1
|
Ginex T, Vázquez J, Estarellas C, Luque FJ. Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design. Curr Opin Struct Biol 2024; 87:102870. [PMID: 38914031 DOI: 10.1016/j.sbi.2024.102870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
The expansion of the chemical space to tangible libraries containing billions of synthesizable molecules opens exciting opportunities for drug discovery, but also challenges the power of computer-aided drug design to prioritize the best candidates. This directly hits quantum mechanics (QM) methods, which provide chemically accurate properties, but subject to small-sized systems. Preserving accuracy while optimizing the computational cost is at the heart of many efforts to develop high-quality, efficient QM-based strategies, reflected in refined algorithms and computational approaches. The design of QM-tailored physics-based force fields and the coupling of QM with machine learning, in conjunction with the computing performance of supercomputing resources, will enhance the ability to use these methods in drug discovery. The challenge is formidable, but we will undoubtedly see impressive advances that will define a new era.
Collapse
Affiliation(s)
- Tiziana Ginex
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Javier Vázquez
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain; Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain
| | - F Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Das S, Tanemura KA, Dinpazhoh L, Keng M, Schumm C, Leahy L, Asef CK, Rainey M, Edison AS, Fernández FM, Merz KM. In Silico Collision Cross Section Calculations to Aid Metabolite Annotation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:750-759. [PMID: 35378036 PMCID: PMC9277703 DOI: 10.1021/jasms.1c00315] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The interpretation of ion mobility coupled to mass spectrometry (IM-MS) data to predict unknown structures is challenging and depends on accurate theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low or atmospheric pressure drift chamber. The sensitivity and reliability of computational prediction of CCS values depend on accurately modeling the molecular state over accessible conformations. In this work, we developed an efficient CCS computational workflow using a machine learning model in conjunction with standard DFT methods and CCS calculations. Furthermore, we have performed Traveling Wave IM-MS (TWIMS) experiments to validate the extant experimental values and assess uncertainties in experimentally measured CCS values. The developed workflow yielded accurate structural predictions and provides unique insights into the likely preferred conformation analyzed using IM-MS experiments. The complete workflow makes the computation of CCS values tractable for a large number of conformationally flexible metabolites with complex molecular structures.
Collapse
Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kiyoto Aramis Tanemura
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Laleh Dinpazhoh
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Mithony Keng
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Christina Schumm
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Lydia Leahy
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Carter K Asef
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Markace Rainey
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Arthur S Edison
- Departments of Genetics and Biochemistry, Institute of Bioinformatics and Complex Carbohydrate Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
4
|
Sprague DJ, Getschman AE, Fenske TG, Volkman BF, Smith BC. Trisubstituted 1,3,5-Triazines: The First Ligands of the sY12-Binding Pocket on Chemokine CXCL12. ACS Med Chem Lett 2021; 12:1773-1782. [PMID: 34795867 PMCID: PMC8592115 DOI: 10.1021/acsmedchemlett.1c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
![]()
CXCL12, a CXC-type
chemokine, binds its receptor CXCR4, and the
resulting signaling cascade is essential during development and subsequently
in immune function. Pathologically, the CXCL12–CXCR4 signaling
axis is involved in many cancers and inflammatory diseases and thus
has sparked continued interest in the development of therapeutics.
Small molecules targeting CXCR4 have had mixed results in clinical
trials. Alternatively, small molecules targeting the chemokine instead
of the receptor provide a largely unexplored space for therapeutic
development. Here we report that trisubstituted 1,3,5-triazines are
competent ligands for the sY12-binding pocket of CXCL12. The initial
hit was optimized to be more synthetically tractable. Fifty unique
triazines were synthesized, and the structure–activity relationship
was probed. Using computational modeling, we suggest key structural
interactions that are responsible for ligand–chemokine binding.
The lipophilic ligand efficiency was improved, resulting in more soluble,
drug-like molecules with chemical handles for future development and
structural studies.
Collapse
Affiliation(s)
- Daniel J. Sprague
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Anthony E. Getschman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Tyler G. Fenske
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| |
Collapse
|
5
|
Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
Collapse
Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
6
|
Gjuroski I, Furrer J, Vermathen M. Probing the Interactions of Porphyrins with Macromolecules Using NMR Spectroscopy Techniques. Molecules 2021; 26:1942. [PMID: 33808335 PMCID: PMC8037866 DOI: 10.3390/molecules26071942] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
Porphyrinic compounds are widespread in nature and play key roles in biological processes such as oxygen transport in blood, enzymatic redox reactions or photosynthesis. In addition, both naturally derived as well as synthetic porphyrinic compounds are extensively explored for biomedical and technical applications such as photodynamic therapy (PDT) or photovoltaic systems, respectively. Their unique electronic structures and photophysical properties make this class of compounds so interesting for the multiple functions encountered. It is therefore not surprising that optical methods are typically the prevalent analytical tool applied in characterization and processes involving porphyrinic compounds. However, a wealth of complementary information can be obtained from NMR spectroscopic techniques. Based on the advantage of providing structural and dynamic information with atomic resolution simultaneously, NMR spectroscopy is a powerful method for studying molecular interactions between porphyrinic compounds and macromolecules. Such interactions are of special interest in medical applications of porphyrinic photosensitizers that are mostly combined with macromolecular carrier systems. The macromolecular surrounding typically stabilizes the encapsulated drug and may also modify its physical properties. Moreover, the interaction with macromolecular physiological components needs to be explored to understand and control mechanisms of action and therapeutic efficacy. This review focuses on such non-covalent interactions of porphyrinic drugs with synthetic polymers as well as with biomolecules such as phospholipids or proteins. A brief introduction into various NMR spectroscopic techniques is given including chemical shift perturbation methods, NOE enhancement spectroscopy, relaxation time measurements and diffusion-ordered spectroscopy. How these NMR tools are used to address porphyrin-macromolecule interactions with respect to their function in biomedical applications is the central point of the current review.
Collapse
Affiliation(s)
| | | | - Martina Vermathen
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (I.G.); (J.F.)
| |
Collapse
|
7
|
Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
Collapse
|
8
|
Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
Collapse
Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| |
Collapse
|
9
|
Abstract
A major challenge for metabolomic analysis is to obtain an unambiguous identification of the metabolites detected in a sample. Among metabolomics techniques, NMR spectroscopy is a sophisticated, powerful, and generally applicable spectroscopic tool that can be used to ascertain the correct structure of newly isolated biogenic molecules. However, accurate structure prediction using computational NMR techniques depends on how much of the relevant conformational space of a particular compound is considered. It is intrinsically challenging to calculate NMR chemical shifts using high-level DFT when the conformational space of a metabolite is extensive. In this work, we developed NMR chemical shift calculation protocols using a machine learning model in conjunction with standard DFT methods. The pipeline encompasses the following steps: (1) conformation generation using a force field (FF)-based method, (2) filtering the FF generated conformations using the ASE-ANI machine learning model, (3) clustering of the optimized conformations based on structural similarity to identify chemically unique conformations, (4) DFT structural optimization of the unique conformations, and (5) DFT NMR chemical shift calculation. This protocol can calculate the NMR chemical shifts of a set of molecules using any available combination of DFT theory, solvent model, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Our protocol reduces the overall computational time by 2 orders of magnitude over methods that optimize the conformations using fully ab initio methods, while still producing good agreement with experimental observations. The complete protocol is designed in such a manner that makes the computation of chemical shifts tractable for a large number of conformationally flexible metabolites.
Collapse
Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA
| | - Arthur S. Edison
- Departments of Genetics and Biochemistry, Institute of Bioinformatics and Complex Carbohydrate Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA
| |
Collapse
|
10
|
Platzer G, Mayer M, Beier A, Brüschweiler S, Fuchs JE, Engelhardt H, Geist L, Bader G, Schörghuber J, Lichtenecker R, Wolkerstorfer B, Kessler D, McConnell DB, Konrat R. PI by NMR: Probing CH-π Interactions in Protein-Ligand Complexes by NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:14861-14868. [PMID: 32421895 PMCID: PMC7496880 DOI: 10.1002/anie.202003732] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/11/2020] [Indexed: 02/02/2023]
Abstract
While CH–π interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH–π interactions in drug–protein complexes. Herein, we present a fast and reliable methodology called PI (π interactions) by NMR, which can differentiate the strength of protein–ligand CH–π interactions in solution. By combining selective amino‐acid side‐chain labeling with 1H‐13C NMR, we are able to identify specific protein protons of side‐chains engaged in CH–π interactions with aromatic ring systems of a ligand, based solely on 1H chemical‐shift values of the interacting protein aromatic ring protons. The information encoded in the chemical shifts induced by such interactions serves as a proxy for the strength of each individual CH–π interaction. PI by NMR changes the paradigm by which chemists can optimize the potency of drug candidates: direct determination of individual π interactions rather than averaged measures of all interactions.
Collapse
Affiliation(s)
- Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Sven Brüschweiler
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| |
Collapse
|
11
|
Platzer G, Mayer M, Beier A, Brüschweiler S, Fuchs JE, Engelhardt H, Geist L, Bader G, Schörghuber J, Lichtenecker R, Wolkerstorfer B, Kessler D, McConnell DB, Konrat R. PI by NMR: Probing CH–π Interactions in Protein–Ligand Complexes by NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology Department of Structural and Computational Biology Max Perutz Labs University of Vienna Campus Vienna Biocenter 5 1030 Vienna Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology Department of Structural and Computational Biology Max Perutz Labs University of Vienna Campus Vienna Biocenter 5 1030 Vienna Austria
| | - Sven Brüschweiler
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology Department of Structural and Computational Biology Max Perutz Labs University of Vienna Campus Vienna Biocenter 5 1030 Vienna Austria
| | - Julian E. Fuchs
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Julia Schörghuber
- Institute of Organic Chemistry University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry University of Vienna Währingerstraße 38 1090 Vienna Austria
| | | | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG Dr. Boehringer Gasse 5–11 1121 Vienna Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology Department of Structural and Computational Biology Max Perutz Labs University of Vienna Campus Vienna Biocenter 5 1030 Vienna Austria
| |
Collapse
|
12
|
Wang Y, Kim J, Hilty C. Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization. Chem Sci 2020; 11:5935-5943. [PMID: 32874513 PMCID: PMC7441707 DOI: 10.1039/d0sc00266f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 11/21/2022] Open
Abstract
Elucidation of small molecule-protein interactions provides essential information for understanding biological processes such as cellular signaling, as well as for rational drug development. Here, multi-dimensional NMR with sensitivity enhancement by dissolution dynamic nuclear polarization (D-DNP) is shown to allow the determination of the binding epitope of folic acid when complexed with the target dihydrofolate reductase. Protein signals are selectively enhanced by polarization transfer from the hyperpolarized ligand. A pseudo three-dimensional data acquisition with ligand-side Hadamard encoding results in protein-side [13C, 1H] chemical shift correlations that contain intermolecular nuclear Overhauser effect (NOE) information. A scoring function based on this data is used to select pre-docked ligand poses. The top five poses are within 0.76 Å root-mean-square deviation from a reference structure for the encoded five protons, showing improvements compared with the poses selected by an energy-based scoring function without experimental inputs. The sensitivity enhancement provided by the D-DNP combined with multi-dimensional NMR increases the speed and potentially the selectivity of structure elucidation of ligand binding epitopes.
Collapse
Affiliation(s)
- Yunyi Wang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Jihyun Kim
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| |
Collapse
|
13
|
Lin Y, Ruan H, Akutse KS, Lai B, Lin Y, Hou Y, Zhong F. Ethylene and Benzaldehyde Emitted from Postharvest Tomatoes Inhibit Botrytis cinerea via Binding to G-Protein Coupled Receptors and Transmitting with cAMP-Signal Pathway of the Fungus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13706-13717. [PMID: 31693347 DOI: 10.1021/acs.jafc.9b05778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tomato storage conditions are difficult largely due to Botrytis cinerea infection which causes gray mold disease. However, the effects of the volatile organic compounds (VOCs) emitted by postharvest tomatoes on this fungus remain unclear. We analyzed the effects of tomato-emitted VOCs on B. cinerea pathogenicity, germination, and hyphal growth with bioassay, predicted the causative active compounds by principle component analysis, identified G-protein-coupled receptors (GPCRs) which captured chemical signals in the B. cinerea genome by stimulating molecular docking, tested the binding affinities of these receptors for the active compounds by fluorescence binding competition assay, and identified an associated signaling pathway by RNA interfere. The VOCs emitted by postharvest tomatoes inhibited B. cinerea; ethylene and benzaldehyde were the active compounds causing this effect. One of the identified GPCRs in B. cinerea, BcGPR3, bound tightly to both active compounds. Two genes associated with the cAMP signaling pathway (BcRcn1 and BcCnA) were downregulated in wild-type B. cinerea exposed to the active compounds, as well as in the ΔBcgpr3 B. cinerea mutant. Exposure to postharvest tomato VOCs reduces B. cinerea pathogenicity due to ethylene and benzaldehyde volatiles. The BcGPR3 protein is inactivated by the active compounds, and thus fails to transmit signals to the cAMP pathway, thereby inhibiting B. cinerea.
Collapse
Affiliation(s)
- Yongwen Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & College of Horticulture , Fujian Agriculture and Forestry University Fujian , 350013 Fuzhou , Fujian , P. R. China
| | - Hongchun Ruan
- Institute of Plant Protection , Fujian Academy of Agricultural Sciences , 350013 Fuzhou , Fujian , P. R. China
| | - Komivi Senyo Akutse
- International Centre of Insect Physiology and Ecology , 30772-00100 Nairobi , Kenya
| | - Baochun Lai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & College of Horticulture , Fujian Agriculture and Forestry University Fujian , 350013 Fuzhou , Fujian , P. R. China
| | - Yizhang Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & College of Horticulture , Fujian Agriculture and Forestry University Fujian , 350013 Fuzhou , Fujian , P. R. China
| | - Youming Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & College of Horticulture , Fujian Agriculture and Forestry University Fujian , 350013 Fuzhou , Fujian , P. R. China
| | - Fenglin Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & College of Horticulture , Fujian Agriculture and Forestry University Fujian , 350013 Fuzhou , Fujian , P. R. China
| |
Collapse
|
14
|
Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
Collapse
Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
| |
Collapse
|
15
|
Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front Chem 2018; 6:150. [PMID: 29868556 PMCID: PMC5952040 DOI: 10.3389/fchem.2018.00150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/16/2018] [Indexed: 01/13/2023] Open
Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.
Collapse
Affiliation(s)
- Xinsheng Jin
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- National Engineering Research Centre for Nanotechnology, Shanghai, China
| |
Collapse
|
16
|
Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. Phys Chem Chem Phys 2018; 20:9543-9553. [PMID: 29577158 PMCID: PMC5892194 DOI: 10.1039/c8cp00647d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical shifts are highly sensitive probes of local conformation and overall structure. Both isotropic shifts and chemical shift tensors are readily accessible from NMR experiments but their quantum mechanical calculations remain challenging. In this work, we report and compare accurately measured and calculated 15NH and 13Cα chemical shift tensors in proteins, using the microcrystalline agglutinin from Oscillatoria agardhii (OAA). Experimental 13Cα and 15NH chemical tensors were obtained by solid-state NMR spectroscopy, employing tailored recoupling sequences, and for their quantum mechanics/molecular mechanics (QM/MM) calculations different sets of functionals were evaluated. We show that 13Cα chemical shift tensors are primarily determined by backbone dihedral angles and dynamics, while 15NH tensors mainly depend on local electrostatic contributions from solvation and hydrogen bonding. In addition, the influence of including crystallographic waters, the molecular mechanics geometry optimization protocol, and the level of theory on the accuracy of the calculated chemical shift tensors is discussed. Specifically, the power of QM/MM calculations in accurately predicting the unusually upfield shifted 1HN G26 and G93 resonances is highlighted. Our integrated approach is expected to benefit structure refinement of proteins and protein assemblies.
Collapse
Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Leonardus M. I. Koharudin
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8087, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| |
Collapse
|