Category Archives: drugs

Summer of High Performance Computing

Summer of High Performance computing (HPC) is a PRACE programme that offers summer placements at HPC centres across Europe. This year 21 top applicants from across Europe were selected to participate and I was lucky to host two excellent students, Samanta and Juan. They spent two months working on projects in my lab related to HPC.

Samanta worked on understanding the dynamics of the protein human Thymidine Kinase 1 (hTK1), which is crucial for DNA biosynthesis, using Molecular Dynamics simulations. She delivered the project and created an excellent video, I hope you enjoy it!


Juan worked on a computer-aided drug design project. One of the initial steps in drug discovery projects is the virtual screening of small molecules against a set of targets to predict their affinity. Juan created a Python tool has been added to our existing ChemBioServer website that filters compounds so as to be specific for a given set of proteins. He successfully completed the projected and brought new functionality to our server. Enjoy his explanatory video.

Free Virtual Symposium: Advances in Drug Discovery and Development

On September 24, 2014, a world-class group of scientists from biotech, pharma and academia will present the latest research findings and new technologies that are driving the design, discovery and development of new drugs – from small molecules and monoclonals to RNA therapeutics and gene-editing technologies.

testtubes3The event is free and organized by the American Chemical Society (ACS) and ACS’s magazine C&EN news.

To register for free please follow this link.  Even if you can’t make the live lectures or the time zone is not convenient for you, all presentations will be archived and available on demand for three months.

You will even have the chance to “Walk the floor” in a virtual exhibition hall, participate in panel discussions and Q&A sessions and do live-chat with peers and vendors

Some of the talks that I find interesting:

Accurate Prediction of Ligand Binding Free Energies – MARK MURCKO, PhD (Disruptive Biomedical LLC)

Design of Protein Structures, Functions and Assemblies – DAVID BAKER, PhD (HHMI/Univ of Washington)

Site-directed ligand discovery for cryptic sites – MICHELLE ARKIN PhD (UCSF)

The Promises and Challenges of Next-Generation Therapeutics – GREG VERDINE, PhD (Warp Drive Bio)

Structure based Drug Design: G-protein coupled receptors using StaR tech – FIONA MARSHALL (Heptares)

Drug Repositioning in the Era of Personalized Medicine – CRAIG WEBB, PhD (NuMedii)

Panel Discussion:The Business of Biotech – LUKE TIMMERMAN, MATT HERPER, MANDY JACKSON

Exploiting cell death for drug discovery – BRENT STOCKWELL, PhD (HHMI/Columbia University)

The VCNDD: CNS Drug Discovery in Academia – CRAIG W. LINDSLEY, PhD (Vanderbilt Center – VCNDD)

Targeting Lysine Acetylation in Cancer – JAY BRADNER, MD (Dana Farber Cancer Institute)

How are drugs designed?

How are drugs designed? Come on Friday 2nd May at 18:00 at the Athens Science Festival, Technopolis Gkazi to listen to my talk! See the detailed program of the festival here.

CADDThis talk will address how drugs are designed to combat a disease – from the discovery of the cause of the disease (e.g. a mutant protein), specialized techniques for the design of small chemical molecules (that are drugs), to clinical trials. We will also discuss advances and progresses in individualized treatment (also known as personalized medicine), i.e. how DNA testing could help each patient receive medication specifically tailored for them.

Πώς σχεδιάζονται τα φάρμακα; Ελάτε την Παρασκευή 2 Μαϊου στις 18:00 στο Athens Science Festival, Τεχνοπολις Γκάζι, να ακούσετε την ομιλία μου.

Η ομιλία έχει θέμα το πώς επιτελείται ο σχεδιασμός φαρμάκων για μία ασθένεια – από την ανακάλυψη του αιτίου που προκαλεί την ασθένεια (π.χ. μια μεταλλαγμένη πρωτεΐνη), εξειδικευμένες τεχνικές για το σχεδιασμό μικρών χημικών μορίων που αποτελούν τα φάρμακα, μεχρι και τις κλινικές δοκιμές. Επίσης θα συζητήσουμε τις προοπτικές και εξελίξεις στην εξατομικευμένη θεραπεία, το πώς δηλαδή με εξέταση DNA μπορεί ο κάθε ασθενής να λαμβάνει ένα φάρμακο που είναι ειδικά κατάλληλο για εκείνον.

Περισσότερες πληροφορίες και μία μικρή περίληψη για το θέμα θα βρείτε σε πρόσφατο άρθρο στην ιστοσελίδα της διοργάνωσης.


A Day in the Life of a Computational Chemist

As you know if you have been following this blog, I have always been fascinated by how the world around us works. Why is the sky blue? Why are bubbles in a soft drink spherical? How do we fall in love? What are we really made of?

This inherent curiosity led me to become a scientist. I studied Chemistry but soon enough I realized that being a chemist makes a huge mess or at least I made one in the lab! Fortunately, I then realized that computers exist and they make things much cleaner. I discovered that today it is possible to build chemicals, study reactions, or even make drugs within a desktop computer by performing virtual experiments in a similar way as the typical chemists. This type of chemistry is called “computational chemistry”. So I became a computational chemist. Indeed, I literally live in a virtual reality world, where everything from chemical reactions to drugs, food, materials, cosmetics, electronics, and prImageoteins is being modeled and simulated. And you won’t believe it, but, yes, I do have a job!

I am a group leader at the Biomedical Research Foundation of the Academy of Athens.  I specialize in “computer-aided drug design”, so the computer is my Virgil in the world of drugs (to paraphrase the original Nobel Committee tagline). The main activity of my lab is the design of anti-cancer candidate drugs. Recent advances in computer-aided drug design allow us to develop drugs specifically designed for a given protein, shortening the development cycle of new drugs.

Do you want to learn more about what it means to be a computational chemist and how I spend my day? For more details and a video on the life of a computational chemist, please read my full blog post at the Wiley Exchanges site.


PS. My Doktorvater, Jeremy Smith, was also kind enough to link to this post in his own blog!

Five new candidate drugs are revealed in the ACS New Orleans meeting

The ACS National Spring Meeting took place 7-11 April in New Orleans.

As is traditional for the Medicinal Chemistry Division, structures of candidate drugs get revealed in the “First-Time Disclosures” session.

This year’s entries are:






More about how where these drugs discovered:


Kalydeco: The most important new drug of 2012

Kalydeco, a drug for cystic fibrosis, is the most important new drug of 2012 according to Forbes magazine and was developed by Vertex pharmaceuticals with seed funding from the Cystic Fibrosis Foundation.

Cystic Fibrosis is a genetic disorder that results in scarring (fibrosis) and cyst formation within the pancreas, lungs, liver, and intestines.


Kalydeco’s chemical structure, costing $294,000 per patient per year

Kalydeco, given alone, will only help a few thousand patients the world over. Like other drugs for very rare diseases, its price is very high: $294,000 per patient per year.

Though its chemical structure could be routinely made by a synthetic chemist, it is covered by a patent so it is illegal to make in a lab.

The efforts to cure cystic fibrosis were spearheaded by a discovery from Francis Collins, later famous for heading the Human Genome Project and then the National Institutes of Health, who discovered the gene that, when mutated, causes cystic fibrosis 23 years ago. Kalydeco is the first drug to directly affect the defects caused by these mutations, leading to improvements in patients’ lung function.

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