Asymmetric Synthesis of New β-Lactam Lipopeptides as Bacterial Signal Peptidase I Inhibitors

International audienceThe transmembrane bacterial enzyme, signal peptidase I, is recognized as being a promising target for reducing the emergence of drug resistance. The asymmetric synthesis and the biological evaluation of original β-lactam lipopeptides have been performed to discover potent signal peptidase inhibitors. The importance of the azetidinone motif of these lipopeptides has been demonstrated and can serve as a starting point to exploit and improve the reactivity of the β-lactam in peptidomimetics

Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization

DNA polymerases from different evolutionary families [Vent (exo−) DNA polymerase from the B-family polymerases, Taq DNA polymerase from the A-family polymerases and HIV reverse transcriptase from the reverse transcriptase family] were examined for their ability to incorporate the sugar-modified cyclohexenyl nucleoside triphosphates. All enzymes were able to use the cyclohexenyl nucleotides as a substrate. Using Vent (exo−) DNA polymerase and HIV reverse transcriptase, we were even able to incorporate seven consecutive cyclohexenyl nucleotides. Using a cyclohexenyl nucleic acid (CeNA) template, all enzymes tested were also able to synthesize a short DNA fragment. Since the DNA-dependent CeNA polymerization and the CeNA-dependent DNA polymerization is possible to a limited extend, we suggest CeNA as an ideal candidate to use in directed evolution methods for the development of a polymerase capable of replicating CeNA

Elaboration of a proprietary thymidylate kinase inhibitor motif towards anti-tuberculosis agents

International audienceWe report the design and synthesis of a series of non-nucleoside MtbTMPK inhibitors (1-14) based on the gram-positive bacterial TMPK inhibitor hit compound 1. A practical synthesis was developed to access these analogues. Several compounds show promising MtbTMPK inhibitory potency and allow the establishment of a structure-activity relationship, which is helpful for further optimization

Iminodiacetic-phosphoramidates as metabolic prototypes for diversifying nucleic acid polymerization in vivo

Previous studies in our laboratory proved that certain functional groups are able to mimic the pyrophosphate moiety and act as leaving groups in the enzymatic polymerization of deoxyribonucleic acids by HIV-1 reverse transcriptase. When the potential leaving group possesses two carboxylic acid moieties linked to the nucleoside via a phosphoramidate bond, it is efficiently recognized by this error-prone enzyme, resulting in nucleotide incorporation into DNA. Here, we present a new efficient alternative leaving group, iminodiacetic acid, which displays enhanced kinetics and an enhanced elongation capacity compared to previous results obtained with amino acid deoxyadenosine phosphoramidates. Iminodiacetic acid phosphoramidate of deoxyadenosine monophosphate (IDA-dAMP) is processed by HIV-1 RT as a substrate for single nucleotide incorporation and displays a typical Michaelis–Menten kinetic profile. This novel substrate also proved to be successful in primer strand elongation of a seven-base template overhang. Modelling of this new substrate in the active site of the enzyme revealed that the interactions formed between the triphosphate moiety, magnesium ions and enzyme's residues could be different from those of the natural triphosphate substrate and is likely to involve additional amino acid residues. Preliminary testing for a potential metabolic accessibility lets us to envision its possible use in an orthogonal system for nucleic acid synthesis that would not influence or be influenced by genetic information from the outside

Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease

Human ubiquitin carboxyl-terminal hydrolase-2 (USP2) inhibitors, such as thiopurine analogs, have been reported to inhibit SARS-CoV papain-like proteases (PLpro). The PLpro have significant functional implications in the innate immune response during SARS-CoV-2 infection and considered an important antiviral target. Both proteases share strikingly similar USP fold with right-handed thumb-palm-fingers structural scaffold and conserved catalytic triad Cys-His-Asp/Asn. In this urgency situation of COVID-19 outbreak, there is a lack of in-vitro facilities readily available to test SARS-CoV-2 inhibitors in whole-cell assays. Therefore, we adopted an alternate route to identify potential USP2 inhibitor through integrated in-silico efforts. After an extensive virtual screening protocol, the best compounds were selected and tested. The compound Z93 showed significant IC50 value against Jurkat (9.67 μM) and MOTL-4 cells (11.8 μM). The binding mode of Z93 was extensively analyzed through molecular docking, followed by MD simulations, and molecular interactions were compared with SARS-CoV-2. The relative binding poses of Z93 fitted well in the binding site of both proteases and showed consensus π-π stacking and H-bond interactions with histidine and aspartate/asparagine residues of the catalytic triad. These results led us to speculate that compound Z93 might be the first potential chemical lead against SARS-CoV-2 PLpro, which warrants in-vitro evaluations.status: publishe

Investigation of the DNA-dependent cyclohexenyl

nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerizatio

Molecular dynamics simulation of polarizable water by an extended lagrangian method

The extended Lagrangian method is applied to incorporate induced polarization effects in pure water, using molecular dynamics simulations, at a cost in computer time which is only twice that of modelling the corresponding pairwise additive system. Thermodynamic, structural and dynamical properties of the mean-field SPC and the polarizable PSPC models are compared. All simulations were performed in the canonical ensemble by use of the Nos6 thermostat method. We confirm that explicitly including induced polarization effects considerably improves the quality of the SPC model for the transport properties. We show that within some difference in simulation conditions, the method of the extended Lagrangian gives quite satisfactory results when compared to the more classical self-consistent iterative/predictive procedure previously used to calculate the non-additive effects. The latter part of this study assesses the importance of many-body effects in determining the properties of liquid water. This question is addressed with simulations, using a water model, where the induced dipole moment of the PSPC is represented by a single fixed point dipole positioned at the oxygen. It is shown that, whereas the many-body effects appear to have little influence on static properties and on the self-diffusion coefficient, their accurate and explicit representation significantly affects the orientational times. © 1992 Taylor & Francis Group, LLC.SCOPUS: ar.jinfo:eu-repo/semantics/publishe