Computational chemistry has been embraced by drug discovery as a key complementary technology to medicinal and organic chemistry [1]. For instance, several big pharmaceutical companies arrange research divisions into smaller groups of cross-disciplinary researchers including computational chemists as primary stakeholders operating in a biotech environment [2].

Medicinal chemistry CROs and computational chemistry

What is the situation in small and medium Contract Research Organizations (CRO) with a deep expertise in medicinal chemistry?  Some of these CROs have already built computational chemistry efforts in-house or have established collaborations with Computer-Aided Drug Design (CADD) service providers, while some are still reluctant to explore this field.  The main reason is unfamiliarity, which often raises two key questions:

• What are the benefits of adding computational chemistry to a drug discovery project?
• Will computational chemistry over-take medicinal chemistry?

There are multiple benefits to consider:

• Computational chemistry can be used to move High-Throughput Screening (HTS) assays from a brute force approach to guided experiments, reducing HTS costs by up to 1,500X as shown by ex-Pharmacia (now Pfizer) [3].
• Synthesis can also be sped up by allowing medicinal and organic chemists to concentrate on fewer compounds [4] since in-silico models have shown successful use in qualifying hits from HTS [5].
• CADD tools allow fast and inexpensive access to different virtual libraries that increase the chances of exploring a wider chemical space.

All the aforementioned examples are translated into the design and optimization of more robust leads.

The answer to the second question is an outright “no”: computational chemistry cannot substitute medicinal chemistry know-how. Computational chemistry provides more insights into ligand-target interactions and this information is very useful for medicinal chemists in the creative process of lead design and optimization.

Collaboration models

There are several ways in which a medicinal chemistry CRO can use CADD as complementary technology: It may either build such an effort in-house or establish external collaborations with a preferred partner.

Alternatively, it may establish relationships with several partners on a per-project basis. In case of external partners, several factors need to be considered such as the technology, area of expertise and know-how, costs, trust, flexibility and geographical influence.

In summary, computational chemistry is used as a complementary technology to reduce the costs and increase the efficiency of target-to-hit, hit-to-lead and lead optimization drug discovery stages. In the new collaborative and fragmented drug discovery ecosystem [6], new opportunities arise to reduce the gap between extremely specialized organizations and consequently improve efficiency in R&D.

Have an open discussion with us!

To find out how Pharmacelera can help you to complement your technology with CADD, contact us for an open discussion.

References

[1] G. Sliwoski, S. Kothiwale, J. Meiler, E. Lowe, “Computational Methods in Drug discovery”, Pharmacological Reviews, January 2014
[2] T.J. Ritchie, I.M. McLay, “Should medicinal chemists do molecular modelling?”, feature in Drug Discovery Today, January 2012

[3] T. Doman, S. McGovern, B. Witherbee, T. Kasten, R. Kurumbail, W. Stallings, D. Connolly, B. Shoichet, “Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B”, Journal of Medicinal Chemistry, April 2002

[4] S. Basak, “Chemobioinformatics: the Advancing Frontier of Computer-Aided Drug Design in the Post-Genomic Era”, Curr Comput Aided Drug Des, March 2012

[5] R. Malik, D. Bunkar, B. S. Choudhary, S. Srivastava, P. Mehta, and M. Sharma, “High throughput virtual screening and in silico ADMET analysis for rapid and efficient identification of potential PAP248-286 aggregation inhibitors as anti-HIV agents,” J. Mol. Struct., vol. 1122, pp. 239–246, Oct. 2016.

[6] S. Mignani, S. Huber, H. Tomás, J. Rodrigues, J-P. Majoral, “Why and How Have Drug Discovery Strategies Changed? What are the New Mindsets?”, Drug Discovery Today, February 2016