In this two-part post, I will give you the guidelines about the methods used for prediction of the properties of molecules.
Basic methods are extremely simple to implement in your daily scientific activities if you in some branch of analytical chemistry (HPLC and related) and can help you when you want to publish the paper as the spice and allow you to have a much better discussion of the results.
Some of the answers include the following questions:
• is that molecule solvable in water/ oil?
• can it enter the bloodstream?
• can it enter the brain, because there is the BBB (blood-brain barrier)
• Does it resemble some known drug?
• What could be its mechanism of action?
• Is it biodegradable?
A relatively precise answer to all these questions can be given simpler than you imagine – you just need to draw the formula.
If you are not a scientist, this post will also help you in real-life because you will be able to personally.
This is for the surface properties, we will do this in Part II, so stay tuned/ follow.
Image was stolen from here
SAR Studies
The abbreviation SAR stands for the Structure-Activity Relationships.
The first practical implementations started in the 80’s, continued during the 90’s but the market exploded in the late 2000’s with more than a million scientific publications, according to scholar.google.
The logic is simple:
• some physicochemical property is measured for various molecules to form the database
• molecules are translated into the fragments (example)
I drow it, no copyright :)
This molecule can be represented as 3 x CH3, 1 x C and 1 x OH
The effect of each group is linear and additive (the simplest imaginable approach)
3 x a x CH3 + b x C + c x OH = some measurement
You can DIY with your personal database, just solve the system of equations (divide the matrices in Matlab, it works fine... \ )
But wait, 3D structure, conformations…
You are right, all those effects are important, but on a bulk scale, when something should be just roughly estimated, this approximation works perfectly fine.
Let’s play together!
Open this website: http://www.swissadme.ch/
and draw the molecule you like.
Just because it’s winter we will draw this lovely bornyl acetate, the smell of the Christmas tree.
The acronym on the right panel, SMILES, is the 1D array that represents the molecules.
Run!
What have we got?
TPSA – total polar surface area is the parameter that is used in medicinal chemistry. If the values is > 140, the permeability into the cells will be poor. It would be good if the value is < 90.
LogP – parameter that describes the lipophilicity (solvability in oils vs water). There are numerous methods how this should be calculated, but more-less all of them give the same results
Pharmacokinetics is fun…
- Can this be absorbed by ingestion – yes
- BBB means can it enter the brain - yes
Drug-likeness apply several filters like the Molecular weight, Number of O and N atoms, LogP, TPSA and compares it with the potential drugs.
Now you know how to test the molecules
And see if the new molecule extracted from some exotic plant really has some logic or it will be forever promising compound.
To read more about "forever promising" molecules, go to this post by @suesa
Sources:
- Website for the predictor link
- Compounds that provides the smell of the Christmas tree, link
- SMILES abbreviation, link
- Ertl, Peter, Bernhard Rohde, and Paul Selzer. "Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties." Journal of medicinal chemistry 43.20 (2000): 3714-3717. link
- Mannhold, Raimund, et al. "Calculation of molecular lipophilicity: State‐of‐the‐art and comparison of log P methods on more than 96,000 compounds." Journal of pharmaceutical sciences 98.3 (2009): 861-893. link
- Lipinski’s rule of five
Stay tuned for the Part II, we will play in 3D
Upvote, good job. I like chemistry a lot. Alex, i don't know how upvote works. Look, i started with +28, after that i had +20, +14+ and now is in +12, why is down every time!!! HELP.
You mean the steem power in the brackets? It goes down with the time, I think that after 50 days I have about 9. Don't worry too much about it because the curation awards for young users are very small < 1 Steem per week and you can upvote yourself with the max 0.01$ per post, thus also not too important.
Good luck with the Nissan ;)
Thanks, i will upload videos fixing it.
The guildlines are perfect.. 👍 am https://steemit.com/@micahkitty
Thank you very much and welcome to SteemIt.
Just be aware when you make the comments with the links directing to you, as many people could consider it to be a spam and flag you.
It's just an unwritten rule, make a nice, long comment, stay with the topic and no links that are not directly related to the post.
keep voting work as a team
But the SteemIt doesn't work like this :(
I have only 10 votes per day, and there is a lot of high-quality content that deserves my votes.
Make some good content, and the results will come.
Vote-for-vote can't work: 10 x 0.01 or less = 0.1 max per day
We can do it for the whole year, make 365 bad posts each and earn less than with one single post well-written post.
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