Discovering NDM-1 inhibitors using molecular substructure embeddings representations

NDM-1 (New-Delhi-Metallo-beta-lactamase-1) is an enzyme developed by bacteria that is implicated in bacteria resistance to almost all known antibiotics. In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison to the classical Machine Learning paradigm. Moreover, we investigate different compact molecular representations, based on atomic or bi-atomic substructures. Finally, we scanned the Drugbank for strongly active compounds and we present the top-15 ranked compounds

Complexity of the Tensegrity Structure for Dynamic Energy and Force Distribution of Cytoskeleton during Cell Spreading

Cytoskeleton plays important roles in intracellular force equilibrium and extracellular force transmission from/to attaching substrate through focal adhesions (FAs). Numerical simulations of intracellular force distribution to describe dynamic cell behaviors are still limited. The tensegrity structure comprises tension-supporting cables and compression-supporting struts that represent the actin filament and microtubule respectively, and has many features consistent with living cells. To simulate the dynamics of intracellular force distribution and total stored energy during cell spreading, the present study employed different complexities of the tensegrity structures by using octahedron tensegrity (OT) and cuboctahedron tensegrity (COT). The spreading was simulated by assigning specific connection nodes for radial displacement and attachment to substrate to form FAs. The traction force on each FA was estimated by summarizing the force carried in sounding cytoskeletal elements. The OT structure consisted of 24 cables and 6 struts and had limitations soon after the beginning of spreading by declining energy stored in struts indicating the abolishment of compression in microtubules. The COT structure, double the amount of cables and struts than the OT structure, provided sufficient spreading area and expressed similar features with documented cell behaviors. The traction force pointed inward on peripheral FAs in the spread out COT structure. The complex structure in COT provided further investigation of various FA number during different spreading stages. Before the middle phase of spreading (half of maximum spreading area), cell attachment with 8 FAs obtained minimized cytoskeletal energy. The maximum number of 12 FAs in the COT structure was required to achieve further spreading. The stored energy in actin filaments increased as cells spread out, while the energy stored in microtubules increased at initial spreading, peaked in middle phase, and then declined as cells reached maximum spreading. The dynamic flows of energy in struts imply that microtubules contribute to structure stabilization

Synthesis of 1,6-dihydropyrrolo[2,3-g]indazoles using Larock indole annulations

International audienceThe synthesis of 1,6-dihydropyrrolo[2,3-g]indazole derivatives is described. The indolic ring system is constructed via a Larock palladium-catalyzed annulation using terminal and internal alkynes. Additionally, when using internal alkynes for this reaction, we found that a directing effect on regioselectivity was mediated by the ester group of alkyl 3-substituted propiolate derivative

The phosphorus-Claisen condensation

International audience1,1-Bisphosphorus compounds are easily synthesized through the phosphorus-Claisen (phospha-Claisen) condensation between a phosphorus-stabilized anion and a phosphorus electrophile. The preliminary scope of this reaction is investigated in terms of employable phosphorus reagents. Valuable intermediates are conveniently prepared in a single step. Overall, the method is competitive with multistep procedures which require the preparation of PCl intermediates derived from the P(OR) reagents we instead employ directly, and it delivers complex organophosphorus compounds in moderate to good isolated yields. An example of the intramolecular version of the reaction, the phospha-Dieckmann condensation, is also reported

Regioselective synthesis of novel substituted indazole-5,6-diamine derivatives

International audienceThe synthesis of a series of novel indazole-5,6-diamine derivatives is described. This indazole ring system was incorporated in an octahydropyrrolo[3,4-b]phenazine scaffold and was diversely and regioselectively substituted on the nitrogen atoms at the 5- and 10-positions. Thus, the nitrogen atom at the 5-position was found to be more reactive toward electrophiles than the one at the 10-position. This difference of reactivity could be attributed to the electronic effect of the pyrazole moiety. Moreover, an unexpected tetrahydropyran protecting group migration was observed from the N-1 atom to the C-11 position of the octahydropyrrolo[3,4-b]phenazine scaffold

Chemistry of the Versatile (Hydroxymethyl)phosphinyl P(O)CH₂OH Functional Group

(Hydroxymethyl)phosphorus compounds are well-known and valuable compounds in general; however the use of (hydroxymethyl)phosphinates R¹P(O)(OR²)CH₂OH in particular has been much more limited. The potential of this functionality has not yet been fully realized because the mild unmasking of the hydroxymethyl group was not available. The mild <i>oxidative</i> conversion of R¹P(O)(OR²)CH₂OH into R¹P(O)(OR²)H using the Corey–Kim oxidation is described. Other reactions preserving the methylene carbon are also reported

Synthesis of (phosphonomethyl)phosphinate pyrophosphate analogues via the phospha-Claisen condensation

International audiencePyrophosphate analogues are of great importance especially for the design of biologically active molecules. The phospha-Claisen condensation allows for the rapid synthesis of (phosphonomethyl)phosphinate pyrophosphate analogues and building blocks that can be employed in numerous applications

Identification of pyrrolo[2,3-g]indazoles as new Pim kinase inhibitors.

International audienceThe synthesis and Pim kinase inhibition potency of a new series of pyrrolo[2,3-g]indazole derivatives is described. The results obtained in this preliminary structure–activity relationship study pointed out that sub-micromolar Pim-1 and Pim-3 inhibitory potencies could be obtained in this series, more particularly for compounds 10 and 20, showing that pyrrolo[2,3-g]indazole scaffold could be used for the development of new potent Pim kinase inhibitors. Molecular modeling experiments were also performed to study the binding mode of these compounds in Pim-3 ATP-binding pocket

Synthesis and biological activities of pyrazolo[3,4-g]quinoxaline derivatives

International audienceThe synthesis of new pyrazolo[3,4-g]quinoxaline derivatives, as well as their Pim kinases (Pim-1, Pim-2, Pim-3) inhibitory potencies and in vitro antiproliferative activities toward a human fibroblast primary culture and three human solid cancer cell lines (PA1, PC3 and DU145) are described. The results obtained in this preliminary structure–activity relationship study have pointed out that most of the compounds in this series exhibited interesting in vitro Pim-3 kinase inhibitory potencies. Moreover, some of the tested compounds have demonstrated favorable antiproliferative potencies

Synthèse et activités biologiques des pyrazolo[3,4-g]quinoxalines

Communication oral