Naphthalene-based bis-N-salicylidene aniline dyes: Crystal structures, Hirshfeld surface analysis, computational study and molecular docking with the SARS-CoV-2 proteins

In this work, we report structural and computational studies of a series of naphthalene-based bis-N-salicylidene aniline dyes, namely N,N′-bis-salicylidene-1,5-diaminonaphthalene (1), N,N′-bis(3-hydroxysalicylidene)-1,5-diaminonaphthalene (2) and N,N′-bis(3-methoxysalicylidene)-1,5-diaminonaphthalene (3). For 3, two polymorphs are known, namely 3red and 3yellow. Both polymorphs of 3 were analyzed and discussed. All the molecules adopt an enol-imine tautomer, stabilized by two intramolecular O–H[Formula: see text] N hydrogen bonds. The structure of 2 is further stabilized by a couple of additional O–H[Formula: see text] O hydrogen bonds and by intermolecular O–H[Formula: see text] O interactions, yielding a 1D zig-zag supramolecular chain. Molecules of 2, 3red and 3yellow are interlinked through intermolecular C–H[Formula: see text] π interactions, while the crystal packing of 1 and 2 is also described by intermolecular π[Formula: see text] π interactions. More than 90% of the total Hirshfeld surface area for all the discussed molecules is occupied by H[Formula: see text] H, H[Formula: see text] C, H[Formula: see text] O and C[Formula: see text] C contacts. The polymorphs 3red and 3yellow, despite being chemically the same, differ geometrically, thus yielding remarkably different Hirshfeld surfaces. The Hirshfeld surface of 3yellow is very similar to that of 2. All structures are mainly characterized by the dispersion energy framework followed by the less significant electrostatic energy framework contribution. Molecular docking studies were employed to inspect the effect of 1–3 on the SARS-CoV-2 protein targets. The docking analysis revealed that the dye 2 showed the best binding energies toward Papain-like protease (PLpro, –10.40 kcal/mol), nonstructural protein 14 (nsp14 (N7-MTase), –10.10 kcal/mol), RdRp-RTP (–9.70 kcal/mol) and nonstructural protein 3 (nsp3_range 207-379-MES, –9.30 kcal/mol). The obtained results can give an insight into chemical and biological activities of the studied molecules that could aid in designing of potent reagents SARS-CoV-2. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13738-021-02438-y.