Analogy of Drug Target in cartoon

My analogy of cat’s face with drug target such as HIV-protease. What makes them look like a cat? Conserved features (ears and whiskers), and Differential features (eyes and the shape of the face)

Drug is an inhibitor that stop the cat from meowing, such as this Star Corps Trooper helmet.

Let’s see what are possibilities if we are to fit cat’s face with a Star Corps Clone Trooper Helmet

 

Bad target arises when Tom’s picture is in complex because Jerry is there and it is of low resolution

Fluff friend cat called Syri and Garfield looks so common. The colour are the same and they have no special features, and they are promiscuous. If we have enough amount of pictures and they are in the same pose without distortion, it help with the design.

To discriminate them for helmet design, we need to understand their special features. If they are too similar, we may misidentify closely related cats such as the two kitties from Sanrio. It shows the reason why something we are targeting can fit the same models (this may cause drug’s side effects in the case of kinases)

Felix and Sylvester are unique. They are easy for the design of specific helmets for masking them.Most of the effort is CRISPR-cas9 is devoted to find a smart synthetic cat or a helmet that can perform our goal to control these mask singers.

 

 

 

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Why drug design researchers need MANORAA?

1. We are in the era with 100,000 protein structures available. Now we need to analyse what the crystallographic community already have rather than predicting probes in the vacuum.
2. When you know the ligand is bound inside the identifiable PDB crystal structure, it is surely affect that protein and we showed you the associated Ki from peer-review literature. So that is how we build the bridge from structures to precision medicine.
3. The residues that you want to fish out from the multiple alignment conservation may be there but may not be a must. The atoms that must be there are atoms that stay there and pair up with the ligand most of the time. The residues that causes the change in binding affinities is what you want to fish for selectivity.
4. What the drug community need is perhaps a linker such as MANORAA to go all the way from ligands to proteins, pathways, SNPs and target human organs plus a bit of help from the collaborative effort from various disciplines.
5. It is the very first attempt that ligand structures can complement the drug discovery pipeline with mostly experimental data source support to the expression levels.
6. It works on your phone, tablet, mac and PC so I can browse my drug on the go.
7. Its ligand superposition function allows you to make programmable code for fragments superposition on the URL so your drug fragment remains anonymous.
8. It is open and free but we will need to survive on citation.

Reference: MANORAA paper

 

 

Designing & Sewing future

 

When I was a young girl I wondered,

How Singer machine can neatly

Help my Mom sew zillion of artistry-

Tailor made and fancy wedding gown.

She was a professional dress maker,

Designer of her own fashion.

How pity she’s in heaven for one,

Life was stunt I’ve never get to sew.

That time I was only eleven

It happened like a flash of memory

I grew up a humble & tiny

Tailor-made drug design researcher.

Machines at present day are very wise.

Poem like this one, can it weave?

I was told AI will replicize

Till human like I will be defeated.

On the origins of enzyme inhibitor selectivity and promiscuity

For students who are interested in helping establishing my projects and laboratory in Thailand, please contact me directly at the Institute of Molecular Biosciences, Mahidol University.

MAHORI tutorial

This is a screenshot from my webservice MAHORI. The service has an aim to assist fragment-based inhibitor design. It is a bit complicate to use and therefore I create a video from a screen capturing program.

The idea is that similar chemical fragments in the binding pocket of proteins should make contact to similar atomic environment. If you choose the set of hetero-atoms that can influence the binding, you will find that they form similar numbers of interactions in various pockets.

The example illustrates the use of staurosporine’s N4 and O6 atoms, which forms similar number of interactions among various kinases. If you have a fragment of interest, you can put those fragments to look for the existing environment in the Protein Data Bank. Maybe those outputs resemble your pocket of interest.