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Garduño-Juárez R, Tovar-Anaya DO, Perez-Aguilar JM, Lozano-Aguirre Beltran LF, Zubillaga RA, Alvarez-Perez MA, Villarreal-Ramirez E. Molecular Dynamic Simulations for Biopolymers with Biomedical Applications. Polymers (Basel) 2024; 16:1864. [PMID: 39000719 PMCID: PMC11244511 DOI: 10.3390/polym16131864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 07/17/2024] Open
Abstract
Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.
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Affiliation(s)
- Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - David O Tovar-Anaya
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | | | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Marco Antonio Alvarez-Perez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Eduardo Villarreal-Ramirez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
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2
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Favaro A, Sturlese M. A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments. J Med Chem 2024; 67:3874-3884. [PMID: 38426508 DOI: 10.1021/acs.jmedchem.3c02222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Fragment-based lead discovery has emerged as one of the most efficient screening strategies for finding hit molecules in drug discovery. Recently, a novel strategy based on a class of fragments characterized by an ultralow molecular weight (ULMW) has been proposed. These fragments bind to the target with a very low affinity, requiring reliable biophysical methods for detection. The most notable application of ULMW used a set of 81 fragments, named MiniFrags, and screened them by X-ray crystallography. We extended the utilization of this novel class of fragments to another gold standard technique for fragment-based screening: nuclear magnetic resonance (NMR). Here, we present a novel NMR protocol to detect and analyze such weak interactions in a challenging real-world scenario: a flexible target with a flat, water-exposed binding site. We identified a subset of 69 highly water-soluble MiniFrags that were screened against the antiapoptotic protein human Bfl-1.
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Affiliation(s)
- Annagiulia Favaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
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3
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Das S, Merz KM. Molecular Gas-Phase Conformational Ensembles. J Chem Inf Model 2024; 64:749-760. [PMID: 38206321 DOI: 10.1021/acs.jcim.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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4
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Schauenburg D, Weil T. Chemical Reactions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303396. [PMID: 37679060 PMCID: PMC10885656 DOI: 10.1002/advs.202303396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?
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Affiliation(s)
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
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5
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Xie B, Xu S, Schecterson L, Gumbiner BM, Sivasankar S. Strengthening E-cadherin adhesion via antibody-mediated binding stabilization. Structure 2024; 32:217-227.e3. [PMID: 38052206 PMCID: PMC10872345 DOI: 10.1016/j.str.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/10/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023]
Abstract
E-cadherins (Ecads) are a crucial cell-cell adhesion protein with tumor suppression properties. Ecad adhesion can be enhanced by the monoclonal antibody 66E8, which has potential applications in inhibiting cancer metastasis. However, the biophysical mechanisms underlying 66E8-mediated adhesion strengthening are unknown. Here, we use molecular dynamics simulations, site-directed mutagenesis, and single-molecule atomic force microscopy experiments to demonstrate that 66E8 strengthens Ecad binding by stabilizing the primary Ecad adhesive conformation: the strand-swap dimer. By forming electrostatic interactions with Ecad, 66E8 stabilizes the swapped β-strand and its hydrophobic pocket and impedes Ecad conformational changes, which are necessary for rupture of the strand-swap dimer. Our findings identify fundamental mechanistic principles for strengthening of Ecad binding using monoclonal antibodies.
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Affiliation(s)
- Bin Xie
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Shipeng Xu
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA
| | - Leslayann Schecterson
- Seattle Children's Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, USA
| | - Barry M Gumbiner
- Seattle Children's Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, USA
| | - Sanjeevi Sivasankar
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA; Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA.
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6
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Dangat Y, Freindorf M, Kraka E. Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study. J Am Chem Soc 2024; 146:145-158. [PMID: 38055807 DOI: 10.1021/jacs.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.
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Affiliation(s)
- Yuvraj Dangat
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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Xie B, Xu S, Schecterson L, Gumbiner BM, Sivasankar S. Strengthening E-cadherin adhesion via antibody mediated binding stabilization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547716. [PMID: 37461464 PMCID: PMC10350017 DOI: 10.1101/2023.07.04.547716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
E-cadherins (Ecads) are a crucial cell-cell adhesion protein with tumor suppression properties. Ecad adhesion can be enhanced by the monoclonal antibody 66E8, which has potential applications in inhibiting cancer metastasis. However, the biophysical mechanisms underlying 66E8 mediated adhesion strengthening are unknown. Here, we use molecular dynamics simulations, site directed mutagenesis and single molecule atomic force microscopy experiments to demonstrate that 66E8 strengthens Ecad binding by stabilizing the primary Ecad adhesive conformation: the strand-swap dimer. By forming electrostatic interactions with Ecad, 66E8 stabilizes the swapped β-strand and its hydrophobic pocket and impedes Ecad conformational changes, which are necessary for rupture of the strand-swap dimer. Our findings identify fundamental mechanistic principles for strengthening of Ecad binding using monoclonal antibodies.
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9
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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023; 18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. AREAS COVERED This review explores the relationship between X-ray crystallography and other modern structural determination methods. It examines the integration of data acquired from diverse biochemical and biophysical techniques with those derived from structural biology. Additionally, the paper offers insights into the influence of AI on X-ray crystallography, emphasizing how integrating AI with experimental approaches can revolutionize our comprehension of biological processes and interactions. EXPERT OPINION Investing in science is crucially emphasized due to its significant role in drug discovery and advancements in healthcare. X-ray crystallography remains an essential source of structural biology data for drug discovery. Recent advances in biochemical, spectroscopic, and bioinformatic methods, along with the integration of AI techniques, hold the potential to revolutionize drug discovery when effectively combined with robust data management practices.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Szczygiel
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
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Palma M. Epitopes and Mimotopes Identification Using Phage Display for Vaccine Development against Infectious Pathogens. Vaccines (Basel) 2023; 11:1176. [PMID: 37514992 PMCID: PMC10384025 DOI: 10.3390/vaccines11071176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional vaccines use inactivated or weakened forms of pathogens which could have side effects and inadequate immune responses. To overcome these challenges, phage display has emerged as a valuable tool for identifying specific epitopes that could be used in vaccines. This review emphasizes the direct connection between epitope identification and vaccine development, filling a crucial gap in the field. This technique allows vaccines to be engineered to effectively stimulate the immune system by presenting carefully selected epitopes. Phage display involves screening libraries of random peptides or gene/genome fragments using serum samples from infected, convalescent, or vaccinated individuals. This method has been used to identify epitopes from various pathogens including SARS-CoV-2, Mycobacterium tuberculosis, hepatitis viruses, H5N1, HIV-1, Human T-lymphotropic virus 1, Plasmodium falciparum, Trypanosoma cruzi, and Dirofilaria repens. Bacteriophages offer advantages such as being immunogenic carriers, low production costs, and customization options, making them a promising alternative to traditional vaccines. The purpose of this study has been to highlight an approach that encompasses the entire process from epitope identification to vaccine production using a single technique, without requiring additional manipulation. Unlike conventional methods, phage display demonstrates exceptional efficiency and speed, which could provide significant advantages in critical scenarios such as pandemics.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain
- Protheragen Inc., Ronkonkoma, NY 11779, USA
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11
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Eaton RM, Zercher BP, Wageman A, Bush MF. A Flexible, Modular Platform for Multidimensional Ion Mobility of Native-like Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1175-1185. [PMID: 37171243 PMCID: PMC10548348 DOI: 10.1021/jasms.3c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Native ion mobility (IM) mass spectrometry (MS) is used to probe the size, shape, and assembly of biomolecular complexes. IM-IM-MS can increase the amount of information available in structural studies by isolating subpopulations of structures for further analysis. Previously, IM-IM-MS has been implemented using the Structures for Lossless Ion Manipulations (SLIM) architecture to probe the structural stability of gas-phase protein ions. Here, a new multidimensional IM instrument constructed from SLIM devices is characterized using multiple operational modes. In this new design, modular devices are used to perform all ion manipulations, including initial accumulation, injection, separation, selection, and trapping. Using single-dimension IM, collision cross section (Ω) values are determined for a set of native-like ions. These Ω values are within 3% of those reported previously based on measurements using RF-confining drift cells. Tandem IM experiments are performed on a sample of ubiquitin ions that contains both compact and partially unfolded structures, demonstrating that this platform can isolate subpopulations of structures. Finally, additional modes of analysis, including multiplexed IM and inverse IM, are demonstrated using this platform. The ability of this platform to quickly switch between different modes of IM analysis makes it a highly flexible tool for studying protein structures and dynamics.
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Affiliation(s)
- Rachel M. Eaton
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Benjamin P. Zercher
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - AnneClaire Wageman
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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12
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Duong SL, Prüss H. Molecular disease mechanisms of human antineuronal monoclonal autoantibodies. Trends Mol Med 2023; 29:20-34. [PMID: 36280535 DOI: 10.1016/j.molmed.2022.09.011] [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: 08/05/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]
Abstract
Autoantibodies targeting brain antigens can mediate a wide range of neurological symptoms ranging from epileptic seizures to psychosis to dementia. Although earlier experimental work indicated that autoantibodies can be directly pathogenic, detailed studies on disease mechanisms, biophysical autoantibody properties, and target interactions were hampered by the availability of human material and the paucity of monospecific disease-related autoantibodies. The emerging generation of patient-derived monoclonal autoantibodies (mAbs) provides a novel platform for the detailed characterization of immunobiology and autoantibody pathogenicity in vitro and in animal models. This Feature Review focuses on recent advances in mAb generation and discusses their potential as powerful scientific tools for high-resolution imaging, antigenic target identification, atomic-level structural analyses, and the development of antibody-selective immunotherapies.
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Affiliation(s)
- Sophie L Duong
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Charitéplatz 1, 10117 Berlin, Germany
| | - Harald Prüss
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany.
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13
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Shen C, Zhang X, Deng Y, Gao J, Wang D, Xu L, Pan P, Hou T, Kang Y. Boosting Protein-Ligand Binding Pose Prediction and Virtual Screening Based on Residue-Atom Distance Likelihood Potential and Graph Transformer. J Med Chem 2022; 65:10691-10706. [PMID: 35917397 DOI: 10.1021/acs.jmedchem.2c00991] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The past few years have witnessed enormous progress toward applying machine learning approaches to the development of protein-ligand scoring functions. However, the robust performance and wide applicability of scoring functions remain a big challenge for increasing the success rate of docking-based virtual screening. Herein, a novel scoring function named RTMScore was developed by introducing a tailored residue-based graph representation strategy and several graph transformer layers for the learning of protein and ligand representations, followed by a mixture density network to obtain residue-atom distance likelihood potential. Our approach was resolutely validated on the CASF-2016 benchmark, and the results indicate that RTMScore can outperform almost all of the other state-of-the-art methods in terms of both the docking and screening powers. Further evaluation confirms the robustness of our approach that can not only retain its docking power on cross-docked poses but also achieve improved performance as a rescoring tool in larger-scale virtual screening.
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Affiliation(s)
- Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China.,CarbonSilicon AI Technology Co., Ltd, Hangzhou, Zhejiang 310018, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd, Hangzhou, Zhejiang 310018, China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dong Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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14
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Gomari MM, Rostami N, Faradonbeh DR, Asemaneh HR, Esmailnia G, Arab S, Farsimadan M, Hosseini A, Dokholyan NV. Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation. Proteins 2022; 90:1908-1925. [DOI: 10.1002/prot.26386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences Tehran Iran
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering Arak University Arak Iran
| | - Davood Rabiei Faradonbeh
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Tehran University of Medical Sciences Tehran Iran
| | - Hamid Reza Asemaneh
- Polymer Research Center, Department of Chemical Engineering Razi University Kermanshah Iran
| | - Giti Esmailnia
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Shahriar Arab
- Department of Biophysics School of Biological Sciences, Tarbiat Modares University Tehran Iran
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences University of Guilan Rasht Iran
| | - Arshad Hosseini
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology Pennsylvania State University College of Medicine Hershey Pennsylvania USA
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15
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Lee J, Li K, Zimmerman SC. A Selective Alkylating Agent for CTG Repeats in Myotonic Dystrophy Type 1. ACS Chem Biol 2022; 17:1103-1110. [PMID: 35483041 DOI: 10.1021/acschembio.1c00949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disease intervention at the DNA level generally has been avoided because of off-target effects. Recent advances in genome editing technologies using CRISPR-Cas9 have opened a new era in DNA-targeted therapeutic approaches. However, delivery of such systems remains a major challenge. Here, we report a selective DNA-modifying small molecule that targets a disease-specific structure and mismatches involved in myotonic dystrophy type 1 (DM1). This ligand alkylates T-T mismatch-containing hairpins formed in the expanded CTG repeats (d(CTG)exp) in DM1. Ligand alkylation of d(CTG)exp inhibits the transcription of d(CAG·CTG)exp, thereby reducing the level of the toxic r(CUG)exp transcript. The bioactivity of the ligand also included a reduction in DM1 pathological features such as disease foci formation and misregulation of pre-mRNA splicing in DM1 model cells. Furthermore, the CTG-alkylating ligand may change the d(CAG·CTG)exp repeat length dynamics in DM1 patient cells. Our strategy of linking an alkylating moiety to a DNA mismatch-selective small molecule may be generally applicable to other repeat expansion diseases such as Huntington's disease and amyotrophic lateral sclerosis.
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Affiliation(s)
- JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ke Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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16
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He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022; 2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg2+ cations stabilizes the compact state. The absence of Mg2+ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, United States
| | - Anja Henning-Knechtel
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Correspondence: Serdal Kirmizialtin,
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17
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Mureddu LG, Vuister GW. Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved? Front Mol Biosci 2022; 9:834453. [PMID: 35252355 PMCID: PMC8895297 DOI: 10.3389/fmolb.2022.834453] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last century, the definitions of pharmaceutical drug and drug discovery have changed considerably. Evolving from an almost exclusively serendipitous approach, drug discovery nowadays involves several distinct, yet sometimes interconnected stages aimed at obtaining molecules able to interact with a defined biomolecular target, and triggering a suitable biological response. At each of the stages, a wide range of techniques are typically employed to obtain the results required to move the project into the next stage. High Throughput Screening (HTS) and Fragment Based Drug Design (FBDD) are the two main approaches used to identify drug-like candidates in the early stages of drug discovery. Nuclear Magnetic Resonance (NMR) spectroscopy has many applications in FBDD and is used extensively in industry as well as in academia. In this manuscript, we discuss the paths of both successful and unsuccessful molecules where NMR had a crucial part in their development. We specifically focus on the techniques used and describe strengths and weaknesses of each stage by examining several case studies. More precisely, we examine the development history from the primary screening to the final lead optimisation of AZD3839 interacting with BACE-1, ABT-199 interacting with BCL2/XL and S64315 interacting with MCL-1. Based on these studies, we derive observations and conclusions regarding the FBDD process by NMR and discuss its potential improvements.
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Affiliation(s)
| | - Geerten W. Vuister
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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18
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Heine V, Dey C, Bojarová P, Křen V, Elling L. Methods of in vitro study of galectin-glycomaterial interaction. Biotechnol Adv 2022; 58:107928. [DOI: 10.1016/j.biotechadv.2022.107928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
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19
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Deciphering the high viscosity of a therapeutic monoclonal antibody in high concentration formulations by microdialysis-hydrogen/deuterium exchange mass spectrometry. J Pharm Sci 2022; 111:1335-1345. [PMID: 34999091 DOI: 10.1016/j.xphs.2021.12.027] [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: 03/17/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 11/22/2022]
Abstract
High concentration formulations of therapeutic monoclonal antibodies (mAbs) are highly desired for subcutaneous injection. However, high concentration formulations can exhibit unusual molecular behaviors, such as high viscosity or aggregation, that present challenges for manufacturing and administration. To understand the molecular mechanism of the high viscosity exhibited by high concentration protein formulations, we analyzed a human IgG4 (mAb1) at high protein concentrations using sedimentation velocity analytical ultracentrifugation (SV-AUC), X-ray crystallography, hydrogen/deuterium exchange mass spectrometry (HDX-MS), and protein surface patches analysis. Particularly, we developed a microdialysis HDX-MS method to determine intermolecular interactions at different protein concentrations. SV-AUC revealed that mAb1 displayed a propensity for self-association of Fab-Fab, Fab-Fc, and Fc-Fc. mAb1 crystal structure and HDX-MS results demonstrated self-association between complementarity-determining regions (CDRs) and Fc through electrostatic interactions. HDX-MS also indicated Fab-Fab interactions through hydrophobic surface patches constructed by mAb1 CDRs. Our multi-method approach, including fast screening of SV-AUC as well as interface analysis by X-ray crystallography and HDX-MS, helped to elucidate the high viscosity of mAb1 at high concentrations as induced by self-associations of Fab-Fc and Fab-Fab.
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20
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McCabe JW, Jones BJ, Walker TE, Schrader RL, Huntley AP, Lyu J, Hoffman NM, Anderson GA, Reilly PTA, Laganowsky A, Wysocki VH, Russell DH. Implementing Digital-Waveform Technology for Extended m/ z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2812-2820. [PMID: 34797072 PMCID: PMC9026758 DOI: 10.1021/jasms.1c00245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Here, we describe a digital-waveform dual-quadrupole mass spectrometer that enhances the performance of our drift tube FT-IMS high-resolution Orbitrap mass spectrometer (MS). The dual-quadrupole analyzer enhances the instrument capabilities for studies of large protein and protein complexes. The first quadrupole (q) provides a means for performing low-energy collisional activation of ions to reduce or eliminate noncovalent adducts, viz., salts, buffers, detergents, and/or endogenous ligands. The second quadrupole (Q) is used to mass-select ions of interest for further interrogation by ion mobility spectrometry and/or collision-induced dissociation (CID). Q is operated using digital-waveform technology (DWT) to improve the mass selection compared to that achieved using traditional sinusoidal waveforms at floated DC potentials (>500 V DC). DWT allows for increased precision of the waveform for a fraction of the cost of conventional RF drivers and with readily programmable operation and precision (Hoffman, N. M. . A comparison-based digital-waveform generator for high-resolution duty cycle. Review of Scientific Instruments 2018, 89, 084101).
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert L Schrader
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Adam P Huntley
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nathan M Hoffman
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | | | - Peter T A Reilly
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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21
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Residue-based pharmacophore approaches to study protein-protein interactions. Curr Opin Struct Biol 2021; 67:205-211. [PMID: 33486430 DOI: 10.1016/j.sbi.2020.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 01/22/2023]
Abstract
This review focuses on pharmacophore approaches in researching protein interfaces that bind protein ligands. Pharmacophore descriptions of binding interfaces that employ molecular dynamics simulation can account for effects of solvation and conformational flexibility. In addition, these calculations provide an approximation to entropic considerations and as such, a better approximation of the free energy of binding. Residue-based pharmacophore approaches can facilitate a variety of drug discovery tasks such as the identification of receptor-ligand partners, identifying their binding poses, designing protein interfaces for selectivity, or defining a reduced mutational combinatorial exploration for subsequent experimental engineering techniques by orders of magnitudes.
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22
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Abstract
Drug transporters are integral membrane proteins that play a critical role in drug disposition by affecting absorption, distribution, and excretion. They translocate drugs, as well as endogenous molecules and toxins, across membranes using ATP hydrolysis, or ion/concentration gradients. In general, drug transporters are expressed ubiquitously, but they function in drug disposition by being concentrated in tissues such as the intestine, the kidneys, the liver, and the brain. Based on their primary sequence and their mechanism, transporters can be divided into the ATP-binding cassette (ABC), solute-linked carrier (SLC), and the solute carrier organic anion (SLCO) superfamilies. Many X-ray crystallography and cryo-electron microscopy (cryo-EM) structures have been solved in the ABC and SLC transporter superfamilies or of their bacterial homologs. The structures have provided valuable insight into the structural basis of transport. This chapter will provide particular focus on the promiscuous drug transporters because of their effect on drug disposition and the challenges associated with them.
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Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, Athens, GA, USA.
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23
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McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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24
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020; 25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58102, USA
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
- Correspondence: ; Tel.: +1-435-222-1403
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND 58102, USA;
| | - Juechen Yang
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Michael Holland
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Tina Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
| | - Gary H. Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
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25
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Zhang Y, Wang S, Jia Z. In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices. Int J Mol Sci 2020; 21:ijms21010308. [PMID: 31906428 PMCID: PMC6981927 DOI: 10.3390/ijms21010308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 12/13/2022] Open
Abstract
Although prevalent in the determination of protein structures; crystallography always has the bottleneck of obtaining high-quality protein crystals for characterizing a wide range of proteins; especially large protein complexes. Stable fragments or domains of proteins are more readily to crystallize; which prompts the use of in situ proteolysis to remove flexible or unstable structures for improving crystallization and crystal quality. In this work; we investigated the effects of in situ proteolysis by chymotrypsin on the crystallization of the XcpVWX complex from the Type II secretion system of Pseudomonas aeruginosa. Different proteolysis conditions were found to result in two distinct lattices in the same crystallization solution. With a shorter chymotrypsin digestion at a lower concentration; the crystals exhibited a P3 hexagonal lattice that accommodates three complex molecules in one asymmetric unit. By contrast; a longer digestion with chymotrypsin of a 10-fold higher concentration facilitated the formation of a compact P212121 orthorhombic lattice with only one complex molecule in each asymmetric unit. The molecules in the hexagonal lattice have shown high atomic displacement parameter values compared with the ones in the orthorhombic lattice. Taken together; our results clearly demonstrate that different proteolysis conditions can result in the generation of distinct lattices in the same crystallization solution; which can be exploited in order to obtain different crystal forms of a better quality
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Affiliation(s)
- Yichen Zhang
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON K7L 3N6, Canada;
| | - Shu Wang
- College of Chemistry, Beijing Normal University, 19 Xinjiekou Outer Street, Beijing 100875, China;
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, 18 Stuart Street, Kingston, ON K7L 3N6, Canada;
- Correspondence: ; Tel.: +86-1-613-533-6277
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26
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Zeng L, Ding W, Hao Q. Using cryo-electron microscopy maps for X-ray structure determination of homologues. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:63-72. [PMID: 31909744 DOI: 10.1107/s2059798319015924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022]
Abstract
The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to handle such cases. The whole process includes three steps: cryo-EM map replacement, phase extension by NCS averaging and dual-space iterative model building. When the resolution gap between the cryo-EM and X-ray crystallographic data is large and the sequence identity is low, an intermediate stage of model building is necessary. Six test cases have been studied with sequence identity between the corresponding molecules in the cryo-EM and X-ray structures ranging from 34 to 52% and with sequence similarity ranging from 86 to 91%. This hybrid method consistently produced models with reasonable Rwork and Rfree values which agree well with the previously determined X-ray structures for all test cases, thus indicating the general applicability of the method for X-ray structure determination of homologues using cryo-EM maps as a starting point.
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Affiliation(s)
- Lingxiao Zeng
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong
| | - Wei Ding
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong
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27
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Dutta S, Ghosh M, Karmakar R, Chakrabarti J. Dynamic signature of ligand binding over a protein surface. Phys Rev E 2019; 100:062411. [PMID: 31962438 DOI: 10.1103/physreve.100.062411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 06/10/2023]
Abstract
We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Rahul Karmakar
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - J Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
- Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
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Sjuts H, Schreuder H, Engel CK, Bussemer T, Gokarn Y. Matching pH values for antibody stabilization and crystallization suggest rationale for accelerated development of biotherapeutic drugs. Drug Dev Res 2019; 81:329-337. [PMID: 31758731 DOI: 10.1002/ddr.21624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 11/11/2022]
Abstract
Monoclonal antibodies (mAbs) are currently leading products in the global biopharmaceutical market. Multiple mAbs are in clinical development and novel biotherapeutic protein scaffolds, based on the canonical immunoglobulin G (IgG) fold, are emerging as treatment options for various medical conditions. However, fast approvals for biotherapeutics are challenging to achieve, because of difficult scientific development procedures and complex regulatory processes. Selecting molecular entities with superior physicochemical properties that proceed into clinical trials and the identification of stable formulations are crucial developability aspects. It is widely accepted that the solution pH has critical influences on both the protein's colloidal stability and its crystallization behavior. Furthermore, proteins usually crystallize best at solution conditions that enable high protein solubility, purity, stability, and monodispersity. Therefore, we hypothesize that the solution pH value is a central parameter that is linking together protein formulation, protein crystallization, and thermal protein stability. In order to experimentally test this hypothesis, we have investigated the effect of the solution pH on the thermal stabilities and crystallizabilities for three different mAbs. Combining biophysical measurements with high throughput protein (HTP) crystallization trials we observed a correlation in the buffer pH values for eminent mAb stability and successful crystallization. Specifically, differential scanning fluorimetry (DSF) was used to determine pH values that exert highest thermal mAb stabilities and additionally led to the identification of unfolding temperatures of individual mAb domains. Independently performed crystallization trials with the same mAbs resulted in their successful crystallization at pH values that displayed highest thermal stabilities. In summary, the presented results suggest a strategy how protein crystallization could be used as a screening method for the development of biotherapeutic protein formulations with improved in vitro stabilities.
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Affiliation(s)
- Hanno Sjuts
- Biologics Research, Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Herman Schreuder
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Christian K Engel
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Till Bussemer
- Biologics Development, Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Yatin Gokarn
- Biologics Development, Sanofi US Services Inc., Framingham, Massachusetts, US
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Porebski PJ, Bokota G, Venkataramany BS, Minor W. Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations. Protein Sci 2019; 29:120-127. [PMID: 31605409 DOI: 10.1002/pro.3747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022]
Abstract
In the Special Issue on Tools for Protein Science in 2018, we presented Molstack: a concept of a cloud-based platform for sharing electron density maps and their interpretations. Molstack is a web platform that allows the interactive visualization of density maps through the simultaneous presentation of multiple datasets and models in a way that allows for easy pairwise comparison. We anticipated that the users of this conceptually simple platform would find many different uses for their projects, and we were not mistaken. We have observed researchers use Molstack to present experimental evidence for their models in the form of electron density maps, omit maps, and anomalous difference density maps. Users also employed Molstack to present alternative interpretations of densities, including rerefinements and speculative interpretations. While we anticipated these types of projects to be the main use cases, we were pleased to see Molstack used to display superpositions of different models, as a tool for story-driven presentations, and for collaboration as well. Here, we present developments in the platform that were driven by user feedback, highlight several cases that used Molstack to enhance the publication, and discuss possible directions for the platform.
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Affiliation(s)
- Przemyslaw J Porebski
- Department of Molecular Physiology & Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Grzegorz Bokota
- Department of Molecular Physiology & Biological Physics, University of Virginia, Charlottesville, Virginia.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Barat S Venkataramany
- Department of Molecular Physiology & Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Wladek Minor
- Department of Molecular Physiology & Biological Physics, University of Virginia, Charlottesville, Virginia
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30
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Bala S, Shinya S, Srivastava A, Ishikawa M, Shimada A, Kobayashi N, Kojima C, Tama F, Miyashita O, Kohda D. Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study. Biochim Biophys Acta Gen Subj 2019; 1864:129418. [PMID: 31449839 DOI: 10.1016/j.bbagen.2019.129418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/02/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules. METHODS We designed an intended crystal contact-free space (CCFS) in protein crystals, and arranged the flexible loop of interest in the CCFS. The yeast Tim 21 protein was chosen as the model protein, because one of the loops (loop 2) is distorted by crystal contacts in the conventional crystal. RESULTS Yeast Tim21 was fused to the MBP protein by a rigid α-helical linker. The space created between the two proteins was used as the CCFS. The linker length provides adjustable freedom to arrange loop 2 in the CCFS. We re-determined the NMR structure of yeast Tim21, and conducted MD simulations for comparison. Multidimensional scaling was used to visualize the conformational similarity of loop 2. We found that the crystal contact-free conformation of loop 2 is located close to the center of the ensembles of the loop 2 conformations in the NMR and MD structures. CONCLUSIONS Loop 2 of yeast Tim21 in the CCFS adopts a representative, dominant conformation in solution. GENERAL SIGNIFICANCE No single powerful technique is available for the characterization of flexible structures in protein molecules. NMR analyses and MD simulations provide useful, but incomplete information. CCFS crystallography offers a third route to this goal.
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Affiliation(s)
- Siqin Bala
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shoko Shinya
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Marie Ishikawa
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Shimada
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan; Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Florence Tama
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; Center for Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.
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Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov 2019; 14:755-768. [DOI: 10.1080/17460441.2019.1623202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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32
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:2906519. [PMID: 30112206 PMCID: PMC6077552 DOI: 10.1155/2018/2906519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.
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Xu D, Li B, Gao J, Liu Z, Niu X, Nshogoza G, Zhang J, Wu J, Su XC, He W, Ma R, Yang D, Ruan K. Ligand Proton Pseudocontact Shifts Determined from Paramagnetic Relaxation Dispersion in the Limit of NMR Intermediate Exchange. J Phys Chem Lett 2018; 9:3361-3367. [PMID: 29864276 DOI: 10.1021/acs.jpclett.8b01443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Delineation of protein-ligand interaction modes is key for rational drug discovery. The availability of complex crystal structures is often limited by the aqueous solubility of the compounds, while lead-like compounds with micromolar affinities normally fall into the NMR intermediate exchange regime, in which severe line broadening to beyond the detection of interfacial resonances limits NMR applications. Here, we developed a new method to retrieve low-populated bound-state 1H pseudocontact shifts (PCSs) using paramagnetic relaxation dispersion (RD). We evaluated using a 1H PCS-RD approach in a BRM bromodomain lead-like inhibitor to filter molecular docking poses using multiple intermolecular structural restraints. Considering the universal presence of proton atoms in druglike compounds, our work will have wide application in structure-guided drug discovery even under an extreme condition of NMR intermediate exchange and low aqueous solubility of ligands.
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Affiliation(s)
- Difei Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Bin Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
- Center of Medical Physics and Technology, Hefei Institute of Physical Science , Cancer Hospital Chinese Academy of Science , Hefei , Anhui 230031 , PR China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai , 201210 , PR China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , PR China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin , 300071 , PR China
| | - Wei He
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , Singapore , 117543 , Singapore
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
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35
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Munsamy G, Ramharack P, Soliman MES. Egress and invasion machinery of malaria: an in-depth look into the structural and functional features of the flap dynamics of plasmepsin IX and X. RSC Adv 2018; 8:21829-21840. [PMID: 35541758 PMCID: PMC9081207 DOI: 10.1039/c8ra04360d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/07/2018] [Indexed: 02/05/2023] Open
Abstract
Plasmepsins, a family of aspartic proteases expressed by Plasmodium falciparum parasite, have been identified as key mediators in the onset of lethal malaria. Precedence has been placed on this family of enzymes due their essential role in the virulence of the parasite, thus highlighting their importance as novel drug targets. A previously published study by our group proposed a set of parameters used to define the flap motion of aspartic proteases. These parameters were used in the study of Plm I-V and focused on the flap flexibility as well as structural dynamics. Recent studies have highlighted the essential role played by Plm IX and X in egress and invasion of the malarial parasite. This study aims to close the gap on the latter family, investigating the flap dynamics of Plms IX and X. Molecular dynamics simulations demonstrated an "open and close" mechanism at the region of the catalytic site. Further computation of the dihedral angles at the catalytic region revealed tractability at both the flap tip and flexible loop. This structural versatility enhances the interaction of variant ligand sizes, in comparison to other Plm family members. The results obtained from this study signify the essential role of structural flap dynamics and its resultant effect on the binding landscapes of Plm IX and X. We believe that this unique structural mechanism may be integrated in the design and development of effective anti-malarial drugs.
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Affiliation(s)
- Geraldene Munsamy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
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37
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Xiao K, Zhao Y, Choi M, Liu H, Blanc A, Qian J, Cahill TJ, Li X, Xiao Y, Clark LJ, Li S. Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping. Nat Protoc 2018; 13:1403-1428. [PMID: 29844522 DOI: 10.1038/nprot.2018.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions. To distinguish between inter- and intramolecular interactions, we use a CXMS method to determine the position of direct interface regions by trapping intermolecular residues in close proximity to various cross-linkers (e.g., disuccinimidyl adipate (DSA)) of different lengths and reactive groups. Both MS-based experiments are performed on high-resolution mass spectrometers (e.g., an Orbitrap Elite hybrid mass spectrometer). The physiological relevance of the interactions identified through HDXMS and CXMS is investigated by transiently co-expressing cysteine mutant pairs, one mutant on each protein at the discovered interfaces, in an appropriate cell line, such as HEK293. Disulfide-trapped protein complexes are formed within cells spontaneously or are facilitated by addition of oxidation reagents such as H2O2 or diamide. Western blotting analysis, in the presence and absence of reducing reagents, is used to determine whether the disulfide bonds are formed in the proposed complex interface in physiologically relevant milieus. The procedure described here requires 1-2 months. We demonstrate this approach using the β2-adrenergic receptor-β-arrestin1 complex as the model system.
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Affiliation(s)
- Kunhong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minjung Choi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adi Blanc
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiang Qian
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas J Cahill
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xue Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Yunfang Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa J Clark
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sheng Li
- Department of Chemistry, University of California at San Diego, La Jolla, California, USA
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Lo YH, Pillon MC, Stanley RE. Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae. J Vis Exp 2018. [PMID: 29364241 DOI: 10.3791/56953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Determination of the full-length structure of ribosome assembly factor Nsa1 from Saccharomyces cerevisiae (S. cerevisiae) is challenging because of the disordered and protease labile C-terminus of the protein. This manuscript describes the methods to purify recombinant Nsa1 from S. cerevisiae for structural analysis by both X-ray crystallography and SAXS. X-ray crystallography was utilized to solve the structure of the well-ordered N-terminal WD40 domain of Nsa1, and then SAXS was used to resolve the structure of the C-terminus of Nsa1 in solution. Solution scattering data was collected from full-length Nsa1 in solution. The theoretical scattering amplitudes were calculated from the high-resolution crystal structure of the WD40 domain, and then a combination of rigid body and ab initio modeling revealed the C-terminus of Nsa1. Through this hybrid approach the quaternary structure of the entire protein was reconstructed. The methods presented here should be generally applicable for the hybrid structural determination of other proteins composed of a mix of structured and unstructured domains.
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Affiliation(s)
- Yu-Hua Lo
- Signal Transduction Laboratory, National Institutes of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health
| | - Monica C Pillon
- Signal Transduction Laboratory, National Institutes of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institutes of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
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Li X, Zhu L, Wang B, Yuan M, Zhu R. Drugs and Targets in Fibrosis. Front Pharmacol 2017; 8:855. [PMID: 29218009 PMCID: PMC5703866 DOI: 10.3389/fphar.2017.00855] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/08/2017] [Indexed: 01/18/2023] Open
Abstract
Fibrosis contributes to the development of many diseases and many target molecules are involved in fibrosis. Currently, the majority of fibrosis treatment strategies are limited to specific diseases or organs. However, accumulating evidence demonstrates great similarities among fibroproliferative diseases, and more and more drugs are proved to be effective anti-fibrotic therapies across different diseases and organs. Here we comprehensively review the current knowledge on the pathological mechanisms of fibrosis, and divide factors mediating fibrosis progression into extracellular and intracellular groups. Furthermore, we systematically summarize both single and multiple component drugs that target fibrosis. Future directions of fibrosis drug discovery are also proposed.
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Affiliation(s)
- Xiaoyi Li
- Department of Gastroenterology, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Lixin Zhu
- Department of Pediatrics, Digestive Diseases and Nutrition Center, State University of New York at Buffalo, Buffalo, NY, United States
- Genome, Environment and Microbiome Community of Excellence, State University of New York at Buffalo, Buffalo, NY, United States
| | - Beibei Wang
- Department of Gastroenterology, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Meifei Yuan
- Center for Drug Discovery, SINO High Goal Chemical Technology Co., Ltd., Shanghai, China
| | - Ruixin Zhu
- Department of Gastroenterology, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China
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Al Nasr K, Jones C, Yousef F, Jebril R. PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models. J Comput Biol 2017; 25:21-32. [PMID: 29140718 DOI: 10.1089/cmb.2017.0191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures. The aim of this method is to reduce the number of native-like candidate conformations and, therefore, reduce the time required for structural evaluation by energy calculations. A test of two datasets was performed. The first dataset contains 10 proteins and shows that our method can successfully detect the correct native structure for the given skeleton among a set of different protein structures. The second dataset contains 12 proteins and shows that our method can filter slightly modified decoy conformations of the same protein. The efficiency of the method is also reported.
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Affiliation(s)
- Kamal Al Nasr
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
| | - Christopher Jones
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
| | - Feras Yousef
- 2 Department of Mathematics, The University of Jordan , Amman, Jordan
| | - Ruba Jebril
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
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Gao J, Liang E, Ma R, Li F, Liu Y, Liu J, Jiang L, Li C, Dai H, Wu J, Su X, He W, Ruan K. Fluorine Pseudocontact Shifts Used for Characterizing the Protein-Ligand Interaction Mode in the Limit of NMR Intermediate Exchange. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jia Gao
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - E Liang
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Yixiang Liu
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Ling Jiang
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Haiming Dai
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collatorative Innovation Center of Chemical Science and Engineering(Tianjin); Nankai University; Tianjin 300071 P. R. China
| | - Wei He
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
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42
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Li XY, Tang HJ, Zhang L, Yang L, Li P, Chen J. A selective knockout method for discovery of minor active components from plant extracts: Feasibility and challenges as illustrated by an application to Salvia miltiorrhiza. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:253-260. [PMID: 29132906 DOI: 10.1016/j.jchromb.2017.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/18/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022]
Abstract
Natural products have been recognized to play an invaluable role in drug discovery. However, efficient discovery of minor active constituents from natural sources is challenging due to the low abundance and complex matrices. In this study, we developed a selective knockout method to discover minor bioactive components from complex phytochemical mixtures, using a Chinese medicine as an example. Based on the chromatographic fingerprint, six major components in the ethyl acetate extract of the root of Salvia miltiorrhiza (EASM) were selectively knocked out via high-resolution peak fraction (HRPF) approach. The remaining extract was automatically enriched and fractionated to generate a chemical library consisting of 62 minor components with contents less than 3‰. Simultaneously, a parallel mass-spectrometry (MS) analysis was performed to ensure purity and to characterize the structure of the compound in each fraction. Via an antioxidant response element (ARE)-driven luciferase reporter system, 33 minor components were screened out as nuclear factor erythroid 2-related factor 2 (Nrf2) activators and 30 components were identified. Here, the Nrf2 activation activities of 21 components have been reported for the first time. Different from the existing methods for discovery of active compounds from natural products, in the developed method of this manuscript, the major components are selectively removed, and the fractions of the minor components are prepared after several times of preparative HPLC enrichment by high-resolution peak fraction approach. It improves the prospective discovery of minor active components from complex medicinal herbs.
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Affiliation(s)
- Xue-Yan Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Hong-Jin Tang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Liu Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Lin Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Jun Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China.
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43
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Gao J, Liang E, Ma R, Li F, Liu Y, Liu J, Jiang L, Li C, Dai H, Wu J, Su X, He W, Ruan K. Fluorine Pseudocontact Shifts Used for Characterizing the Protein-Ligand Interaction Mode in the Limit of NMR Intermediate Exchange. Angew Chem Int Ed Engl 2017; 56:12982-12986. [DOI: 10.1002/anie.201707114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/15/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jia Gao
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - E Liang
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Yixiang Liu
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Ling Jiang
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Haiming Dai
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collatorative Innovation Center of Chemical Science and Engineering(Tianjin); Nankai University; Tianjin 300071 P. R. China
| | - Wei He
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
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44
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Xia J, Hsieh JH, Hu H, Wu S, Wang XS. The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. J Chem Inf Model 2017; 57:1414-1425. [PMID: 28511009 DOI: 10.1021/acs.jcim.6b00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Jui-Hua Hsieh
- Kelly Government Solutions , Research Triangle Park, North Carolina 27709, United States
| | - Huabin Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University , Washington, D.C. 20059, United States
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45
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Zhou RB, Cao HL, Zhang CY, Yin DC. A review on recent advances for nucleants and nucleation in protein crystallization. CrystEngComm 2017. [DOI: 10.1039/c6ce02562e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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46
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Janero DR, Korde A, Makriyannis A. Ligand-Assisted Protein Structure (LAPS): An Experimental Paradigm for Characterizing Cannabinoid-Receptor Ligand-Binding Domains. Methods Enzymol 2017; 593:217-235. [DOI: 10.1016/bs.mie.2017.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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47
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Pichlo C, Montada AA, Schacherl M, Baumann U. Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD. J Vis Exp 2016. [PMID: 28060332 DOI: 10.3791/55022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a target for future development of inhibitors to decrease the virulence of the pathogen. To perform biophysical and structural characterization as well as inhibitor screening, large amounts of pure and active protein will be needed. We have developed a protocol for efficient production and purification of PPEP-1 by the use of E. coli as the expression host yielding sufficient amounts and purity of protein for crystallization and structure determination. Additionally, using microseeding, highly intergrown crystals of PPEP-1 can be grown to well-ordered crystals suitable for X-ray diffraction analysis. The methods could also be used to produce other recombinant proteins and to study the structures of other proteins producing intergrown crystals.
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48
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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49
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Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review. Anal Chim Acta 2016; 940:8-20. [DOI: 10.1016/j.aca.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/25/2016] [Accepted: 08/07/2016] [Indexed: 01/14/2023]
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50
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Molecular docking for drug discovery and development: a widely used approach but far from perfect. Future Med Chem 2016; 8:1707-10. [PMID: 27578269 DOI: 10.4155/fmc-2016-0143] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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