Antibiotics are the most powerful weapon available to treat bacterial infections. Since being discovered in the 1940s, bacteria have become resistant to these substances due to their unconscious and excessive use. For this reason, diseases that were previously treated with antibiotics have become untreatable, and new diseases have begun to appear [1]. This is a situation that threatens human health. According to the World Health Organization, 700,000 people die annually due to antibiotic resistance. It is estimated that 10 million people will die annually after 2050. This number of deaths is equal to the number of people who die from cancer each year today [2].

Naphthoquinones are members of the quinone class, such as benzoquinone or anthroquinone. These compounds are secondary metabolites produced by plants. Lawsone (Lawsonia inermis), juglone (Juglans regia L.), and plumbagin (Plumbago zeylanica) are compounds containing natural naphthoquinone scaffolds [3]. 1,4-Naphthoquinone and 2,3-dichloro-1,4-naphthoquinone are used as starting materials for the production of new derivatives. New naphthoquinones are obtained from the nucleophilic addition–elimination reactions of them with nitrogen, oxygen, and sulfur-containing nucleophiles [4], [5]. Natural and synthetic naphthoquinones show powerful antibacterial activity [1], [6], as well as many different biological properties such as antifungal [7], antivirus [8], antimycobacterial [9], antimalarial [10], antitrypanosomal [11], antiinflammatory [12], anticancer [13], [14], and anti-Alzheimer's [15]. The reason why naphthoquinones show so much biological activity is due to their electrochemical behavior. While naphthoquinone derivatives undergo enzymatic reduction in the presence of molecular oxygen and turn into semiquinone and hydroquinone derivatives, oxidation of molecular oxygen leads to creation of reactive oxygen species (ROS). Reactive oxygen species can be hydroxyl radicals, hydrogen peroxide, superoxide anion, and singlet oxygen. ROS can damage macromolecules such as lipids and proteins and can trigger apoptosis, depending on their doses.

Tandon et al.[16] performed the synthesis of novel 2-arylamino-3-halo-1,4-naphthoquinones as potential antibacterial agent 1 Yamashita et al. [17] reported the synthesis and antibacterial evaluation of new naphtho[2,3-b]furan-4,9-diones 2 Chan et al. [18] described the synthesis and biological evaluation of newly cationic anthraquinones 3 that displayed important antibacterial activity. Lopez-Lopez et al. [19] reported 2-(anilino)-5-hydroxy-1,4-naphthoquinones 4 and their resistance toward both Gram-positive or Gram-negative strains. Kim et al. [20] also performed the synthesis of new pyrimidinone-fused 1,4-naphthoquinones 5 as potential antibacterial compound (Fig. 1).

Piperazine is one of the most widely used heterocyclics for the development of new medicinal candidates with a range of applications. Biologically active substances utilized in numerous therapeutic domains frequently contain piperazine scaffolds [21]. The anthraquinone-derived molecule with the propanyl benzyl piperazine group was shown to have the best selectivity for inhibiting hTERT expression in H1299 cells among these compounds [22]. Furthermore, it is well-known that the combination of benzyl piperazine and flavonoid naringenin derivatives inhibits the hypoxic-induced IL6/JAK2/STAT3 [23].

Despite the widespread availability of antibiotics, the growth of antibiotic-resistant bacterial species highlights the critical need for synthesizing and developing more potent antimicrobial medicines. DNA gyrase enzyme, which is from the topoisomerase enzyme class, plays an important role in DNA replication and transcription processes. Inhibiting this enzyme hinders DNA synthesis, eventually leading to bacterial cell death. Karkare et al. have shown that naphthoquinone derivatives exhibit antibacterial effects by inhibiting the DNA gyrase enzyme [24]. Dissanayake et al. discovered that plumbagin, a naphthoquinone produced from Plumbago species plants, inhibits the DNA gyrase enzyme [25], [26].

The fact that propanyl spacer derivatives in the literature data show selectivity in activity investigations, benzyl piperazine derivatives are strong therapeutic prospects, and halo-naphthoquinone 1 is a strong antibacterial agent guided the design of this investigation. In this study, 2,3-dichloro-1,4-naphthoquinone was chosen as the starting material, and N-benzyl piperazines were bound with a 1,3 dipropanyl spacer. The structures of derivatives were elucidated by 1H NMR, 13C NMR, FTIR, and HRMS analysis. Molecular docking studies of the most potent derivatives were performed to better understand the interaction of compounds with DNA gyrase B active site. We have also employed molecular dynamics (MD) simulations for selected docked complexes to see how stable are each system. Furthermore, the synthesized compounds underwent in silico ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) assessments, and their drug potentials were determined using the Golden Triangle and Lipinski's rule of five filters (Pfizer).