Paolo Monciardini - Academia.edu (original) (raw)

Papers by Paolo Monciardini

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

International Journal of Systematic and Evolutionary Microbiology

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and... more The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter , with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinc...

Journal of Natural Products

The increasing incidence of infections caused by drug-resistant pathogens requires new efforts fo... more The increasing incidence of infections caused by drug-resistant pathogens requires new efforts for the discovery of novel antibiotics. By screening microbial extracts in an assay aimed at identifying compounds interfering with cell wall biosynthesis, based on differential activity against a Staphylococcus aureus strain and its isogenic L-form, the potent enduracyclinones (1, 2), containing the uncommon amino acid enduracididine linked to a six-ring aromatic skeleton, were discovered from different Nonomuraea strains. The structures of 1 and 2 were established through a combination of derivatizations, oxidative cleavages, and NMR analyses of natural and 13 C− 15 N-labeled compounds. Analysis of the biosynthetic cluster provides the combination of genes for the synthesis of enduracididine and type II polyketide synthases. Enduracyclinones are active against Gram-positive pathogens (especially Staphylococcus spp.), including multi-drug-resistant strains, with minimal inhibitory concentrations in the range of 0.0005 to 4 μg mL −1 and with limited toxicity toward eukaryotic cells. The combined results from assays and macromolecular syntheses suggest a possible dual mechanism of action in which both peptidoglycan and DNA syntheses are inhibited by these molecules.

Cell, Jan 15, 2017

Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the disco... more Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits...

BMC Genomics, 2016

 Users may download and print one copy of any publication from the public portal for the purpose... more  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Methods in Enzymology, 2009

Journal of natural products, Jan 29, 2015

We identified an Actinoallomurus strain producing NAI-107, a chlorinated lantibiotic effective ag... more We identified an Actinoallomurus strain producing NAI-107, a chlorinated lantibiotic effective against multidrug-resistant Gram-positive pathogens and previously reported from the distantly related genus Microbispora. Inclusion of KBr in the production medium of either the Actinoallomurus or the Microbispora producer readily afforded brominated variants of NAI-107, which were designated as NAI-108. The other post-translational modifications naturally occurring in this lantibiotic family (i.e., hydroxylation of Pro-14 and C-terminal decarboxylation) were unaffected by the presence of a brominated tryptophan. In addition to being the first example of a bromine-containing lantibiotic, NAI-108 displayed a small but consistent improvement in antibacterial activity against all tested strains. The brominated lantibiotic maintained the same rapid bactericidal activity as NAI-107 but at reduced concentrations, consistent with its increased potency and with the role played by the hydrophobici...

Journal of Industrial Microbiology & Biotechnology, 2015

Natural products represent a major source of approved drugs and still play an important role in s... more Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity. Consistently, 2014 has seen new, natural product-derived antibiotics approved for human use by the US Food and Drug Administration. One of the recently approved second-generation glycopeptides is dalbavancin, a semi-synthetic derivative of the natural product A40,926. This compound inhibits bacterial growth by binding to lipid intermediate II (Lipid II), a key intermediate in peptidoglycan biosynthesis. Like other recently approved antibiotics, dalbavancin has a complex history of preclinical and clinical development, with several companies contributing to different steps in different years. While our work on dalbavancin development stopped at the previous company, intriguingly our current pipeline includes two more Lipid II-binding natural products or derivatives thereof. In particular, we will focus on the properties of NAI-107 and related lantibiotics, whi...

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

International Journal of Phytoremediation, 1999

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

Methods in enzymology, 2009

The need for novel antibiotics to fight multidrug-resistant pathogens calls for a return to natur... more The need for novel antibiotics to fight multidrug-resistant pathogens calls for a return to natural product screening, but novel approaches must be implemented to increase the chances of discovering novel compounds. This chapter illustrates strategic considerations and the required ingredients for screening programs: microbial diversity, samples for screening, targets and assays, assay development and implementation, hit identification and follow-up. When appropriate, we highlight the impact that chemical diversity consisting of mixtures of different compounds, amid a large background of known antibiotics, has on the screening process. Examples of detailed procedures are described for strain isolation and preservation, sample preparation, primary and secondary assays, and extract fractionation. While these limited examples are not sufficient to organize a complete screening program, they provide a basis for understanding the details of microbial product screening in the anti-infecti...

Ernst Schering Research Foundation Workshop, 2005

... We also acknowl-edge the contribution of Julie De Keyser to the characterization of the Gamma... more ... We also acknowl-edge the contribution of Julie De Keyser to the characterization of the Gamma strains. ... 169 Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen ...

Expert Opinion on Drug Discovery, 2007

There is a need to develop novel antibiotics for treating infections caused by multiresistant pat... more There is a need to develop novel antibiotics for treating infections caused by multiresistant pathogens. Notwithstanding a plethora of novel targets and intensive high-throughput screening, conventional chemistry has yet to deliver these badly needed new drugs. Microorganisms have provided many of the existing antibiotics, but there is a general feeling that the large majority of compounds have already been discovered. Novel assays, used to screen common microbes, can provide novel structural scaffolds for antibiotic discovery. However, the highest impact may come from unexplored microbial sources. Fortunately, there is plenty of previously undescribed, antibiotic-producing bacteria in the environment.

Genome announcements, Jan 23, 2014

We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that... more We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.

Microbial cell factories, Jan 10, 2014

BackgroundNAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising la... more BackgroundNAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising lantibiotic active against Gram-positive bacteria and currently in late preclinical-phase. Lantibiotics (lanthionine-containing antibiotics) are ribosomally synthesized and post-translationally modified peptides (RiPPs), encoded by structural genes as precursor peptides.The biosynthesis of biologically active compounds is developmentally controlled and it depends upon a variety of environmental stimuli and conditions. Inorganic phosphate (Pi) usually negatively regulates biologically-active molecule production in Actinomycetes, while it has been reported to have a positive control on lantibiotic production in Firmicutes strains. So far, no information is available concerning the Pi effect on lantibiotic biosynthesis in Actinomycetes.ResultsAfter having developed a suitable defined medium, Pi-limiting conditions were established and confirmed by quantitative analysis of polyphosphate accumu...

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

International Journal of Systematic and Evolutionary Microbiology

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and... more The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter , with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinc...

Journal of Natural Products

The increasing incidence of infections caused by drug-resistant pathogens requires new efforts fo... more The increasing incidence of infections caused by drug-resistant pathogens requires new efforts for the discovery of novel antibiotics. By screening microbial extracts in an assay aimed at identifying compounds interfering with cell wall biosynthesis, based on differential activity against a Staphylococcus aureus strain and its isogenic L-form, the potent enduracyclinones (1, 2), containing the uncommon amino acid enduracididine linked to a six-ring aromatic skeleton, were discovered from different Nonomuraea strains. The structures of 1 and 2 were established through a combination of derivatizations, oxidative cleavages, and NMR analyses of natural and 13 C− 15 N-labeled compounds. Analysis of the biosynthetic cluster provides the combination of genes for the synthesis of enduracididine and type II polyketide synthases. Enduracyclinones are active against Gram-positive pathogens (especially Staphylococcus spp.), including multi-drug-resistant strains, with minimal inhibitory concentrations in the range of 0.0005 to 4 μg mL −1 and with limited toxicity toward eukaryotic cells. The combined results from assays and macromolecular syntheses suggest a possible dual mechanism of action in which both peptidoglycan and DNA syntheses are inhibited by these molecules.

Cell, Jan 15, 2017

Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the disco... more Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits...

BMC Genomics, 2016

 Users may download and print one copy of any publication from the public portal for the purpose... more  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Methods in Enzymology, 2009

Journal of natural products, Jan 29, 2015

We identified an Actinoallomurus strain producing NAI-107, a chlorinated lantibiotic effective ag... more We identified an Actinoallomurus strain producing NAI-107, a chlorinated lantibiotic effective against multidrug-resistant Gram-positive pathogens and previously reported from the distantly related genus Microbispora. Inclusion of KBr in the production medium of either the Actinoallomurus or the Microbispora producer readily afforded brominated variants of NAI-107, which were designated as NAI-108. The other post-translational modifications naturally occurring in this lantibiotic family (i.e., hydroxylation of Pro-14 and C-terminal decarboxylation) were unaffected by the presence of a brominated tryptophan. In addition to being the first example of a bromine-containing lantibiotic, NAI-108 displayed a small but consistent improvement in antibacterial activity against all tested strains. The brominated lantibiotic maintained the same rapid bactericidal activity as NAI-107 but at reduced concentrations, consistent with its increased potency and with the role played by the hydrophobici...

Journal of Industrial Microbiology & Biotechnology, 2015

Natural products represent a major source of approved drugs and still play an important role in s... more Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity. Consistently, 2014 has seen new, natural product-derived antibiotics approved for human use by the US Food and Drug Administration. One of the recently approved second-generation glycopeptides is dalbavancin, a semi-synthetic derivative of the natural product A40,926. This compound inhibits bacterial growth by binding to lipid intermediate II (Lipid II), a key intermediate in peptidoglycan biosynthesis. Like other recently approved antibiotics, dalbavancin has a complex history of preclinical and clinical development, with several companies contributing to different steps in different years. While our work on dalbavancin development stopped at the previous company, intriguingly our current pipeline includes two more Lipid II-binding natural products or derivatives thereof. In particular, we will focus on the properties of NAI-107 and related lantibiotics, whi...

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

International Journal of Phytoremediation, 1999

Bergey's Manual of Systematics of Archaea and Bacteria, 2015

Methods in enzymology, 2009

The need for novel antibiotics to fight multidrug-resistant pathogens calls for a return to natur... more The need for novel antibiotics to fight multidrug-resistant pathogens calls for a return to natural product screening, but novel approaches must be implemented to increase the chances of discovering novel compounds. This chapter illustrates strategic considerations and the required ingredients for screening programs: microbial diversity, samples for screening, targets and assays, assay development and implementation, hit identification and follow-up. When appropriate, we highlight the impact that chemical diversity consisting of mixtures of different compounds, amid a large background of known antibiotics, has on the screening process. Examples of detailed procedures are described for strain isolation and preservation, sample preparation, primary and secondary assays, and extract fractionation. While these limited examples are not sufficient to organize a complete screening program, they provide a basis for understanding the details of microbial product screening in the anti-infecti...

Ernst Schering Research Foundation Workshop, 2005

... We also acknowl-edge the contribution of Julie De Keyser to the characterization of the Gamma... more ... We also acknowl-edge the contribution of Julie De Keyser to the characterization of the Gamma strains. ... 169 Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen ...

Expert Opinion on Drug Discovery, 2007

There is a need to develop novel antibiotics for treating infections caused by multiresistant pat... more There is a need to develop novel antibiotics for treating infections caused by multiresistant pathogens. Notwithstanding a plethora of novel targets and intensive high-throughput screening, conventional chemistry has yet to deliver these badly needed new drugs. Microorganisms have provided many of the existing antibiotics, but there is a general feeling that the large majority of compounds have already been discovered. Novel assays, used to screen common microbes, can provide novel structural scaffolds for antibiotic discovery. However, the highest impact may come from unexplored microbial sources. Fortunately, there is plenty of previously undescribed, antibiotic-producing bacteria in the environment.

Genome announcements, Jan 23, 2014

We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that... more We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.

Microbial cell factories, Jan 10, 2014

BackgroundNAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising la... more BackgroundNAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising lantibiotic active against Gram-positive bacteria and currently in late preclinical-phase. Lantibiotics (lanthionine-containing antibiotics) are ribosomally synthesized and post-translationally modified peptides (RiPPs), encoded by structural genes as precursor peptides.The biosynthesis of biologically active compounds is developmentally controlled and it depends upon a variety of environmental stimuli and conditions. Inorganic phosphate (Pi) usually negatively regulates biologically-active molecule production in Actinomycetes, while it has been reported to have a positive control on lantibiotic production in Firmicutes strains. So far, no information is available concerning the Pi effect on lantibiotic biosynthesis in Actinomycetes.ResultsAfter having developed a suitable defined medium, Pi-limiting conditions were established and confirmed by quantitative analysis of polyphosphate accumu...