Drug design is an expensive and laborious process to develop new drugs. But pharmacophore modeling is a successful and very diverse subfield of computer-aided drug design. With the support of our advanced protein engineering platform established for many years, Creative BioMart has successfully applied pharmacophore to a wide range of rational design of new drugs. Our scientists provide you with fully customized pharmacophore modeling and screening service to identify similar active molecules against specific target proteins based on structure and ligand pharmacophore models, in which the binding affinity of large-scale compounds to target macromolecules can be determined by in silico Molecular docking process is easily evaluated.

A pharmacophore is a collection of steric and electronic features necessary to ensure optimal supramolecular interaction with a specific biological target and trigger (or block) its biological response. Each type of atom or group in a molecule that exhibits certain properties relevant to molecular recognition can be reduced to a pharmacophore feature. Pharmacophores are now one of the most advanced techniques widely used in various ways in computer-aided drug design projects. Pharmacophore modeling methods have been widely used in virtual screening, lead optimization, target identification, toxicity prediction, and lead de novo design due to their simplicity and versatility. In addition, it is also of great significance in the research of fragment-based drug design and lead design for protein-protein interaction interface and target-based chemical spatial classification. Today, a series of automated pharmacophore modeling and screening tools continue to emerge, and pharmacophore modeling and screening is one of the appropriate choices for researchers in drug discovery and design.

Fig 1. The full framework of pharmacophore architecture. (Yang S Y, 2010)

Services

Pharmacophore modeling has become a well-established method for computer-aided drug design with many different applications in drug discovery. Creative BioMart is committed to developing pharmacophore modeling and screening platforms to identify similar active molecules against specific target proteins, and to simulate the binding mode of bioactive molecules to target binding sites, including HB formation, columbium interactions, metal interactions interaction, hydrophobic contact, aromatic stacking, or charge transfer interactions. Pharmacophore models can be built in a ligand-based manner by stacking a set of active molecules and extracting common interaction features necessary for their biological activity. On the other hand, if the three-dimensional structures of the receptors have been reported, they can be constructed in a structure-based manner by probing possible interaction points in the receptor binding pocket. We offer the following pharmacophore modeling and screening services, including but not limited to:

• Ligand-Based Pharmacophore Modeling
• Structure-Based Pharmacophore Modeling

Our pharmacophore modeling and screening services have been widely used for similarity measurement, virtual screening, ligand optimization, scaffold hopping, target identification, etc. In addition, our scientists will strive to further develop the role of the pharmacophore in protein engineering for different applications to maximize their utilization.

(1) Fragment-based drug design: using computational pharmacophore methods to identify novel derivatives. For example, pharmacophore fingerprint-based similarity searches and generation of 3D pharmacophore queries identify larger and more potent molecules from small molecule libraries.

(2) Protein-protein interaction (PPI) inhibition: different approaches can be used to map pharmacophore signatures to amino acids present at the PPI interface.

(3) Protein design: pharmacophores can be used simply by reversing the small molecule drug design process of known protein structures.

Service Principle

Creative BioMart is based on innovative, pragmatic and honest, adhering to the tenet of "Quality is our life, providing customers with the best quality service", providing customized services to customers around the world.

We will be glad to discuss details of intended interaction studies with you and develop experimental strategies/methods tailored to your requirement. Our customer service representatives are enthusiastic and trustworthy 24 hours a day, Monday to Friday. If you are interested in our services, please do not hesitate to contact us for more information or to discuss in detail.

References

1. Choudhury, C., & Narahari Sastry, G. (2019). Pharmacophore modelling and screening: concepts, recent developments and applications in rational drug design. In Structural bioinformatics: Applications in preclinical drug discovery process (pp. 25-53). Springer, Cham.
2. Yang S Y. (2010) Pharmacophore modeling and applications in drug discovery: challenges and recent advances[J]. Drug discovery today. 15(11-12): 444-450.

• Computational Drug Discovery and Development Service