Tuberculosis (TB) is an infectious bacterial disease caused by Mycobacterium tuberculosis (Mtb). Despite being around for thousands of years, TB remains one of the world's biggest killers. Under the World Health Organization's short-course regimen, 85 % of patients can be cured within 6 months, but 1.6 million people still died of TB in 2021 [1]. Defaulting and irregular anti-TB medicine intake are the major barriers to effective treatment. In addition, the emergence of drug-resistant strains around the world poses a major threat to the successful treatment of TB [2], [3]. According to statistics from the WHO, there were about 450,000 cases of drug resistant TB worldwide in 2021. Thus, new anti-TB drugs are needed to address the challenges posed by drug-resistant Mtb [4].

It is well known that gut microbes interact closely with components of the immune system [5]. Microecological dysregulation in the gut microbiota community could lead to increased TB susceptibility or relapse [6], [7]. Long-term anti-TB treatment with four first-line anti-TB drugs, isoniazid (INH), rifampicin (RIF), pyrazinamide (PZA), and ethambutol (EMB), has been found to result in pronounced and long-lasting microecological dysbiosis of the gut bacterial microbiota [8]. Since RIF is a broad-spectrum antimicrobial agent, it may be the main drug contributing to the dysbiosis of the intestinal microbiota of TB patients in short-course treatment chemotherapy regimen. A study showed that RIF induced significant changes in the diversity and composition of the intestinal microbiota of Mtb-infected mice [9]. Séraphin and colleagues administered prophylaxis with RIF to patients with latent TB infection (LTBI), and after 2 months the LTBI patients developed significant gut microbiota dysbiosis [10]. Therefore, we hypothesized that altering the broad-spectrum antimicrobial properties of RIF would reduce its intervention in the diversity and composition of the gut microbiota community.

It is well known that small molecules must overcome the obstacles of the bacterial cell wall structure to enter the bacterial cytoplasm [11]. The cell wall structure of Mtb is very special, consisting of a large number of mycolic acids, and this structural feature imposes a restriction on the entry of many small molecules into the cells of Mtb [12]. It is generally believed that the same small molecule enters the cells of different species of bacteria at different rates of diffusion, and therefore, the differences in diffusion of small molecules can be utilized to design specific anti-Mtb molecules.

Based on the complete structure of RIF, it is undoubtedly very difficult to modify it into a narrow-spectrum antibiotic that is specifically anti-Mtb. Structurally RIF is divided into 3 parts, the naphthalene core, the polyketide backbone and N-methyl piperazine (Fig. 1a). RIF is one of the rifamycin derivatives. Previous studies indicated that modification of C7 or C8 of the naphthalene ring of rifamycin usually yielded derivatives with high antibacterial activity. However, modification of the free hydroxyl group of polyketide backbone failed to yield derivatives with potential antimicrobial activity [13], [14], [15], [16]. Thus the naphthalene ring is an important pharmacophore of RIF [17]. In addition, there are reports that the binding between RIF and RNA polymerase (RNAP) was mainly controlled by hydrophobic forces between the naphthalene ring and the amino acid residues in the active site [18], [19]. Based on the above foundation, we designed and synthesized 16 compounds (Fig. 1b, Scheme 1) with naphthalene ring. In addition, 2 phenyl ring-containing compounds (Fig. 1c) were synthesized to verify whether the naphthalene ring-containing compounds had stronger anti-Mtb effects.

In this study, we attempted to address 2 questions, firstly, whether the synthesized compounds have a specific anti-Mtb activity and secondly, whether the synthesized narrow-spectrum antibiotics disrupt the gut bacterial community.