Design of a fused triazolyl 2-quinolinone unnatural nucleoside via tandem CuAAC-Ullmann coupling reaction and study of photophysical property

Targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) with synthetic/designer unnatural nucleoside analogs: an in silico study

CONTEXT

Since the outbreak of COVID-19 in December 2019, it developed into a pandemic affecting all the countries and millions of people around the globe. Until now, there is no medicine available to contain the spread of the virus. As an aid to drug discovery, the molecular docking and molecular dynamic tools were applied extensively. In silico studies made it possible for rapid screening of potential molecules as possible inhibitors/drugs against the targeted proteins. As a continuation of our drug discovery research, we have carried out molecular docking studies of our 12 reported unnatural nucleosides and 14 designer Avigan analogs with SARS-CoV-2, RNA-dependent RNA polymerase (RdRp), which we want to report herein. The same calculation was also carried out, taking 11 known/under trail/commercial nucleoside drug molecules for a comparison of the binding interactions in the catalytic site of RdRp. The docking results and binding efficiencies of our reported nucleosides and designer nucleosidic were compared with the binding energy of commercially available drugs such as remdesevir and favipiravir. Furthermore, we evaluated the protein-drug binding efficiency and stability of the best docked molecules by molecular dynamic studies (MD). From our study, we have found that few of our proposed drugs show promising binding efficiency at the catalytic pocket of SARS-CoV-2 RdRp and can be a promising RdRp inhibitor drug candidate. Hence, this study will be of importance to make progress toward developing successful nucleoside-based drugs and conduct the antiviral test in the wet lab to understand their efficacy against COVID-19.

METHOD

All the docking studies were carried out with AutoDock 4.2, AutoDock Vina and Molegro Virtual Docker. Following the docking studies, the MD simulations were carried out following the standard protocol with the GROMACS ver. 2019.6. by applying the CHARMM36 all-atom biomolecular force field. The drug-protein interaction was studied using the Biovia Discovery Studio suite, Ligplot software, and Protein-Ligand Interaction Profiler (PLIP).

Synthesis and photophysical characterization of fluorescent indole nucleoside analogues

Fluorescent nucleosides are useful chemical tools for biochemical research and are frequently incorporated into nucleic acids for a variety of applications. The most widely utilized fluorescent nucleoside is 2-aminopurine-2'-deoxyribonucleoside (2APN). However, 2APN is limited by a moderate Stokes shift, molar extinction coefficient, and quantum yield. We recently reported 4-cyanoindole-2'-deoxyribonucleoside (4CIN), which offers superior photophysical characteristics in comparison to 2APN. To further improve upon 4CIN, a focused library of additional analogues combining the structural features of 2APN and 4CIN were synthesized and their photophysical properties were quantified. Nucleosides 2-6 were found to possess diverse photophysical properties with some features superior to 4CIN. In addition, the structure-function relationship data gained from 1-6 can inform the design of next-generation fluorescent indole nucleosides.

One-pot construction of carbohydrate scaffolds mediated by metal catalysts

Owing to the environmental concern worldwide and also due to cost, time and labour issues, use of one-pot reactions [domino/cascade/tandem/multi-component (MC) or sequential] has gained much attention among the scientific and industrial communities for the generation of compound libraries having different scaffolds. Inclusion of sugars in such compounds is expected to increase the pharmacological efficacy because of the possibility of better interactions with the receptors of such unnatural glycoconjugates. In many of the one-pot transformations, the presence of a metal salt/complex can improve the reaction/change the course of reaction with remarkable increase in chemo-/regio-/stereo-selectivity. On the other hand because of the importance of natural polymeric glycoconjugates in life processes, the development and efficient synthesis of related oligosaccharides, particularly utilising one-pot MC-glycosylation techniques are necessary. The present review is an endeavour to discuss one-pot transformations involving carbohydrates catalysed by a metal salt/complex.

Synthetic and computational studies on CuI/ligand pair promoted activation of C(Aryl)-Cl bond in C-N coupling reactions

Cu/ligand-mediated coupling reactions have been widely investigated in the recent past. However, activation of cheaper aryl chlorides is still a great limitation of these reactions. During the course of present investigations efforts have been made to develop a normal and facile CuI/ligand pair protocol for arylation of phthalimide using aryl chlorides. The protocol has also been extended for arylation of amines. On the basis of experimental and theoretical results, a catalytic cycle has also been proposed and it has been established that these reactions follow oxidative addition-reductive elimination (OA-RE) pathway. These studies have indicated that tetracoordinated [Cu(L1)(L2)]⁺ complex is active catalytic species in these reactions.

Guanine and 8-Azaguanine in Anomeric DNA Hybrid Base Pairs: Stability, Fluorescence Sensing, and Efficient Mismatch Discrimination with α-d-Nucleosides

The α-anomers of 8-aza-2'-deoxyguanosine (αG_d*) and 2'-deoxyguanosine (αG_d) were site-specifically incorporated in 12-mer duplexes opposite to the four canonical DNA constituents dA, dG, dT, and dC. Oligodeoxyribonucleotides containing αG_d* display significant fluorescence at slightly elevated pH (8.0). Oligodeoxyribonucleotides incorporating β-anomeric 8-aza-2'-deoxyguanosine (G_d*) and canonical dG were studied for comparison. For αG_d* synthesis, an efficient purification of anomeric 8-azaguanine nucleosides was developed on the basis of protected intermediates, and a new αG_d* phosphoramidite was prepared. Differences were observed for sugar conformations ( N vs S) and p K_a values of anomeric nucleosides. Duplex stability and mismatch discrimination were studied employing UV-dependent melting and fluorescence quenching. A gradual fluorescence change takes place in duplex DNA when the α-nucleoside αG_d* was positioned opposite to the four canonical β-nucleosides. The strongest fluorescence decrease appeared in duplexes incorporating αG_d*-C_d base pair matches. Decreasing fluorescence corresponds to increasing T_m values. For mismatch discrimination, the α-anomers αG_d* and αG_d are more efficient than the corresponding β-nucleosides. Duplexes with single "purine-purine" αG_d*-αG_d* or αG_d-αG_d base pairs are significantly more stable than those displaying β-d configuration. CD spectra indicate that single mutations by α-anomeric nucleosides do not affect the global structure of B-DNA.