Covalent Docking

At CD ComputaBio, we offer cutting-edge Covalent Docking services to cater to the needs of our clients in the pharmaceutical, biotechnology, and academic research fields. Our experienced team of experts is dedicated to providing high-quality solutions that drive innovation and accelerate drug discovery processes. With our state-of-the-art technology and customized approach, we strive to meet and exceed the expectations of our clients. Below, we outline the key aspects of our Covalent Docking Service, including service items, applications, and the software and tools we utilize.

Applications of Covalent Docking

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  Targeted Drug Design

  Covalent Docking plays a pivotal role in the rational design of targeted therapies by enabling the identification of covalent inhibitors that selectively bind to the desired target protein. This approach enhances the specificity and efficacy of drug candidates.
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  Fragment-Based Drug Discovery

  Covalent Docking is instrumental in fragment-based drug discovery by assisting in the identification and optimization of fragment hits that can form covalent bonds with the target protein. This strategy accelerates the development of novel therapeutics with enhanced potency.
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  Mechanism of Action Studies

  Covalent Docking facilitates elucidating the mechanism of action of covalent inhibitors by predicting the binding mode and interactions at the atomic level. This information aids in understanding the structural basis of target engagement and guiding subsequent optimization efforts.

Our Services

• Covalent Docking Simulation
  Using molecular docking techniques, we simulate the binding interactions between the target protein and the ligand. Our Covalent Docking simulations provide valuable insights into the covalent bond formation and stability, aiding in the design of potent inhibitors.

Fig 1. Covalent docking

• Reactivity Assessment
  We conduct in-depth reactivity assessments to evaluate the stability and reactivity of the covalent adduct formed between the ligand and the target protein. This analysis helps in predicting the pharmacokinetic properties and safety profile of the covalent inhibitors.
• Hit-to-Lead Optimization
  Through iterative cycles of virtual screening and molecular docking, we facilitate the hit-to-lead optimization process to identify lead compounds with improved binding affinity and selectivity. Our tailored approach ensures the rapid progression of promising candidates towards preclinical studies.

Fig 2. Lead optimization

Software and Tools

Schrödinger Suite

We harness the power of Schrödinger's advanced modeling tools, such as Maestro and Glide, for molecular docking simulations and binding affinity predictions. This suite enables us to perform high-throughput screening and lead optimization efficiently.

MOE (Molecular Operating Environment)

MOE's comprehensive set of modules for structure-based drug design and molecular modeling allows us to visualize complex protein-ligand interactions, analyze binding affinity, and optimize lead compounds for covalent interactions.

Service Features

• Accurate Binding Mode Prediction - Using AIPharmX^TM platform, our scientists can quickly sample initial poses of a large number of pre-reacted species while optimizing ligand poses and attached residues to produce reasonable physicochemistry. The resulting accuracy is superior to other docking programs, achieving lower RMS deviations from native co-crystallized structures.
• Complete Workflow - First, on the AIPharmX^TM platform, our scientists dock pre-reacted ligands to determine feasible poses that bring the reactive groups into proximity with the reactive receptor residues. Then, covalent bonds are formed for the top-scoring complex structures, covalently attached ligands are sampled, and the complexes are scored using all-atom molecular mechanics, OPLS force field, and VSGB2.0 implicit solvent model.

At CD ComputaBio, our Covalent Docking Service is designed to empower researchers and drug discovery professionals with the tools and insights needed to accelerate their projects and achieve success in developing novel therapeutic agents. By combining our expertise, state-of-the-art technologies, and a customer-centric approach, we are committed to delivering tailored solutions that drive innovation and promote scientific advancement. If you are interested in our services or have any questions, please feel free to contact us.