in silico drug discovery

Hi,

I am new to in silico drug discovery. I am trying to learn the things. So I am looking for some one who can guide me.

In my experiments I found one compound, very potent on cacer cells, no deviations from Lipinski's rule of five. So I would like to proceed as follows:

1. Searching for similar compounds in a database.

2. Docking the similar compounds on a possible targets to determine the relative scores.

3. Optimising the lead compound.

I am not sure whether chemaxon softwares would be sufficient to try my ideas.

I appreciate if anyone lends helping hand.

Kindest regards

 

Hi,

1. You can search for similar compounds in many ways. Apart from fingerprint based chemical similarity, the Screen tool provides other flexible decriptors (like pharmacophores) as a basis of the similarity. You can read more details of the features in the technical presentation.

You might be interested in, the Flexible 3D alignment tool as well, that can be use to compare the spacial overlap of the identified molecules with your active one.

2. We have no docking application, but we support many file formats, that the docking tools can accept.

3. The optimization of the lead is a complex issue, the selection of applicable software applications depend on your goals, so entire toolkit is available. However, the calculation plugins offer countless functions for the estimation of physicochemical properties. I would advise to take a look at the Chemical Terms presentation that allows you to easily create your custom property filters by the combination of properties. The Chemical Terms filters can be used in many applications, such as Instant JChem or JChem for Excel to filter compounds in databases or chemical spreadsheets. The jcsearch command tool can filter molecules directly in your files. You can calculate the Chemical Terms values using the evaluate command line tool.

I am very interested to have some feedback from you to learn what were the most useful components and how you could use them in your project. Might you need any assistance or have questions, please do not hesitate to contact us. If you prefer we can arrange a web meeting with our scientists to discuss how we can help in your discovery.

 

Best regards

Hi, 

Though it's not docking, but flexible 3D alignment might be useful. With this you can model the receptor by a pharmacophore hypothesis and you can align your structures onto this model.

Regards

Miklos