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Hargreaves D, Carbajo RJ, Bodnarchuk MS, Embrey K, Rawlins PB, Packer M, Degorce SL, Hird AW, Johannes JW, Chiarparin E, Schade M. Design of rigid protein-protein interaction inhibitors enables targeting of undruggable Mcl-1. Proc Natl Acad Sci U S A 2023; 120:e2221967120. [PMID: 37186857 PMCID: PMC10214187 DOI: 10.1073/pnas.2221967120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The structure-based design of small-molecule inhibitors targeting protein-protein interactions (PPIs) remains a huge challenge as the drug must bind typically wide and shallow protein sites. A PPI target of high interest for hematological cancer therapy is myeloid cell leukemia 1 (Mcl-1), a prosurvival guardian protein from the Bcl-2 family. Despite being previously considered undruggable, seven small-molecule Mcl-1 inhibitors have recently entered clinical trials. Here, we report the crystal structure of the clinical-stage inhibitor AMG-176 bound to Mcl-1 and analyze its interaction along with clinical inhibitors AZD5991 and S64315. Our X-ray data reveal high plasticity of Mcl-1 and a remarkable ligand-induced pocket deepening. Nuclear Magnetic Resonance (NMR)-based free ligand conformer analysis demonstrates that such unprecedented induced fit is uniquely achieved by designing highly rigid inhibitors, preorganized in their bioactive conformation. By elucidating key chemistry design principles, this work provides a roadmap for targeting the largely untapped PPI class more successfully.
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Affiliation(s)
- David Hargreaves
- Discovery Sciences, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | | | - Kevin Embrey
- Discovery Sciences, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | - Martin Packer
- Chemistry, Oncology R&D, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | | | | | | | - Markus Schade
- Chemistry, Oncology R&D, AstraZeneca, CambridgeCB4 0WG, United Kingdom
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2
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Structures Controlled by Entropy: The Flexibility of Strychnine as Example. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227987. [PMID: 36432085 PMCID: PMC9692940 DOI: 10.3390/molecules27227987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and 3JHH couplings as well.
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Li XL, Ru T, Navarro-Vázquez A, Lindemann P, Nazaré M, Li XW, Guo YW, Sun H. Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D. JOURNAL OF NATURAL PRODUCTS 2022; 85:1730-1737. [PMID: 35792821 DOI: 10.1021/acs.jnatprod.2c00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).
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Affiliation(s)
- Xiao-Lu Li
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Tong Ru
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Peter Lindemann
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Marc Nazaré
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
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Sternberg U, Farès C. Statistical evaluation of simulated NMR data of flexible molecules. Phys Chem Chem Phys 2022; 24:9608-9618. [PMID: 35403649 DOI: 10.1039/d2cp00330a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new probability score-named χ-probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the χ-probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the χ-probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility. The NMR data (which include RDCs, NOE distances and 3J couplings) are calculated from MDOC (Molecular Dynamics with Orientational Constraints) trajectories and are investigated against experimentally measured data. It is demonstrated that this approach singles out the correct stereochemical configuration with probabilities more than 98%, even for highly mobile molecules. In more demanding cases, a decisive χ-probability test requires that the datasets include high-quality NOE distances in addition to RDC values.
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Affiliation(s)
- Ulrich Sternberg
- Research Partner of Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,COSMOS-Software, Jena, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany.
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Bohle F, Grimme S. Hydrocarbon Macrocycle Conformer Ensembles and 13 C-NMR Spectra. Angew Chem Int Ed Engl 2022; 61:e202113905. [PMID: 35099097 PMCID: PMC9303527 DOI: 10.1002/anie.202113905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 12/27/2022]
Abstract
NMR as a routine analytical method provides important three-dimensional structure information of compounds in solution. Here we apply the recently released CRENSO computational workflow for the automated generation of conformer ensembles to the quantum mechanical calculation of 13 C-NMR spectra of a series of flexible cycloalkanes up to C20 H40 . We evaluate the computed chemical shifts in comparison with corresponding experimental data in chloroform. It is shown that accurate and properly averaged theoretical NMR data can be obtained in about a day of computation time on a standard workstation computer. The excellent agreement between theory and experiment enables one to deduce preferred conformations of large, non-rigid macrocycles under ambient conditions from our automated procedure.
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Affiliation(s)
- Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115, Bonn, Germany
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Bohle F, Grimme S. Hydrocarbon Macrocycle Conformer Ensembles and
13
C‐NMR Spectra. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fabian Bohle
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich-Wilhelms-Universität Bonn Beringstr. 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich-Wilhelms-Universität Bonn Beringstr. 4 53115 Bonn Germany
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Roth FA, Schmidts V, Thiele CM. TITANIA: Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds. J Org Chem 2021; 86:15387-15402. [PMID: 34677977 DOI: 10.1021/acs.joc.1c01926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) become increasingly important as additional NMR parameters in the structure elucidation of organic compounds but are usually used in fitting procedures to discriminate between (computed) structures that are in accordance with RDCs and others that can be ruled out. Thus, the determination of configurations requires prior structural information. The direct use of RDCs as restraints to construct structures based on RDCs has only recently begun also in organic compounds. No protocol has been published though that uses the vector and dynamics information available in multialignment data sets directly for the joint determination of conformation and configuration of organic compounds. This is proposed in the current study. We show that by employing these data, even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. The requirements in terms of the number of RDCs and alignment media necessary are discussed in detail.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
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Balazs A, Davies N, Longmire D, Packer M, Chiarparin E. Nuclear magnetic resonance free ligand conformations and atomic resolution dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:489-498. [PMID: 37904764 PMCID: PMC10539760 DOI: 10.5194/mr-2-489-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/28/2021] [Indexed: 11/01/2023]
Abstract
Knowledge of free ligand conformational preferences (energy minima) and conformational dynamics (rotational energy barriers) of small molecules in solution can guide drug design hypotheses and help rank ideas to bias syntheses towards more active compounds. Visualization of conformational exchange dynamics around torsion angles, by replica exchange with solute tempering molecular dynamics (REST-MD), gives results in agreement with high-resolution 1 H nuclear magnetic resonance (NMR) spectra and complements free ligand conformational analyses. Rotational energy barriers around individual bonds are comparable between calculated and experimental values, making the in-silico method relevant to ranking prospective design ideas in drug discovery programs, particularly across a series of analogs. Prioritizing design ideas, based on calculations and analysis of measurements across a series, efficiently guides rational discovery towards the "right molecules" for effective medicines.
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Affiliation(s)
- Amber Y. S. Balazs
- Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nichola L. Davies
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
| | - David Longmire
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
| | - Martin J. Packer
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
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Sager E, Tzvetkova P, Gossert AD, Piechon P, Luy B. Determination of Configuration and Conformation of a Reserpine Derivative with Seven Stereogenic Centers Using Molecular Dynamics with RDC-Derived Tensorial Constraints*. Chemistry 2020; 26:14435-14444. [PMID: 32744785 PMCID: PMC7702126 DOI: 10.1002/chem.202002642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/22/2020] [Indexed: 11/11/2022]
Abstract
NMR-based determination of the configuration of complex molecules containing many stereocenters is often not possible using traditional NOE data and coupling patterns. Making use of residual dipolar couplings (RDCs), we were able to determine the relative configuration of a natural product containing seven stereocenters, including a chiral amine lacking direct RDC data. To identify the correct relative configuration out of 32 possible ones, experimental RDCs were used in three different approaches for data interpretation: by fitting experimental data based singular value decomposition (SVD) using a single alignment tensor and either (i) a single conformer or (ii) multiple conformers, or alternatively (iii) using molecular dynamics simulations with tensorial orientational constraints (MDOC). Even though in all three approaches one and the same configuration could be selected and clear discrimination between possible configurations was achieved, the experimental data was not fully satisfied by the methods based on single tensor approaches. While these two approaches are faster, only MDOC is able to fully reproduce experimental results, as the obtained conformational ensemble adequately covers the conformational space necessary to describe the molecule with inherent flexibility.
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Affiliation(s)
- Emine Sager
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Pavleta Tzvetkova
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
| | - Alvar D. Gossert
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
- Institut für Molekularbiologie und BiophysikETH Zürich8093ZürichSwitzerland
| | - Philippe Piechon
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Burkhard Luy
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
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Sternberg U, Tzvetkova P, Muhle-Goll C. The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints. Phys Chem Chem Phys 2020; 22:17375-17384. [PMID: 32705098 DOI: 10.1039/d0cp01905d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone). In the case of sagittamide A, one-bond 1H-13C residual dipolar couplings (RDC) are used as orientational constraints that reorient the molecule or parts of it. In addition, NOE distances and 3J scalar couplings are used as constraints. Five possible configurations of sagittamide A (labelled a to e) are considered. One experimental RDC value per flexible unit was available and this was not sufficient to single out one valid configuration. The problem could be solved by including NOE distances as well as 3J couplings as complementary constraints into the MDOC simulations. In accordance with former investigations, we confirmed the configuration a for the natural product. A detailed analysis of conformers of the central chain of 6 chiral carbon atoms could be given by inspecting the MDOC trajectory. The relative abundance of these conformers is crucial in fulfilling all three sets of constraints.
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Affiliation(s)
- Ulrich Sternberg
- Research Partner of Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. and COSMOS-Software, Jena, Germany
| | - Pavleta Tzvetkova
- Institute of Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute of Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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