1
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Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024; 64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [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: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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2
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La CC, Smith SA, Vappala S, Adili R, Luke CE, Abbina S, Luo HD, Chafeeva I, Drayton M, Creagh LA, de Guadalupe Jaraquemada-Peláez M, Rhoads N, Kalathottukaren MT, Henke PK, Straus SK, Du C, Conway EM, Holinstat M, Haynes CA, Morrissey JH, Kizhakkedathu JN. Smart thrombosis inhibitors without bleeding side effects via charge tunable ligand design. Nat Commun 2023; 14:2177. [PMID: 37100783 PMCID: PMC10133246 DOI: 10.1038/s41467-023-37709-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/28/2023] [Indexed: 04/28/2023] Open
Abstract
Current treatments to prevent thrombosis, namely anticoagulants and platelets antagonists, remain complicated by the persistent risk of bleeding. Improved therapeutic strategies that diminish this risk would have a huge clinical impact. Antithrombotic agents that neutralize and inhibit polyphosphate (polyP) can be a powerful approach towards such a goal. Here, we report a design concept towards polyP inhibition, termed macromolecular polyanion inhibitors (MPI), with high binding affinity and specificity. Lead antithrombotic candidates are identified through a library screening of molecules which possess low charge density at physiological pH but which increase their charge upon binding to polyP, providing a smart way to enhance their activity and selectivity. The lead MPI candidates demonstrates antithrombotic activity in mouse models of thrombosis, does not give rise to bleeding, and is well tolerated in mice even at very high doses. The developed inhibitor is anticipated to open avenues in thrombosis prevention without bleeding risk, a challenge not addressed by current therapies.
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Affiliation(s)
- Chanel C La
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Stephanie A Smith
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sreeparna Vappala
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Reheman Adili
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
- Bloodworks Research Institute, 1551 Eastlake Avenue E.; Ste. 100, Seattle, WA, 98102, USA
| | - Catherine E Luke
- Department of Surgery, Section of Vascular Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Srinivas Abbina
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Haiming D Luo
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Irina Chafeeva
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Drayton
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Louise A Creagh
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | | | - Nicole Rhoads
- Bloodworks Research Institute, 1551 Eastlake Avenue E.; Ste.100, Seattle, WA, 98102, USA
| | - Manu Thomas Kalathottukaren
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter K Henke
- Department of Surgery, Section of Vascular Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Caigan Du
- Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Edward M Conway
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- The School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Michael Holinstat
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Charles A Haynes
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - James H Morrissey
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- The School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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3
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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4
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Pushkarev SV, Vinnik VA, Shapovalova IV, Švedas VK, Nilov DK. Modeling the Structure of Human tRNA-Guanine Transglycosylase in Complex with 7-Methylguanine and Revealing the Factors that Determine the Enzyme Interaction with Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:443-449. [PMID: 35790378 DOI: 10.1134/s0006297922050054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
tRNA-guanine transglycosylase, an enzyme catalyzing replacement of guanine with queuine in human tRNA and participating in the translation mechanism, is involved in the development of cancer. However, information on the small-molecule inhibitors that can suppress activity of this enzyme is very limited. Molecular dynamics simulations were used to determine the amino acid residues that provide efficient binding of inhibitors in the active site of tRNA-guanine transglycosylase. It was demonstrated using 7-methylguanine molecule as a probe that the ability of the inhibitor to adopt a charged state in the environment of hydrogen bond acceptors Asp105 and Asp159 plays a key role in complex formation. Formation of the hydrogen bonds and hydrophobic contacts with Gln202, Gly229, Phe109, and Met259 residues are also important. It has been predicted that introduction of the substituents would have a different effect on the ability to inhibit tRNA-guanine transglycosylase, as well as the DNA repair protein poly(ADP-ribose) polymerase 1, which can contribute to the development of more efficient and selective compounds.
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Affiliation(s)
- Sergey V Pushkarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Valeriia A Vinnik
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Shapovalova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vytas K Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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5
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment‐Bindung an die Kinase‐Scharnier‐Region: Wenn Ladungsverteilung und lokale p
K
a
‐Verschiebungen etablierte Bioisosterie‐Konzepte fehlleiten. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Christof Siefker
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Björn Wagner
- Roche Innovation Center Grenzacherstr. 124 4070 Basel Schweiz
| | - Andreas Heine
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
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6
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew Chem Int Ed Engl 2021; 60:252-258. [PMID: 33021032 PMCID: PMC7821265 DOI: 10.1002/anie.202011295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 12/25/2022]
Abstract
Medicinal-chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well-established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pKa values are modulated influencing protonation states and bioavailability. Considering the adjacent H-bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono-dentate pyridine nitrogen out-performs bi-dentate functionalities. The importance of correctly designing pKa values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.
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Affiliation(s)
- Matthias Oebbeke
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Christof Siefker
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Björn Wagner
- Roche Innovation CenterGrenzacherstr. 1244070BaselSwitzerland
| | - Andreas Heine
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
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7
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Hassaan E, Hohn C, Ehrmann FR, Goetzke FW, Movsisyan L, Hüfner-Wulsdorf T, Sebastiani M, Härtsch A, Reuter K, Diederich F, Klebe G. Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT. J Med Chem 2020; 63:6802-6820. [PMID: 32515955 DOI: 10.1021/acs.jmedchem.0c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1-recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1-recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Frederik R Ehrmann
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - F Wieland Goetzke
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Levon Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tobias Hüfner-Wulsdorf
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Maurice Sebastiani
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Klaus Reuter
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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8
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Klebe G. Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option? Drug Discov Today 2019; 24:943-948. [PMID: 30708050 DOI: 10.1016/j.drudis.2019.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
Thermodynamic profiles of ligand binding, particularly enthalpically favored binding signatures, have been suggested as a criterion to support the decision-making process around which compounds to select for further optimization in drug development. The concept was enthusiastically taken up, but turned out to be too superficial, either because many aspects determining thermodynamic profiles are insufficiently appreciated or because it is difficult to compare such data on a global scale. The impact of water, changes in protonation states, along with buffer dependencies and incompatible measurement conditions that are far from standard conditions hamper such broad-scale comparisons. However, thermodynamic signatures can make us aware of the impact of these aspects and provide important hints for improving our understanding of the binding process and defining criteria for drug optimization.
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Affiliation(s)
- Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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9
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Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des 2018; 32:937-963. [PMID: 30415285 PMCID: PMC6301044 DOI: 10.1007/s10822-018-0170-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/07/2018] [Indexed: 10/27/2022]
Abstract
Accurately predicting the binding affinities of small organic molecules to biological macromolecules can greatly accelerate drug discovery by reducing the number of compounds that must be synthesized to realize desired potency and selectivity goals. Unfortunately, the process of assessing the accuracy of current computational approaches to affinity prediction against binding data to biological macromolecules is frustrated by several challenges, such as slow conformational dynamics, multiple titratable groups, and the lack of high-quality blinded datasets. Over the last several SAMPL blind challenge exercises, host-guest systems have emerged as a practical and effective way to circumvent these challenges in assessing the predictive performance of current-generation quantitative modeling tools, while still providing systems capable of possessing tight binding affinities. Here, we present an overview of the SAMPL6 host-guest binding affinity prediction challenge, which featured three supramolecular hosts: octa-acid (OA), the closely related tetra-endo-methyl-octa-acid (TEMOA), and cucurbit[8]uril (CB8), along with 21 small organic guest molecules. A total of 119 entries were received from ten participating groups employing a variety of methods that spanned from electronic structure and movable type calculations in implicit solvent to alchemical and potential of mean force strategies using empirical force fields with explicit solvent models. While empirical models tended to obtain better performance than first-principle methods, it was not possible to identify a single approach that consistently provided superior results across all host-guest systems and statistical metrics. Moreover, the accuracy of the methodologies generally displayed a substantial dependence on the system considered, emphasizing the need for host diversity in blind evaluations. Several entries exploited previous experimental measurements of similar host-guest systems in an effort to improve their physical-based predictions via some manner of rudimentary machine learning; while this strategy succeeded in reducing systematic errors, it did not correspond to an improvement in statistical correlation. Comparison to previous rounds of the host-guest binding free energy challenge highlights an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds. The data suggests that further refinement of force field parameters, as well as improved treatment of chemical effects (e.g., buffer salt conditions, protonation states), may be required to further enhance predictive accuracy.
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Affiliation(s)
- Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - John N McNeill
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Wei Yao
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Matthew Sullivan
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael W Chiu
- Qualcomm Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA.
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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10
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Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
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Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
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11
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Ehrmann FR, Stojko J, Metz A, Debaene F, Barandun LJ, Heine A, Diederich F, Cianférani S, Reuter K, Klebe G. Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition. PLoS One 2017; 12:e0175723. [PMID: 28419165 PMCID: PMC5395182 DOI: 10.1371/journal.pone.0175723] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/30/2017] [Indexed: 01/05/2023] Open
Abstract
For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT) is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed. Thus, soaked structures may be misleading and suggest irrelevant binding modes. Accordingly, we re-investigated these complexes by co-crystallization. The obtained structures revealed large conformational rearrangements not visible in the soaked complexes. They result from spatial perturbations in the ribose-34/phosphate-35 recognition pocket and, consequently, an extended loop-helix motif required to prevent access of water molecules into the dimer interface loses its geometric integrity. Thermodynamic profiles of ligand binding in solution indicate favorable entropic contributions to complex formation when large conformational adaptations in the dimer interface are involved. Native MS titration experiments reveal the extent to which the homodimer is destabilized in the presence of each inhibitor. Unexpectedly, one ligand causes a complete rearrangement of subunit packing within the homodimer, never observed in any other TGT crystal structure before. Likely, this novel twisted dimer is catalytically inactive and, therefore, suggests that stabilizing this non-productive subunit arrangement may be used as a further strategy for TGT inhibition.
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Affiliation(s)
| | - Johann Stojko
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - François Debaene
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | | | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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Neeb M, Hohn C, Ehrmann FR, Härtsch A, Heine A, Diederich F, Klebe G. Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding? Bioorg Med Chem 2016; 24:4900-4910. [DOI: 10.1016/j.bmc.2016.07.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/24/2016] [Indexed: 11/29/2022]
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13
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Zheng L, Ding X, Liu K, Feng S, Tang B, Li Q, Huang D, Yang S. Molecular imaging of fibrosis using a novel collagen-binding peptide labelled with 99mTc on SPECT/CT. Amino Acids 2016; 49:89-101. [PMID: 27633720 DOI: 10.1007/s00726-016-2328-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 09/07/2016] [Indexed: 12/18/2022]
Abstract
Fibrosis, closely related to chronic various diseases, is a pathological process characterised by the accumulation of collagen (largely collagen type I). Non-invasive methods are necessary for the diagnosis and follow-up of fibrosis. This study aimed to develop a collagen-targeted probe for the molecular imaging of fibrosis. We identified CPKESCNLFVLKD (CBP1495) as an original collagen-binding peptide using isothermal titration calorimetry and enzyme-linked immunosorbent assay. CBP1495 effectively bound to collagen type I (K d = 861 nM) and (GPO)9 (K d = 633 nM), a collagen mimetic peptide. Western blot and histochemistry validated CBP1495 targeting collagen in vitro and ex vivo. (Gly-(D)-Ala-Gly-Gly) was introduced to CBP1495 for coupling 99mTc. Labelling efficiency of 99mTc-CBP1495 was 95.06 ± 1.08 %. The physico-chemical properties, tracer kinetics and biodistribution of 99mTc-CBP1495 were carried out, and showed that the peptide stably chelated 99mTc in vitro and in vivo. SPECT/CT imaging with 99mTc-CBP1495 was performed in rat fibrosis models, and revealed that 99mTc-CBP1495 significantly accumulated in fibrotic lungs or livers of rats. Finally, 99mTc-CBP1495 uptake and hydroxyproline (Hyp), a specific amino acid of collagen, were quantitatively analysed. The results demonstrated that 99mTc-CBP1495 uptake was positvely correlated with Hyp content in lungs (P < 0.0001, r 2 = 0.8266) or livers (P < 0.0001, r 2 = 0.7581). Therefore, CBP1495 is a novel collagen-binding peptide, and 99mTc-labelled CBP1495 may be a promising radiotracer for the molecular imaging of fibrosis.
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Affiliation(s)
- Lei Zheng
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.,Department of Nuclear Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Xiaojiang Ding
- Department of Nuclear Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Kaiyun Liu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, 400038, China
| | - Shibin Feng
- Department of Cardiology, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Qianwei Li
- Department of Nuclear Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Dingde Huang
- Department of Nuclear Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
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Falconer RJ. Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015. J Mol Recognit 2016; 29:504-15. [PMID: 27221459 DOI: 10.1002/jmr.2550] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x-ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion-π and π-π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Robert J Falconer
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK.
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15
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Hohn C, Härtsch A, Ehrmann FR, Pfaffeneder T, Trapp N, Dumele O, Klebe G, Diederich F. An Immucillin-Based Transition-State-Analogous Inhibitor of tRNA-Guanine Transglycosylase (TGT). Chemistry 2016; 22:6750-4. [PMID: 26991861 DOI: 10.1002/chem.201600883] [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] [Received: 03/15/2016] [Indexed: 11/06/2022]
Abstract
Shigellosis is one of the most severe diarrheal diseases worldwide without any efficient treatment so far. The enzyme tRNA-guanine transglycosylase (TGT) has been identified as a promising target for small-molecule drug design. Herein, we report a transition-state analogue, a small, immucillin-derived inhibitor, as a new lead structure with a novel mode of action. The complex inhibitor synthesis was accomplished in 18 steps with an overall yield of 3 %. A co-crystal structure of the inhibitor bound to Z. mobilis TGT confirmed the predicted conformation of the immucillin derivative in the enzyme active site.
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Affiliation(s)
- Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Oliver Dumele
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland.
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Callies O, Hernández Daranas A. Application of isothermal titration calorimetry as a tool to study natural product interactions. Nat Prod Rep 2016; 33:881-904. [DOI: 10.1039/c5np00094g] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular interactions of natural products by isothermal titration calorimetry (ITC) is a potent tool to get new insights of the underpinning driving forces.
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Affiliation(s)
- O. Callies
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
| | - A. Hernández Daranas
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
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17
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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Klebe G. The Use of Thermodynamic and Kinetic Data in Drug Discovery: Decisive Insight or Increasing the Puzzlement? ChemMedChem 2014; 10:229-31. [DOI: 10.1002/cmdc.201402521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 11/07/2022]
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21
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Barandun LJ, Ehrmann FR, Zimmerli D, Immekus F, Giroud M, Grünenfelder C, Schweizer WB, Bernet B, Betz M, Heine A, Klebe G, Diederich F. Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Chemistry 2014; 21:126-35. [DOI: 10.1002/chem.201405764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/09/2022]
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22
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Neeb M, Betz M, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G. Beyond Affinity: Enthalpy–Entropy Factorization Unravels Complexity of a Flat Structure–Activity Relationship for Inhibition of a tRNA-Modifying Enzyme. J Med Chem 2014; 57:5566-78. [DOI: 10.1021/jm5006868] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Neeb
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Michael Betz
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Luzi Jakob Barandun
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Christoph Hohn
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - François Diederich
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
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