In Silico

To identify the ligand that binds to a target protein with high affinity is a nontrivial task in computer-assisted approaches. Antiviral drugs have been identified for NS2B/NS3 protease enzyme on the mechanism to cleave the viral protein using the computational tools. The consequence of the molecular docking, free energy calculations, and simulation protocols explores the better ligand. It provides in-depth structural insights with the catalytic triad of His51, Asp75, Ser135, and Gly133. The MD simulation was employed here to predict the stability of the complex. The alanine mutation has been performed and its stability was monitored by using the molecular dynamics simulation. The minimal RMSD value suggests that the derived complexes are close to equilibrium. The DFT outcome reveals that the HOMO-LUMO gap of Ligand19 is 2.86 kcal/mol. Among the considered ligands, Ligand19 shows the lowest gap and it is suggested that the HOMO of Ligand19 may transfer the electrons to the LUMO in the active regions. The calculated binding energy of Ligand19 using the DFT method is in good agreement with the docking studies. The pharmacological activity of ligand was performed and satisfies Lipinski rule of 5. Moreover, the computational results are compared with the available IC50 values of experimental results

Acid/Base and H₂PO₄^– Controllable High-Contrast Optical Molecular Switches with a Novel BODIPY Functionalized [2]Rotaxane

A novel multifunctional mechanically interlocked switchable [2]­rotaxane <b>R4</b> containing two molecular stations and rotaxane arms terminated with boron-dipyrromethene (BODIPY) fluorophores and its derivatives were synthesized for the first time by CuAAC click reaction. The shuttling motion of macrocycle between the dibenzylammonium and triazolium recognition sites and the distance dependent photoinduced electron transfer process of <b>R4</b> is demonstrated by utilizing external chemical stimuli (acid/base). Interestingly, the reversible self-assembly process of <b>R4</b> was recognized by the acid–base molecular switch strategy. Notably, two symmetrical triazolium groups acted as molecular stations, H₂PO₄^– receptors, and H-bonded donors. Both [2]­rotaxane <b>R4</b> and thread <b>R2</b> demonstrated excellent optical responses and high selectivity toward H₂PO₄^– ion. The specific motion and guest–host interactions of mechanically interlocked machines (MIMs) were also further explored by quantum mechanical calculations. The thread <b>R2</b> also demonstrated to enable the detection of H₂PO₄^– in RAW 264.7 cells successfully