• BSC
  • BSC
  • BSC

Computational study of coffee compounds for cancer prevention

The Project

Did you know that some molecules present in your breakfast are potential inhibitors of cancer cell proliferation? Unfortunately, their concentration in your coffee and cereals is very low, making extraction an unpractical way to obtain them. Nonetheless, we can produce them with enzymes. Learn how the reaction happens and take the chance to design your own enzyme to speed up the catalysis.

Experts believe that the next emerging biotechnological field is computer-aided protein engineering; proteins that are designed and edited on computers and then synthesized to produce novel types of medicines, catalysts and materials. State of the art softwares and supercomputing facilities open a new world on protein design, making the production of protein variants that satisfy specific industrial needs feasible. The growing popularity of enzymes resides in the need to substitute contaminating chemical processes to green biological reactions, since all the side-products formed are not harmful for the environment.  

In this project, we intend you to work as a real investigator. The main goal here is to design your own enzyme variant in order to speed up the production of a compound of industrial interest with applications in cancer prevention, among others, from molecules present in coffee plants. As in a real investigation, the most promising results (once the project is over) will be brought to an experimental lab to validate them and if it succeeds, you will be part of a scientific publication!

First of all, you will learn the role of proteins in industry and why they are becoming more and more important every day. Then, you will get familiarized with proteins and ligands and specifically with our working problem, the hydrolysis of esters to its respective alcohol and acid by means of a lipase protein. You will also use a database, the Protein Data Bank, to visualize and manipulate the 3D structure of a protein. Moreover, several bioinformatic tools will be provided to gather information about the system.

Therefore, you will acquire familiarity with regularly used softwares and the concepts behind them. First, you will learn how to prepare a protein in such a way that the simulation will reproduce the specified industrial conditions, like the working pH. Then, a Monte Carlo-based technique (PELE) will be used to simulate the interaction between several substrates and the protein in order to differentiate between a good binder and a non-binder. Moreover, you will learn to analyze the data obtained from your simulations and draw conclusions.

Finally, you will apply the techniques you learned for a real case. You will simulate the interaction between lipases and a putative, not previously tested, substrate. Then, you will propose your own mutations to tailor the protein to speed up anticancer molecules, considering the data obtained in the previous simulations. At the end, you will check your hypothesis comparing the simulations between the wild type and the mutant variant.

Besides the experience of being a computational researcher, you will have the opportunity of visiting MareNostrum, which consists in a guided tour through the infrastructures of one of the largest supercomputers in the world.

Join this project and be part of a real anticancer investigation!

Matching profiles

Chemistry, biology, biochemistry, computer science, bioinformatics

Required materials

Laptop

Coordinator of the project
Víctor Guallar

Víctor Guallar

Víctor Guallar studied as an undergraduate at the Autonomous University of Barcelona (Spain), major in Chemistry, followed by a joined PhD in physical chemistry at UC Berkeley and Autonomous University of Barcelona, with Professors Josep M. Lluch, Miquel Moreno and William H. Miller (November 1999 thesis defense). Then he moved to NYC for a postdoc (2000-2003) at Columbia University with Prof. Richard Friesner. After NYC, he got a tenured position as an assistant Professor at Washington University in St. Louis (2003-2006). In 2006 he was appointed Professor at the Catalan Institution for Research and Advanced Studies (ICREA) in the Life Science Department at the Barcelona Supercomputing Center (BSC).

Gerard Santiago

Gerard Santiago

Gerard Santiago obtained his Biochemistry degree by University of Barcelona (UB) in 2013, and a Bioengineering Master by Institut Químic de Sarrià (IQS) in 2015. He is currently a PhD candidate in Barcelona Supercomputing Center (BSC-CNS). His scientific career revolves around different levels of Green Biotechnology, such as: new enzyme discovery for industrial applications in extreme environments, production of high-value compounds on eukaryotic strains grow it in waste materials and enzyme design (focused on oxidoreductases) for eco-friendly industry.

Ferran Sancho

Ferran Sancho

Ferran Sancho obtained his Chemistry degree in 2013 followed by a Master’s degree in Theoretical Chemistry and Computational Modelling in 2015 at the University of Barcelona (UB). He is currently carrying on a PhD project at Barcelona Supercomputing Center (BSC-CNS) in the Life Science department. His open investigation lines are oxidoreductases catalysis, mainly flavoproteins and laccases, and the designing of new variants for industrial eco friendly applications.

The center
BSC

The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain.