Paradisi Rese@rch

Discovery Evolution Application
Francesca Paradisi
Prof. Francesca Paradisi

Associate Professor in Biocatalysis and Enzyme Engineering

About me...

I completed my MSc in Organic Chemistry from the University of Bologna in 1998 under the supervision of Prof. Cainelli. In 2002 I completed my PhD at the same institution with a thesis on the synthesis of non-natural amino acids via diketopiperazine scaffolds. During my PhD I spent a summer in Dublin as a visiting student in Trinity College working with Prof. Thorri Gunnlaugsson and it was a fantastic experience. So after my PhD I had no doubt I wanted to go abroad and I joined the group of Prof. Paul Engel at University College Dublin as Post-Doctoral Fellow where I discovered the wonders of biocatalysis. I remained in Paul’s group until 2005 developing several projects mainly focused on amino acid dehydrogenases and their applications in the synthesis of non-natural amino acids. I owe Paul all I know about enzymes and their reaction mechanisms!

I spent then a few months in Enzolve Technologies in 2005, a spin-off company of UCD where I worked on the use of mutant dehydrogeanse enzymes for neonatal screening of metabolic disorders. In 2006 I won the lotto and was appointed College Lecturer in Chemical Biology at the UCD School of Chemistry. I was promoted in 2014 to Senior Lecturer. I was fortunate to be always surrounded by a team of excellent students that made my research always interesting, certainly challenging, and thankfully rewarding.

A had the great opportunity to spend the summer of 2015 in UC Davis in California as a visiting academic and I joined the group of Dr. Justin Siegel who gave me the possibility of expanding my research to a different class of enzymes (glycosyl hydrolyses) and getting my hands dirty in the lab again was awesome as they say.  While I was in Davis and I thought things couldn’t get any better, I was offered the position of Associate Professor in Biocatalysis and Enzyme Engineering in the School of Chemistry at the Univeristy of Nottingham. I have started this new adventure since February 2016.

Outside my work life, I have a husband and two children, Oliver and Martina, and a cat. I love skiing and swimming and travelling too.

Research Highlights

Amino Acids (2017): Stabilization of Angiotensin-(1–7) by key substitution with a cyclic non-natural amino acid

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Green Chemistry (2017) : “Continuous flow biocatalysis: production and in-line purification of amines by immobilised transaminase from Halomonas elongata”

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OBC (2016) : “Stereoelectronic effects in the reaction of aromatic substrates catalysed by Halomonas elongata transaminase and its mutants”

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Latest Post

Biotrans 2017

Larah, Jenni, Martina and Benni with Fran at Biotrans 2017. We participated with 4 posters and one pitch talk. Great fun was had by all and the company was probably the best aspect of the Budapest experience.
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Research Highlights

Amino Acids (2017): Stabilization of Angiotensin-(1–7) by key substitution with a cyclic non-natural amino acid

Well done to Anita! Her work finally rewarded! This paper was the result of our collaborative work...
See more

Green Chemistry (2017) : “Continuous flow biocatalysis: production and in-line purification of amines by immobilised transaminase from Halomonas elongata”

Great achievement for the group! Matteo, Martina and Jenni, together with our collaborators in...
See more

OBC (2016) : “Stereoelectronic effects in the reaction of aromatic substrates catalysed by Halomonas elongata transaminase and its mutants”

Well done for Martina e Matteo, the work of the last few months has been successfully...
See more

Latest Post

Biotrans 2017

Larah, Jenni, Martina and Benni with Fran at Biotrans 2017. We participated with 4 posters and one pitch talk. Great fun was had by all and the company was probably the best aspect of the Budapest experience.

See more

Research

Our Projects :
Flow Biocatalysis

Enzymes are amazing catalysts which effortlessly and with extreme precision regulate reactions of biosynthetic pathways in a biological system. We are taking enzymes from different sources, those that offer the optimal characteristics for our chemistry, and recreate artificial cascades ex-vivo using a flow reactor. Enzymes we produce, are directly and covalently immobilised onto solid supports and packed into column reactors. Each enzymatic biotransformation can be individually optimised so that the starting material is fully converted into the product by the time the flow takes it out of the column. Two, three more columns containing different enzymes can be connected sequencially, and several steps can be performed with high efficiency and fast flow.  Continuous flow biocatalysis is the ultimate evolution of continuous processing and has brought enzymes to a whole new dimension. Have a look at the enzymes we work with below.

Enzyme Toolbox

 

We have a special interest in enzymes from extremophilic microbes which have adapted to life in  high salt environments (Dead Sea, salterns, etc). The mechanism developed by the organisms to  withstand molar concentrations of NaCl is either by accumulation of high amounts of KCl in the cytoplasm, or by efficient production of soluble organic molecules. In both cases the enzymes expressed by these bacteria or achaea have evolved structurally to be able to perform in a water depleted system and therfore are excellent candidates for synthetic applications which normally require organic solvents.

Transaminases are a family of enzymes with high potential in biotechnological applications. They can be very useful for the enantioselective production of a series of compounds with high value such as chiral amines and enantiopure amino alcohols which find use in many chemical fields; above all, for the synthesis of biologically active compounds. The synthesis of enantiopure amines by enzymatically catalyzed reactions presents several advantages as an alternative to traditional approaches such as mild reaction conditions, high stereoselectivity, fewer synthetic steps, potential total substrate conversion and no environmental issues unlike in the case of transition metal catalysts. 

The reaction is reversible and transaminases can also be used for the mild oxidation of amines into aldehydes and ketones.

We have isolated and investigated a transaminase from Halomonas elongata (HEWT) which has shown high enantioselectivity, large substrate spectra and stability in organic solvents, HEWT a highly suitable enzyme for biotechnological applications in the production of chiral amines. For these reasons, we are currently developing different projects regarding its application, including continuous flow biotransformation and enzyme evolution to improve its catalytic performance against non natural substrates.

Redox enzymes encompass a number of different biocatalysts of great industrial interest. We have a collection of enzymes from both salt adapted and mesophilic sources such as alcohol dehydrogenases (ADHs) and ketoreductases (KR) which we have used to synthesise chiral alcohols (in the reductive direction) and in the dynamic kinetic resolution of profenic aldehydes. These enzymes pose an additional challenge as they are cofactor dependent (NAD(P)H). The cofactor cannot be used stoichiometrically as it is prohibitively expensive. We have therefore developed simple recycling strategies which are easily adaptable to flow biocatalysis.

 

Hydrolytic enzymes are another large family of very useful biocatalysts. We have recently expanded our research into reactions which include ester and amide hydrolysis (and eventually also synthesis) as part of an artificial enzymatic cascade. A selection of esterases and amidases are now part of our library. In a separate project six ß-glycosyl hydrolyses, all classified as GH1, have been selected to investigate how environmental adaptation affects biocatalytic properties, as well as stability at different temperatures, pHs and in the presence of solvents. Furthermore, we analysed whether the subtle differences in the active site of the proteins may indicate a pattern for a preferential substrate recognition. GH1 from Thermobaculum terrenum (Tte) and Thermus Nonproteolyticus (Tno) have been chosen as thermophilic examples, Halothermothrix orenii (Hor) and Halobacillus halophilus (Hha) as two halophilic proteins (with Hor being also thermophilic), and finally Colwellia psychrerythraea (Cps) and Marinomonas profundimaris (Mpr) as psychrophilic ones. 

 

Semi-synthetic enzymes

Metals are part of biological molecules and cover different roles. It is fascinating how inorganic elements are pivotal in many cases for biological activity. In collaboration with Prof. Albrecht in Switzerland we have started looking at the amino acid residues that hold in place the metal in the active site of a number of enzymes. Specifically we are investigating the role of histidine as a ligand in copper proteins such as azurin. Azurin is a bacterial blue copper protein that acts as electron shuttle in bacteria denitrification process, where its metal center undergoes oxidation-reduction between Cu(I) and Cu (II) during the electron transfer. We have taken azurin as a model to evaluate the hypothesis that carbon-metal bonding in proteins (other than nitrogen-metal bonding) could play an important role since the interconversion of histidine between the weakly π-acidic imine (N-bound form) and the strongly σ-donating C-bound carbene tautomer2 will have substantial implications on the activity and oxidation-reduction chemistry of the coordinated metal center.

Under this same heading it is worth mentioning that our ADH proteins contain a catalytic zinc in the active site which coordinated to the substrate and facilitate the biotransformation. We are interested in investigating better the role of the zinc and its role in substrate selectivity. What happens if we change the metal for a different one? Can substrates other than alcohols/carbonyls be accommodated and transformed?

Peptido-mimeticts

Peptidomimetics are widely used in medicinal chemistry as therapeutic agents to act as agonists or antagonists on receptor or enzyme targets. They are also valuable tools for investigating the relationship between peptide structure and function as they elucidate key residues that are required to achieve a desired biological response. The incorporation of cyclic structures into peptidomimetics was shown to decrease their conformational flexibility resulting in increased selectivity and affinity with their target and improved enzymatic stability and bioavailability.

While trying to synthesise the side chain of an non-natural amino acid, we serendipitously discovered a side product of our reaction which looked more interestingly than the product we wanted to make. In 2013 we published the synthesis of the non-natural δ-amino acid ACCA (cis-3-(aminomethyl)cyclobutanecarboxylic acid) (O’Reilly et al. 2013, Amino acids, 511-518). ACCA contains a cyclobutane ring that gives the molecule conformational rigidity and locks the amino and carboxylic acid group in a cis conformation.

ACCA shows structural similarity to glutamate, making it an interesting building block for the synthesis of glutamate analogues. A set of dipeptides containing ACCA and a natural amino acid (glycine, valine, phenylalanine, cysteine) have been synthesized and are evaluated for their application as glutamate analogues selectively targeting the cystine-glutamate exchanger (Xc).

Angiotensin-(1-7) is a heptapeptide hormone of the renin-angiotensin system (RAS). We are particularly interested in the potential use of Angiotensin-(1-7) in anti-cancer therapy. Its anti-angiogenic and anti-proliferative properties have been investigated Prof. Gallagher at Wake Forest University (NC, USA). A phase II clinical trial recently completed by the Wake Forest School of Medicine successfully showed its therapeutic potential as a second or third line treatment of patients with unresectable or metastatic sarcomas.

Ang-(1-7) mediates its biological responses by interacting with the G protein-coupled mas. It is readily cleaved by the dipeptidyl carboxypeptidase angiotensin-converting enzyme (ACE) resulting in short-half life. We have synthesised a series of Ang-(1-7) analogues incorporating ACCA to decrease enzymatic metabolism thereby overcoming the problem of the short half-life of the endogenous heptapeptide and improving its properties as a therapeutic agent. This work has led to a patent application (Gallagher et al. U.S. Provisional Application No. 62/266,410, 2015).

 

Group Members

Dr. Jennifer Cassidy

I am currently a Post-Doctoral researcher with Dr Paradisi. During my PhD in this group, my research focussed on the discovery and characterisation of novel enzymes from halophilic organisms.

Research area

My research interests include protein expression, purification, mutagenesis, homology modelling and in silico docking. At present, I am studying the effects of mutations on the substrate scope of alcohol dehydrogenases and how ionic liquids can be applied as green solvents.

Larah Bruen

I am a 3rd year PhD student focused on the area of biocatalysis, following a B.Sc. Chemistry degree in National University of Ireland, Galway.

Research area

My research is focused on an alcohol dehydrogenase from a halophilic archaea, and currently I am working to expand the substrate scope of this enzyme through in-silico docking and site-directed mutagenesis. In parallel, I am currently working on a novel method of screening mutant libraries of alcohol dehydrogenases.

Eimear Hegarty

I have recently joined the Paradisi Research Group as a 1st year PhD student having just completed my B.Sc. in Industrial Biochemistry at the University of Limerick (Ireland).

Research area

With a keen interest in biocatalysis and enzyme engineering my research will focus on exploiting the hyper-salinity requirements of Haloferax volcanii to the advantage of biotechnology by developing it as a new expression system for proteins of industrial relevance.

Dr. Martina Contente

I am a post-doctoral researcher currently working in Professor Francesca Paradisi’s research group at the University of Nottingham.

Research area

I am very interested in Biocatalysis research in particular in using enzymes or engineered whole cells as catalysts for the preparation of chiral pharmaceutical intermediates. I am working on immobilized transaminase from halophilic microorganism and its different mutants for the transformation of various substrates, interesting building blocks for the synthesis of pharmaceuticals. I am also exploring new synthetic techniques for flow chemistry reactors.

Benedetta Guidi

I am a PhD student in chemistry at University of Milan (Italy) currently visiting Dr. Paradisi’s research group

Research area

I am currently attempting to express the halophilic enzymes from the marine bacterium Virgibacillus pantothenticus in the archaea host Haloferax volcanii. Specifically, my PhD project is focused on the marine environment potential as a source of new and unusual biocatalysts. The idea concerns in exploiting the ability of these novel enzymes to catalyse enantioselective conversion of pharmaceutical chiral intermediates.

Matteo Planchestainer

I am a 3rd year PhD student in Biocatalysis, in the context of enzymology and protein engineering mostly of enzyme from extremophiles.

Research area

I am interested in redesigning enzymes by engineering novel properties and understanding their structural behaviour. I am working on the evolution of a halophilic amino transaminase to accept non-natural substrates. I am carrying out a comparative study on glycosyl ydrolases from different extreme organisms to investigate how environmental adaptation affects enzymatic properties. Finally, I am also investigating metallo-enzymes in attempt to understand the role of the residues involved metal coordination by developing semi-synthetic biocatalysts.

David Roura Padrosa

I am a 1st year PhD student focused on the area of flow chemistry combined with biocatalysis. I studied a Bachelor degree in Biology and an MSc in Molecular Biology and Biomedicine at the University of Girona.

Research area

I joined Dr. Paradisi group to widen my professional horizons by gaining new  knowledge and experience in the study and application of enzymes. My main interests are protein expression and characterization, directed mutagenesis and in silico approaches for the optimizati on and better understanding of enzyme functions.

Alessandro Orlandini

I joined Dr. Paradisi group to widen my professional horizons by gaining new knowledge and experience in the study and application of enzymes. My main interests are protein expression and characterization, directed mutagenesis and in silico approaches for the optimization and better understanding of enzyme functions.

Research area

I am collaborating with the Synthetic Biology Research Centre on the assembly of biosynthetic pathways for the production of 3-hydroxypropionic acid (3-HPO) and its derivatives. Within this project my efforts will focus on trying to evolve a specific aminomutase capable of a biotransformation that doesn’t occur in nature. The evolution of this enzyme will significantly impact the overall process.

Dr. Jennifer Cassidy

I am currently a Post-doctoral researcher with Dr Paradisi. During my PhD in this group, my research focussed on the discovery and characterisation of novel enzymes from halophilic organisms.

Research area

My research interests include protein expression, purification, mutagenesis, homology modelling and in silico docking. At present, I am studying the effects of mutations on the substrate scope of alcohol dehydrogenases and how ionic liquids can be applied as green solvents.

Matteo Planchestainer

I am a 3rd year PhD student in Biocatalysis, in the context of enzymology and protein engineering mostly of enzyme from extremophiles.

Research area

I am interested in redesigning enzymes by engineering novel properties and understanding their structural behaviour. I am working on the evolution of a halophilic amino transaminase to accept non-natural substrates. I am carrying out a comparative study on glycosyl ydrolases from different extreme organisms to investigate how environmental adaptation affects enzymatic properties. Finally, I am also investigating metallo-enzymes in attempt to understand the role of the residues involved metal coordination by developing semi-synthetic biocatalysts.

Larah Bruen

I am a 3rd year PhD student focused on the area of biocatalysis, following a B.Sc. Chemistry degree in National University of Ireland, Galway.

Research area

My research is focused on an alcohol dehydrogenase from a halophilic archaea, and currently I am working to expand the substrate scope of this enzyme through in-silico docking and site-directed mutagenesis. In parallel, I am currently working on a novel method of screening mutant libraries of alcohol dehydrogenases.

Dr. Martina Contente

I am a post-doctoral researcher currently working in Professor Francesca Paradisi’s research group at the University of Nottingham.

Research area

I am very interested in Biocatalysis research in particular in using enzymes or engineered whole cells as catalysts for the preparation of chiral pharmaceutical intermediates. I am working on immobilized transaminase from halophilic microorganism and its different mutants for the transformation of various substrates, interesting building blocks for the synthesis of pharmaceuticals. I am also exploring new synthetic techniques for flow chemistry reactors.

Benedetta guidi

I am a PhD student in chemistry at University of Milan (Italy) currently visiting Dr. Paradisi’s research group.

Research area

I am currently attempting to express the halophilic enzymes from the marine bacterium Virgibacillus pantothenticus in the archaea host Haloferax volcanii. Specifically, my PhD project is focused on the marine environment potential as a source of new and unusual biocatalysts. The idea concerns in exploiting the ability of these novel enzymes to catalyse enantioselective conversion of pharmaceutical chiral intermediates.

Eimear Hegarty

I have recently joined the Paradisi Research Group as a 1st year PhD student having just completed my B.Sc. in Industrial Biochemistry at the University of Limerick (Ireland). 

Research area

With a keen interest in biocatalysis and enzyme engineering my research will focus on exploiting the hyper-salinity requirements of Haloferax volcanii to the advantage of biotechnology by developing it as a new expression system for proteins of industrial relevance.

David Roura Padrosa

I am a 1st year PhD student focused on the area of flow chemistry combined with biocatalysis. I studied a Bachelor degree in Biology and an MSc in Molecular Biology and Biomedicine at the University of Girona.

Research area

I joined Dr. Paradisi group to widen my professional horizons by gaining new knowledge and experience in the study and application of enzymes. My main interests are protein expression and characterization, directed mutagenesis and in silico approaches for the optimization and better understanding of enzyme functions.

Alessandro Orlandini

I am a 1st year PhD student working in Paradisi Research Lab at the University of Nottingham. I completed both my Bachelor in Biotechnology and my MSc in Industrial and Molecular Biotechnology at the University of Bologna (Italy).

Research area

I am collaborating with the Synthetic Biology Research Centre on the assembly of biosynthetic pathways for the production of 3-hydroxypropionic acid (3-HPO) and its derivatives. Within this project my efforts will focus on trying to evolve a specific aminomutase capable of a biotransformation that doesn’t occur in nature. The evolution of this enzyme will significantly impact the overall process.

Those that shared the journey

Dr. Kevin Devine, Senior Lecturer, London Metropolitan University, UK
Dr. Daniele Balducci
Dr. Elena Lestini, Post Doc, Dublin City University, IE
Dr. Ann-Kathrin Liliensiek, Researcher, Federal Institute of Hydrology, Essen, DE
Dr. Maeve O’Neill, Team Leader, Biocatalysts Ltd, Cardiff, UKK

Dr. Elaine O’Reilly (2010), Assistant Professor, University of Nottingham, UK
Dr. Gabriele Gucciardo (2010), Team Leader, Almac Group, Northern Ireland, UK
Dr. Sabrina Devereux (2010), Project Manager, Horizon Pharma Ireland, IE
Dr. Leanne Timpson (2011), Novozymes,  Nottingham, UK
Dr. Daniela Quaglia (2012), Post Doctoral Researcher, Université de Montréal, Canada
Dr. Philip Conway (2012), Technical Development Chemist, GSK, Cork, IE
Dr. Lara Pes (2013), Post Doctoral Researcher, Weill Cornell Medical College, NY, USA
Dr. Keith Robertson (2013), Technical Development Chemist, GSK, Cork, IE
Dr. Diya Alsafadi (2013), Researcher, Royal Scientific Society, Jordan
Dr. Jennifer Cassidy (2015), Post Doctoral Researcher, University College Dublin, IE
Dr. Anita Wester (2016).

Cillin Mac Donnchadha (2009), LEO Pharma, Dublin, IE

Outputs

Journal Articles

Reviews & Book

Patents

June 2016: The Tromsø Experience
Read more.
October 2016: Shiny New Lab
Here we are! After a lot of unpacking and patience too, our lab is ready to run!      
Read more.
December 2016: Jenni’s poster astonishes at CSCB symposium
Read more.
October 2016: Well done Anita!
Massive congratulations to Anita who successfully defended her thesis on the 4th of October 2016. Wishing you all the very
Read more.
June 2017: Corbella Summer School Keynote Lecture
Read more.
March 2017: Lab B11 road trip
Read more.
October 2016: Nott’s crew… Check!
Here we are! The group is finally complete and ready to kick off this new adventure!!        
Read more.
August 2016: Big changes ahead!
The group will shortly officially move to Nottingham, and we will have a number of new researchers joining us, so we
Read more.
September 2016: Leaving UCD
Emotional moment during Francesca’s leaving lecture in UCD few weeks ago. Many students, colleagues, and friends attended her fascinating summary of ten
Read more.
May 2017: Well done Larah!
Read more.
October 2016: Ben Feringa in Groningen
Pleasant surprise for Francesca e Matteo during the Novel Enzyme conference in Groningen (The Netherland) last week.   Bernard Lucas
Read more.
Biotrans 2017
Read more.

Collaborations

“A knotty puzzle may hold a scientist up for a century, when it may be that a colleague has

the solution already and is not even aware of the puzzle that it might solve.”

(Isaac Asimov, The Robots of Dawn)

Dr. Justin Siegel and Dr. Marc Facciotti, UC Davis, California, USA

Dr. Justin Siegel and Dr. Marc Facciotti, UC Davis, California, USA

Prof. Peg Gallagher and Dr. Ann Tallant

Prof. Peg Gallagher and Dr. Ann Tallant, Wake Forest University, North Carolina, USA

Dr. Cormac Murphy

Dr. Cormac Murphy, University College Dublin, Ireland

Prof. Prem Puri

Prof. Prem Puri, National Children’s Research Centre, Dublin, Ireland

Dr. Thorsten Allers

Dr. Thorsten Allers, University of Nottingham, UK

Dr. Adele Williamson

Dr. Adele Williamson, Tromso University, Norway

Prof. Martin Albrecht

Prof. Martin Albrecht, University of Bern, Switzerland

Prof. Francesco Molinari

Prof. Francesco Molinari, University of Milan, Italy

Dr. Alessandra Tolomelli

Dr. Alessandra Tolomelli, University of Bologna, Italy

Prof. Francesca Paradisi

Associate Professor in Biocatalysis and Enzyme Engineering

School of Chemistry |University of Nottingham| University Park Nottingham | NG7 2RD| UK

Phone: +44(0)115 74 86267

Email: francesca.paradisi@nottingham.ac.uk

School of Chemistry

University Park, Nottingham NG7 2RD, Regno Unito

Prof. Francesca Paradisi

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THANKS FOR VISITING US

Francesca Paradisi Research © 2016-2017  - School of Chemistry - University of Nottingham

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