Computational Modeling in the service of health

Technological evolution is increasingly present in all areas of our lives. In today’s article we look at how its application in the chemical sciences through what is known as Computational Chemistry influences the development of modern chemistry, biochemistry, physics and materials science.

This role has been widely recognized by the international scientific community and this recognition was forged in the 1998 awarding of the Nobel Prize in Chemistry to John A. Pople, precisely for having made Computational Chemistry a predictive tool and therefore practically indispensable in any field of Chemistry and Physics.

This year’s Nobel Prize in Chemistry also goes to Martin Karplus, Michael Levitt and Arieh Warshel for “the development of computational models for the description of complex chemical systems”. His work is part of computational chemistry, a discipline that uses computers instead of traditional test tubes to study the properties, behavior and reactivity of chemical substances.

One of the partners of the OLIGOFASTX consortium in Spain stands out in this field: Nostrum Biodiscovery. In particular, his expertise lies in the application of computational chemistry tools aimed at accelerating, streamlining and optimizing the design of small biomolecules.

NOSTRUM BIODISCOVERY S.L. is a spin-off of the Barcelona Supercomputing Center (BSC) and the Institute for Research in Biomedicine (IRB), dedicated to the development and exploitation of state-of-the-art computational biochemistry and simulation tools for the design of next-generation biotechnological products and therapies.

In particular, NOSTRUM BIODISCOVERY has developed strong expertise (internationally) in early stage drug discovery and enzyme/protein engineering (including direct in silico evolution and antibody design/optimization), PROTAC, PPI, Molecular Glues, small molecule RNA and aptamers.

“The impact of computational simulation on the drug discovery process is increasingly significant. Public and private research groups are making increasing use of in silico technologies which, being directly related to the increased computing power of computers, are becoming more and more powerful and significantly reduce the time and cost of drug development,” explains Modesto Orozco, president of NBD.

All this experience is embodied in a co-development strategy to bring to market new assets that address unmet medical needs. These include, but are not limited to, the following therapeutic areas:

  • Ischemia
  • Oncology
  • Aging
  • Schizofrenia
  • Parkinson
  • Rare diseases
Pipeline NBD. Source:

R&D&I in its purest form

To this end, NOSTRUM BIODISCOVERY has created the NBDSuite® Platform: an end-to-end software solution for life sciences that encompasses molecular modeling in drug discovery and enzyme engineering with bioinformatics powered by explainable Artificial Intelligence.

At its heart is PELE, an in-house Monte Carlo algorithm that can explore a wide range of the conformational space of biological systems within a few hours. It is suitable for determining the binding mode of small molecules at a protein binding site, taking into account the flexibility of the surrounding side chains.

This platform can be combined with other computational techniques, such as molecular dynamics simulations, to obtain a time-resolved picture of macromolecules that explicitly describes their accessible conformational space and the coupling of their dynamics with the potential ligand(s) and solvent.

Thanks to partners such as NBD, the OLIGOFASTX consortium combines synergies of its components and allows for faster and safer project progress while covering all areas and stages of development of solutions for untreated rare diseases.