Fluoro-Aryl Substituted α,β2,3-Peptides in the Development of Foldameric Antiparallel β-Sheets: A Conformational Study

\u3b1,\u3b22,3 -Disteroisomeric foldamers of general formula Boc(S-Ala-\u3b2-2R,3R-Fpg)n OMe or Boc(S-Ala-\u3b2-2S,3S-Fpg)n OMe were prepared from both enantiomers of syn H-2-(2-F-Phe)-h-PheGly-OH (named \u3b2-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 \u3c0-stacking. A conformational study was performed, using IR, NMR and computational studies of diastereoisomeric tetra- and hexapeptides containing the \u3b22,3-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 \u3b2-amino acid. Combining S-Ala with \u3b2-2R,3R-Fpg, a stable extended \u3b2-strand conformation was obtained. Furthermore, \u3b2-2R,3R-Fpg containing hexapeptide self-assembles to form antiparallel \u3b2-sheet structure stabilized by intermolecular H-bonds and \u3c0,\u3c0-interactions. These features make peptides containing the \u3b22,3-fluoro amino acid very appealing for the development of bioactive proteolytically stable foldameric \u3b2-sheets as modulators of protein-protein interaction (PPI)

Genetic background and immunological status influence B cell repertoire diversity in mice

International audienceThe 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 × 10 9 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. The adaptive immune system is capable of producing antibodies against a large number of immunogens. This vast diversity of immunoglobulin sequences is not provided by the limited number of genes present in the genome, but by rearrangements of the germline at specific loci. In the case of B cell receptors, rearrangement of variable (V), diversity (D), and joining (J) gene segments in V-Domain creates a combinatorial diversity for the immu-noglobulin heavy chain (IGH), whereas rearrangement of V and J gene segments provides a similar diversity for the lambda or kappa light chains (IGL/IGK) 1 (Fig. 1). Additionally, at the junctions of V-D and D-J segments, a process of random deletion and addition of nucleotides creates an immense junctional diversity. Finally, somatic hypermutations focused on Complementary Determining Regions (CDR) supplement the mechanisms of immu-noglobulin maturation, expanding still further the diversity and leading to affine and specific antibodies. Studies have shown that this vast diversity, as well as other characteristics of the immune repertoire, can be influenced by factors such as immunization 2,3 or pathology, notably autoimmune diseases 4-6. Generation of antibody libraries is a crucial step in the attempt to study in vivo immune repertoires 7,8. Care needs to be taken to ensure the coverage of a large antibody sequence diversity in order to mimic the natural B cell repertoire as close as possible. Recently, we have described an original strategy allowing to improve the library construction process and increase its diversity 9. This strategy is based on a technological optimization relying on Rolling Circle Amplification (RCA), combined with a newly designed set of oligonucleotide primers based on a thorough analysis of the IMGT/LIGM-DB database 10. In the present study, we have used this strategy to generate libraries form two murine inbred strains were used, namely Balb/C (healthy) and SJL/J (susceptible to autoimmune disease), together representing 4 different IgG immune repertoires: i) healthy and naïve (NB for naïve Balb/C), ii) healthy and immunized (IB for immunized Balb/C), iii) autoimmune prone and naïve (NS for naïve SJL/J), and iv) autoimmune prone and immunized (IS for immunized SJL/J) 11. We have decidedly chosen t

A novel genetic variant in PTGS1 affects N-glycosylation of cyclooxygenase-1 causing a dominant-negative effect on platelet function and bleeding diathesis.

During platelet activation, arachidonic acid (AA) is released from membrane phospholipids and metabolized to thromboxane A2 (TXA2) through the actions of cyclooxygenase-1 (COX-1) and TXA2 synthase. Note, TXA2 binds to the platelet TXA2 receptor, causing shape change, secretion and platelet aggregation.1 Also, COX-1 (599aa; 70 kDa) has cyclooxygenase and peroxidase activities and it is functionally active as a homodimer, with each COX-1 monomer consisting of four highly conserved domains: an N-terminal signal peptide, a dimerization domain, a membrane-binding domain (MBD) and a large C-terminal catalytic domain2 (Figure 1A). Irreversible COX-1 inhibition by aspirin is a widely established anti-platelet therapy in cardiovascular disease.Fundación Mutua Madrileña, Grant/Award Number: AP172142019; Fundación Séneca, Grant/Award Number: 19873/GERM/15; Gerencia Regional de Salud, Grant/Award Numbers: 1647/A/17, 2061A/19; Instituto de Salud Carlos III (ISCIII) & Feder, Grant/Award Numbers: CB15/00055, PI17/01966, PI18/00598, PI20/00926, PI17/01311; Junta de Castilla y León; British Heart Foundation, Grant/Award Number: PG/17/40/33028; Ayuda a Grupos de Trabajo en Patología Hemorrágica; Premio López Borrasca 2019; Sociedad Española de Trombosis y Hemostasia

Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities

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 Δ<i>G</i>_bind, 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 (<i>N</i>_wat) 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

Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method

A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein–protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides the Nwat parameter, the effect of the force field, the molecular dynamics simulation length, and the implicit solvent model used in the MMGBSA analysis have been also evaluated. We found that considering 30 interfacial water molecules improved the correlation between predicted and experimental binding energies by up to 30%, compared to the standard approach. Moreover, the correlation resulted in being rather sensitive to the force field and, to a minor extent, to the implicit solvent model and to the length of the MD simulation

Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method

A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein–protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides the Nwat parameter, the effect of the force field, the molecular dynamics simulation length, and the implicit solvent model used in the MMGBSA analysis have been also evaluated. We found that considering 30 interfacial water molecules improved the correlation between predicted and experimental binding energies by up to 30%, compared to the standard approach. Moreover, the correlation resulted in being rather sensitive to the force field and, to a minor extent, to the implicit solvent model and to the length of the MD simulation

An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β‑Hairpin, and Intrinsically Disordered Peptides

Replica exchange molecular dynamics simulations were performed to test the ability of six AMBER force fields and three implicit solvent models of predicting the native conformation of two helical peptides, three β-hairpins, and three intrinsically disordered peptides. Although a combination of the force field and implicit solvation models able to accurately predict the native structure of all the considered peptides was not identified, we found that the GB-Neck2 model seems to well compensate for some of the conformational biases showed by ff96 and ff99SB/ildn/ildn-φ. Indeed, the force fields of the ff99SB series coupled with GB-Neck2 reasonably discriminated helices from disordered peptides, while a good prediction of β-hairpin conformations was only achieved by performing two independent simulations: one with the ff96/GB-Neck2 combination and the other with GB-Neck2 coupled with any of the ff99SB/ildn/ildn-φ force fields

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

The Nwat-MMGBSA method, whose theory has been described in Maffucci & Contini, JCTC 2013, 9, 2706, is based on the inclusion as part of the receptor of a given number of water molecules (Nwat) which are the closest to a residue (generally the ligand) or to a selection of residues (the contact interface) in each frame of the MD simulation. The method was shown to improve the correlation between predicted and experimental binding energy in both ligand-receptor and protein-protein complexes (Maffucci & Contini, JCIM 2016, 56, 1692). Here, we report on the optimization of the Nwat-MMGBSA protocol for its use to rescore docking results. We also report an automatic workflow, based on three independent scripts (which can be concatenated in a fully automated procedure) to easily employ Nwat-MMGBSA rescoring in virtual screening application. The protocol has been tuned using three different examples, and then tested in two retrospective virtual screening examples. In each example, the Nwat-MMGBSA method has been compared with the standard MMGBSA approach (Nwat=0). A link to download the scripts, working examples and tutorials is also provided.<br /

Differences in Thermal Structural Changes and Melting Between Mesophilic and Thermophilic Dihydrofolate Reductase Enzymes

A key aspect of life\u27s evolution on Earth is the adaptation of proteins to be stable and work in a very wide range of temperature conditions. A detailed understanding of the associated molecular mechanisms would also help to design enzymes optimized for biotechnological processes. Despite important advances, a comprehensive picture of how thermophilic enzymes succeed in functioning under extreme temperatures remains incomplete. Here, we examine the temperature dependence of stability and of flexibility in the mesophilic monomeric Escherichia coli (Ec) and thermophilic dimeric Thermotoga maritima (Tm) homologs of the paradigm dihydrofolate reductase (DHFR) enzyme. We use all-atom molecular dynamics simulations and a replica-exchange scheme that allows to enhance the conformational sampling while providing at the same time a detailed understanding of the enzymes\u27 behavior at increasing temperatures. We show that this approach reproduces the stability shift between the two homologs, and provides a molecular description of the denaturation mechanism by identifying the sequence of secondary structure elements melting as temperature increases, which is not straightforwardly obtained in the experiments. By repeating our approach on the hypothetical TmDHFR monomer, we further determine the respective effects of sequence and oligomerization in the exceptional stability of TmDFHR. We show that the intuitive expectation that protein flexibility and thermal stability are correlated is not verified. Finally, our simulations reveal that significant conformational fluctuations already take place much below the melting temperature. While the difference between the TmDHFR and EcDHFR catalytic activities is often interpreted via a simplified two-state picture involving the open and closed conformations of the key M20 loop, our simulations suggest that the two homologs\u27 markedly different activity temperature dependences are caused by changes in the ligand-cofactor distance distributions in response to these conformational changes