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The Chemical Biology Research in France
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The Chemical Biology Research in France

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 18423

Special Issue Editor

Dr. Paola Arimondo

E-Mail Website
Guest Editor
CNRS Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
Interests: chemical biology; medicinal chemistry; drug discovery in the field of epigenetics and gene regulation applied to cancer and infectious diseases

Special Issue Information

Dear Colleagues,

Chemistry at the interface of biology has played an important role in research in France since the end of the 19th century with the discoveries made by Louis Pasteur and their application to medicine and biotechnology. Chemical biology opens many possibilities for innovative findings and to develop new cutting-edge technologies to understand biology and discover, for example, new treatments for human diseases or new agronomical applications. The development of chemical reactions that occur in living systems has been a breakthrough and has enabled the observation and study of all types of biomolecules in living systems. An important application is detection: these chemical tools allow the detection and following of biological macromolecules, events and organisms in living cells and animals. With the implementation of the “omics” approaches and phenotypic technologies, chemical biology has revealed large numbers of uncharacterized potential drug targets that can be addressed with chemical probes. Chemical probes can reveal the function of a specific biomolecule without suppressing it. The effect is rapid, potentially reversible, and does not necessarily disrupt the entire interactome of the biomolecule in the biological context. Thus, they constitute a valuable toolbox for in detail studies of biological processes. Notably, when combined with a medicinal chemistry program, chemical probes can favour the emergence of drug candidates. Another explored area is the chemical modulation of biomolecules that can for example trigger the immune response and open the way to new therapeutic strategies. The present Special Issue is aimed at covering novel developments of chemical tools and chemical probes ongoing in French laboratories and their applications.

Dr. Paola Arimondo
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • chemical biology
  • France
  • chemical tools
  • detection
  • drug discovery
  • mechanism of action
  • novel targets

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Published Papers (5 papers)

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Research

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17 pages, 5240 KiB  
Article
Crossing of the Cystic Barriers of Toxoplasma gondii by the Fluorescent Coumarin Tetra-Cyclopeptide
by Céline Dard, Baptiste Leforestier, Flaviane Francisco Hilário, Mohamed Dit Mady Traoré, Marie-Ange Lespinasse, Basile Pérès, Marie-Carmen Molina, Rossimiriam Pereira de Freitas, Anne Milet, Danièle Maubon and Yung-Sing Wong
Molecules 2021, 26(24), 7506; https://doi.org/10.3390/molecules26247506 - 11 Dec 2021
Cited by 4 | Viewed by 2473
Abstract
FR235222 is a natural tetra-cyclopeptide with a strong inhibition effect on histone deacetylases, effective on mammalian cells as well as on intracellular apicomplexan parasites, such as Toxoplasma gondii, in the tachyzoite and bradyzoite stages. This molecule is characterized by two parts: the zinc-binding [...] Read more.
FR235222 is a natural tetra-cyclopeptide with a strong inhibition effect on histone deacetylases, effective on mammalian cells as well as on intracellular apicomplexan parasites, such as Toxoplasma gondii, in the tachyzoite and bradyzoite stages. This molecule is characterized by two parts: the zinc-binding group, responsible for the binding to the histone deacetylase, and the cyclic tetrapeptide moiety, which plays a crucial role in cell permeability. Recently, we have shown that the cyclic tetrapeptide coupled with a fluorescent diethyl-amino-coumarin was able to maintain properties of cellular penetration on human cells. Here, we show that this property can be extended to the crossing of the Toxoplasma gondii cystic cell wall and the cell membrane of the parasite in its bradyzoite form, while maintaining a high efficacy as a histone deacetylase inhibitor. The investigation by molecular modeling allows a better understanding of the penetration mechanism. Full article
(This article belongs to the Special Issue The Chemical Biology Research in France)
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22 pages, 6392 KiB  
Article
Synthesis and Biological Activity of a Cytostatic Inhibitor of MLLr Leukemia Targeting the DOT1L Protein
by Corentin Bon, Yang Si, Melanie Pernak, Magdalena Barbachowska, Eva Levi-Acobas, Veronique Cadet Daniel, Corinne Jallet, Dusan Ruzic, Nemanja Djokovic, Teodora Djikić, Katarina Nikolic, Ludovic Halby and Paola B. Arimondo
Molecules 2021, 26(17), 5300; https://doi.org/10.3390/molecules26175300 - 31 Aug 2021
Cited by 8 | Viewed by 4503
Abstract
Histone methyltransferase DOT1L catalyzes mono-, di- and trimethylation of histone 3 at lysine residue 79 (H3K79) and hypermethylation of H3K79 has been linked to the development of acute leukemias characterized by the MLL (mixed-lineage leukemia) rearrangements (MLLr cells). The inhibition of H3K79 methylation [...] Read more.
Histone methyltransferase DOT1L catalyzes mono-, di- and trimethylation of histone 3 at lysine residue 79 (H3K79) and hypermethylation of H3K79 has been linked to the development of acute leukemias characterized by the MLL (mixed-lineage leukemia) rearrangements (MLLr cells). The inhibition of H3K79 methylation inhibits MLLr cells proliferation, and an inhibitor specific for DOT1L, pinometostat, was in clinical trials (Phase Ib/II). However, the compound showed poor pharmacological properties. Thus, there is a need to find new potent inhibitors of DOT1L for the treatment of rearranged leukemias. Here we present the design, synthesis, and biological evaluation of a small molecule that inhibits in the nM level the enzymatic activity of hDOT1L, H3K79 methylation in MLLr cells with comparable potency to pinometostat, associated with improved metabolic stability and a characteristic cytostatic effect. Full article
(This article belongs to the Special Issue The Chemical Biology Research in France)
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Review

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16 pages, 4012 KiB  
Review
Molecular Design in Practice: A Review of Selected Projects in a French Research Institute That Illustrates the Link between Chemical Biology and Medicinal Chemistry
by Benoit Deprez, Damien Bosc, Julie Charton, Cyril Couturier, Rebecca Deprez-Poulain, Marion Flipo, Florence Leroux, Baptiste Villemagne and Nicolas Willand
Molecules 2021, 26(19), 6083; https://doi.org/10.3390/molecules26196083 - 8 Oct 2021
Cited by 2 | Viewed by 3128
Abstract
Chemical biology and drug discovery are two scientific activities that pursue different goals but complement each other. The former is an interventional science that aims at understanding living systems through the modulation of its molecular components with compounds designed for this purpose. The [...] Read more.
Chemical biology and drug discovery are two scientific activities that pursue different goals but complement each other. The former is an interventional science that aims at understanding living systems through the modulation of its molecular components with compounds designed for this purpose. The latter is the art of designing drug candidates, i.e., molecules that act on selected molecular components of human beings and display, as a candidate treatment, the best reachable risk benefit ratio. In chemical biology, the compound is the means to understand biology, whereas in drug discovery, the compound is the goal. The toolbox they share includes biological and chemical analytic technologies, cell and whole-body imaging, and exploring the chemical space through state-of-the-art design and synthesis tools. In this article, we examine several tools shared by drug discovery and chemical biology through selected examples taken from research projects conducted in our institute in the last decade. These examples illustrate the design of chemical probes and tools to identify and validate new targets, to quantify target engagement in vitro and in vivo, to discover hits and to optimize pharmacokinetic properties with the control of compound concentration both spatially and temporally in the various biophases of a biological system. Full article
(This article belongs to the Special Issue The Chemical Biology Research in France)
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30 pages, 8661 KiB  
Review
Convertible and Constrained Nucleotides: The 2’-Deoxyribose 5’-C-Functionalization Approach, a French Touch
by Crystalle Chardet, Corinne Payrastre, Béatrice Gerland and Jean-Marc Escudier
Molecules 2021, 26(19), 5925; https://doi.org/10.3390/molecules26195925 - 30 Sep 2021
Cited by 3 | Viewed by 3047
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position [...] Read more.
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids. Full article
(This article belongs to the Special Issue The Chemical Biology Research in France)
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15 pages, 2379 KiB  
Review
The Cellular and Chemical Biology of Endocytic Trafficking and Intracellular Delivery—The GL–Lect Hypothesis
by Ludger Johannes
Molecules 2021, 26(11), 3299; https://doi.org/10.3390/molecules26113299 - 31 May 2021
Cited by 9 | Viewed by 3915
Abstract
Lipid membranes are common to all forms of life. While being stable barriers that delimitate the cell as the fundamental organismal unit, biological membranes are highly dynamic by allowing for lateral diffusion, transbilayer passage via selective channels, and in eukaryotic cells for endocytic [...] Read more.
Lipid membranes are common to all forms of life. While being stable barriers that delimitate the cell as the fundamental organismal unit, biological membranes are highly dynamic by allowing for lateral diffusion, transbilayer passage via selective channels, and in eukaryotic cells for endocytic uptake through the formation of membrane bound vesicular or tubular carriers. Two of the most abundant fundamental fabrics of membranes—lipids and complex sugars—are produced through elaborate chains of biosynthetic enzymes, which makes it difficult to study them by conventional reverse genetics. This review illustrates how organic synthesis provides access to uncharted areas of membrane glycobiology research and its application to biomedicine. For this Special Issue on Chemical Biology Research in France, focus will be placed on synthetic approaches (i) to study endocytic functions of glycosylated proteins and lipids according to the GlycoLipid–Lectin (GL–Lect) hypothesis, notably that of Shiga toxin; (ii) to mechanistically dissect its endocytosis and intracellular trafficking with small molecule; and (iii) to devise intracellular delivery strategies for immunotherapy and tumor targeting. It will be pointed out how the chemical biologist’s view on lipids, sugars, and proteins synergizes with biophysics and modeling to “look” into the membrane for atomistic scale insights on molecular rearrangements that drive the biogenesis of endocytic carriers in processes of clathrin-independent endocytosis. Full article
(This article belongs to the Special Issue The Chemical Biology Research in France)
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