We follow a holistic approach to discovery projects by studying the target of interest and the different pathways. We have standardized procedures and highly-skilled scientists for solving complex problems related to discovery. The CADD facility routinely supports discovery projects starting from target identification to clinical positioning of the candidate compound. We have a wide range of tools available for compound optimization. Also, we have proven expertise in collaborative small molecule, PROTAC and peptide drug discovery projects.
Virtual screening is a powerful modeling technique to identify novel hit compounds in any discovery program. It is routinely deployed in drug discovery projects for compound ideation and conceptualization. Virtual screening has multiple applications including hit scouting and hit-to-lead optimization.
The techniques deal with computational or in silico analog of biological screening to score, rank, and/or filter a set of structures using one or more computational procedures. This helps to decide which compounds to screen, which libraries to synthesize, and which compounds to purchase from an external source. Virtual screening uses both structures, ligand or compound-guided computational methods, or a combination of both.
We have access to more than two billion commercially available compounds’ databases. This database is routinely used to carry out virtual screening studies to facilitate the compound design and ideation.
Structure-based design approach exploits disease-related targets by experimentally determining 3-dimensional structure (e.g. X-ray, NMR, or Cryo-EM) or homology model (in case of unavailability of experimental structure). This method is performed to predict the binding pose of the molecule in the binding site and estimate probable binding affinity or a score representing the strength of binding.
We use docking and molecular dynamics simulation to shortlist compounds that may become a good hit or lead for a project.
Ligand or compound-based design is another powerful modeling technique used in CADD. Some of the most used techniques routinely deployed at Aurigene include pharmacophore modeling, quantitative structure-activity relationship (QSAR), or knowledge-based expert methods, for compound design and ideation. We use a ligand-based design approach in de novo, scaffold hopping, ligand hybridization, fragment-linking and related techniques. The ligand-based approach is not limited to compound designs but is also deployed in a predictive model. Predictive models built using AI/ML techniques are used at our facility to determine compound potency, selectivity and Physico-chemical properties. This in turn facilitates project progress.
Our CADD and bioinformatics facility are equipped with a state-of-the-art “Nanome” interactive virtual reality platform. This is supplemented by the acclaimed "MolSoft" commercial suite of software to carry out all modeling studies. Additionally, our team uses open-source CADD-related software (e.g. KNIME, Cytoscape and Datawarrior) to enrich modeling and simulation-related work. We use a public-domain database to enrich our understanding of disease biology and chemical space. Our facility is equipped with a high-end workstation to cater to the need for CPU/GPU intensive simulation and AI/ML-related activity.
3-D virtual reality facility
High-end software for simulation & modelling (MolSoft)
Team lead by domain expert in CADD and Informatics
JUNE 28, 2022
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