.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer-Ingelheim (Canada) Ltd., Research and Development , Laval, Québec H7S 2G5, Canada
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12
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13
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Hughes TS, Chalmers MJ, Novick S, Kuruvilla DS, Chang MR, Kamenecka TM, Rance M, Johnson BA, Burris TP, Griffin PR, Kojetin DJ. Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism. Structure 2012; 20:139-50. [PMID: 22244763 DOI: 10.1016/j.str.2011.10.018] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 12/31/2022]
Abstract
Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution nuclear magnetic resonance (NMR) studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators.
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Affiliation(s)
- Travis S Hughes
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
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14
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Pagano K, Torella R, Foglieni C, Bugatti A, Tomaselli S, Zetta L, Presta M, Rusnati M, Taraboletti G, Colombo G, Ragona L. Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule. PLoS One 2012; 7:e36990. [PMID: 22606323 PMCID: PMC3351436 DOI: 10.1371/journal.pone.0036990] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/11/2012] [Indexed: 11/18/2022] Open
Abstract
Fibroblast growth factors (FGFs) are recognized targets for the development of therapies against angiogenesis-driven diseases, including cancer. The formation of a ternary complex with the transmembrane tyrosine kinase receptors (FGFRs), and heparan sulphate proteoglycans (HSPGs) is required for FGF2 pro-angiogenic activity. Here by using a combination of techniques including Nuclear Magnetic Resonance, Molecular Dynamics, Surface Plasmon Resonance and cell-based binding assays we clarify the molecular mechanism of inhibition of an angiostatic small molecule, sm27, mimicking the endogenous inhibitor of angiogenesis, thrombospondin-1. NMR and MD data demonstrate that sm27 engages the heparin-binding site of FGF2 and induces long-range dynamics perturbations along FGF2/FGFR1 interface regions. The functional consequence of the inhibitor binding is an impaired FGF2 interaction with both its receptors, as demonstrated by SPR and cell-based binding assays. We propose that sm27 antiangiogenic activity is based on a twofold-direct and allosteric-mechanism, inhibiting FGF2 binding to both its receptors.
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Affiliation(s)
- Katiuscia Pagano
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Rubben Torella
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Chiara Foglieni
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Bergamo, Italy
| | - Antonella Bugatti
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Simona Tomaselli
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Lucia Zetta
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Marco Presta
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Marco Rusnati
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Giulia Taraboletti
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Bergamo, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
- * E-mail: (LR); (GC)
| | - Laura Ragona
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
- * E-mail: (LR); (GC)
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15
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Fernández A, Fraser C, Scott LR. Purposely engineered drug–target mismatches for entropy-based drug optimization. Trends Biotechnol 2012; 30:1-7. [DOI: 10.1016/j.tibtech.2011.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/13/2011] [Accepted: 07/13/2011] [Indexed: 12/11/2022]
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16
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Nichols SE, Swift RV, Amaro RE. Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem 2012; 12:2002-12. [PMID: 23110535 PMCID: PMC3636520 DOI: 10.2174/156802612804910313] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/27/2012] [Accepted: 08/27/2012] [Indexed: 12/05/2022]
Abstract
Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline.
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Affiliation(s)
- Sara E Nichols
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
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17
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Bieri M, Gooley PR. Automated NMR relaxation dispersion data analysis using NESSY. BMC Bioinformatics 2011; 12:421. [PMID: 22032230 PMCID: PMC3215250 DOI: 10.1186/1471-2105-12-421] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/27/2011] [Indexed: 11/11/2022] Open
Abstract
Background Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR) relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. Results The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. Conclusions NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.
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Affiliation(s)
- Michael Bieri
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic 3010, Australia
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18
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Carroll MJ, Gromova AV, Miller KR, Tang H, Wang XS, Tripathy A, Singleton SF, Collins EJ, Lee AL. Direct detection of structurally resolved dynamics in a multiconformation receptor-ligand complex. J Am Chem Soc 2011; 133:6422-8. [PMID: 21469679 DOI: 10.1021/ja2005253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structure-based drug design relies on static protein structures despite significant evidence for the need to include protein dynamics as a serious consideration. In practice, dynamic motions are neglected because they are not understood well enough to model, a situation resulting from a lack of explicit experimental examples of dynamic receptor-ligand complexes. Here, we report high-resolution details of pronounced ~1 ms time scale motions of a receptor-small molecule complex using a combination of NMR and X-ray crystallography. Large conformational dynamics in Escherichia coli dihydrofolate reductase are driven by internal switching motions of the drug-like, nanomolar-affinity inhibitor. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments and NOEs revealed the crystal structure to contain critical elements of the high energy protein-ligand conformation. The availability of accurate, structurally resolved dynamics in a protein-ligand complex should serve as a valuable benchmark for modeling dynamics in other receptor-ligand complexes and prediction of binding affinities.
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Affiliation(s)
- Mary J Carroll
- Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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19
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LaPlante SR, Gillard JR, Jakalian A, Aubry N, Coulombe R, Brochu C, Tsantrizos YS, Poirier M, Kukolj G, Beaulieu PL. Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B. J Am Chem Soc 2011; 132:15204-12. [PMID: 20942454 DOI: 10.1021/ja101358s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view must evolve to also include ligand shape and conformational changes. Here, we describe an example where a ligand's "structural hinge" influences potency by inducing an "L-shape" bioactive conformation, and due to its solvent exposure in the complex, reasonable conformation-activity-relationships can be qualitatively attributed. From a ligand design perspective, this feature was exploited by successful linker hopping to an alternate "structural hinge" that led to a new and promising chemical series which matched the ligand bioactive conformation and the pocket bioactive space. Using a combination of X-ray crystallography, NMR and modeling with support from binding-site resistance mutant studies and photoaffinity labeling experiments, we were able to derive inhibitor-polymerase complexes for various chemical series.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard St., Laval, Quebec, Canada, H7S2G5.
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20
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Stark JL, Powers R. Application of NMR and molecular docking in structure-based drug discovery. Top Curr Chem (Cham) 2011; 326:1-34. [PMID: 21915777 DOI: 10.1007/128_2011_213] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug discovery is a complex and costly endeavor, where few drugs that reach the clinical testing phase make it to market. High-throughput screening (HTS) is the primary method used by the pharmaceutical industry to identify initial lead compounds. Unfortunately, HTS has a high failure rate and is not particularly efficient at identifying viable drug leads. These shortcomings have encouraged the development of alternative methods to drive the drug discovery process. Specifically, nuclear magnetic resonance (NMR) spectroscopy and molecular docking are routinely being employed as important components of drug discovery research. Molecular docking provides an extremely rapid way to evaluate likely binders from a large chemical library with minimal cost. NMR ligand-affinity screens can directly detect a protein-ligand interaction, can measure a corresponding dissociation constant, and can reliably identify the ligand binding site and generate a co-structure. Furthermore, NMR ligand affinity screens and molecular docking are perfectly complementary techniques, where the combination of the two has the potential to improve the efficiency and success rate of drug discovery. This review will highlight the use of NMR ligand affinity screens and molecular docking in drug discovery and describe recent examples where the two techniques were combined to identify new and effective therapeutic drugs.
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Affiliation(s)
- Jaime L Stark
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
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Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 346] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
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Dynameomics: a comprehensive database of protein dynamics. Structure 2010; 18:423-35. [PMID: 20399180 DOI: 10.1016/j.str.2010.01.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 12/15/2022]
Abstract
The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (approximately 11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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