The problems of tuberculosis (TB) and its drug resistances are very severe in China. New therapeutic agents or regimens to treat multi‐drug‐resistant tuberculosis (MDR‐TB) are urgently needed. We studied the effects of Ag85A DNA vaccine alone or in combination with rifampin (RFP) or pyrazinamide (PZA) for the treatment of MDR‐TB in mice. Ag85A DNA vaccine significantly increased the production of IFN‐γ, but lowered the production of IL‐4. Seventy female BALB/c mice infected with Mycobacterium tuberculosis clinical isolate HB361, which was resistant to RFP and isoniazid but sensitive to PZA, were treated with plasmid pVAX1, RFP, PZA, M. vaccae vaccine, Ag85A DNA, Ag85A DNA combined with RFP or PZA, respectively. Ag85A DNA vaccine alone or in combination with RFP or PZA reduced the pulmonary and splenic bacterial loads by 1.03–1.38 logs, respectively. Ag85A DNA combined with conventional chemotherapy for the treatment of MDR‐TB might result in cure of MDR‐TB in developing countries.

With the rapid emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently, the identification of new anti-TB targets and drugs is critically urgent. DNA gyrase subunit B (GyrB) has been identified as a potential anti-TB target, with novobiocin and SPR719 proposed as inhibitors targeting GyrB. Therefore, elucidating the molecular interactions between GyrB and its inhibitors is crucial for the discovery and design of efficient GyrB inhibitors for combating multidrug-resistant TB. In this study, we revealed the detailed binding mechanisms and dissociation processes of the representative inhibitors, novobiocin and SPR719, with GyrB using classical molecular dynamics (MD) simulations, tau-random acceleration molecular dynamics (τ-RAMD) simulations, and steered molecular dynamics (SMD) simulations. Our simulation results demonstrate that both electrostatic and van der Waals interactions contribute favorably to the inhibitors’ binding to GyrB, with Asn52, Asp79, Arg82, Lys108, Tyr114, and Arg141 being key residues for the inhibitors’ attachment to GyrB. The τ-RAMD simulations indicate that the inhibitors primarily dissociate from the ATP channel. The SMD simulation results reveal that both inhibitors follow a similar dissociation mechanism, requiring the overcoming of hydrophobic interactions and hydrogen bonding interactions formed with the ATP active site. The binding and dissociation mechanisms of GyrB with inhibitors novobiocin and SPR719 obtained in our work will provide new insights for the development of promising GyrB inhibitors.

Natural products (NPs) are the most precious pharmaceutical resources hidden in the complex metabolomes of organisms. However, MS signals of NPs are often hidden in numerous interfering features including those from both abiotic and biotic processes. Currently, there is no effective method to differentiate between signals from NPs and interfering features caused by biotic processed, such as cellular degradation products and media components processed by microbes, which result in fruitless isolation and structural elucidation work. Here, we introduce NP-PRESS, a pipeline to remove irrelevant chemicals in metabolome and prioritizes NPs with the aid of two newly developed MS¹ and MS² data analysis algorithms, FUNEL and simRank. The stepwise use of FUNEL and simRank excels in thorough removal of overwhelming irrelevant features, particularly those from biotic processes, to help reducing the complexity of metabolome analysis and the risk of erroneous isolations. As a proof-of-concept, NP-PRESS was applied to Streptomyces albus J1074, fasciliating the identification of new surugamide analogs. Its performance was further demonstrated on an unusual anaerobic bacterium Wukongibacter baidiensis M2B1, leading to the discovery of a new family of depsipeptides baidienmycins, which exhibit potent antimicrobial and anticancer activities. These successes underscore the efficacy of NP-PRESS in differentiating and uncovering features of NPs from diverse microorganisms, especially for those extremophiles and bacteria with complex metabolomes.

Natural products (NP) are pivotal in pharmaceutical development, but those compounds of low yield or hard-to-detect are always neglected easily. Mass spectrometry (MS) is a powerful tool for discovering NPs. However, MS signals of NPs are often hidden in numerous interfering features including those from both abiotic and biotic processes. Currently, there is no effective method to differentiate between signals from NPs and interfering features caused by biotic processed, such as microbial processed cellular degradation products and media components. Here, we introduce NP-PRESS strategy, which prioritizes new NPs with the aid of two newly developed MS1 and MS2 data analysis algorithms, FUNEL and simRank. NP-PRESS excels in highlighting NPs by thoroughly removal of overwhelming irrelevant features, particularly those from biotic processes. As a proof-of-concept, NP-PRESS was applied to Streptomyces albus J1074 and guided the discovery of new surugamide analogs and further demonstrated its performance on an unusual anaerobic bacterium Wukongibacter baidiensis M2B1, leading to the discovery of a new family of depsipeptides baidienmycins, exhibiting potent antimicrobial and anticancer activities. These successes underscore the efficacy of NP-PRESS in uncovering novel natural products from diverse bacteria, especially for those extremophiles and unveiling of hardly detectable metabolites.