1
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Hautiere M, Maffucci I, Costa N, Herbet A, Essono S, Padiolleau-Lefevre S, Boquet D. The functionality of a therapeutic antibody candidate restored by a single mutation from proline to threonine in the variable region. Hum Vaccin Immunother 2023; 19:2279867. [PMID: 38012091 PMCID: PMC10760395 DOI: 10.1080/21645515.2023.2279867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
mAbs play an essential role in the therapeutic arsenal. Our laboratory has patented the Rendomab-B49 mAb targeting the endothelin B receptor (ETB). This G protein-coupled receptor plays a driving role in the progression of numerous cancers. We chimerized our mAb (xiRB49) to evaluate its preclinical therapeutic efficacy in different ETB+ tumor models with an antibody drug conjugate approach. As previously reported, the chimerization process of an antibody can alter its functionality. In this article, we present the chimerization of RB49. xiRB49 purified by Protein A remained perfectly soluble and did not aggregate, but it lost all its ability to recognize ETB. A detailed analysis of its variable region using IMGT tools allowed us to identify an unusual proline at position 125. In silico mAb modeling and in vitro experiments were performed for a better understanding of xiRB49 structure-function relationships. Our results show that the proline in position 125 on the heavy chain alters the xiRB49 CDR3 light chain conformation and its mutation to threonine allows complete functional recovery.
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Affiliation(s)
- Marie Hautiere
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, Gif-sur-Yvette, France
| | - Irene Maffucci
- Centre de Recherche de Royallieu, CNRS UMR 7025, Génie Enzymatique et Cellulaire, Compiègne Cedex, France
- Centre de Recherche de Royallieu, Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire, Compiègne Cedex, France
| | - Narciso Costa
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, Gif-sur-Yvette, France
| | - Amaury Herbet
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, Gif-sur-Yvette, France
| | | | - Séverine Padiolleau-Lefevre
- Centre de Recherche de Royallieu, CNRS UMR 7025, Génie Enzymatique et Cellulaire, Compiègne Cedex, France
- Centre de Recherche de Royallieu, Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire, Compiègne Cedex, France
| | - Didier Boquet
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, Gif-sur-Yvette, France
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2
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Binet T, Padiolleau-Lefèvre S, Octave S, Avalle B, Maffucci I. Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools. BMC Bioinformatics 2023; 24:422. [PMID: 37940855 PMCID: PMC10634105 DOI: 10.1186/s12859-023-05532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial conformations they can assume. The first level of ssNAs spatial organisation corresponds to their base pairs pattern, i.e. their secondary structure. Many computational tools have been developed to predict the ssNAs secondary structures, making the choice of the appropriate tool difficult, and an up-to-date guide on the limits and applicability of current secondary structure prediction tools is missing. Therefore, we performed a comparative study of the performances of 9 freely available tools (mfold, RNAfold, CentroidFold, CONTRAfold, MC-Fold, LinearFold, UFold, SPOT-RNA, and MXfold2) on a dataset of 538 ssNAs with known experimental secondary structure. RESULTS The minimum free energy-based tools, namely mfold and RNAfold, and some tools based on artificial intelligence, namely CONTRAfold and MXfold2, provided the best results, with [Formula: see text] of exact predictions, whilst MC-fold seemed to be the worst performing tool, with only [Formula: see text] of exact predictions. In addition, UFold and SPOT-RNA are the only options for pseudoknots prediction. Including in the analysis of mfold and RNAfold results 5-10 suboptimal solutions further improved the performances of these tools. Nevertheless, we could observe issues in predicting particular motifs, such as multiple-ways junctions and mini-dumbbells, or the ssNAs whose structure has been determined in complex with a protein. In addition, our benchmark shows that some effort has to be paid for ssDNA secondary structure predictions. CONCLUSIONS In general, Mfold, RNAfold, and MXfold2 seem to currently be the best choice for the ssNAs secondary structure prediction, although they still show some limits linked to specific structural motifs. Nevertheless, actual trends suggest that artificial intelligence has a high potential to overcome these remaining issues, for example the recently developed UFold and SPOT-RNA have a high success rate in predicting pseudoknots.
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Affiliation(s)
- Thomas Binet
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Séverine Padiolleau-Lefèvre
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Stéphane Octave
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France
| | - Bérangère Avalle
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France.
| | - Irene Maffucci
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319, 60203, Compiègne Cedex, France.
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3
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Herrera León C, Kalacas NA, Mier A, Sakhaii P, Merlier F, Prost E, Maffucci I, Montagna V, Mora-Radó H, Dhal PK, Tse Sum Bui B, Haupt K. Synthetic Peptide Antibodies as TNF-α Inhibitors: Molecularly Imprinted Polymer Nanogels Neutralize the Inflammatory Activity of TNF-α in THP-1 Derived Macrophages. Angew Chem Int Ed Engl 2023; 62:e202306274. [PMID: 37338464 DOI: 10.1002/anie.202306274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023]
Abstract
Tumor Necrosis Factor-α (TNF-α) is a cytokine that is normally produced by immune cells when fighting an infection. But, when too much TNF-α is produced as in autoimmune diseases, this leads to unwanted and persistent inflammation. Anti-TNF-α monoclonal antibodies have revolutionized the therapy of these disorders by blocking TNF-α and preventing its binding to TNF-α receptors, thus suppressing the inflammation. Herein, we propose an alternative in the form of molecularly imprinted polymer nanogels (MIP-NGs). MIP-NGs are synthetic antibodies obtained by nanomoulding the 3-dimensional shape and chemical functionalities of a desired target in a synthetic polymer. Using an in-house developed in silico rational approach, epitope peptides of TNF-α were generated and 'synthetic peptide antibodies' were prepared. The resultant MIP-NGs bind the template peptide and recombinant TNF-α with high affinity and selectivity, and can block the binding of TNF-α to its receptor. Consequently they were applied to neutralize pro-inflammatory TNF-α in the supernatant of human THP-1 macrophages, leading to a downregulation of the secretion of pro-inflammatory cytokines. Our results suggest that MIP-NGs, which are thermally and biochemically more stable and easier to manufacture than antibodies, and cost-effective, are very promising as next generation TNF-α inhibitors for the treatment of inflammatory diseases.
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Affiliation(s)
- Claudia Herrera León
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Noel Angelo Kalacas
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Peyman Sakhaii
- Global CMC Early Development, Synthetics Platform, Sanofi-Aventis Deutschland GmbH, Industrial Park Hoechst, Building G849, 65926, Frankfurt/Main, Germany
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Helena Mora-Radó
- Global CMC Early Development, Synthetics Platform, Sanofi-Aventis Deutschland GmbH, Industrial Park Hoechst, Building G849, 65926, Frankfurt/Main, Germany
| | - Pradeep K Dhal
- Global CMC Early Development, Synthetics Platform, Sanofi Global R&D, 350 Water Street, Cambridge, MA 02141, USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
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4
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Guérin M, Shawky M, Zedan A, Octave S, Avalle B, Maffucci I, Padiolleau-Lefèvre S. Lyme borreliosis diagnosis: state of the art of improvements and innovations. BMC Microbiol 2023; 23:204. [PMID: 37528399 PMCID: PMC10392007 DOI: 10.1186/s12866-023-02935-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023] Open
Abstract
With almost 700 000 estimated cases each year in the United States and Europe, Lyme borreliosis (LB), also called Lyme disease, is the most common tick-borne illness in the world. Transmitted by ticks of the genus Ixodes and caused by bacteria Borrelia burgdorferi sensu lato, LB occurs with various symptoms, such as erythema migrans, which is characteristic, whereas others involve blurred clinical features such as fatigue, headaches, arthralgia, and myalgia. The diagnosis of Lyme borreliosis, based on a standard two-tiered serology, is the subject of many debates and controversies, since it relies on an indirect approach which suffers from a low sensitivity depending on the stage of the disease. Above all, early detection of the disease raises some issues. Inappropriate diagnosis of Lyme borreliosis leads to therapeutic wandering, inducing potential chronic infection with a strong antibody response that fails to clear the infection. Early and proper detection of Lyme disease is essential to propose an adequate treatment to patients and avoid the persistence of the pathogen. This review presents the available tests, with an emphasis on the improvements of the current diagnosis, the innovative methods and ideas which, ultimately, will allow more precise detection of LB.
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Affiliation(s)
- Mickaël Guérin
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Marc Shawky
- Connaissance Organisation Et Systèmes TECHniques (COSTECH), EA 2223, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Ahed Zedan
- Polyclinique Saint Côme, 7 Rue Jean Jacques Bernard, 60204, Compiègne, France
| | - Stéphane Octave
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Bérangère Avalle
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Irene Maffucci
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Séverine Padiolleau-Lefèvre
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France.
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5
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Binet T, Avalle B, Dávila Felipe M, Maffucci I. AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures. Bioinformatics 2022; 39:6849515. [PMID: 36440922 PMCID: PMC9805580 DOI: 10.1093/bioinformatics/btac752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Comparing single-stranded nucleic acids (ssNAs) secondary structures is fundamental when investigating their function and evolution and predicting the effect of mutations on their structures. Many comparison metrics exist, although they are either too elaborate or not sensitive enough to distinguish close ssNAs structures. RESULTS In this context, we developed AptaMat, a simple and sensitive algorithm for ssNAs secondary structures comparison based on matrices representing the ssNAs secondary structures and a metric built upon the Manhattan distance in the plane. We applied AptaMat to several examples and compared the results to those obtained by the most frequently used metrics, namely the Hamming distance and the RNAdistance, and by a recently developed image-based approach. We showed that AptaMat is able to discriminate between similar sequences, outperforming all the other here considered metrics. In addition, we showed that AptaMat was able to correctly classify 14 RFAM families within a clustering procedure. AVAILABILITY AND IMPLEMENTATION The python code for AptaMat is available at https://github.com/GEC-git/AptaMat.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Binet
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compiègne Cedex, France
| | - Bérangère Avalle
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compiègne Cedex, France
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6
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Medina Rangel PX, Mier A, Moroni E, Merlier F, Gheber LA, Vago R, Maffucci I, Tse Sum Bui B, Haupt K. Molecularly imprinted polymer nanogels targeting the HAV motif in cadherins inhibit cell-cell adhesion and migration. J Mater Chem B 2022; 10:6688-6697. [PMID: 35583238 DOI: 10.1039/d2tb00680d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cadherins are cell-surface proteins that mediate cell-cell adhesion. By regulating their grip formation and strength, cadherins play a pivotal role during normal tissue morphogenesis and homeostasis of multicellular organisms. However, their dysfunction is associated with cell migration and proliferation, cancer progression and metastasis. The conserved amino acid sequence His-Ala-Val (HAV) in the extracellular domain of cadherins is implicated in cadherin-mediated adhesion and migration. Antagonists of cadherin adhesion such as monoclonal antibodies and small molecule inhibitors based on HAV peptides, are of high therapeutic value in cancer treatment. However, antibodies are not stable outside their natural environment and are expensive to produce, while peptides have certain limitations as a drug as they are prone to proteolysis. Herein, we propose as alternative, a synthetic antibody based on molecularly imprinted polymer nanogels (MIP-NGs) to target the HAV domain. The MIP-NGs are biocompatible, have high affinity for N-cadherin and inhibit cell adhesion and migration of human cervical adenocarcinoma (HeLa) cells, as demonstrated by cell aggregation and Matrigel invasion assays, respectively. The emergence of MIPs as therapeutics for fighting cancer is still in its infancy and this novel demonstration reinforces the fact that they have a rightful place in cancer treatment.
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Affiliation(s)
- Paulina X Medina Rangel
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Elena Moroni
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Levi A Gheber
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Razi Vago
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203 Compiègne Cedex, France.
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz‐Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Guillermo U. Ruiz‐Esparza
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joseph V. Bonventre
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Pradeep K. Dhal
- US Early Development Sanofi Global R&D 153 Second Avenue Waltham MA 02451 USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Peyman Sakhaii
- R&D Global CMC Development—Synthetics—Early Development Frankfurt Sanofi-Aventis (Deutschland) GmbH Industriepark Hoechst Frankfurt am Main Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
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8
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz-Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021; 60:20849-20857. [PMID: 34296498 PMCID: PMC8562893 DOI: 10.1002/anie.202106507] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Molecularly imprinted polymers (MIPs) are tailor-made synthetic antibodies possessing specific binding cavities designed for a target molecule. Currently, MIPs for protein targets are synthesized by imprinting a short surface-exposed fragment of the protein, called epitope or antigenic determinant. However, finding the epitope par excellence that will yield a peptide "synthetic antibody" cross-reacting exclusively with the protein from which it is derived, is not easy. We propose a computer-based rational approach to unambiguously identify the "best" epitope candidate. Then, using Saturation Transfer Difference (STD) and WaterLOGSY NMR spectroscopies, we prove the existence of specific binding sites created by the imprinting of this peptide epitope in the MIP nanogel. The optimized MIP nanogel could bind the epitope and cognate protein with a high affinity and selectivity. The study was performed on Hepatitis A Virus Cell Receptor-1 protein, also known as KIM-1 and TIM-1, for its ubiquitous implication in numerous pathologies.
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Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Guillermo U Ruiz-Esparza
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Joseph V Bonventre
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Pradeep K Dhal
- US Early Development, Sanofi Global R&D, 153 Second Avenue, Waltham, MA, 02451, USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Peyman Sakhaii
- R&D Global CMC Development-Synthetics-Early Development Frankfurt, Sanofi-Aventis (Deutschland) GmbH, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
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Abstract
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The pandemic caused
by SARS-CoV-2 is currently representing a major
health and economic threat to humanity. So far, no specific treatment
to this viral infection has been developed and the emergency still
requires an efficient intervention. In this work, we used virtual
screening to facilitate drug repurposing against SARS-CoV-2, targeting
viral main proteinase and spike protein with 3000 existing drugs.
We used a protocol based on a docking step followed by a short molecular
dynamic simulation and rescoring by the Nwat-MMGBSA approach. Our
results provide suggestions for prioritizing in vitro and/or in vivo tests of already available compounds.
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Affiliation(s)
- Irene Maffucci
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu - CS 60 319 - 60 203 Compiègne Cedex, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Via Venezian, 21 20133 Milano, Italy
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10
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Maffucci I, Laage D, Sterpone F, Stirnemann G. Cover Feature: Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature (Chem. Eur. J. 44/2020). Chemistry 2020. [DOI: 10.1002/chem.202003018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Irene Maffucci
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
- Present address: Centre de recherche Royallieu Université de Technologie de Compiègne, UPJV CNRS, Enzyme and Cell Engineering CS 60319-60203 Compiègne Cedex France
| | - Damien Laage
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
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11
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Maffucci I, Laage D, Sterpone F, Stirnemann G. Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature. Chemistry 2020; 26:10045-10056. [DOI: 10.1002/chem.202001973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Irene Maffucci
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
- Present address: Centre de recherche Royallieu Université de Technologie de Compiègne, UPJV CNRS, Enzyme and Cell Engineering CS 60319-60203 Compiègne Cedex France
| | - Damien Laage
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
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12
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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13
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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14
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Chaaya N, Shahsavarian MA, Maffucci I, Friboulet A, Offmann B, Léger JB, Rousseau S, Avalle B, Padiolleau-Lefèvre S. Genetic background and immunological status influence B cell repertoire diversity in mice. Sci Rep 2019; 9:14261. [PMID: 31582818 PMCID: PMC6776527 DOI: 10.1038/s41598-019-50714-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 09/16/2019] [Indexed: 01/08/2023] Open
Abstract
The relationship between the immune repertoire and the physiopathological status of individuals is essential to apprehend the genesis and the evolution of numerous pathologies. Nevertheless, the methodological approaches to understand these complex interactions are challenging. We performed a study evaluating the diversity harbored by different immune repertoires as a function of their physiopathological status. In this study, we base our analysis on a murine scFv library previously described and representing four different immune repertoires: i) healthy and naïve, ii) healthy and immunized, iii) autoimmune prone and naïve, and iv) autoimmune prone and immunized. This library, 2.6 × 109 in size, is submitted to high throughput sequencing (Next Generation Sequencing, NGS) in order to analyze the gene subgroups encoding for immunoglobulins. A comparative study of the distribution of immunoglobulin gene subgroups present in the four libraries has revealed shifts in the B cell repertoire originating from differences in genetic background and immunological status of mice.
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Affiliation(s)
- Nancy Chaaya
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Melody A Shahsavarian
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Alain Friboulet
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Bernard Offmann
- Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR 6286 CNRS, UFR Sciences et Techniques, 2, chemin de la Houssinière, 44322, Nantes, France
| | - Jean-Benoist Léger
- CNRS UMR 7253, Heudiasyc; Université de Technologie de Compiègne. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Heudiasyc. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Sylvain Rousseau
- CNRS UMR 7253, Heudiasyc; Université de Technologie de Compiègne. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Heudiasyc. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Bérangère Avalle
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Séverine Padiolleau-Lefèvre
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France. .,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.
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15
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Bucci R, Contini A, Clerici F, Beccalli EM, Formaggio F, Maffucci I, Pellegrino S, Gelmi ML. Fluoro-Aryl Substituted α,β 2,3-Peptides in the Development of Foldameric Antiparallel β-Sheets: A Conformational Study. Front Chem 2019; 7:192. [PMID: 31001518 PMCID: PMC6454073 DOI: 10.3389/fchem.2019.00192] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/13/2019] [Indexed: 01/08/2023] Open
Abstract
α,β2,3-Disteroisomeric foldamers of general formula Boc(S-Ala-β-2R,3R-Fpg)nOMe or Boc(S-Ala-β-2S,3S-Fpg)nOMe were prepared from both enantiomers of syn H-2-(2-F-Phe)-h-PheGly-OH (named β-Fpg) and S-alanine. Our peptides show two appealing features for biomedical applications: the presence of fluorine, attractive for non-covalent interactions, and aryl groups, crucial for π-stacking. A conformational study was performed, using IR, NMR and computational studies of diastereoisomeric tetra- and hexapeptides containing the β2,3-amino acid in the R,R- and S,S-stereochemistry, respectively. We found that the stability of peptide conformation is dependent on the stereochemistry of the β-amino acid. Combining S-Ala with β-2R,3R-Fpg, a stable extended β-strand conformation was obtained. Furthermore, β-2R,3R-Fpg containing hexapeptide self-assembles to form antiparallel β-sheet structure stabilized by intermolecular H-bonds and π,π-interactions. These features make peptides containing the β2,3-fluoro amino acid very appealing for the development of bioactive proteolytically stable foldameric β-sheets as modulators of protein-protein interaction (PPI).
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Affiliation(s)
- Raffaella Bucci
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
| | - Alessandro Contini
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
| | - Francesca Clerici
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
| | - Egle Maria Beccalli
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
| | | | - Irene Maffucci
- CNRS UMR 7025, Génie Enzymatique et Cellulaire, Centre de Recherche de Royallieu, Compiègne, France.,Génie Enzymatique et Cellulaire, Centre de Recherche de Royallieu, Sorbonne Universités, Université de Technologie de Compiègne, Compiègne, France
| | - Sara Pellegrino
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
| | - Maria Luisa Gelmi
- Department of Pharmaceutical Sciences (DISFARM), University of Milan, Milan, Italy
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16
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Maffucci I, Hu X, Fumagalli V, Contini A. An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings. Front Chem 2018; 6:43. [PMID: 29556494 PMCID: PMC5844977 DOI: 10.3389/fchem.2018.00043] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/19/2018] [Indexed: 01/05/2023] Open
Abstract
Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases. Calculations were performed in triplicates on both classic HPC environments and on standard workstations equipped by a GPU card, evidencing no statistical differences in the results. No relevant differences in correlation to experiments were also observed when performing Nwat-MMGBSA calculations on 4 or 1 ns long trajectories. A fully automatic workflow for structure-based virtual screening, performing from library set-up to docking and Nwat-MMGBSA rescoring, has then been developed. The protocol has been tested against no rescoring or standard MM-GBSA rescoring within a retrospective virtual screening of inhibitors of AmpC β-lactamase and of the Rac1-Tiam1 protein-protein interaction. In both cases, Nwat-MMGBSA rescoring provided a statistically significant increase in the ROC AUCs of between 20 and 30%, compared to docking scoring or to standard MM-GBSA rescoring.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Xiao Hu
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Valentina Fumagalli
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
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17
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Tomsett M, Maffucci I, Le Bailly BAF, Byrne L, Bijvoets SM, Lizio MG, Raftery J, Butts CP, Webb SJ, Contini A, Clayden J. A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal. Chem Sci 2017; 8:3007-3018. [PMID: 28451368 PMCID: PMC5380885 DOI: 10.1039/c6sc05474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/24/2017] [Indexed: 11/21/2022] Open
Abstract
Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.
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Affiliation(s)
- Michael Tomsett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Bryden A F Le Bailly
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Stefan M Bijvoets
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - M Giovanna Lizio
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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18
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21, 20133 Milano, Italy
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19
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Staniland S, Adams RW, McDouall JJW, Maffucci I, Contini A, Grainger DM, Turner NJ, Clayden J. Biocatalytic Dynamic Kinetic Resolution for the Synthesis of Atropisomeric Biaryl N-Oxide Lewis Base Catalysts. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605486] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Ralph W. Adams
- School of Chemistry; University of Manchester; Manchester M13 9PL UK
| | | | - Irene Maffucci
- Università di Milano, Dipartimento Scienze Farmaceutiche-Sezione di Chimica Generale e Organica “Alessandro Marchesini”; Università degli Studi di Milano; 20133 Milano Italy
| | - Alessandro Contini
- Università di Milano, Dipartimento Scienze Farmaceutiche-Sezione di Chimica Generale e Organica “Alessandro Marchesini”; Università degli Studi di Milano; 20133 Milano Italy
| | | | - Nicholas J. Turner
- School of Chemistry; University of Manchester, Manchester Institute of Biotechnology; 131 Princess Street Manchester M1 7DN UK
| | - Jonathan Clayden
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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20
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Staniland S, Adams RW, McDouall JJW, Maffucci I, Contini A, Grainger DM, Turner NJ, Clayden J. Biocatalytic Dynamic Kinetic Resolution for the Synthesis of Atropisomeric Biaryl N-Oxide Lewis Base Catalysts. Angew Chem Int Ed Engl 2016; 55:10755-9. [DOI: 10.1002/anie.201605486] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Indexed: 12/17/2022]
Affiliation(s)
| | - Ralph W. Adams
- School of Chemistry; University of Manchester; Manchester M13 9PL UK
| | | | - Irene Maffucci
- Università di Milano, Dipartimento Scienze Farmaceutiche-Sezione di Chimica Generale e Organica “Alessandro Marchesini”; Università degli Studi di Milano; 20133 Milano Italy
| | - Alessandro Contini
- Università di Milano, Dipartimento Scienze Farmaceutiche-Sezione di Chimica Generale e Organica “Alessandro Marchesini”; Università degli Studi di Milano; 20133 Milano Italy
| | | | - Nicholas J. Turner
- School of Chemistry; University of Manchester, Manchester Institute of Biotechnology; 131 Princess Street Manchester M1 7DN UK
| | - Jonathan Clayden
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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21
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Maffucci I, Contini A. An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides. J Chem Theory Comput 2016; 12:714-27. [DOI: 10.1021/acs.jctc.5b01211] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
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22
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Maffucci I, Clayden J, Contini A. Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides. J Phys Chem B 2015; 119:14003-13. [PMID: 26457452 DOI: 10.1021/acs.jpcb.5b07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Jonathan Clayden
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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Maffucci I, Pellegrino S, Clayden J, Contini A. Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids. J Phys Chem B 2015; 119:1350-61. [PMID: 25528885 DOI: 10.1021/jp510775e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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Ruffoni A, Contini A, Soave R, Lo Presti L, Esposto I, Maffucci I, Nava D, Pellegrino S, Gelmi ML, Clerici F. Model peptides containing the 3-sulfanyl-norbornene amino acid, a conformationally constrained cysteine analogue effective inducer of 310-helix secondary structures. RSC Adv 2015. [DOI: 10.1039/c5ra03805g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Two model peptides containing the 3-benzylsulfanylnorbornene amino acid (NRB) was prepared. Theoretical calculations, spectroscopic and X-ray analyses confirmed that both NRB enantiomers possess a strong right-handed helicogenic effect.
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Ruffoni A, Ferri N, Bernini SK, Ricci C, Corsini A, Maffucci I, Clerici F, Contini A. 2-Amino-3-(phenylsulfanyl)norbornane-2-carboxylate: An Appealing Scaffold for the Design of Rac1–Tiam1 Protein–Protein Interaction Inhibitors. J Med Chem 2014; 57:2953-62. [DOI: 10.1021/jm401924s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alessandro Ruffoni
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Nicola Ferri
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
- Multimedica IRCCS, Milan, Italy
| | - Sergio K. Bernini
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Chiara Ricci
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Alberto Corsini
- Dipartimento
di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Irene Maffucci
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Francesca Clerici
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento
di Scienze Farmaceutiche—Sezione di Chimica Generale e Organica
“Alessandro Marchesini”, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy
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Maffucci I, Contini A. Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities. J Chem Theory Comput 2013; 9:2706-17. [PMID: 26583864 DOI: 10.1021/ct400045d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) methods are widely used for drug design/discovery purposes. However, it is not clear if the correlation between predicted and experimental binding affinities can be improved by explicitly considering selected water molecules in the calculation of binding energies, since different and sometimes diverging opinions are found in the literature. In this work, we evaluated how variably populated hydration shells explicitly considered around the ligands may affect the correlation between MM-PB/GBSA computed binding energy and biological activities (IC50 and ΔGbind, depending on the available experimental data). Four different systems-namely, the DNA-topoisomerase complex, α-thrombin, penicillopepsin, and avidin-were considered and ligand hydration shells populated by 10-70 water molecules were systematically evaluated. We found that the consideration of a hydration shell populated by a number of water residues (Nwat) between 30 and 70 provided, in all of the considered examples, a positive effect on correlation between MM-PB/GBSA calculated binding affinities and experimental activities, with a negligible increment of computational cost.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche-Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche-Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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