Computational Chemistry Services

Effective drug candidates by design

Utilising computational chemistry can significantly improve the efficiency of drug discovery, especially when it is well integrated with a dynamic medicinal chemistry team, as at Domainex. The ongoing development of theoretical models, based on the most up-to-date results, ensures that scientists have the best opportunity of designing relevant novel chemical entities.

Through its dedicated computer-aided drug design (CADD) team led by Drs. Christine Richardson and Stuart Firth-Clark, Domainex provides integrated and stand-alone expertise in a range of computational chemistry solutions including:

Computational chemistry at Domainex – computer modelling of target and inhibitor  Computational chemistry at Domainex – computer modelling of target and inhibitor

Hit finding through our proven LeadBuilder approach

This involves the virtual screening of our lead-like (Number of Interesting Chemical entities, NICE) database of over 1.6 million compounds using a combination of pharmacophore- and structure-based techniques (such as docking). See 'LeadBuilder' for more information.

 

Ligand-Based Drug Design 

Our CADD team can assist you in analysing the similarity of active compounds and identifying whether there are common pharmacophore features (such as hydrogen-bond donors, hydrogen-bond acceptors, aromatic rings, etc) across a range of active compounds. Such information can be very useful as input into a virtual screening approach, such as LeadBuilder.

Our experts will work closely with you to analyse and prioritise your data – for example, they could cluster your dataset and identify a subset of molecules for further development.

If you have a small dataset and need to explore some Structure Activity Relationships (SAR), our CADD team could search our curated proprietary databases of commercially available suppliers for nearest neighbour analogues which can be subsequently purchased and tested.

Computational chemistry at Domainex – scaffold hopping techniques

Structure-based drug design (SBDD)

Our CADD team can assist you in analysing any available structural information on biomolecules of interest and help you design and prioritise possible ligands which bind to your nominated target. The CADD team can also use their expertise to modify existing biomolecular structures.  This could include building a ligand into an apo structure that requires some conformational adjustment to allow the ligand to fit the proposed binding site (for an example of this see our protease inhibitor case study). Additionally, if your target is a member of a large protein family, then our CADD team can overlay the protein structures, and identify any unique hot-spots of interaction for that target.

 

Novel Molecule Design

Our CADD team can design novel compounds and using techniques such as docking, ensure that these molecules are appropriate for your target. Our medicinal chemistry team would also be involved to identify potential synthesis routes for these compounds. The methodology can be applied to fragments, lead- or drug-like compounds, depending on your requirements. Our CADD team can also employ Scaffold Hopping approaches which will help you to explore chemical space for active compounds that are not covered by patent restrictions.

 

Fragment Library Design

Our CADD team can help you design a fragment library using their proprietary fragment analysis tools and can be used in conjunction with Novel Molecule Design to provide a bespoke fragment library for you. If required, our medicinal chemistry team can synthesize the novel fragments, while our FragmentBuilder team can provide fragment screening services.

 

Virtual Library Design

Our CADD team can design library arrays that are tailored to your target. By enumerating the possibilities by virtually reacting available reagents together, and subsequently docking and analysing the output, our CADD and medicinal chemistry teams can provide you with a list of reagents which would result in ligands well suited to the target of interest.

 

Physical Property Modelling/QSAR

Our CADD team has access to physical property calculators such as LogP, LogD, and Polar Surface Area. They can also flag chemical groups which potentially show toxicity, reactivity or assay interference liabilities. In addition to the physical property calculators, they can train new physical property models based on your data, thereby producing calculated properties that are potentially more reliable for your project.

 

Homology Modelling

Our CADD team would be happy to assist you in generating a 3D model if there is no current structural data of your target available. They can identify closely related proteins which do have a structure, and while checking to ensure that these structures are appropriate to be used as a template, they can build a 3D model that could be subsequently used for SBDD analysis, virtual screening and virtual library design.

 

Molecular Dynamics (MD)

Our CADD team has expertise and access to Molecular Dynamics tools which can be used to generate different conformations of the target and/or identify regions of the target that are likely to show mobility. MD can also be used to explore the conformational potential energy surface of ligands to identify low-energy conformers in vacuo, or in the presence of solvent water.

 

The examples we have described here are a selection of our capabilities. Our experienced CADD team would be happy to discuss additional requirements you have and provide you with a bespoke CADD service that is tailored to your needs. If you would like to discover more about our computational chemistry services, discuss specific research, or receive a proposal, please contact us or email enquiries@domainex.co.uk