Final Demonstration of the Co-Identity of Lipiarmycin A3 and Tiacumicin B (Fidaxomicin) through Single Crystal X-ray Analysis

Serra, Stefano; Malpezzi, Luciana; Bedeschi, Angelo; Fuganti, Claudio; Fonte, Piera

doi:10.3390/antibiotics6010007

Cited by 19 publications

(9 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The error bars denote the standard error from a minimum of three experiments (for some points, the error bars are smaller than the width of the point and are not shown). ( B ) Chemical structure of Fdx ( Serra et al, 2017 ). ( C ) Synthetic us-fork promoter fragment used for cryo-EM experiments.…”

Section: Resultsmentioning

confidence: 99%

“…For the high-resolution structures, the rigid-body refined models were subsequently refined with secondary structure restraints. A model of Fdx was generated from a crystal structure ( Serra et al, 2017 ), edited in Phenix REEL, and refined into the cryo-EM density. Refined models were inspected and modified in Coot ( Emsley and Cowtan, 2004 ) according to cryo-EM maps, followed by further real-space refinement with PHENIX.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

Boyaci

Chen

Lilić

et al. 2018

eLife

132

View full text Add to dashboard Cite

Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

Boyaci

Chen

Lilić

et al. 2018

eLife

132

View full text Add to dashboard Cite

show abstract

“…Fidaxomicin is an antibacterial drug in clinical use in treatment of Clostridium difficile diarrhea (Lancaster and Matthews, 2012; Venugopal and Johnson, 2012). The active pharmaceutical ingredient of fidaxomicin, lipiarmycin A3 (Lpm; Kaufmann et al, 2015; Serra et al, 2017; Fig. S1A), is a macrocyclic antibiotic with bactericidal activity against Gram-positive bacteria and efflux-deficient strains of Gram-negative bacteria (Lancaster and Matthews, 2012; Venugopal and Johnson, 2012; Srivastava et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)

et al. 2018

View full text Add to dashboard Cite

Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.

show abstract

“…The latter synthetic compound proved identical to a commercial sample of tiacumicin B from Dactylosporangium aurantiacum , thus confirming the structure assigned. Finally, a study on the comparative X-ray analysis of lipiarmycin A3 and tiacumicin B was published in 2017, providing the definitive proof that these pharmaceutical compounds are identical in all respects and confirmed the previous assigned chemical structure of lipiarmycin A3 [ 162 ].…”

Section: Antibiotics From Actinomycetes : From Isolation To Chemical Characterization Total Synthesis and Industrial Pmentioning

confidence: 58%

Actinomycetes: A Never-Ending Source of Bioactive Compounds—An Overview on Antibiotics Production

Simeis¹,

Serra²

2021

Antibiotics

Self Cite

105

View full text Add to dashboard Cite

The discovery of penicillin by Sir Alexander Fleming in 1928 provided us with access to a new class of compounds useful at fighting bacterial infections: antibiotics. Ever since, a number of studies were carried out to find new molecules with the same activity. Microorganisms belonging to Actinobacteria phylum, the Actinomycetes, were the most important sources of antibiotics. Bioactive compounds isolated from this order were also an important inspiration reservoir for pharmaceutical chemists who realized the synthesis of new molecules with antibiotic activity. According to the World Health Organization (WHO), antibiotic resistance is currently one of the biggest threats to global health, food security, and development. The world urgently needs to adopt measures to reduce this risk by finding new antibiotics and changing the way they are used. In this review, we describe the primary role of Actinomycetes in the history of antibiotics. Antibiotics produced by these microorganisms, their bioactivities, and how their chemical structures have inspired generations of scientists working in the synthesis of new drugs are described thoroughly.

show abstract

Final Demonstration of the Co-Identity of Lipiarmycin A3 and Tiacumicin B (Fidaxomicin) through Single Crystal X-ray Analysis

Cited by 19 publications

References 20 publications

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)

Actinomycetes: A Never-Ending Source of Bioactive Compounds—An Overview on Antibiotics Production

Contact Info

Product

Resources

About