Tether influence on the binding properties of tRNALys3 ligands designed by a fragment-based approach

Probing the structure of human tRNA3Lys in the presence of ligands using docking, MD simulations and MSM analysis

The tRNA3Lys, which acts as a primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription, undergoes structural changes required for the formation of a primer-template complex. Small molecules have been targeted against tRNA3Lys to inhibit the primer-template complex formation. The present study aims to understand the kinetics of the conformational landscape spanned by tRNA3Lys in apo form using molecular dynamics simulations and Markov state modeling. The study is taken further to investigate the effect of small molecules like 1,4T and 1,5T on structural conformations and kinetics of tRNA3Lys, and comparative analysis is presented. Markov state modeling of tRNA3Lys apo resulted in three metastable states where the conformations have shown the non-canonical structures of the anticodon loop. Based on analyses of ligand-tRNA3Lys interactions, crucial ion and water mediated H-bonds and free energy calculations, it was observed that the 1,4-triazole more strongly binds to the tRNA3Lys compared to 1,5-triazole. However, the MSM analysis suggest that the 1,5-triazole binding to tRNA3Lys has brought rigidity not only in the binding pocket (TΨC arm, D-TΨC loop) but also in the whole structure of tRNA3Lys. This may affect the easy opening of primer tRNA3Lys required for HIV-1 reverse transcription.

Small-Molecule 3D Ligand for RNA Recognition: Tuning Selectivity through Scaffold Hopping

Targeting RNAs with small molecules is considered the next frontier for drug discovery. In this context, the development of compounds capable of binding RNA structural motifs of low complexity with high affinity and selectivity would greatly expand the number of targets of potential therapeutic value. In this study, we demonstrate that tuning the three-dimensional shape of promiscuous nucleic acid binders is a valuable strategy for the design of new selective RNA ligands. Indeed, starting from a known cyanine, the simple replacement of a phenyl ring with a [2.2]paracyclophane moiety led to a new compound able to discriminate between nucleic acids showing different structural characteristics with a marked affinity and selectivity for an octahairpin loop RNA sequence. This shape modification also affected the in cellulo behavior of the cyanine. These results suggest that scaffold hopping is a valuable strategy to improve the selectivity of RNA/small-molecule interactions and highlight the need to explore a new chemical space for the design of selective RNA ligands.

Dual Roles of Azide: Dearomative Dimerization of Furfuryl Azides

A dearomative dimerization of furfuryl azides for the construction of furfuryl triazoles is developed. As a rare leaving group, azide is capable of initiating the generation of a furfuryl cation under the Lewis acid-catalyzed conditions, followed by reacting with the other azide to realize an intermolecular [3 + 2] cycloaddition/furan ring-opening cascade. By extending the reaction time, a fragmentation reaction of resulting furfuryl triazoles occurs to afford 1H-triazoles in high yield. Control studies demonstrated that key furfuryl cations also can be obtained from furfuryl triazoles. Furthermore, a chemoselective cross-cycloaddition can be achieved between furfuryl azides and a benzyl azide.

Synthesis of New Fused 4H-Thieno[3,2-b]pyrrole Derivatives via Decomposition of Methyl 4-Azido-5-arylthiophene-2-carboxylates

This article is focused on the development of practical approaches to the synthesis of 4-azido-5-arylthiophene-2-carboxylates and 4-amino-5-arylthiophene-2-carboxylates using the Fiesselmann reaction. The photochemical and thermal (including microwave-assisted) decomposition of 4-azido-5-arylthiophene-2-carboxylates have been studied in order to synthesize fused 4H-thieno[3,2-b]pyrrole derivatives. The proposed approaches allow to obtain functionally substituted heteroacenes, which are of interest as building blocks for organic semiconductors.

Acid-catalyzed three-component addition of carbonyl compounds with 1,2,3-triazoles and indoles

A facile and efficient acid-catalyzed three-component reaction of indoles, 1-tosyl-1,2,3-triazoles and carbonyl compounds has been developed. The use of TsOH with a small amount of water significantly promoted the reaction yield. This method provided a general and one-pot approach for the synthesis of structurally diverse C3-alkylated indole derivatives. The alkylation exclusively occurred at the N² position of triazoles. Various functional groups were tolerated under the optimized simple reaction conditions.

Cyclic cis-1,3-Diamines Derived from Bicyclic Hydrazines: Synthesis and Applications

Cyclic cis-1,3-diamines are versatile building blocks frequently found in natural molecules or biologically active compounds. In comparison with widely studied 1,2-diamines, and despite their chemical similarity, 1,3-diamines have been investigated less intensively probably because of a lack of general synthetic procedures giving access to these compounds with good levels of chemo-, regio-, and stereocontrol. In this Account we will give a general overview of the biological interest of cyclic cis-1,3-diamines. We will then describe the synthesis and potential applications of these compounds with a particular focus on the work realized in our laboratory.

1 Introduction

2 Biological Relevance of the cis-1,3-Diamine Motif

3 Classical Synthetic Strategies towards cis-1,3-Diamines

4 N–N Bond Cleavage of Bicyclic Hydrazines: A Versatile Method to Access cis-1,3-Diamines

4.1 Preparation of Five-Membered Cyclic cis-1,3-Diamino Alcohols

4.2 Access to Fluorinated 1,3-cis-Diaminocyclopentanes

4.3 Synthesis of cis-1,3-Diaminocyclohexitols

4.4 Formation of Cyclic cis-3,5-Diaminopiperidines

5 Applications of Cyclic cis-1,3-Diamines

5.1 Small-Molecular RNA Binders

5.2 Fluorinated 1,3-Diamino Cyclopentanes as NMR Probes

6 Concluding Remarks

Synthesis of β-triazolylenones via metal-free desulfonylative alkylation of N-tosyl-1,2,3-triazoles

Desulfonylative alkylation of N-tosyl-1,2,3-triazoles under metal-free conditions leading to β-triazolylenones is reported here. The present study encompasses the synthesis of triazoles with a new substitution pattern in a single step from cyclic 1,3-dicarbonyl compounds and N-tosyl triazole in moderate to high yields. Our synthesis takes place with complete regioselectivity as confirmed by crystallographic analysis which is rationalized by a suitable mechanistic proposal. This method provides an efficient, versatile and straightforward strategy towards the synthesis of new functionalized 1,2,3-triazoles.

Transition-Metal-Free One-Pot Tandem Synthesis of 3-Ketoisoquinolines from Aldehydes and Phenacyl Azides

An efficient and transition-metal-free strategy for the synthesis of 3-keto-isoquinolines in one pot has been developed from the easily accessible 2-(formylphenyl)acrylates and phenacyl azides. Various substituted aldehydes and phenacyl azides were successfully employed in this transformation to furnish a variety 3-keto-isoquinolines in very good yields. A number of controlled experiments were conducted to postulate the reaction mechanism. Secondary functionalizations of 2-keto-isoquinolins were also performed to showcase the synthetic utility.

Modular Access to N-Substituted cis 5-Amino-3-hydroxypiperidines

A sequence of oxidative cleavage/reductive amination/reductive cleavage enables the preparation of N-substituted cis 5-amino-3-hydroxypiperidines from a readily available bicyclic adduct. This new route provides straightforward and versatile access to drug-relevant scaffolds or fragments.

N1-Selective alkenylation of 1-sulfonyl-1,2,3-triazoles with alkynes via gold catalysis

A N¹-selective alkenylation of 1-sulfonyl-1,2,3-triazoles with alkynes via gold catalysis is reported. N¹-Vinyl substituted 1,2,3-triazoles were selectively prepared in up to 92% yield through the sulfonyl group of 1,2,3-triazole derivatives transformed to alkenyl groups in a "one-pot two steps" manner. This method provided a new method for the synthesis of potentially biological-active vinyl-triazole building blocks.

N-2-Selective gold-catalyzed alkylation of 1-sulfonyl-1,2,3-trizoles

An efficient new method was developed to synthesis N-2-alkyl-1,2,3-trizoles via gold catalyzed alkylation of 1-sulfonyl-1,2,3-trizoles with vinyl ethers.

Various structures of complexes fabricated using transition metals and triazole ligands and their inhibition effects on xanthine luminescence

The interaction between novel transition metal complexes and xanthine luminescence was studied for the first time.

Green organocatalytic α-hydroxylation of ketones

An efficient and green method for the α-hydroxylation of substituted ketones has been developed.

2- and 3-substituted imidazo[1,2-a]pyrazines as inhibitors of bacterial type IV secretion

A novel series of 8-amino imidazo[1,2-a]pyrazine derivatives has been developed as inhibitors of the VirB11 ATPase HP0525, a key component of the bacterial type IV secretion system. A flexible synthetic route to both 2- and 3-aryl substituted regioisomers has been developed. The resulting series of imidazo[1,2-a]pyrazines has been used to probe the structure-activity relationships of these inhibitors, which show potential as antibacterial agents.

Rapid access to novel 1,2,3-triazolo-heterocyclic scaffolds via tandem Knoevenagel condensation/azide-alkyne 1,3-dipolar cycloaddition reaction in one pot

An operationally simple, one-pot, two-step cascade method has been developed to afford biologically important fused 1,2,3-triazolo-heterocyclic scaffolds from 2-alkynyl aryl(heteroaryl) aldehydes and phenacyl azides. This unique atom economical transformation engages four reactive centers (aldehyde, alkyne, active methylene, and azide) under metal-free catalysis.

The design of RNA binders: targeting the HIV replication cycle as a case study

The human immunodeficiency virus 1 (HIV-1) replication cycle is finely tuned with many important steps involving RNA-RNA or protein-RNA interactions, all of them being potential targets for the development of new antiviral compounds. This cycle can also be considered as a good benchmark for the evaluation of early-stage strategies aiming at designing drugs that bind to RNA, with the possibility to correlate in vitro activities with antiviral properties. In this review, we highlight different approaches developed to interfere with four important steps of the HIV-1 replication cycle: the early stage of reverse transcription, the transactivation of viral transcription, the nuclear export of partially spliced transcripts and the dimerization step.

Design and synthesis of anti-cancer cyclopeptides containing triazole skeleton

We describe the design and synthesis of some hypothetical heptapeptides specifically to overcome the neoplastic activity of ras oncogene and their anti-cancer activities were studied. To improve the anti-cancer activity of the synthesized peptides, their structure modifications were done based on a sequential Ugi/Huisgen 1,3-Dipolar cyclization reaction. The cyclopeptides which contained triazole skeleton showed significant anti-cancer activity against cancer cells with mutated ras oncogene such as A549, PC3 and C26 cells. This study clearly shows the importance of triazole skeleton in biological activity of the peptides. It might be possible to overcome the difficulties involved in making complex peptides by employing this elegant chemistry.

A fragment-based approach to the SAMPL3 Challenge

The success of molecular fragment-based design depends critically on the ability to make predictions of binding poses and of affinity ranking for compounds assembled by linking fragments. The SAMPL3 Challenge provides a unique opportunity to evaluate the performance of a state-of-the-art fragment-based design methodology with respect to these requirements. In this article, we present results derived from linking fragments to predict affinity and pose in the SAMPL3 Challenge. The goal is to demonstrate how incorporating different aspects of modeling protein-ligand interactions impact the accuracy of the predictions, including protein dielectric models, charged versus neutral ligands, ΔΔGs solvation energies, and induced conformational stress. The core method is based on annealing of chemical potential in a Grand Canonical Monte Carlo (GC/MC) simulation. By imposing an initially very high chemical potential and then automatically running a sequence of simulations at successively decreasing chemical potentials, the GC/MC simulation efficiently discovers statistical distributions of bound fragment locations and orientations not found reliably without the annealing. This method accounts for configurational entropy, the role of bound water molecules, and results in a prediction of all the locations on the protein that have any affinity for the fragment. Disregarding any of these factors in affinity-rank prediction leads to significantly worse correlation with experimentally-determined free energies of binding. We relate three important conclusions from this challenge as applied to GC/MC: (1) modeling neutral ligands--regardless of the charged state in the active site--produced better affinity ranking than using charged ligands, although, in both cases, the poses were almost exactly overlaid; (2) simulating explicit water molecules in the GC/MC gave better affinity and pose predictions; and (3) applying a ΔΔGs solvation correction further improved the ranking of the neutral ligands. Using the GC/MC method under a variety of parameters in the blinded SAMPL3 Challenge provided important insights to the relevant parameters and boundaries in predicting binding affinities using simulated annealing of chemical potential calculations.