key: cord-0798353-qcu38m49 authors: Al-Janabi, Ahmed S.M.; Elzupir, Amin O.; Yousef, Tarek A. title: Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases date: 2020-10-17 journal: J Mol Struct DOI: 10.1016/j.molstruc.2020.129454 sha: 3bbf9364924fbcef161f4d623730b432bae0fd5e doc_id: 798353 cord_uid: qcu38m49 New Schiff bases {N'-(phenyl(pyridin-2-yl)methylene) isonicotinohydrazide (L(1)H), N(1)-(naphthalen-1-yl)-N(2)-(phenyl(pyridin-2-yl) methylidene) ethane-1,2-diamine (L(2)H), N-(6-chlorobenzo[d]thiazol-2-yl)-1-phenyl-1-(pyridin-2-yl) methanimine (L(3)H)}were synthesized by reaction of 2-benzoylpyridine with different amines (2-amino-6-chlorobenzothiazole, isonicotinohydrazide and N(1)-(naphthalen-1-yl)ethane-1,2-diamine) and characterized by (1)H-NMR, (13)C-NMR, IR mass spectroscopy and elemental analysis. The compounds were assayed by the disc diffusion method for anti-bacterial against five pathogenic bacteria species (Staphylococcus aureus, Micrococcus luteus, Staphylococcus pyogenes, Bacillus subtilis, and E. coli). All prepared Schiff bases showed good activity compared to positive control (streptomycin), Moreover the L(3)H showed the highest activity against S. aureus, and M. luteus than the other compounds and streptomycin. In additional molecular docking studies with 3-chymotrypsin-like protease (3CLpro), the essential enzyme for SARS-CoV-2 proliferation. The rest of compounds have shown promising results as 3CLpro inhibitors interacting with the active sites of the enzymes. Finally, DFT 's estimated electrostatic molecular potential results were used to illustrate the molecular docking findings. The DFT calculations showed that L(3)H has the highest dipole moment and electrophilicity index. Interestingly, L(2)H of the largest energy gap ∆E = 2.49 eV, there are several hydrophilic interactions that could facilitate the binding with the receptors. All of these parameters could be shared to significantly affect the protein sites of binding affinity with different extent. Novel coronavirus has arisen as an infectious disease and spread rapidly throughout the world and is transmitted mainly through contact with contaminated saliva droplets or by nose discharge while Patients diagnosed with cough or sneeze. Human coronaviruses were first described in the mid-1960s [1, 2] . Coronaviruses belong to the Coronaviridae family, a family of single stranded enveloped-positive sense RNA viruses. In addition, the Coronaviridae family was divided into four genera: α, β, γ, and δ. Coronaviruses of ubiquitous and genera commonly infect mammals and humans while birds are primarily infected by the form and generations. That specification is in line with coronavirus phylogenetic analysis and genome structure [3] . Computational features of the novel coronavirus [4, 5] or more generally new testable theories for standard drugs involved. A virtual screening technique has recently been performed to identify the active site on the viral protease for the binding of many natural compounds by molecular docking and cell-based assays [6] . Our research group recently concentrated on determining the molecular geometry of synthesized materials by comparing the desired properties from experimental evaluation to estimated parameters from computational calculations [7] . Schiff bases have been reported to possess a wide range of biological properties such as being anti-tumor, antiviral, anti-bacterial, anti-fungal and anti-inflammatory etc. [8] Schiff bases containing N, S, and O atoms in structures show an important role in biological systems because they have unusual electronic properties [9] . 2-phenylquinazoline-4(3)H-one Schiff bases are confirmed to have antiviral activity against certain strains of viruses, such as feline corona virus, influenza Viruses, and type 1 and type 2 herpes simplex viruses [10] . From published literature, the antiviral ability of these Schiff bases is evident and thus further focused work will help to discover and improve new potential lead compounds to use them as drug candidates. Recently a novel SARS-CoV-2 virus properly originated from bat was reported, cause the severe acute respiratory syndrome, known as COVID-19 [11] [12] [13] . The enzyme 3chymotrypsin-like protease (3CL pro ) cleaves at least 11 sites on the polyproteins translated from the viral RNA of SARS-CoV-2. Thus, the compounds having ability to inhibit this enzyme can be considering as an effective therapeutic agent for COVID-19. This work describes the synthesis and spectroscopic characterization of new Schiff bases and evaluated as anti-bacterial, besides, the synthetic compounds have also been studied as 3CLpro inhibitors. L 3 H was prepared by a similar method to that of L 1 H using 2-amino-6chlorobenzothiazole in place of isonicotinohydrazide. The anti-bacterial activities of the complexes were tested by agar disc diffusion method originally described by Bauer [14] against five bacteria types, Nutrient broth for bacteria by the two-fold serial dilution method [15] . The bacterial suspension was attuned with sterile saline to a concentration of 1*10 -5 -10 -6 CFU. The tested compounds and standard control (Streptomycin) were prepared by two-fold serial dilution to obtain the essential concentrations of 200, 100, 50, 25, 12.5 and 6.25 g/mL. The tubes were incubated in incubators at 37 C. The MICs were recorded by visual observations after 24 h. The three-dimensional structures of the L 1 H, L 2 H, and L 3 H were generated and optimized by Gaussian 09 program package [16] software. The crystal structure of 3CL pro of SARS-CoV-2 was obtained from the Protein Data Bank database (PDB ID: 6Y2E). Molecular docking experiments were carried out using the AutoDock Vina tool plugin UCSF Chimera software (v 1.14), adopting the default values for the parameters, and a grid box (-16 × -24.0 × 17) Å was centered at (35, 65, 65) Å. In order to represents the real environment, water was added as a solvent, with accessible surface area of 14358.5. The predicted binding affinity score was explored utilizing the View Dock tool. The binding to active sites and images were processed by the UCSF Chimera [17] [18] [19] . The Schiff bases have been synthesized by condensation of 2-benzoylpyridine with 2amino-6-chlorobenzothiazole or isonicotinohydrazide or N 1 -(naphthalen-1-yl)ethane-1,2-diamine to afford a dark creamy with L 1 H, light brown-yellow in L 2 H, and a brownish yellow with L 3 H (Scheme 1). The prepared Schiff bases are stable in air and soluble in EtOH, DMSO and DMF. The compounds were characterized by using elemental analysis, 1 H, 13 C NMR, and IR techniques. All attempts to get crystals suitable for X-ray diffraction studies were unsuccessful. The IR spectra of the prepared Schiff bases (Fig. 1 ) displayed a strong band within the 1627-1639 cm -1 range for the azomethine group (C=N) [20] [21] [22] . And disappeared the (C=O) of 2-phenylpyridine, and (NH2)sy, asy stretching vibration of amine, indicates the formation of the proposed compounds. The (C=C) vibration of the aromatic rings showed within the 1529-1554 cm -1 range [22] . The spectra of L 1 H and L 2 H displayed a medium band at 3110cm -1 and 3131cm -1 assigned to the (N-H). And the L 1 H spectrum appeared the (C=O) of isonicotine group at 1668cm -1 [23] Also the spectrum of L 2 H showed the stretching vibration of aliphatic group at 2945cm -1 [22] . Other vibrations are listed in experimental section. The 1 H-NMR spectrum of L 1 H in DMSO-d6 displayed the NH proton at 11.53 ppm as a singlet peak. And four doublet peaks at 8.92ppm, 7.92ppm, 7.71ppm and 7.62ppm, assigned to the H15,16, H14,17, H4, and H2, corresponding to 2,1,2,1 protons respectively. Also the spectrum showed two doublet of doublets peaks at 8.74ppm, and 8.12ppm for the H1 and H3, respectively. A multiplet peak was showed at 7.39ppm assigned to protons in position 8-12 (phenyl ring) (Fig. SI1, supporting information). The 1 H-NMR spectrum of L 2 H (Fig 2) , clearly display the phenyl protons belong to the pyridyl, phenyl and naphthyl rings. A two doublet peaks displayed at 7.21ppm and 7.32ppm due to a H14 and H19,22, corresponding to one and two protons, respectively. And two doublet of doublet of doublets at 8.72ppm, and 8.07ppm for the H2 and H3, respectively. Also the spectrum displayed two multiplets peaks at 7.98ppm and 7.67ppm, due to the protons in position (1, 4, 15, 16) and (9) (10) (11) , respectively. The protons in position 20 and 21 appeared as doublet of doublets at 7.01ppm (JHH = 7.8 Hz). And the H8,12 showed as triplet peak at 7.54ppm with coupling constant to the neighboring protons (JHH = 7.7 Hz). The NH proton was showed at 7.43 ppm as a singlet peak, whereas the methylene groups displayed as two singlet at 2.302 and 2.295 ppm, due to the NH-CH2 and CH2N=C, respectively, corresponding to four protons. The 1 H-NMR spectrum of L 3 H in DMSO-d6 showed two doublet of doublets peaks at 8.80ppm, and 7.98ppm for the H1 and H3, respectively. And two doublet peaks at 7.72ppm, and 7.56ppm, due to the H4 and H2, corresponding to one proton of each peak, respectively. Also the spectrum showed two multiplet peaks were showed at 7.56ppm and 7.36ppm due to protons in position (8, 12, 15, 16) and (9) (10) (11) . The H18 was showed as a singlet peak at 8.12ppm (Fig. SI 3, supporting information). The above results were supported by 13 C NMR and elemental analysis data (Fig. 3) . (Fig. SI 2 and 4, supporting information) . The MICs are given in Table 2 At B3LYP 6-311G (d,p) basis set, the theoretical DFT calculations were carried out in gas phase by DFT method. The results of the theoretical DFT calculations for all the compounds under investigation (Figs 4-6) showed the non-planarity. Table 3 summarizes the approximate calculations of DFT for Electronic Energy, Heat Capacity, Entropy (S), Thermal Energy, polarizability, and dipole moment of L 1 H, L 2 H, and L 3 H. binding, of all the major thermodynamic variables calculated for proteins. It gives entropy and enthalpy a temperature dependency which will alter their signs and determine which of them will dominate. The heat capacity order is as follows: L 3 H < L 1 H < L 2 H. The unfolding protein typically has a positive Cp, which results in optimum stability and often cold denaturation [26] . The frontier molecular orbitals (FMO) can provide objective qualitative information about the HOMO electrons being susceptible to transfer to the LUMO. In addition, HOMO and LUMO are very useful quantum chemical parameters to assess the molecules' reactivity and are used to measure other parameters, such as the descriptors for chemical reactivity. The energies of the studied compounds' HOMOs and LUMOs were measured using DFT method at the base set of B3LYP 6-311 G (d, p) and are tabled in Table 5 . The isodensity surface plots of HOMO and LUMO for L 1 H, L 2 H, and L 3 H are shown in Fig. 5 . The results of the FMOs energy analysis revealed that the energies of HOMOs of L 3 H is higher compared with L 1 H and L 2 H. However, the destabilization of the LUMO level is found to be higher in L 3 H than the others. Consequently, the energy gap is in the order of L 1 H < L 3 H < L 2 H. This suggests that such hydrophilic interactions considerably impact the binding affinity of such small drugs to the receptors. The HOMO of a certain drug and the LUMO with the adjacent residues could share the orbital interactions during the binding process. Calculations, such as the energy of the highest occupied molecular orbital, µ= -χ =1/2 (ELUMO + EHOMO) S =1/2 η (4) The inverse value of the global hardness is designed as the softness (σ) as follow: The molecular electrostatic potential (MEP) is important to quantify in order to validate the evidence regarding the reactivity of the compounds studied as inhibitors. Even though the MEP provides an indication of the molecular size and shape of both the positive, negative and neutral electrostatic potential. This may be a method for predicting relationships of physicochemical properties with the molecular structure of the drugs being investigated. In addition, the electrostatic molecular potential is a valuable method for estimating drug reactivity against electrophilic and nucleophilic attacks. Under the same base sets, the molecular electrostatic potential of the L 1 H, L 2 H, and L 3 H is determined using the same process and is seen in Fig. 6 . The maximum negative area within the MEP is the chosen electrophilic attack sites, indicated as red color. So, the negatively charged sites, and the reverse satiation for the blue regions, should draw an attacking electrophile. It is apparent that the molecular size and shape as well as the orientation of the negative, positive, and neutral electrostatic potential differed by product due to the type of atoms and their electronic existence. The difference in mapping the electrostatic potential around the compound may be primarily responsible for variation of its binding receptor affinities. The Mulliken atomic charges of the estimated compounds (1-3) were calculated the DFT using B3LYP 6-311G (d,p) at a basis set, the data were tabulated in inhibitors. Serial interval of novel coronavirus (COVID-19) infections Emerging understanding of etiology and epidemiology of the novel coronavirus (COVID-19) China Novel Coronavirus I, Research T. A novel coronavirus from patients with pneumonia in China In silico oncology drug repositioning and polypharmacology Computational network biology: Data, model, and applications In silico and in vitro analysis of small molecules and natural compounds targeting the 3CL protease of feline infectious peritonitis virus N-alkyl 2-pyridone versus O-alkyl 2-pyridol: Ultrasonic synthesis, DFT, docking studies and their antimicrobial evaluation A new chiral Boron-dipyrromethene (BODIPY)-based fluorescent probe: Molecular docking, DFT, antibacterial and antioxidant approaches Computational and molecular docking approaches of a New axially chiral BODIPY fluorescent dye Synthesis, antiviral activity and cytotoxicity evaluation of Schiff bases of some 2-phenyl quinazoline-4(3)H-ones Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin The 2019-new coronavirus epidemic: evidence for virus evolution Single-Disk Antibiotic-Sensitivity Testing Staphylococci Gaussian 09, Revision a. 02 UCHIME improves sensitivity and speed of chimera detection UCSF Chimera-a visualization system for exploratory research and analysis AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading Ligational behavior of Schiff bases towards transition metal ion and metalation effect on their antibacterial activity Synthesis, characterization, fluorescence and catalytic activity of some new complexes of unsymmetrical Schiff base of 2-pyridinecarboxaldehyde with 2,6-diaminopyridine Spectrometric Identification of Organic Compounds Schiff bases of indoline-2,3-dione (isatin) derivatives and nalidixicacidcarbohydrazide, synthesis, antitubercular activity and pharmacophoricmodelbuilding Synthesis and antimycobacterial activity of some coupling products from 4-aminobenzoic acid hydrazones Synthesis and antibacterial screening of hydrazones, Schiff and Mannich bases of isatin derivatives Heat capacity in proteins Specific interactions between tauprotein and curcumin derivatives: Molecular docking and abinitio molecular orbital simulations DFT investigations of linear Zn3-typecomplexwithcompartmentalN/O-donor Schiff base: Synthesis, characterizations, crystal structure, fluorescence and molecular docking Spectroscopic identification, structural features, Hirshfeld surface analysis and molecular docking studies on stiripentol: An orphan antiepileptic drug Quantum chemical calculations, experimental investigations and DNA studies on (E)-2-((3-hydroxynaphthalen-2-yl) methylene)-N-(pyridin-2-yl) hydrazinecarbothioamide and its Mn (II) Semiempirical studies, spectral analysis, in vitro antibacterial and DNA degradation studies of heterocyclic thiosemicarbazone ligand and its metal complexes Structural, optical, morphology characterization and DFT studies of nano sized Cu (II) complexes containing schiff base using green synthesis Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors The authors declare no conflict of interest.