1
|
Nedielkov R, Möller HM. Detecting and Characterizing Interactions of Metabolites with Proteins by Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Spectroscopy. Methods Mol Biol 2023; 2554:123-139. [PMID: 36178624 DOI: 10.1007/978-1-0716-2624-5_9] [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] [Indexed: 06/16/2023]
Abstract
Saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy is an established technique for detecting and characterizing the binding of small molecules, such as metabolites, to biological macromolecules like proteins and nucleic acids. STD NMR allows detection of binding in complex mixtures of potential ligands, which is often used for library screening in the pharmaceutical industry but may also be beneficial for binding studies with metabolite mixtures. The nature of the ligand is normally restricted to small molecules in terms of NMR spectroscopy, and the size of the macromolecule on the other side should be larger than 10-15 kDa. This technique is especially applicable to detecting binders of intermediate to low affinity with the dissociation constant (KD) above 1 μM. In this chapter, we focus on recent developments and the applications of STD NMR to studying interactions of natural products and metabolites, in particular. The reader is also referred to excellent reviews of the field and the literature cited therein. This chapter also provides a detailed experimental protocol for performing the STD NMR measurement based on the example of the subunit A of the Na+-transporting NADH/ubiquinone oxidoreductase (Na+-NQR) from V. cholerae interacting with its natural quinone substrate and inhibitors.
Collapse
Affiliation(s)
- Ruslan Nedielkov
- University of Potsdam, Institute for Chemistry, Potsdam, Germany.
| | - Heiko M Möller
- University of Potsdam, Institute for Chemistry, Potsdam, Germany
| |
Collapse
|
2
|
Camargo PG, Fabris M, Tatsuta Nakamae MY, Germano de Freitas Oliveira B, Henrique da Silva Lima C, de Fátima Â, de Lima Ferreira Bispo M, Macedo F. Thiohydantoins and hydantoins derived from amino acids as potent urease inhibitors: Inhibitory activity and ligand-target interactions. Chem Biol Interact 2022; 365:110045. [PMID: 35853540 DOI: 10.1016/j.cbi.2022.110045] [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: 03/01/2022] [Revised: 06/10/2022] [Accepted: 07/13/2022] [Indexed: 11/03/2022]
Abstract
We report the investigation of hydantoins and thiohydantoins derived from L and d-amino acids as inhibitors against the Canavalia ensiformis urease (CEU). The biochemical in vitro assay against CEU revealed a promising inhibitory potential for most thiohydantoins with six of them showing %I higher than the reference inhibitor thiourea (56.5%). In addition, thiohydantoin derived from l-valine, 1b, as well as the hydantoin 2d, derived from l-methionine, were identified as the most potent inhibitors with %I = 90.5 and 85.9 respectively. Enzyme kinetic studies demonstrated a mixed and uncompetitive inhibition profile for these compounds with Ki values of 0.42 mM for 1b and 0.99 mM for 2d. These kinetic parameters, obtained from traditional colorimetric assay, were strictly related to the KD values measured spectroscopically by the Saturation Transfer Difference (STD) technique for the urease complex. STD was also used to evince the moieties of the ligands responsible for the binding with the enzyme. Molecular docking studies showed that the thiohydantoin and hydantoin rings can act as a pharmacophoric group due to their binding affinity by hydrogen bonding interactions with critical amino acid residues in the enzyme active and/or allosteric site. These findings agreed with the experimental alpha values, demonstrating that 1b has affinity by free enzyme, and 2d derivative, an uncompetitive inhibitor, has great binding affinity at the allosteric site. The results for the thiohydantoin 1a, derived from d-valine, demonstrated a drastic stereochemical influence on inhibition, kinetics, and binding parameters in comparison to its enantiomer 1b.
Collapse
Affiliation(s)
- Priscila Goes Camargo
- Departament of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, PR, Brazil
| | - Marciéli Fabris
- Departament of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, PR, Brazil
| | | | | | | | - Ângelo de Fátima
- Departament of Chemistry Institute of Exact Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Fernando Macedo
- Departament of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, PR, Brazil.
| |
Collapse
|
3
|
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
|
4
|
Chen JL, Zhang P, Abe M, Aikawa H, Zhang L, Frank AJ, Zembryski T, Hubbs C, Park H, Withka J, Steppan C, Rogers L, Cabral S, Pettersson M, Wager TT, Fountain MA, Rumbaugh G, Childs-Disney JL, Disney MD. Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing. J Am Chem Soc 2020; 142:8706-8727. [PMID: 32364710 PMCID: PMC7357857 DOI: 10.1021/jacs.0c00768] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Approximately 95% of human genes are alternatively spliced, and aberrant splicing events can cause disease. One pre-mRNA that is alternatively spliced and linked to neurodegenerative diseases is tau (microtubule-associated protein tau), which can cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) and can contribute to Alzheimer's disease. Here, we describe the design of structure-specific lead small molecules that directly target tau pre-mRNA from sequence. This was followed by hit expansion and analogue synthesis to further improve upon these initial lead molecules. The emergent compounds were assessed for functional activity in a battery of assays, including binding assays and an assay that mimics molecular recognition of tau pre-mRNA by a U1 small nuclear ribonucleoprotein (snRNP) splicing factor. Compounds that emerged from these studies had enhanced potency and selectivity for the target RNA relative to the initial hits, while also having significantly improved drug-like properties. The compounds are shown to directly target tau pre-mRNA in cells, via chemical cross-linking and isolation by pull-down target profiling, and to rescue disease-relevant splicing of tau pre-mRNA in a variety of cellular systems, including primary neurons. More broadly, this study shows that lead, structure-specific compounds can be designed from sequence and then further optimized for their physicochemical properties while at the same time enhancing their activity.
Collapse
Affiliation(s)
- Jonathan L. Chen
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Masahito Abe
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Haruo Aikawa
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Liying Zhang
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Alexander J. Frank
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Timothy Zembryski
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Christopher Hubbs
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - HaJeung Park
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jane Withka
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Claire Steppan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Lucy Rogers
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Shawn Cabral
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Martin Pettersson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Travis T. Wager
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Matthew A. Fountain
- Department of Chemistry & Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Gavin Rumbaugh
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry and Neuroscience, The Scripps Research Institute, Jupiter
| |
Collapse
|
5
|
Raingeval C, Cala O, Brion B, Le Borgne M, Hubbard RE, Krimm I. 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery. J Enzyme Inhib Med Chem 2019; 34:1218-1225. [PMID: 31286785 PMCID: PMC6691826 DOI: 10.1080/14756366.2019.1636235] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
WaterLOGSY is a sensitive ligand-observed NMR experiment for detection of interaction between a ligand and a protein and is now well-established as a screening technique for fragment-based lead discovery. Here we develop and assess a protocol to derive ligand epitope mapping from WaterLOGSY data and demonstrate its general applicability in studies of fragment-sized ligands binding to six different proteins (glycogen phosphorylase, protein peroxiredoxin 5, Bcl-xL, Mcl-1, HSP90, and human serum albumin). We compare the WaterLOGSY results to those obtained from the more widely used saturation transfer difference experiments and to the 3D structures of the complexes when available. In addition, we evaluate the impact of ligand labile protons on the WaterLOGSY data. Our results demonstrate that the WaterLOGSY experiment can be used as an additional confirmation of the binding mode of a ligand to a protein.
Collapse
Affiliation(s)
- Claire Raingeval
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Olivier Cala
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Béatrice Brion
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Marc Le Borgne
- b Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7 , Lyon , France
| | - Roderick Eliot Hubbard
- c YSBL, University of York , Heslington , York , UK.,d Vernalis (R&D) Ltd, Granta Park, Abington , Cambridge , UK
| | - Isabelle Krimm
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| |
Collapse
|
6
|
Zhang Y, Xu H, Casabianca LB. Interaction between cyanine dye IR-783 and polystyrene nanoparticles in solution. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1054-1060. [PMID: 29771468 DOI: 10.1002/mrc.4751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
The interactions between small molecule drugs or dyes and nanoparticles are important to the use of nanoparticles in medicine. Noncovalent adsorption of dyes on nanoparticle surfaces is also important to the development of nanoparticle dual-use imaging contrast agents. In this work, solution-state NMR is used to examine the noncovalent interaction between a near-infrared cyanine dye and the surface of polystyrene nanoparticles in solution. Using 1D proton NMR, we can approximate the number of dye molecules that associate with each nanoparticle for different sized nanoparticles. Saturation-Transfer Difference NMR was also used to show that protons near the positively charged nitrogen in the dye are more strongly associated with the negatively charged nanoparticle surface than protons near the negatively charged sulfate groups of the dye. The methods described here can be used to study similar drug or dye molecules interacting with the surface of organic nanoparticles.
Collapse
Affiliation(s)
- Yunzhi Zhang
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Hui Xu
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | | |
Collapse
|
7
|
Szlag VM, Jung S, Rodriguez RS, Bourgeois M, Bryson S, Schatz GC, Reineke TM, Haynes CL. Isothermal Titration Calorimetry for the Screening of Aflatoxin B1 Surface-Enhanced Raman Scattering Sensor Affinity Agents. Anal Chem 2018; 90:13409-13418. [DOI: 10.1021/acs.analchem.8b03221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Victoria M. Szlag
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Seyoung Jung
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Rebeca S. Rodriguez
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Marc Bourgeois
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel Bryson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - George C. Schatz
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Theresa M. Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christy L. Haynes
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|