Pyrido[1,2-e]purine: Design and Synthesis of Appropriate Inhibitory Candidates against the Main Protease of COVID-19

Design and synthesis of novel main protease inhibitors of COVID-19: quinoxalino[2,1-b]quinazolin-12-ones

The COVID-19 pandemic represents a substantial global challenge, being a significant cause of mortality in numerous countries. Thus, it is imperative to conduct research to develop effective therapies to combat COVID-19. The primary aim of this study is to employ a two-step tandem reaction involving 2,3-dichloroquinoxaline and 2-amino-N-substituted benzamides in alkaline media/DMF at an elevated temperature to design and synthesize a series of polycyclic derivatives endowed with quinoxalino[2,1-b]quinazolin-12-one framework. Following synthesis, the newly synthesized heterocycles were evaluated for their potential as inhibitors of the main protease of SARS-CoV-2 by means of molecular docking and dynamic simulation techniques. The in silico investigation demonstrated that all tested compounds effectively establish stable binding interactions, primarily through multiple hydrogen bonding and hydrophobic interactions, at the active site of the enzyme. These findings offer crucial structural insights that can be employed in future endeavors toward designing potent inhibitors targeting the main protease (Mpro). Among the investigated compounds, the p-tolylamino-substituted quinoxalino[2,1-b]quinazolinone derivative exhibited the most promise as an inhibitor of the main protease in COVID-19. Consequently, it warrants further investigation both in vitro and in vivo to identify it as a prospective candidate for anti-SARS-CoV-2 drug development.

Insight into crystal structures and identification of potential styrylthieno[2,3-b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach

Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.

Synthesis, molecular docking and dynamics studies of pyridazino[4,5-b]quinoxalin-1(2H)-ones as targeting main protease of COVID-19

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a crisis in public health. Because, the 3CLpro, the main protease of SARS-CoV-2, possesses a critical role in coronavirus replication, many efforts have been devoted to developing various inhibitors to prevent the fast spread of COVID-19. In the current work, a number of various pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives bearing thiadiazine and thiadiazole fragments has been prepared via a straightforward and practical strategy involving the reaction of 2-(ethoxycarbonyl)-3-formylquinoxaline 1,4-dioxide with thiocarbohydrazide under reflux conditions. To determine the bioavailability of pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives, Lipinski's rule of five has been carried out. Regarding this rule, none of the synthesized compounds exhibit any deviation from Lipinski's rule of five. Furthermore, molecular docking and molecular dynamics approaches have been implemented to figure out the potential interactions of products with SARS-CoV-2 main protease. The outcomes of molecular docking studies demonstrate that the phenyl and nitrophenyl substituted pyridazino[4,5-b]quinoxalin-1(2H)-one show the lowest binding affinity among the other compounds, indicating a favorable orientation in the active site of the chymotrypsin-like cysteine protease. In addition, the MD simulation performed to evaluate the stability of the protein-ligand complex represents that the average binding energy of the nitrophenyl complex is less than that of the phenyl complex. Therefore, according to the in silico results, the inhibitory effect of the nitrophenyl complex is more significant than the phenyl complex.Communicated by Ramaswamy H. Sarma.