Service Offering

Moleculomics offers a bespoke protein structure prediction service for individual or small sets of proteins.

Using the world-leading protein modelling platform developed at Swansea University over a period of 15 years and reviewed in over 50+ peer reviewed publications[1], and access to the comprehensive Human3DProteome platform, 3D structural models may be  produced directly from sequence for any protein of interest from any organism, including protein variants (mutations) due to single nucleotide polymorphisms.

An accurate 3D model is the basis to understanding how the protein of interest interacts with other molecules; synthetic and/or organic.  Popular workflows offered by Moleculomics include the following which may be customised to suit the scientific questions being addressed;

• Structure-function annotation
• Active site delineation
• Molecular docking (small molecule, peptide and biologics)
• Addition of cofactors and prosthetic groups
• Prediction of protein-protein interactions
• Peptide design and docking
• In silico pathway analysis (mapping proteins of interest to pathways and disease areas)
• Assessment of resistance and protein evolution
• Identification of homologous regions for repurposing and broad spectrum therapeutic development
• In silico protein engineering

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For further information, please contact info@moleculomics.com to discuss your specific requirements.

High throughput affinity screening and docking of compounds against panels of proteins of known toxicity to identify and eliminate problem compounds earlier within the R&D cycle

The prevailing approach to active molecule discovery in recent decades is that of rational molecular design, involving the development of new ligands for a specific target (normally a specific site in a single protein or a small number of targets that bind with the ligand).  Adverse events due to off-target interactions are not widely assessed by in silico approaches.  In vitro approaches are increasingly employed, typically involving toxicology panels comprising binding assays for around 44 protein receptors [Bowes et al., (2012)]. Such in vitro toxicology panel data provide valuable validation information for in silico approaches.

Moleculomics offer an in silico screening platform that will enable analysis of the predicted interaction between any compound and panels of selected target proteins. Two such panels are offered which may be used at any point during the R&D cycle, although best suited to preclinical or phase zero pharmaceutical profiling:

Panel 44 – A target panel of 44 receptors adopted as the industry standard first step in the drug discovery process, as recommended by four major pharmaceutical companies (Joanne Bowes and colleagues^[1]).

Panel 331 – A panel of similar concept to Panel 44, this time based upon the in silico screening of 331 enzymatic and receptor signalling assays featured in Sipes et al., 2013^[2] and collated in the ToxCast database.

The products described above offer the following benefits:

• A wealth of extremely valuable molecular knowledge which enables a paradigm shift from reliance on observing effects at cellular (in vitro) and animal (in vivo) level, to predicting effects based on an understanding of the whole system at the molecular level.

• A reduction in both drug development time and costs through the ability to screen for toxic or adverse reactions to enable users to identify and eliminate problem compounds sooner within the R&D cycle.

• Substantially reduced lead times and lower screening costs to the equivalent in vitro

• A reduced reliance upon animal testing.

This quantitative simulation method offers significant savings in time, money and material over expensive in vitro and in vivo studies as the first step in the drug discovery process for the identification of the most problematic off-target interactions.

[1] Bowes et al (2012), Nature reviews: Drug Discovery, 11: 909-922

[2] Profiling 976 ToxCast Chemicals across 331Enzymatic and Receptor Signaling Assays – Sipes et al 2013.

High throughput affinity screening and docking of specified compounds against any of 47 tissue specific panels of proteins to provide molecular and structural information to evaluate compound efficacy and toxicity

Drugs fail for a number of reasons.  Challenged fundamentally by a lack of efficacy and/or high toxicity, the underlying problem is that interactions between proteins and chemical compounds are highly complex.

Moleculomics have developed tools to assist the development of compounds by supplementing the R&D process with information relating to the structural and functional interactions of compounds with whole tissue panels.

This service provides predicted affinities for any given compound or libraries of compounds through assessment of the affinity of a given interaction, normalised to an extensive validation exercise involving the high throughput screening of vast libraries to calculate binding affinity “hit thresholds”.  This system offers a proven and extensively validated process which not only predicts hits, but also supplements R&D processes with data such as the 3D structural models, and assessment of the binding site to confirm whether or not a ligand is bound at the normal activation site or an alternative docking site. This approach is able to rationalise both silent antagonists and agonists whereby ligands are predicted to bind with the target, but not activating the associated pathway.  Finally, Structure-Activity relationship data is provided for each hit, where possible.

Moleculomics offer 47 separate tissue panels which are equally powerful in the understanding of both efficacious and toxic effects.  Popular panels include; skin and eye for the assessment of toxic effects and also the liver panel to assess and understand the metabolism of the compound.

Screening novel compounds against specific tissue panels provides an efficient and cost effective method to accelerate the R&D process, however this fails to predict the interaction of the compound/s across the whole proteome which is critical in understanding off target interactions.

High throughput affinity screening and docking of compounds against whole proteomes to provide comprehensive molecular and structural information to evaluate compound efficacy and toxicity

The ability to predict the interaction between a limited number of proteins and compounds provides a wealth of structural and functional information to assist drug design, however it fails to realise the full potential of in silico approaches. Moleculomics have developed innovative high throughput algorithms to provide a comprehensive screen against the whole human proteome.

This approach provides information pertaining to every “hit” within the human proteome, which when analysed in conjunction with Pathway Analysis provides full knowledge of potential adverse outcomes at whole proteome scale.

Annotated Protein-Protein Interaction data pertaining to link Molecular Initiation Events with understanding of Modes of Action and tissue specific pathway analysis

Moleculomics offer Pathway Analysis tools to facilitate the understanding of molecular events from the Molecular Initiation Event (the first interaction of a chemical with a biological system) through a series of events to identify the mechanism of a given outcome; efficacious or toxic.

This approach advances compound development processes from assessment of traditional endpoints to mechanistic understanding of chemical interactions at a molecular level.

At whole proteome level, pathway analysis spans multiple levels of biological organisation from the initial exposure to a chemical through to the systemic outcome(s).

This tool is offered as an extension to tissue specific screening and/or whole proteome screening (link to each) to facilitate comprehensive understanding, not only of the interaction of a chemical with a receptor, but an understanding of the associated consequences; the activation or deactivation of specific pathways.

These novel approaches will need to advance the design of currently available predictive tools to enable:

• Screening of chemicals for interaction with numerous receptors.

• Identification, qualitative and quantitative assessment of receptor binding.

• Understanding of the (potential) consequences of binding (e.g. is binding likely to result in an adverse event?).

• Improved, human-relevant safety assessment across the bioscience sector.

The current Pathway Analysis tool is focussed upon toxicology studies.  A similar tool is currently being developed to identify efficacious pathways, linked to disease networks which will be released soon…

Prepopulated platforms of protein-ligand or protein-protein interactions developed to your specification providing high value molecular and structural information, integrated to your existing workflow

Moleculomics appreciate the limitations of outsourcing and understand that a “black box” solution is not always required.  For this reason we have created an interface to allow easy integration into your workflow to empower your researchers to extract answers to the questions of relevance to your R&D programmes.

The interface is designed to accommodate any of the Moleculomics services described in Service Offering.  The system is fully customisable, the full potential of the system is indicated below:

Re-Drug is a comprehensive Artificial Intelligence-based screening technology for the assessment of both on-target (efficacy) and off-target (potential toxicity) of a candidate therapeutic drawn from the pool of around 1400 FDA approved drugs, screened for repositioning opportunities across more than 1400 known drug targets.

This whole system framework provides an assessment of the candidate drug’s predicted behaviour based upon comparison with the established mechanistic data for a broad range of currently used drugs, encompassing both drug efficacy and potential toxicity.

Re-Drug outputs comprehensive reports on FDA-approved drugs which inform drug discovery and repositioning research including the following:

• Repositioning FDA approved drugs for new targets of interest
• Identification of combinations of downstream pathway events and therapeutic actions for repositioning of drugs targeting multiple sites and effects
• Identification of marketed drugs and reference compounds with similar pharmacological profiles to that of a candidate (currently non-approved) compound
• Opportunities for therapeutic switching by prediction of clinical effects of new drug candidates based on the well characterized in vivo effects of drugs with similar profiles
• Characterization of individual interactions of a candidate (non-approved) compound in the context of similar interactions of currently marketed drugs and reference compounds
• Down-selection of candidate drugs and the preliminary identification of potential efficacious applications and/or toxicity issues by profiling to currently approved drugs

The Re-Drug screening technology is available on both a per compound report basis or as a full web-enabled system interface.

For more information, please contact info@moleculomics.com

Cross-species comparative in silico platform
Comparing liver protein interactions across human, mouse and rat

This tool helps researchers compare compound interactions with liver proteins across 3 species.
A compound can be chosen, and a report is produced showing protein interactions in humans, associated pathways, and which proteins are most similar in mouse and rat.

This is intended to help inform decisions about whether rat or mouse, or neither, is the most appropriate animal model for studying a specific interaction in humans.

Click here to access the free version of CRISP for FDA approved compounds. This has been created with support from the NC3Rs: CRISP (Free Version)

For your own proprietary compounds, click here to go to our Hit To Lead Portal website to purchase a report: CRISP (purchase)