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.
The four modules contain multiple talks on the drug discovery process and are delivered by expert chemists working in top pharmaceutical companies in the world. Attendants will learn about Strategies to Improve Solubility of Drug Candidates, PAINS filters, using PET for Labeling in Drug Discovery & Development, Pharmacokinetic Considerations in Drug Design and Development, and more.
Module 1: Improving Drug Design Efficiency and Efficacy
Module 2: Activity/Potency Screening for Drug Lead and Candidate Optimization
Module 3: Enabling Drug Delivery
Module 4: Pharmacokinetics
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.
The 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? 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.
This 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.
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 proteins 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.
Love at first sight? Desire in a bottle? There have been a lot of claims about what pheromones can do, but what is the science? Dr. George Preti and Dr. Charles J. Wysocki of the Monell Chemical Senses Center discuss the chemistry of pheromones and how mood and emotion can be communicated through chemical signals.
“SMEs- The new tools/opportunities for access to finance introduced by Horizon 2020” by Jean-David Malo, Head of Unit SMEs, Financial Instruments and State Aid, Directorate General for Research and Innovation, EC.
“Access to risk finance”
Part of the horizon 2020 budget, that is 3,69% (2.7 billion euros) will be provided though grant funding but in the form of risk sharing for loans and guarantees and by providing risk finance (equity).
Goal: stimulate more investment in research and innovation To attract additional finance and multiply horizon 2020 budget resources for SMEs
Because of enduring difficulties in SMEs in accessing startup/Grant finance and because of the need to build an integrated European VC market
They cover a broad range of interventions such as :
- Guarantees to mutual guarantee societies and banks lending to companies incl SMEs
- Equity participation for early and growth stage investments
This funding will be typically delivered via financial intermediaries (banks funds etc) but also directly Operated by the EIB group but may also be operated by other financial institutions
Debt finance can be achieved through the following schemes:
- Loans service for R&I (called “RSFFII”) Loans and guarantees for investments in research and innovation; targeted at midcaps and larger companies, research institutes and Stand alone projects Loan amounts over 7,5 million
- Sme and small midcaps R&I loans service Loan guarantee facility between 25,000 to 7.5 million
- SME initiative : Joint guarantee instrument an securitization for loans to innovative SMEs and small midcaps
Equity finance (next year):
-Early stage finance for innovative enterprises
-Pilot facility for tech transfer , creation of spin offs
More info on the initiatives can be also found here.
For the full presentation of Horizon 2020’s Financial Instruments, check this link.
The new drug approvals for 2013 were mostly cancer drugs and drugs for orphan diseases.
Other therapeutic areas included metabolic and endocrinological therapies (two type 2 diabetes drugs and one dyslipidaemia drug), antivirals (two hepatitis C virus (HCV) drugs and an HIV drug) and medical imaging products (three approvals).
Several of these new drugs are scientifically novel.
Gilead’s sofosbuvir is first-in-class NS5B polymerase inhibitor and the first oral HCV drug (Nature Rev. Drug Discov. 12, 409–411; 2013).
Pharmacyclics and Janssen’s ibrutinib is a first-in-class Bruton’s tyrosine kinase (BTK) inhibitor, which entered the clinic in 2009, and is now approved for an aggressive form of B cell non-Hodgkin’s lymphoma, but it is now being also tested for other types of cancers such as chronic lymphocytic leukaemia (CLL). Ibrutinib is the second irreversible kinase inhibitor to be approved after afatinib, setting new hope for the development of irreversible agents that have been thought difficult to reach the market in earlier years (Nature Rev. Drug Discov. 12, 649–651; 2013).
Biogen Idec’s dimethyl fumarate (formerly BG-12) is an extremely small molecule (MW only 144 Da) that had been approved as an anti-psoriasis drug in Germany as well as for preventing the growth of mold in furniture! Now Biogen Idec gets its approval for dimethyl fumarate as the third oral drug for multiple sclerosis. Drug mechanism remains unclear.
GSK’s trametinib is a first-in-class MAPK/ERK kinase (MEK) inhibitor that overcame bioavailability, pharmacokinetics and toxicity problems of previous drug candidates (Nature Rev. Drug Discov. 11, 819–820; 2012). Trametinib is approved for cancers bearing specific BRAF mutations (such as metastatic melanoma). GSK picked up five approvals from the FDA last year (counting the approval granted to ViiV), more than any other drug developer in 2013.
Janssen’s canagliflozin, is the first-FDA approved sodium-dependent glucose cotransporter 2 (SGLT2) inhibitor, against type 2 diabetes space.
Genzyme and Isis’s mipomersen acts on a novel target, binding apolipoprotein B mRNA, reducing protein synthesis and thereby lowering low-density lipoprotein (LDL) levels. Because of its side effects it may be used only as an orphan disease drug agains homozygous familial hypercholesterolaemia and not as a general cholesterol-lowering agent. Regulators in the European Union (EU) have rejected mipomersen because of its side-effects.