RSC Advances Blog

We are very pleased to introduce Atmika Paudel and Kazuhisa Sekimizu, authors of the paper ‘GPI0363 inhibits the interaction of RNA polymerase with DNA in Staphylococcus aureus’. Their article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles. Atmika and Kazuhisa were kind enough to tell us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

Meet the Authors

Dr Atmika Paudel received her undergraduate degree in Pharmacy in 2005 from Tribhuvan University in Nepal and went on to complete a Masters and PhD in Pharmaceutical Biology under the supervision of Professor Kazuhisa Sekimizu from the University of Tokyo in 2010 and 2013, respectively. Since graduation, Dr. Paudel has been a Research Fellow at the University of Tokyo and Teikyo University in Japan. Her research interest includes the discovery of novel therapeutically active antimicrobial agents active against drug-resistant superbugs using the silkworm infection model.

Professor Kazuhisa Sekimizu received his PhD in 1979 from the University of Tokyo by under the supervision of Professor Den’ichi Mizuno and is currently serving as the professor and director of Teikyo University Institute of Medical Mycology Japan. In his early years, Professor Sekimizu studied RNA polymerase and transcription elongation factor S-II in mammalian cells under the supervision of Professor Shunji Natori and initiation of DNA replication in Escherichia coli under the supervision of Professor Arthur Kornberg. His current research interest includes the development of silkworm as an animal model for the identification of therapeutic drugs and functional foods.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
SigA, an essential enzyme required for bacterial transcription, does not exist in human beings and can be targeted for the development of antibiotics that specifically inhibit microbial growth. In this study, we found that GPI0363, a SigA binding antibiotic, inhibits transcription in a different manner compared to other transcription inhibitors recently in clinical use.

How big an impact could your results potentially have?
Microorganisms regularly acquire resistance against antibiotics used in the clinic. To overcome this problem, we should be ready to provide another antibiotic with a novel mode of action and a narrow spectrum of activity. The activity of GPI0363 against drug-resistant Staphylococcus aureus will allow us to develop this molecule as a therapeutic approach against drug-resistant pathogens.

Could you explain the motivation behind this study?
GPI0363 was identified in our laboratory by using the silkworm infection model in 2017. In our earlier study, we found that a single mutation in SigA was responsible for resistance to this antibiotic. This suggested that SigA can be a druggable target for antimicrobial agents and GPI0363 could be a new kind of SigA inhibitor. Thus, we were intrigued to study the underlying mechanism of the antistaphylococcal action of GPI0363. In this study, we explain the proof of concept for the utilization of SigA as a target of antimicrobial agents.

In your opinion, what are the key design considerations for your study?
Due to several problems associated with absorption, distribution, metabolism, excretion, and toxicity (ADMET), most of the antimicrobial agents that display activity in vitro do not show the in vivo activity. For this reason, we use silkworms at the beginning of screening so that the compounds that do not display therapeutic activity can quickly be discarded at the early stage.

In your article you mention that GPI0363 can serve as a promising lead molecule to develop staphylococcal RNA polymerase inhibitors. Please could you tell us more about this?
SigA is present in bacteria and differs among bacterial species. Our findings suggest that GPI0363 is selective towards the inhibition of staphylococcal RNA polymerase via SigA, thus can be used for the development of tailor-made medicines for the same. Further studies in GPI0363 through the structure-activity relationship study should lead to the discovery of compounds with more potent inhibitory activity and better therapeutic activity.

Which part of the work towards this paper proved to be most challenging?
The experiment to prove which step of transcription is inhibited was the most challenging to us. Our purified RNA polymerase fraction of Staphylococcus aureus contained a small amount of SigA and it was difficult to identify if GPI0363 inhibited the interaction of SigA with RNA polymerase core enzyme. To overcome this issue, we used Escherichia coli RNA polymerase core enzyme and S. aureus SigA to prepare a hybrid RNA polymerase holoenzyme.

What aspect of your work are you most excited about at the moment?
At this moment, I am excited for two reasons:
a. GPI0363 does not harbor cross-resistance against clinically used inhibitors of RNA polymerase.
b. We have a lead molecule to start with for the development of antimicrobial agents with therapeutic activity.

What is the next step? What work is planned?
As the next step, we plan to perform a structureactivity relationship study through the synthesis of a large number of GPI0363 derivatives; and perform crystal structure analysis of staphylococcal SigA in the presence of GPI0363.

GPI0363 inhibits the interaction of RNA polymerase with DNA in Staphylococcus aureus
Atmika Paudel, Suresh Panthee, Hiroshi Hamamoto and Kazuhisa Sekimizu
RSC Adv., 2019, 9, 37889-37894
DOI: 10.1039/C9RA06844A, Paper

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We are very pleased to introduce Takeharu Haino, co-author of the paper ‘A protocol for size separation of nanographenes’ along with Ikuya Matsumoto and Ryo Sekiya. His article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles. Professor Takeharu Haino was kind enough to tell us more about the work that went into this article and what he hopes to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

Meet the Author

Takeharu Haino is a Professor in the Department of Chemistry, Graduate School of Science, Hiroshima University. His research field is supramolecular chemistry.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
Oxidative cutting method basically results in various sizes of graphenes which are tough to separate easily. This paper describes quick and convenient method that separates various sized graphenes via dialysis.

How big an impact could your results potentially have?
A chromatographic method is potentially effective for separation purpose; but, it is very time-consuming and tedious. This method is very convenient and quick to obtain practical amount of graphenes in various sizes.

Could you explain the motivation behind this study?
We needed to have uniform size graphenes to obtain reproducible results.

In your opinion, what are the key design considerations for your study?
A key point for this study is to obtain uniform graphenes in a practical scale.

In your article you mention that the separated nanographenes can be employed as starting materials for carbon-based functional materials. . Do you have a particular application in mind?
One of my dreams is to make efficient catalysts with these graphenes.

Which part of the work towards this paper proved to be most challenging?
The quality of graphenes is often a trade-off in relation to its quantity. It is challenging to obtain high quality graphenes in a practical scale using dyalisis.

What aspect of your work are you most excited about at the moment?
What we prepared in this paper, we believe, is one of the highest quality graphenes via such a easy method.

What is the next step? What work is planned?
We would like to functionalize these graphenes for functional material with chirality.

A protocol for size separation of nanographenes
Ikuya Matsumoto, Ryo Sekiya and Takeharu Haino
RSC Adv., 2019, 9, 33843-33846
DOI: 10.1039/C9RA07528C, Paper

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Meet the Author
We are very pleased to introduce Jawameer R. Hama, co-author of the paper ‘Pyrrolizidine alkaloids quantified in soil and water using UPLC-MS/MS‘ with Bjarne W. Strobel. His article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles. Jawameer was kind enough to tell us more about the work that went into this article and what he hopes to achieve in the future. You can find out more about Jawameer and his article below and find more HOT articles in our online collection.

Hama received his Master degree in Analytical Chemistry from Bangor University (UK), 2013. In 2017, He became a PhD fellow at University of Copenhagen, Denmark, under the supervision of Dr. Bjarne W. Strobel. His research project focuses on quantification of crop produced natural toxins in groundwater.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
The article reports a fast, reliable, and sensitive analytical method to analyse pyrrolizidine alkaloids (PAs) in environmental samples, such as water and soil. To do this we optimised the sample preparation and analytical parameters.

How big an impact could your results potentially have?
There is a substantial impact of the study. We have pointed out that PAs can contaminate surface water, especially where there is a lot of vegetation containing PAs. This is because the concentration is much higher when compared with the pesticide concentration limits in water.

Could you explain the motivation behind this study?
We were motivated to know the fate of PAs in environmental samples, especially water, as my whole project is about water analysis. PAs are reported in food and feed – meaning they are stable and persist.

In your opinion, what are the key design considerations for your study?
There are several key designs in the study including planning and using the capacities in the house. Using an analytical system that is not in our house would be too costly. On the other hand, the capacity we have is moderately up to date.  In addition, we considered how the analytical platform could be improved compared to those already reported before by other authors. Thus, we have listed parameters to optimize the platform that haven’t been done before. The location and time of sampling are crucial too.

In your article you mention that the findings may be used as platform to further study PAs in natural water and aquifers. Do you have a particular application in mind? How does it work?
The method is validated for environmental samples, further applications would look at and analyse water samples in the areas close to water bodies where the plants containing PAs are the main vegetation. It would also test the efficiency of waste water treatment plant stations to test if PAs end up in the drinking water as well as screen and monitor the groundwater – especially in places where groundwater is used as drinking water. For that only a sample from the location is required, then the rest of the work would be quickly done in the lab.

Which part of the work towards this paper proved to be most challenging?
The sample type was challenging because this was the first time we have optimized the method for environmental samples (soil and water). When you analyse soil and water samples, it is crucial to eliminate the matrix effect during sample preparation and analysis. In addition, the sample volume was also challenging as it determines the limit of lab work and analysis.

What aspect of your work are you most excited about at the moment?
The concentration and the compound types are very exciting, because we proved our hypothesis that PAs are stable and persist in the environment. If not, we would have given up or changed the route of the project long before.

What is the next step? What work is planned?
We plan to collect lists of samples from potential locations and design the field scale of the locations to know what the main factors that drive PAs in water are. We also plan to correlate seasonal growth of plants, weather (precipitation, snow, temperature) and time of sampling to understand the effect of them.

Pyrrolizidine Alkaloids Quantified in Soil and Water using UPLC-MS/MS
Jawameer R. Hama and Bjarne W. Strobel
RSC Adv., 2019, 9, 30350-30357
DOI: 10.1039/C9RA05301H, Paper

Submit to RSC Advances today! Check out our author guidelines for information on our article types or find out more about the advantages of publishing in a Royal Society of Chemistry journal.

Keep up to date with our latest HOT atricles, Reviews, Collections & more by following us on Twitter. You can also keep informed by signing up to our E-Alerts.