A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure, HSA/DFT/XRD and cytotoxicity

Synthesis, crystal structure and Hirshfeld surface of ethyl 2-[2-(methyl-sulfan-yl)-5-oxo-4,4-diphenyl-4,5-di-hydro-1H-imidazol-1-yl]acetate (thio-phenytoin derivative)

The di-hydro-imidazole ring in the title mol-ecule, C20H20N2O3S, is slightly distorted and the lone pair on the tri-coordinate nitro-gen atom is involved in intra-ring π bonding. The methyl-sulfanyl substituent lies nearly in the plane of the five-membered ring while the ester substituent is rotated well out of that plane. In the crystal, C-H⋯O hydrogen bonds form inversion dimers, which are connected along the a- and c-axis directions by additional C-H⋯O hydrogen bonds, forming layers parallel to the ac plane. The major contributors to the Hirshfeld surface are C⋯H/H⋯C, O⋯H/H⋯O and S⋯H/H⋯S contacts at 20.5%, 14.7% and 4.9%, respectively.

Synthesis, crystal structure and Hirshfeld surface analysis of 1-[3-(2-oxo-3-phenyl-1,2-di-hydro-quinoxalin-1-yl)prop-yl]-3-phenyl-1,2-di-hydro-quinoxalin-2-one

In the title compound, C31H24N4O2, the di-hydro-quinoxaline units are both essentially planar with the dihedral angle between their mean planes being 64.82 (4)°. The attached phenyl rings differ significantly in their rotational orientations with respect to the di-hydro-quinoxaline planes. In the crystal, one set of C-H⋯O hydrogen bonds form chains along the b-axis direction, which are connected in pairs by a second set of C-H⋯O hydrogen bonds. Two sets of π-stacking inter-actions and C-H⋯π(ring) inter-actions join the double chains into the final three-dimensional structure.

Synthesis, crystal structure and Hirshfeld surface analysis of 2-phenyl-3-(prop-2-yn-1-yl-oxy)quin-oxaline

In the title compound, C17H12N2O, the quinoxaline moiety shows deviations of 0.0288 (7) to -0.0370 (7) Å from the mean plane (r.m.s. deviation of fitted atoms = 0.0223 Å). In the crystal, corrugated layers two mol-ecules thick are formed by C-H⋯N hydrogen bonds and π-stacking inter-actions.

Crystal structure and Hirshfeld surface analysis of ethyl 2-(7-chloro-3-methyl-2-oxo-1,2-di-hydro-quinoxalin-1-yl)acetate

The quinoxaline moiety in the title mol-ecule, C13H13ClN2O3, is almost planar (r.m.s. deviation of the fitted atoms = 0.033 Å). In the crystal, C-H⋯O hydrogen bonds plus slipped π-stacking and C-H⋯π(ring) inter-actions generate chains of mol-ecules extending along the b-axis direction. The chains are connected by additional C-H⋯O hydrogen bonds. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (37.6%), H⋯O/O⋯H (22.7%) and H⋯Cl/Cl⋯H (13.1%) inter-actions.

Recent Methods for the Synthesis of Quinoxaline Derivatives and their Biological Activities

Quinoxaline derivatives have been incorporated into numerous marketed drugs used for the treatment of various diseases. Examples include glecaprevir (Mavyret), voxilaprevir (Vosevi), Balversa (L01EX16) (erdafitinib), carbadox, XK469R (NSC698215), and becampanel (AMP397). These quinoxaline derivatives exhibit a diverse range of pharmacological activities, including antibacterial, antitubercular, antiviral, anti-HIV, anti-inflammatory, antifungal, anticancer, antiproliferative, antitumor, kinase inhibition, antimicrobial, antioxidant, and analgesic effects. Recognizing the significance of these bioactive quinoxaline derivatives, researchers have dedicated their efforts to developing various synthetic methods for their production. This review aimed to compile the most recent findings on the synthesis and biological properties of quinoxaline derivatives from 2015 to 2023.

Synthesis and in Silico Investigation of Organoselenium-Clubbed Schiff Bases as Potential Mpro Inhibitors for the SARS-CoV-2 Replication

Since the first report of the organoselenium compound, ebselen, as a potent inhibitor of the SARS-CoV-2 Mpro main protease by Z. Jin et al. (Nature, 2020), different OSe analogs have been developed and evaluated for their anti-COVID-19 activities. Herein, organoselenium-clubbed Schiff bases were synthesized in good yields (up to 87%) and characterized using different spectroscopic techniques. Their geometries were studied by DFT using the B3LYP/6–311 (d, p) approach. Ten FDA-approved drugs targeting COVID-19 were used as model pharmacophores to interpret the binding requirements of COVID-19 inhibitors. The antiviral efficiency of the novel organoselenium compounds was assessed by molecular docking against the 6LU7 protein to investigate their possible interactions. Our results showed that the COVID-19 primary protease bound to organoselenium ligands with high binding energy scores ranging from −8.19 to −7.33 Kcal/mol for 4c and 4a to −6.10 to −6.20 Kcal/mol for 6b and 6a. Furthermore, the docking data showed that 4c and 4a are good Mpro inhibitors. Moreover, the drug-likeness studies, including Lipinski’s rule and ADMET properties, were also assessed. Interestingly, the organoselenium candidates manifested solid pharmacokinetic qualities in the ADMET studies. Overall, the results demonstrated that the organoselenium-based Schiff bases might serve as possible drugs for the COVID-19 epidemic.

Crystal structure and Hirshfeld surface analysis of N-(2,6-di-methyl-phen-yl)-2-[3-hy-droxy-2-oxo-3-(2-oxoprop-yl)indolin-1-yl]acetamide

The cup-shaped conformation of the title mol-ecule, C21H22N2O4, is largely determined by an intra-molecular N-H⋯O hydrogen bond. In the crystal, double layers of mol-ecules are formed by O-H⋯O and C-H⋯O hydrogen bonds. A Hirshfeld surface analysis was performed, which confirms the regions that are active for inter-molecular inter-actions.

Crystal structure and Hirshfeld surface analysis of 2-azido-N-(4-fluoro-phen-yl)acetamide

The asymmetric unit of the title compound, C8H7FN4O, consists of two independent mol-ecules differing in the orientation of the azido group. Each mol-ecule forms N-H⋯O hydrogen-bonded chains along along the c-axis direction with its symmetry-related counterparts and the chains are connected by C-F⋯π(ring), C=O⋯π(ring) and slipped π-stacking inter-actions. A Hirshfeld surface analysis of these inter-actions was performed.

Crystal structure of ethyl 2-{4-[(2-oxo-3-phenyl-1,2-di-hydro-quinoxalin-1-yl)meth-yl]-1H-1,2,3-triazol-1-yl}acetate

The quinoxaline portion of the title mol-ecule, C21H19N5O3, is not quite planar as indicated by a dihedral angle of 3.38 (7)° between the constituent rings. The mol-ecule is 'U-shaped', which is consolidated by an intra-molecular anti-parallel carbonyl electrostatic inter-action with C··O distances of 2.8905 (16) and 3.0221 (15) Å, in the crystal forms corrugated layers through C-H⋯O and C-H⋯N hydrogen bonds and C-H⋯π(ring) and π-stacking inter-actions.

2-Azido-N-(4-methyl-phen-yl)acetamide

The asymmetric unit of the title compound, C9H10N4O, comprises three independent mol-ecules, two pairs of which differ significantly in the rotational orientation of the azido group and one pair having very similar conformations; the N-N-C-C torsion angles are -173.9 (2), -102.7 (2) and -173.6 (2)°. In the crystal, each independent mol-ecule forms N-H⋯O hydrogen bonds with its glide-plane-related counterparts, forming zigzag chains extending along the c-axis direction.

Crystal structure and Hirshfeld surface analysis of 2-chloro-N-(4-meth-oxy-phen-yl)acetamide

In the title mol-ecule, C9H10ClNO2, the meth-oxy group lies very close to the plane of the phenyl ring while the acetamido group is twisted out of this plane by 28.87 (5)°. In the crystal, a three-dimensional structure is generated by N-H⋯O, C-H⋯O and C-H⋯Cl hydrogen bonds plus C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis of the inter-molecular inter-actions was performed and indicated that C⋯H/H⋯C inter-actions make the largest contribution to the surface area (33.4%).

Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2

A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.

Crystal structure and Hirshfeld surface analysis of (E)-3-benzyl-idene-4-oxo-penta-noic acid

The asymmetric unit of the title mol-ecule, C12H12O3, contains two independent mol-ecules having opposite conformations and each forming self-dimers through complementary O-H⋯O hydrogen bonds. These dimers are linked by weak C-H⋯π inter-actions and C-H⋯O hydrogen bonds into a three-dimensional structure in which one can discern layers parallel to the bc plane. A Hirshfeld surface analysis of the inter-molecular inter-actions is included.

Synthesis of indole-based oxadiazoles and their interaction with bacterial peptidoglycan and SARS-CoV-2 main protease: In vitro, molecular docking and in silico ADME/Tox study

In the present study, Indole-based-oxadiazole (1A-17A) compounds were successfully synthesized. The structures of all synthesized compounds were fully characterized by different sophisticated spectroscopic techniques such 1H NMR, 13C NMR, and HREI-MS. Further, the synthesized compounds were explored to investigate their broad-spectrum antibacterial and antibiofilm potential against multidrug resistant Pseudomonas aeruginosa (MDR-PA) and methicillin resistant Staphylococcus aureus (MRSA). The compounds possessed a broad spectrum of antibacterial activity having MIC values of values 1–8 mg/ml against the tested microorganisms. Compound A6 and A7 shows maximum antibacterial activity against MDR-PA, whereas A6, A7 and A11 shows highest activity against MRSA. Furthermore, antibiofilm assay shows that A6, A7 and A11 showed maximum inhibition of biofilm formation and it was found that at 4 mg/ml; A6, A7 and A11 inhibit MRSA biofilm formation by 81.1, 77.5 and 75.9%, respectively; whereas in case of P. aeruginosa; A6 and A7 showed maximum biofilm inhibition and inhibit biofilm formation by 81.5 and 73.7%, respectively. Molecular docking study showed that compounds A6, A7, A8, A10, and A11 had high binding affinity to bacterial peptidoglycan, indicating their potential inhibitory activity against tested bacteria, whereas A6 and A11 were found to be the most effective inhibitors of SARS CoV-2 main protease (3CLpro), with a binding affinity of − 7.78 kcal/mol. Furthermore, SwissADME and pkCSM-pharmacokinetics online tools was applied to calculate the ADME/Tox profile of the synthesized compounds and the toxicity of these chemicals was found to be low. The Lipinski, Veber, Ghose, and Consensus LogP criteria were also used to predict drug-likeness levels of the compounds. Our findings imply that the synthesized compounds could be a useful for the preventing and treating biofilm-related microbial infection as well as SARS-CoV2 infections.

New styrylquinoxaline: synthesis, structural, biological evaluation, ADMET prediction and molecular docking investigations

The organic compound (E)-3-(4-methylstyryl)quinoxalin-2(1H)-one (SQO) with molecular formula C₁₇H₁₄N₂O was synthesized and analyzed using single crystal X-ray diffraction, ¹H, ¹³C NMR and FTIR spectroscopic techniques. The geometric parameters of the molecule was optimized by density-functional theory (DFT) choosing B3LYP with 6-31++G(d,p) basis set. For compatibility, the theoretical structure and experimental structure were overlapped with each other. Frontier molecular orbitals of the title compound were made, and energy gap between HOMO and LUMO was calculated. Molecular electrostatic potential map was generated finding electrophilic and nucleophilic attack centers using DFT method. Hirshfeld surface analysis (HSA) confirms active regions at the circumference of N1 atoms and O1 atoms that form intermolecular N1-H1···O1 hydrogen bond. The acute oral toxicity study was carried out according to OECD guideline, which approve that the compound SQO was non-toxic. In addition, this quinoxaline derivative was evaluated for its in vitro antidiabetic activity against α-glucosidase and α-amylase enzymes and for antioxidant activity by utilizing several tests as 1,1-diphenyl-2-picryl hydrazyl, (2,2'-azino-bis(3-ethyl benzthiazoline-6-sulfonicacid), reducing power test (FRAP) and hydrogen peroxide activity H₂O₂. The molecular docking studies were performed to investigate the antidiabetic activity of SQO and compared with the experimental results. SQO is a potent antidiabetic from both the experimental and molecular docking results. Finally, the physicochemical, pharmacokinetic and toxicological properties of SQO have been evaluated by using in silico absorption, distribution, metabolism, excretion and toxicity analysis prediction.