1
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Yokomine M, Morimoto J, Fukuda Y, Ueda T, Takeuchi K, Umezawa K, Ago H, Matsuura H, Ueno G, Senoo A, Nagatoishi S, Tsumoto K, Sando S. A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2. Chem Sci 2024; 15:7051-7060. [PMID: 38756815 PMCID: PMC11095393 DOI: 10.1039/d4sc01540a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024] Open
Abstract
Peptoids are a promising drug modality targeting disease-related proteins, but how a peptoid engages in protein binding is poorly understood. This is primarily due to a lack of high-resolution peptoid-protein complex structures and systematic physicochemical studies. Here, we present the first crystal structure of a peptoid bound to a protein, providing high-resolution structural information about how a peptoid binds to a protein. We previously reported a rigid peptoid, oligo(N-substituted alanine) (oligo-NSA), and developed an oligo-NSA-type peptoid that binds to MDM2. X-ray crystallographic analysis of the peptoid bound to MDM2 showed that the peptoid recognizes the MDM2 surface predominantly through the interaction of the N-substituents, while the main chain acts as a scaffold. Additionally, conformational, thermodynamic, and kinetic analysis of the peptoid and its derivatives with a less rigid main chain revealed that rigidification of the peptoid main chain contributes to improving the protein binding affinity. This improvement is thermodynamically attributed to an increased magnitude of the binding enthalpy change, and kinetically to an increased association rate and decreased dissociation rate. This study provides invaluable insights into the design of protein-targeting peptoids.
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Affiliation(s)
- Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Koji Umezawa
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University 8304 Minami-Minowa, Kami-Ina Nagano 399-4598 Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University 8304 Minami-Minowa, Kami-Ina Nagano 399-4598 Japan
| | - Hideo Ago
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Go Ueno
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | - Akinobu Senoo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai Minato-ku Tokyo 108-8639 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
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2
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Kalathingal M, Rhee YM. Thermodynamic consequences of stapling side-chains on a peptide ligand using a lactam-bridge: A theoretical study on anti-angiogenic peptides targeting VEGF. Proteins 2024. [PMID: 38602129 DOI: 10.1002/prot.26692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
Peptides are promising therapeutic agents for various biological targets due to their high efficacy and low toxicity, and the design of peptide ligands with high binding affinity to the target of interest is of utmost importance in peptide-based drug design. Introducing a conformational constraint to a flexible peptide ligand using a side-chain lactam-bridge is a convenient and efficient method to improve its binding affinity to the target. However, in general, such a small structural modification to a flexible ligand made with the intent of lowering the configurational entropic penalty for binding may have unintended consequences in different components of the binding enthalpy and entropy, including the configurational entropy component, which are still not clearly understood. Toward probing this, we examine different components of the binding enthalpy and entropy as well as the underlying structure and dynamics, for a side-chain lactam-bridged peptide inhibitor and its flexible analog forming complexes with vascular endothelial growth factor (VEGF), using all-atom molecular dynamics simulations. It is found that introducing a side-chain lactam-bridge constraint into the flexible peptide analog led to a gain in configurational entropy change but losses in solvation entropy, solute internal energy, and solvation energy changes upon binding, pinpointing the opportunities and challenges in drug design. The present study features an interplay between configurational and solvation entropy changes, as well as the one between binding enthalpy and entropy, in ligand-target binding upon imposing a conformational constraint into a flexible ligand.
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Affiliation(s)
- Mahroof Kalathingal
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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3
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Summa CM, Langford DP, Dinshaw SH, Webb J, Rick SW. Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding. J Chem Theory Comput 2024; 20:2812-2819. [PMID: 38538531 DOI: 10.1021/acs.jctc.4c00057] [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: 04/10/2024]
Abstract
Computer simulation methods can aid in the rational design of drugs aimed at a specific target, typically a protein. The affinity of a drug for its target is given by the free energy of binding. Binding can be further characterized by the enthalpy and entropy changes in the process. Methods exist to determine exact free energies, enthalpies, and entropies that are dependent only on the quality of the potential model and adequate sampling of conformational degrees of freedom. Entropy and enthalpy are roughly an order of magnitude more difficult to calculate than the free energy. This project combines a replica exchange method for enhanced sampling, designed to be efficient for protein-sized systems, with free energy calculations. This approach, replica exchange with dynamical scaling (REDS), uses two conventional simulations at different temperatures so that the entropy can be found from the temperature dependence of the free energy. A third replica is placed between them, with a modified Hamiltonian that allows it to span the temperature range of the conventional replicas. REDS provides temperature-dependent data and aids in sampling. It is applied to the bromodomain-containing protein 4 (BRD4) system. We find that for the force fields used, the free energies are accurate but the entropies and enthalpies are not, with the entropic contribution being too positive. Reproducing the entropy and enthalpy of binding appears to be a more stringent test of the force fields than reproducing the free energy.
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Affiliation(s)
- Christopher M Summa
- Department of Computer Science, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Dillon P Langford
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Sam H Dinshaw
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Jennifer Webb
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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4
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Khuttan S, Gallicchio E. What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling. J Chem Theory Comput 2024; 20:1489-1501. [PMID: 38252868 PMCID: PMC10867849 DOI: 10.1021/acs.jctc.3c01250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024]
Abstract
We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a ligand and a copy of the same ligand, and its true value is zero. Nevertheless, because the two copies of the ligand move independently, the self-RBFE value produced by a finite-length simulation fluctuates and can be used to measure the variance of the model. The results of this validation provide evidence that a significant fraction of the errors observed in benchmark studies reflect the statistical fluctuations of unconverged estimates rather than the models' accuracy. Furthermore, we find that ligand reorganization is a significant contributing factor to the statistical variance of binding free energy estimates and that metadynamics-accelerated conformational sampling of the torsional degrees of freedom of the ligand can drastically reduce the time to convergence.
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Affiliation(s)
- Sheenam Khuttan
- Department
of Chemistry and Biochemistry, Brooklyn
College of the City University of New York, New York, New York 11210, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
| | - Emilio Gallicchio
- Department
of Chemistry and Biochemistry, Brooklyn
College of the City University of New York, New York, New York 11210, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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5
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Komarov IV, Bugrov VA, Cherednychenko A, Grygorenko OO. Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules. CHEM REC 2024; 24:e202300276. [PMID: 37847887 DOI: 10.1002/tcr.202300276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/29/2023] [Indexed: 10/19/2023]
Abstract
In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some "rules of thumb" have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Volodymyr A Bugrov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Anton Cherednychenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
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6
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Valdivia V, Recio R, Lerena P, Pozo E, Serrano R, Calero R, Pintado C, Leal MP, Moreno-Rodríguez N, Organero JÁ, Khiar N, Fernández I. Biological evaluation of carbohydrate-based aprepitant analogs for neuroblastoma treatment. Eur J Med Chem 2024; 264:116021. [PMID: 38086194 DOI: 10.1016/j.ejmech.2023.116021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023]
Abstract
Different studies using Aprepitant, a NK1R antagonist currently used as a clinical drug for treating chemotherapy-related nausea and vomiting, have demonstrated that pharmacological inhibition of NK1R effectively reduces the growth of several tumor types such as neuroblastoma (NB). In a previous work, we demonstrated that a series of carbohydrate-based Aprepitant analogs, derived from either d-galactose or l-arabinose, have shown high affinity and NK1R antagonistic activity with a broad-spectrum anticancer activity and an important selectivity. In this new study, we explore the selective cytotoxic effects of these derivatives for the treatment of NB. Furthermore, we describe the design and stereoselective synthesis of a new generation of d-glucose derivatives as Aprepitant analogs, supported by docking studies. This approach showed that most of our carbohydrate-based analogs are significantly more selective than Aprepitant. The galactosyl derivative 2α, has demonstrated a marked in vitro selective cytotoxic activity against NB, with IC50 values in the same range as those of Aprepitant and its prodrug Fosaprepitant. Interestingly, the derivative 2α has shown similar apoptotic effect to that of Aprepitant. Moreover, we can select the glucosyl amino derivative 10α as an interesting hit exhibiting higher in vitro cytotoxic activity against NB than Aprepitant, being 1.2 times more selective.
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Affiliation(s)
- Victoria Valdivia
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Rocío Recio
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain.
| | - Patricia Lerena
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Esther Pozo
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Rosario Serrano
- Departamento de Química Inorgánica, Química Orgánica y Bioquímica, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Raúl Calero
- Departamento de Química Inorgánica, Química Orgánica y Bioquímica, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Cristina Pintado
- Departamento de Química Inorgánica, Química Orgánica y Bioquímica, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Manuel Pernia Leal
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Nazaret Moreno-Rodríguez
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Juan Ángel Organero
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímicas and INAMOL, Universidad de Castilla-La Mancha, Avda. Carlos III, s.n., 45071, Toledo, Spain
| | - Noureddine Khiar
- Instituto de Investigaciones Químicas (IIQ), CSIC-Universidad de Sevilla. Avda. Américo Vespucio, 49, Isla de la Cartuja, 41092, Sevilla, Spain
| | - Inmaculada Fernández
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, C/ Profesor García González, 2, 41012, Sevilla, Spain
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7
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Kalinin MA, Evsiunina MV, Kalle P, Lyssenko KA, Matveev PI, Borisova NE. Small Cyclic Diglycolamides: Tautomerism, Solvent Extraction and Coordination with f-Elements: One Strain to Rule Them All. Inorg Chem 2024; 63:602-612. [PMID: 38112309 DOI: 10.1021/acs.inorgchem.3c03488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The search for new effective extractants is an important task for the management of high-level liquid waste (HLW) generated during the reprocessing of spent nuclear fuel. Here, we synthesized a series of diglycolamides with cyclic substituents for the first time. We disclosed their coordination with f-element nitrates [La(NO3)3 and UO2(NO3)2] by SC-XRD study and complexation properties toward Am(III), Ln(III), and U(VI) during solvent extraction from nitric acid solutions. Using dynamic nuclear magnetic resonance (NMR) and density functional theory (DFT) calculations, the importance of tautomerism in the extraction properties of diglycolamides was shown.
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Affiliation(s)
- Mikhail A Kalinin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Mariia V Evsiunina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Paulina Kalle
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr. 31, Moscow 119991, Russia
| | - Konstantin A Lyssenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Petr I Matveev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Nataliya E Borisova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
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8
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Danelius E, Bu G, Wieske LHE, Gonen T. MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations. ACS Chem Biol 2023; 18:2582-2589. [PMID: 37944119 PMCID: PMC10728894 DOI: 10.1021/acschembio.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as to act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally, and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles that have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material and that different conformations of flexible compounds can be derived from the same experiment. These results will have an impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- Emma Danelius
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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9
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Çınaroğlu S, Biggin PC. Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. J Chem Inf Model 2023; 63:6095-6108. [PMID: 37759363 PMCID: PMC10565830 DOI: 10.1021/acs.jcim.3c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Indexed: 09/29/2023]
Abstract
Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (R2 of 0.88 and an RMSE of 1.48 kcal/mol overall). Although one cannot know prospectively whether computed ITC values will be correct or not, this work shows that if experimental ITC data are available, then this in conjunction with computed ITC, can be used as a tool to know if the ensemble being simulated is representative of the true ensemble or not. That is important for allowing the correct interpretation of the detailed dynamics of the system with respect to the measured enthalpy. The results also suggest that computational calorimetry is becoming increasingly feasible. We provide the data set as a resource for the community, which could be used as a benchmark to help further progress in this area.
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Affiliation(s)
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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10
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Danelius E, Bu G, Wieske H, Gonen T. MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551405. [PMID: 37577574 PMCID: PMC10418104 DOI: 10.1101/2023.07.31.551405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles which have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material, and that different conformations of flexible compounds can be derived from the same experiment. These results will have impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- E Danelius
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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11
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Hammerschmidt SJ, Huber S, Braun NJ, Lander M, Steinmetzer T, Kersten C. Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs. Arch Pharm (Weinheim) 2022; 356:e2200518. [PMID: 36480352 DOI: 10.1002/ardp.202200518] [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: 10/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.
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Affiliation(s)
- Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
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12
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Deng L, Mo J, Zhang Y, Peng K, Li H, Ouyang S, Feng Z, Fang W, Wei J, Rong D, Zhang X, Wang Y. Boronic Acid: A Novel Pharmacophore Targeting Src Homology 2 (SH2) Domain of STAT3. J Med Chem 2022; 65:13094-13111. [PMID: 36170649 DOI: 10.1021/acs.jmedchem.2c00940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SH2 domains have been recognized as promising targets for various human diseases. However, targeting SH2 domains with phosphopeptides or small-molecule inhibitors derived from bioisosteres of the phosphate group is still challenging. Identifying novel bioisosteres of the phosphate group to achieve favorable in vivo potency is urgently needed. Here, we report the feasibility of targeting the STAT3-SH2 domain with a boronic acid group and the identification of a highly potent inhibitor compound 7 by replacing the carboxylic acid of compound 4 with a boronic acid. Compound 7 shows higher binding affinity, better cellular potency, more favorable PK profiles, and higher in vivo antitumor activity than 4. The stronger anticancer effect of 7 partially stems from its covalent binding mode with the SH2 domain, verified by the washout experiments. The relatively high level of sequence conservation among SH2 domains makes the results presented here of general significance.
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Affiliation(s)
- Lin Deng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianshan Mo
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yi Zhang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Keren Peng
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huaxuan Li
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shumin Ouyang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zongbo Feng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wei Fang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianwei Wei
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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13
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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14
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Gaucher J, Reille‐Seroussi M, Broussy S. Structural and ITC Characterization of Peptide‐Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands. Chemistry 2022; 28:e202200465. [PMID: 35665969 PMCID: PMC9543606 DOI: 10.1002/chem.202200465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jean‐François Gaucher
- CiTCoM UMR CNRS 8038 Université Paris Cité, Faculté de Santé, UFR de Pharmacie 4 av. de l'Observatoire 75006 Paris France
| | - Marie Reille‐Seroussi
- CitCoM UMR CNRS 8038 U1268 INSERM Université Paris Cité, Faculté de Santé, UFR de Pharmacie 4 av. de l'Observatoire 75006 Paris France
| | - Sylvain Broussy
- CitCoM UMR CNRS 8038 U1268 INSERM Université Paris Cité, Faculté de Santé, UFR de Pharmacie 4 av. de l'Observatoire 75006 Paris France
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15
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Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies. Mar Drugs 2022; 20:md20060397. [PMID: 35736200 PMCID: PMC9230156 DOI: 10.3390/md20060397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 01/29/2023] Open
Abstract
Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.
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16
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Reek JNH, de Bruin B, Pullen S, Mooibroek TJ, Kluwer AM, Caumes X. Transition Metal Catalysis Controlled by Hydrogen Bonding in the Second Coordination Sphere. Chem Rev 2022; 122:12308-12369. [PMID: 35593647 PMCID: PMC9335700 DOI: 10.1021/acs.chemrev.1c00862] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transition metal catalysis is of utmost importance for the development of sustainable processes in academia and industry. The activity and selectivity of metal complexes are typically the result of the interplay between ligand and metal properties. As the ligand can be chemically altered, a large research focus has been on ligand development. More recently, it has been recognized that further control over activity and selectivity can be achieved by using the "second coordination sphere", which can be seen as the region beyond the direct coordination sphere of the metal center. Hydrogen bonds appear to be very useful interactions in this context as they typically have sufficient strength and directionality to exert control of the second coordination sphere, yet hydrogen bonds are typically very dynamic, allowing fast turnover. In this review we have highlighted several key features of hydrogen bonding interactions and have summarized the use of hydrogen bonding to program the second coordination sphere. Such control can be achieved by bridging two ligands that are coordinated to a metal center to effectively lead to supramolecular bidentate ligands. In addition, hydrogen bonding can be used to preorganize a substrate that is coordinated to the metal center. Both strategies lead to catalysts with superior properties in a variety of metal catalyzed transformations, including (asymmetric) hydrogenation, hydroformylation, C-H activation, oxidation, radical-type transformations, and photochemical reactions.
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Affiliation(s)
- Joost N H Reek
- Homogeneous and Supramolecular Catalysis, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.,InCatT B.V., Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bas de Bruin
- Homogeneous and Supramolecular Catalysis, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sonja Pullen
- Homogeneous and Supramolecular Catalysis, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tiddo J Mooibroek
- Homogeneous and Supramolecular Catalysis, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | | | - Xavier Caumes
- InCatT B.V., Science Park 904, 1098 XH Amsterdam, The Netherlands
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17
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Máximo P, Colaço M, Pauleta SR, Costa PJ, Pischel U, Parola AJ, Basílio N. Photomodulation of ultrastable host–guest complexes in water and their application in light-controlled steroid release. Org Chem Front 2022. [DOI: 10.1039/d2qo00423b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Host–guest complexation of dithienylethene photoswitches with cucurbit[8]uril leads to photoresponsive binding pairs with picomolar affinity in water.
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Affiliation(s)
- Patrícia Máximo
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Miriam Colaço
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Microbial Stress Lab, UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry/Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Paulo J. Costa
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Uwe Pischel
- CIQSO – Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - A. Jorge Parola
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Nuno Basílio
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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18
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Xiao T, Sun L, Zhang M, Li Z, Haura EB, Schonbrunn E, Ji H. Synthesis and structural characterization of a monocarboxylic inhibitor for GRB2 SH2 domain. Bioorg Med Chem Lett 2021; 51:128354. [PMID: 34506932 DOI: 10.1016/j.bmcl.2021.128354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]
Abstract
A monocarboxylic inhibitor was designed and synthesized to disrupt the protein-protein interaction (PPI) between GRB2 and phosphotyrosine-containing proteins. Biochemical characterizations show compound 7 binds with the Src homology 2 (SH2) domain of GRB2 and is more potent than EGFR1068 phosphopeptide 14-mer. X-ray crystallographic studies demonstrate compound 7 occupies the GRB2 binding site for phosphotyrosine-containing sequences and reveal key structural features for GRB2-inhibitor binding. This compound with a -1 formal charge offers a new direction for structural optimization to generate cell-permeable inhibitors for this key protein target of the aberrant Ras-MAPK signaling cascade.
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Affiliation(s)
- Tao Xiao
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Luxin Sun
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Min Zhang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Zilu Li
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States; Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Ernst Schonbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States.
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States; Department of Chemistry, University of South Florida, Tampa, FL, United States.
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19
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Kumar A, Jernigan RL. Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations. Front Mol Biosci 2021; 8:733148. [PMID: 34540902 PMCID: PMC8440829 DOI: 10.3389/fmolb.2021.733148] [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: 06/29/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Allostery is usually considered to be a mechanism for transmission of signals associated with physical or dynamic changes in some part of a protein. Here, we investigate the changes in fluctuations across the protein upon ligand binding based on the fluctuations computed with elastic network models. These results suggest that binding reduces the fluctuations at the binding site but increases fluctuations at remote sites, but not to fully compensating extents. If there were complete conservation of entropy, then only the enthalpies of binding would matter and not the entropies; however this does not appear to be the case. Experimental evidence also suggests that energies and entropies of binding can compensate but that the extent of compensation varies widely from case to case. Our results do however always show transmission of an allosteric signal to distant locations where the fluctuations are increased. These fluctuations could be used to compute entropies to improve evaluations of the thermodynamics of binding. We also show the allosteric relationship between peptide binding in the GroEL trans-ring that leads directly to the release of GroES from the GroEL-GroES cis-ring. This finding provides an example of how calculating these changes to protein dynamics induced by the binding of an allosteric ligand can regulate protein function and mechanism.
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Affiliation(s)
- Ambuj Kumar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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20
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Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat Commun 2021; 12:3384. [PMID: 34099674 PMCID: PMC8185074 DOI: 10.1038/s41467-021-23609-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
Abstract
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational "anchor extension" methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC50 values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.
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21
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New RRC, Bui TTT, Bogus M. Binding Interactions of Peptide Aptamers. Molecules 2020; 25:molecules25246055. [PMID: 33371475 PMCID: PMC7767479 DOI: 10.3390/molecules25246055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Affiliation(s)
- Roger R. C. New
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, Hendon, London NW4 4BT, UK
- Correspondence: or
| | - Tam T. T. Bui
- Centre for Biomolecular Spectroscopy and Institute of Pharmaceutical Science, King’s College, London SE1 1UL, UK;
| | - Michal Bogus
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
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22
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Cramer DL, Cheng B, Tian J, Clements JH, Wypych RM, Martin SF. Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions. Eur J Med Chem 2020; 208:112771. [PMID: 32916312 DOI: 10.1016/j.ejmech.2020.112771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 12/18/2022]
Abstract
Understanding how making structural changes in small molecules affects their binding affinities for targeted proteins is central to improving strategies for rational drug design. To assess the effects of varying the nature of nonpolar groups upon binding entropies and enthalpies, we designed and prepared a set of Grb2-SH2 domain ligands, Ac-pTyr-Ac6c-Asn-(CH2)n-R, in which the size and electrostatic nature of R groups at the pTyr+3 site were varied. The complexes of these ligands with the Grb2-SH2 domain were evaluated in a series of studies in which the binding thermodynamics were determined using isothermal titration calorimetry, and binding interactions were examined in crystallographic studies of two different complexes. Notably, adding nonpolar groups to the pTyr+3 site leads to higher binding affinities, but the magnitude and energetic origins of these effects vary with the nature of the R substituent. For example, enhancements to binding affinities using aliphatic R groups are driven by more favorable changes in binding entropies, whereas aryl R groups improve binding free energies through a combination of more favorable changes in binding enthalpies and entropies. However, enthalpy/entropy compensation plays a significant role in these associations and mitigates against any significant variation in binding free energies, which vary by only 0.8 kcal•mol-1, with changes in the electrostatic nature and size of the R group. Crystallographic studies show that differences in ΔG° or ΔH° correlate with buried nonpolar surface area, but they do not correlate with the total number of polar or van der Waals contacts. The relative number of ordered water molecules and relative order in the side chains at pTyr+3 correlate with differences in -TΔS°. Overall, these studies show that burial of nonpolar surface can lead to enhanced binding affinities arising from dominating entropy- or enthalpy-driven hydrophobic effects, depending upon the electrostatic nature of the apolar R group.
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Affiliation(s)
- David L Cramer
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Bo Cheng
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Jianhua Tian
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Rachel M Wypych
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA.
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23
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Wypych RM, LaPlante SR, White PW, Martin SF. Structure-thermodynamics-relationships of hepatitis C viral NS3 protease inhibitors. Eur J Med Chem 2020; 192:112195. [PMID: 32151833 DOI: 10.1016/j.ejmech.2020.112195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
Thermodynamic parameters were determined for structurally-related inhibitors of HCV NS3 protease to assess how binding entropies and enthalpies vary with incremental changes at the P2 and P3 inhibitor subsites. Changing the heterocyclic substituent at P2 from a pyridyl to a 7-methoxy-2-phenyl-4-quinolyl group leads to a 710-fold increase in affinity. Annelating a benzene ring onto a pyridine ring leads to quinoline-derived inhibitors having higher affinities, but the individual enthalpy and entropy contributions are markedly different for each ligand pair. Introducing a phenyl group at C2 of the heterocyclic ring at P2 uniformly leads to higher affinity analogs with more favorable binding entropies, while adding a methoxy group at C7 of the quinoline ring at P2 provides derivatives with more favorable binding enthalpies. Significant enthalpy/entropy compensation is observed for structural changes made to inhibitors lacking a 2-phenyl substituent, whereas favorable changes in both binding enthalpies and entropies accompany structural modifications when a 2-phenyl group is present. Overall, binding energetics of inhibitors having a 2-phenyl-4-quinolyl group at P2 are dominated by entropic effects, whereas binding of the corresponding norphenyl analogs are primarily enthalpy driven. Notably, the reversal from an entropy driven association to an enthalpy driven one for this set of inhibitors also correlates with alternate binding modes. When the steric bulk of the side chain at P3 is increased from a hydrogen atom to a tert-butyl group, there is a 770-fold improvement in affinity. The 30-fold increase resulting from the first methyl group is solely the consequence of a more favorable change in entropy, whereas subsequent additions of methyl groups leads to modest increases in affinity that arise primarily from incremental improvements in binding enthalpies accompanied with smaller favorable entropic contributions.
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Affiliation(s)
- Rachel M Wypych
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA
| | - Steven R LaPlante
- Université du Québec, INRS-Centre Armand Frappier Santé et Biotechnologie, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
| | - Peter W White
- Boehringer Ingelheim (Canada) Limited, Research and Development, 2100 rue Cunard, Laval, Quebec, H7S 2G5, Canada
| | - Stephen F Martin
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA.
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24
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Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood. Biomolecules 2019; 9:biom9110740. [PMID: 31731771 PMCID: PMC6920920 DOI: 10.3390/biom9110740] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
Natural products from plants, such as chemopreventive agents, attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure-based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide-based therapeutics have been developed to combat several health disorders, including cancers, metabolic disorders, heart-related diseases, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, the in silico activities of cyclic peptides towards molecular targets, such as protein kinases, proteases, and apoptosis related proteins have not been extensively investigated. In this study, we explored the in silico kinase and protease inhibitor potentials of cyclosaplin, and studied the interactions of cyclosaplin with other apoptosis-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that were used in the current study as well. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 kcal/mol indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB, and p38, indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis-related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein–ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands, especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave the insights of cyclosaplin being a potential apoptosis inducer and protein kinase inhibitor.
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25
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Sandner A, Hüfner-Wulsdorf T, Heine A, Steinmetzer T, Klebe G. Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem 2019; 62:9753-9771. [PMID: 31633354 DOI: 10.1021/acs.jmedchem.9b01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Tobias Hüfner-Wulsdorf
- 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
| | - Torsten Steinmetzer
- 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
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26
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Hosoe Y, Numoto N, Inaba S, Ogawa S, Morii H, Abe R, Ito N, Oda M. Structural and functional properties of Grb2 SH2 dimer in CD28 binding. Biophys Physicobiol 2019; 16:80-88. [PMID: 30923665 PMCID: PMC6435016 DOI: 10.2142/biophysico.16.0_80] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/30/2019] [Indexed: 01/06/2023] Open
Abstract
Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein that plays a critical role in cellular signal transduction. It contains a central Src homology 2 (SH2) domain flanked by two Src homology 3 (SH3) domains. Binding of Grb2 SH2 to the cytoplasmic region of CD28, phosphorylated Tyr (pY) containing the peptide motif pY-X-N-X, is required for costimulatory signaling in T cells. In this study, we purified the dimer and monomer forms of Grb2 SH2, respectively, and analyzed their structural and functional properties. Size exclusion chromatography analysis showed that both dimer and monomer exist as stable states. Thermal stability analysis using circular dichroism showed that the dimer mostly dissociates into the monomer around 50°C. CD28 binding experiments showed that the affinity of the dimer to the phosphopeptide was about three fold higher than that of the monomer, possibly due to the avidity effect. The present crystal structure analysis of Grb2 SH2 showed two forms; one is monomer at 1.15 Å resolution, which is currently the highest resolution analysis, and another is dimer at 2.00 Å resolution. In the dimer structure, the C-terminal region, comprising residues 123–152, was extended towards the adjacent molecule, in which Trp121 was the hinge residue. The stable dimer purified using size exclusion chromatography would be due to the C-terminal helix “swapping”. In cases where a mutation caused Trp121 to be replaced by Ser in Grb2 SH2, this protein still formed dimers, but lost the ability to bind CD28.
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Affiliation(s)
- Yuhi Hosoe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satomi Inaba
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.,Research & Utilization Division, Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - Shuhei Ogawa
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Hisayuki Morii
- College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Ichikawa, Chiba 272-0827, Japan
| | - Ryo Abe
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan.,Present address: Strategic Innovation and Research Center, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
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27
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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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28
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Jobin S, Beaumont C, Biron E. Development of a solid-phase traceless-Ugi multicomponent reaction for backbone anchoring and cyclic peptide synthesis. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Steve Jobin
- Faculté de Pharmacie, Université Laval, Pavillon Ferdinand-Vandry, 1050 Avenue de la Médecine; Québec G1V 0A6 Canada
- Laboratoire de Chimie Médicinale, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier; Québec G1V 4G2 Canada
| | - Catherine Beaumont
- Faculté de Pharmacie, Université Laval, Pavillon Ferdinand-Vandry, 1050 Avenue de la Médecine; Québec G1V 0A6 Canada
- Laboratoire de Chimie Médicinale, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier; Québec G1V 4G2 Canada
| | - Eric Biron
- Faculté de Pharmacie, Université Laval, Pavillon Ferdinand-Vandry, 1050 Avenue de la Médecine; Québec G1V 0A6 Canada
- Laboratoire de Chimie Médicinale, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier; Québec G1V 4G2 Canada
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29
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Li A, Gilson MK. Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. J Chem Phys 2018; 149:072311. [PMID: 30134726 DOI: 10.1063/1.5027439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Calorimetric studies of protein-ligand binding sometimes yield thermodynamic data that are difficult to understand. Today, molecular simulations can be used to seek insight into such calorimetric puzzles, and, when simulations and experiments diverge, the results can usefully motivate further improvements in computational methods. Here, we apply near-millisecond duration simulations to estimate the relative binding enthalpies of four peptidic ligands with the Grb2 SH2 domain. The ligands fall into matched pairs, where one member of each pair has an added bond that preorganizes the ligand for binding and thus may be expected to favor binding entropically, due to a smaller loss in configurational entropy. Calorimetric studies have shown that the constrained ligands do in fact bind the SH2 domain more tightly than the flexible ones, but, paradoxically, the improvement in affinity for the constrained ligands is enthalpic, rather than entropic. The present enthalpy calculations yield the opposite trend, as they suggest that the flexible ligands bind more exothermically. Additionally, the small relative binding enthalpies are found to be balances of large differences in the energies of structural components such as ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers and hence may be particularly susceptible to error, due, for example, to approximations in the force field. We also computed first-order estimates of changes in configurational entropy on binding. These too are, arguably, paradoxical, as they tend to favor binding of the flexible ligands. The paradox is explained in part by the fact that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do, at least in the simulations. This result offers a rather general counterargument to the expectation that preorganized ligands should be associated with more favorable binding entropies, other things being equal.
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Affiliation(s)
- Amanda Li
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0419, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
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30
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Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K. Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. J Biochem 2018; 164:65-76. [PMID: 29924367 DOI: 10.1093/jb/mvy032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/06/2018] [Indexed: 02/06/2023] Open
Abstract
Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.
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Affiliation(s)
- Kazuhiro Miyanabe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Akiba
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Osamu Kusano-Arai
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroko Iwanari
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan.,Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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31
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Chen SL, Zhu XF, Yang FY, Pan XC, Gan W, Yuan QH. Order-Disorder transition of carboxyl terminated chains in polydiacetylenes vesicles probed by second harmonic generation and two-photon fluorescence. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1712238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shun-li Chen
- Laboratory of Environmental Science and Technology, Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xue-feng Zhu
- Laboratory of Environmental Science and Technology, Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
| | - Fang-yuan Yang
- Laboratory of Environmental Science and Technology, Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xue-cong Pan
- Laboratory of Environmental Science and Technology, Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wei Gan
- Laboratory of Environmental Science and Technology, Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
- School of Sciences, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Qun-hui Yuan
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
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32
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Che X, Zhang J, Quan H, Yang L, Gao YQ. CDNs-STING Interaction Mechanism Investigations and Instructions on Design of CDN-Derivatives. J Phys Chem B 2018; 122:1862-1868. [PMID: 29361230 DOI: 10.1021/acs.jpcb.7b12276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic dinucleotides (CDNs) present thousand-fold differences of dissociation constants to STING, a pivotal protein in cytosolic dsDNA immunity. To understand how subtle chemical changes in CDNs lead to these substantial variances, a precise ranking of binding affinity is needed. However, the large size and flexibility of CDNs elevate the entropic effect and pose a challenge for this precise prediction. Therefore, in this paper, we developed a new protocol, a combination of selective-integrated tempering sampling of ligands and molecular docking, to take into account the entropic effects originating from extensive ligand configurational space and solvation on binding affinity evaluations. The calculated ranking orders of CDNs and CDN-derivatives to wild type STING and R232H mutant are in agreement with experimental measurements. Further molecular dynamics analysis revealed that the interaction between phosphonate groups and 232R differentiates the binding affinities. The 2'-5' linked phosphonate groups have a larger tendency to form hydrogen bonds with 232R than those with 3'-5' linkages. Moreover, the new protocol identified structural features that enhanced CDNs-STING binding, such as anti-glycosidic bonds and large pro-R distances, which explains the high binding affinity of dithio-RpRp-2'3'-CDA to STING and is expected to provide valuable guidance in the lead-drug optimization.
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Affiliation(s)
- Xing Che
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Jun Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
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33
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Abstract
Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Here, we review the relationship between measures of fast side-chain motion and the underlying conformational entropy. The dynamical proxy reveals that the contribution of conformational entropy can range from highly favorable to highly unfavorable and demonstrates the potential of this key thermodynamic variable to modulate protein-ligand interactions. The dynamical so-called entropy meter also refines the role of solvent entropy and directly determines the loss in rotational-translational entropy that occurs upon formation of high-affinity complexes. The ability to quantify the roles of entropy through an entropy meter based on measurable dynamical properties promises to highlight its role in protein function.
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Affiliation(s)
- A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
| | - Kim A Sharp
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
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34
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Sun S, Compañón I, Martínez‐Sáez N, Seixas JD, Boutureira O, Corzana F, Bernardes GJL. Enhanced Permeability and Binding Activity of Isobutylene-Grafted Peptides. Chembiochem 2018; 19:48-52. [PMID: 29105291 PMCID: PMC5813187 DOI: 10.1002/cbic.201700586] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 01/09/2023]
Abstract
We present a new peptide-macrocyclization strategy with an isobutylene graft. The reaction is mild and proceeds rapidly and efficiently both for linear and cyclic peptides. The resulting isobutylene-grafted peptides possess improved passive membrane permeability due to the shielding of the polar backbone of the amides, as demonstrated by NMR spectroscopy and molecular dynamics simulations. The isobutylene-stapled structures are fully stable in human plasma and in the presence of glutathione. This strategy can be applied to bioactive cyclic peptides such as somatostatin. Importantly, we found that structural preorganization forced by the isobutylene graft leads to a significant improvement in binding. The combined advantages of directness, selectivity, and smallness could allow application to peptide macrocyclization based on this attachment of the isobutylene graft.
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Affiliation(s)
- Shuang Sun
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Ismael Compañón
- Departamento de QuímicaCentro de Investigación en Síntesis QuímicaUniversidad de La RiojaMadre de Dios, 5326006LogroñoSpain
| | - Nuria Martínez‐Sáez
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - João D. Seixas
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Omar Boutureira
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Francisco Corzana
- Departamento de QuímicaCentro de Investigación en Síntesis QuímicaUniversidad de La RiojaMadre de Dios, 5326006LogroñoSpain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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35
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Abstract
Diverse structural types of natural products and their mimics have served as targets of opportunity in our laboratory to inspire the discovery and development of new methods and strategies to assemble polyfunctional and polycyclic molecular architectures. Furthermore, our efforts toward identifying novel compounds having useful biological properties led to the creation of new targets, many of which posed synthetic challenges that required the invention of new methodology. In this Perspective, selected examples of how we have exploited a diverse range of natural products and their mimics to create, explore, and solve a variety of problems in chemistry and biology will be discussed. The journey was not without its twists and turns, but the unexpected often led to new revelations and insights. Indeed, in our recent excursion into applications of synthetic organic chemistry to neuroscience, avoiding the more-traveled paths was richly rewarding.
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Affiliation(s)
- Stephen F Martin
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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36
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Babii O, Afonin S, Schober T, Komarov IV, Ulrich AS. Flexibility vs rigidity of amphipathic peptide conjugates when interacting with lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2505-2515. [PMID: 28958778 PMCID: PMC5667891 DOI: 10.1016/j.bbamem.2017.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 01/17/2023]
Abstract
For the first time, the photoisomerization of a diarylethene moiety (DAET) in peptide conjugates was used to probe the effects of molecular rigidity/flexibility on the structure and behavior of model peptides bound to lipid membranes. The DAET unit was incorporated into the backbones of linear peptide-based constructs, connecting two amphipathic sequences (derived from the β-stranded peptide (KIGAKI)3 and/or the α-helical peptide BP100). A β-strand-DAET-α-helix and an α-helix-DAET-α-helix models were synthesized and studied in phospholipid membranes. Light-induced photoisomerization of the linker allowed the generation of two forms of each conjugate, which differed in the conformational mobility of the junction between the α-helical and/or the β-stranded part of these peptidomimetic molecules. A detailed study of their structural, orientational and conformational behavior, both in isotropic solution and in phospholipid model membranes, was carried out using circular dichroism and solid-state 19F-NMR spectroscopy. The study showed that the rigid and flexible forms of the two conjugates had appreciably different structures only when embedded in an anisotropic lipid environment and only in the gel phase. The influence of the rigidity/flexibility of the studied conjugates on the lipid thermotropic phase transition was also investigated by differential scanning calorimetry. Both models were found to destabilize the lamellar gel phases. DAET building blocks can be used to study rigidity/flexibility effects in supramolecular model systems. Photoswitchable DAET linkers perturb only up to 3–4 adjacent amino acid residues. Membrane-bound amphiphilic secondary structure elements exert a negligible influence on each other when linked by DAET. The rigidity of peptide conjugates affected their structural behavior only in the lipid gel phase.
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Affiliation(s)
- Oleg Babii
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Tim Schober
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Igor V Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Volodymyrska 60, 01601 Kyiv, Ukraine.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany.
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37
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Huang Y, Cui G, Zhao Y, Wang H, Li Z, Dai S, Wang J. Preorganization and Cooperation for Highly Efficient and Reversible Capture of Low-Concentration CO 2 by Ionic Liquids. Angew Chem Int Ed Engl 2017; 56:13293-13297. [PMID: 28857376 DOI: 10.1002/anie.201706280] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/20/2017] [Indexed: 12/12/2022]
Abstract
A novel strategy based on the concept of preorganization and cooperation has been designed for a superior capacity to capture low-concentration CO2 by imide-based ionic liquids. By using this strategy, for the first time, an extremely high gravimetric CO2 capacity of up to 22 wt % (1.65 mol mol-1 ) and excellent reversibility (16 cycles) have been achieved from 10 vol. % of CO2 in N2 when using an ionic liquid having a preorganized anion. Through a combination of quantum-chemical calculations and spectroscopic investigations, it is suggested that cooperative interactions between CO2 and multiple active sites in the preorganized anion are the driving force for the superior CO2 capacity and excellent reversibility.
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Affiliation(s)
- Yanjie Huang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Guokai Cui
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yuling Zhao
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Huiyong Wang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Zhiyong Li
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Sheng Dai
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jianji Wang
- Henan Key Laboratory of Green Chemistry, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
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38
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Huang Y, Cui G, Zhao Y, Wang H, Li Z, Dai S, Wang J. Preorganization and Cooperation for Highly Efficient and Reversible Capture of Low-Concentration CO2
by Ionic Liquids. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yanjie Huang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Guokai Cui
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Yuling Zhao
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Huiyong Wang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Zhiyong Li
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
| | - Sheng Dai
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
- Department of Chemistry; University of Tennessee; Knoxville TN 37996 USA
| | - Jianji Wang
- Henan Key Laboratory of Green Chemistry; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals; Key Laboratory of Green Chemical Media and Reactions; Ministry of Education; School of Chemistry and Chemical Engineering; Henan Normal University; Xinxiang Henan 453007 China
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39
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Mizuno A, Matsui K, Shuto S. From Peptides to Peptidomimetics: A Strategy Based on the Structural Features of Cyclopropane. Chemistry 2017. [PMID: 28632330 DOI: 10.1002/chem.201702119] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptidomimetics, non-natural mimicries of bioactive peptides, comprise an important class of drug molecules. The essence of the peptidomimetic design is to mimic the key conformation assumed by the bioactive peptides upon binding to their targets. Regulation of the conformation of peptidomimetics is important not only to enhance target binding affinity and selectivity, but also to confer cell-membrane permeability for targeting protein-protein interactions in cells. The rational design of peptidomimetics with suitable three-dimensional structures is challenging, however, due to the inherent flexibility of peptides and their dynamic conformational changes upon binding to the target biomolecules. In this Minireview, a three-dimensional structural diversity-oriented strategy based on the characteristic structural features of cyclopropane to address this challenging issue in peptidomimetic chemistry is described.
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Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka, 561-0825, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
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40
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Suárez D, Díaz N. Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes. J Chem Inf Model 2017; 57:2045-2055. [PMID: 28737392 DOI: 10.1021/acs.jcim.7b00355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using extensive molecular dynamics simulations, we investigate the structure and dynamics of the complexes formed between penicillopepsin and two peptidomimetic inhibitors: a linear compound, isovaleryl(P4)-valine(P3)-asparagine(P2)-leucine(P1)-phosphonate-phenylalanine(P1'), and its macrocylic analog that includes a methylene bridge between the Asn(P2) and Phe(P1') side chains. The macrocyclic inhibitor, which has a 420-fold stronger affinity than that of the acyclic one, has been considered to lower the entropic penalty for binding. To better understand this binding preference, the solution structure of the inhibitors is studied by molecular dynamics simulations. Subsequently, we assess the influence of the enzyme/inhibitor contacts, the enzyme-induced inhibitor strain, the variation of the ligand configurational entropy and the enzyme reorganization by combining molecular-mechanics Poisson-Boltzmann surface area and normal mode calculations with conformational entropy calculations. We find that there is no relevant entropic stabilization on the binding of the cyclic inhibitor with respect to the acyclic analog because the methylene bridge does not reduce appreciably the conformational flexibility of the free inhibitor. The most important factors explaining the stronger affinity of the macrocyclic inhibitor are the conformational filtering and the lower ligand strain induced by the methylene bridge.
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Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo , Avda. Julián Claveria 8, 33006 Oviedo, Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo , Avda. Julián Claveria 8, 33006 Oviedo, Spain
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41
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Rossmann M, J Greive S, Moschetti T, Dinan M, Hyvönen M. Development of a multipurpose scaffold for the display of peptide loops. Protein Eng Des Sel 2017; 30:419-430. [PMID: 28444399 PMCID: PMC5897841 DOI: 10.1093/protein/gzx017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/26/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions (PPIs) determine a wide range of biological processes and analysis of these dynamic networks is increasingly becoming a mandatory tool for studying protein function. Using the globular ATPase domain of recombinase RadA as a scaffold, we have developed a peptide display system (RAD display), which allows for the presentation of target peptides, protein domains or full-length proteins and their rapid recombinant production in bacteria. The design of the RAD display system includes differently tagged versions of the scaffold, which allows for flexibility in the protein purification method, and chemical coupling for small molecule labeling or surface immobilization. When combined with the significant thermal stability of the RadA protein, these features create a versatile multipurpose scaffold system. Using various orthogonal biophysical techniques, we show that peptides displayed on the scaffold bind to their natural targets in a fashion similar to linear parent peptides. We use the examples of CK2β/CK2α kinase and TPX2/Aurora A kinase protein complexes to demonstrate that the peptide displayed by the RAD scaffold can be used in PPI studies with the same binding efficacy but at lower costs compared with their linear synthetic counterparts.
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Affiliation(s)
- Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Michael Dinan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. Correspondence:
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42
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Peng G, McEwen AG, Olieric V, Schmitt C, Albrecht S, Cavarelli J, Tarnus C. Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis. Proteins 2017; 85:1413-1421. [DOI: 10.1002/prot.25301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Guanya Peng
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Alastair G. McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Vincent Olieric
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Celine Schmitt
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Sebastien Albrecht
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Celine Tarnus
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
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43
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Mizuno A, Kameda T, Kuwahara T, Endoh H, Ito Y, Yamada S, Hasegawa K, Yamano A, Watanabe M, Arisawa M, Shuto S. Cyclopropane-Based Peptidomimetics Mimicking Wide-Ranging Secondary Structures of Peptides: Conformational Analysis and Their Use in Rational Ligand Optimization. Chemistry 2017; 23:3159-3168. [PMID: 28000361 DOI: 10.1002/chem.201605312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/16/2022]
Abstract
Detailed conformational analyses of our previously reported cyclopropane-based peptidomimetics and conformational analysis-driven ligand optimization are described. Computational calculations and X-ray crystallography showed that the characteristic features of cyclopropane function effectively to constrain the molecular conformation in a three-dimensionally diverse manner. Subsequent principal component analysis revealed that the diversity covers the broad chemical space filled by peptide secondary structures in terms of both main-chain and side-chain conformations. Based on these analyses, a lead stereoisomer targeting melanocortin receptors was identified, and its potency and subtype selectivity were improved by further derivatization. The presented strategy is effective not only for designing non-peptidic ligands from a peptide ligand but also for the rational optimization of these ligands based on the plausible target-binding conformation without requiring the three- dimensional structural information of the target and its peptide ligands.
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Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Tomoshi Kameda
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7, Aomi, Koutou-ku, Tokyo, 135-0064, Japan
| | - Tomoki Kuwahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Hideyuki Endoh
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yoshihiko Ito
- School of Pharmaceutical Sciences, University of Shizuoka, Yata, Suruga-ku, Shizuoka, Shizuoka, 422-8526, Japan
| | - Shizuo Yamada
- School of Pharmaceutical Sciences, University of Shizuoka, Yata, Suruga-ku, Shizuoka, Shizuoka, 422-8526, Japan
| | - Kimiko Hasegawa
- Rigaku Corporation, Application Laboratories, 3-9-12, Matsubara-cho, Akishima, Tokyo, 196-8666, Japan
| | - Akihito Yamano
- Rigaku Corporation, Application Laboratories, 3-9-12, Matsubara-cho, Akishima, Tokyo, 196-8666, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Mitsuhiro Arisawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
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44
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Ricci L, Sernissi L, Scarpi D, Bianchini F, Contini A, Occhiato EG. Synthesis and conformational analysis of peptides embodying 2,3-methanopipecolic acids. Org Biomol Chem 2017; 15:6826-6836. [DOI: 10.1039/c7ob01617d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
When 2,3-methanopipecolic acids replace a proline in peptides, a marked preference (42–92%) for thecisgeometry around the pipecolic amide bond is observed in both water and organic solvents.
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Affiliation(s)
- Luciano Ricci
- Department of Chemistry “U. Schiff”
- University of Florence
- Sesto Fiorentino
- Italy
| | - Lorenzo Sernissi
- Department of Chemistry “U. Schiff”
- University of Florence
- Sesto Fiorentino
- Italy
| | - Dina Scarpi
- Department of Chemistry “U. Schiff”
- University of Florence
- Sesto Fiorentino
- Italy
| | - Francesca Bianchini
- Department of Biomedical
- Experimental and Clinical Sciences “Mario Serio”
- University of Florence
- Florence
- Italy
| | - Alessandro Contini
- Department of Pharmaceutical Sciences
- University of Milan
- I-20133 Milan
- Italy
| | - Ernesto G. Occhiato
- Department of Chemistry “U. Schiff”
- University of Florence
- Sesto Fiorentino
- Italy
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45
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Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. PLoS Comput Biol 2016; 12:e1005057. [PMID: 27560145 PMCID: PMC4999267 DOI: 10.1371/journal.pcbi.1005057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/07/2016] [Indexed: 01/17/2023] Open
Abstract
Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design. Promiscuous proteins are commonly observed in biological systems, such as modular domains that recognize phosphopeptides during signal transduction. The use of phosphopeptides and compounds with phosphate groups as inhibitors to protein–protein interactions have attracted increasing interest for years. By using atomistic molecular dynamics simulations, we are able to perform detailed analyses of the dihedral space to explore protein fluctuation upon ligand binding to better understand promiscuous molecular recognition. Free energy calculation can further provide insights into the mechanism of binding, including both enthalpic and entropic contributions for molecular recognition, which assist in inhibitor design. Our calculation results show that pre-rigidifying a ligand is not always advantageous, suggesting the challenge in retaining optimized intermolecular interactions in pre-rigidified ligand. Instead, certain flexible ligands with multiple binding conformations can reduce entropic penalty, and therefore improves binding affinity. According to our computations, we can introduce new intermolecular interactions to flexible ligand to strengthen attractions while maintaining small entropic penalty by retaining its plasticity in the bound conformation. The study might cast light on a new general strategy for designing inhibitors targeting promiscuous modular domains and protein–protein interactions.
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46
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Affiliation(s)
- Debasis Saha
- Department
of Chemistry, Indian Institute of Science Education and Research, Pune, 411008 Maharashtra India
| | - Arnab Mukherjee
- Department
of Chemistry, Indian Institute of Science Education and Research, Pune, 411008 Maharashtra India
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47
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Hickey JL, Zaretsky S, St. Denis MA, Kumar Chakka S, Morshed MM, Scully CCG, Roughton AL, Yudin AK. Passive Membrane Permeability of Macrocycles Can Be Controlled by Exocyclic Amide Bonds. J Med Chem 2016; 59:5368-76. [DOI: 10.1021/acs.jmedchem.6b00222] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jennifer L. Hickey
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Serge Zaretsky
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Megan A. St. Denis
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Sai Kumar Chakka
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - M. Monzur Morshed
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Conor C. G. Scully
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Andrew L. Roughton
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Andrei K. Yudin
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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48
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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49
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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50
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Rühmann EH, Rupp M, Betz M, Heine A, Klebe G. Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. ChemMedChem 2016; 11:309-19. [PMID: 26762840 DOI: 10.1002/cmdc.201500531] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/14/2015] [Indexed: 01/19/2023]
Abstract
Structural preorganization to fix bioactive conformations at protein binding sites is a popular strategy to enhance binding affinity during late-stage optimization. The rationale for this enhancement relates to entropic advantages assigned to rigidified versus flexible ligands. We analyzed a narrow series of peptidomimetics binding to thrombin. The individual ligands exhibit at P2 a conformationally flexible glycine, more restricted alanine, N-methylglycine, N-methylhomoalanine, and largely rigidified proline moiety. Overall, affinity was found to increase by a factor of 1000, explained partly by an entropic advantage. All ligands adopt the same binding mode with small deviations. The residual mobility of the bound ligands is decreased across the series, and a protein side chain differs in its order/disorder behavior along with changes in the surface-water network pattern established across the newly generated protein-ligand surfaces. The enthalpy/entropy inventory displays a rather complex picture and emphasizes that thermodynamics can only be compared in terms of relative differences within a structurally similar ligand series.
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Affiliation(s)
- Eggert H Rühmann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Melinda Rupp
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Michael Betz
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037, Marburg, Germany.
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