Design of a novel peptide inhibitor

[bionerd]

Hi,

I was wondering if you all could help me design a project:

I was thinking of designing a CXCR4 antagonist as a potential HIV therapeutic. Today, most anti-retroviral therapies hinge on the use of non nucleotide reverse transcriptase inhibitors (NRTIs) or protease inhibitors (PIs) as therapeutics against HIV. However, many of these are extremely expensive, bear large side effects, and lead to drug resistance. As a result, a new class of inhibitors is urgently needed. The identification of entry inhibitors of HIV pose a promising new approach to curbing HIV propagation. HIV relies on two chemokine receptors on CD4+ T cells for entry: CXCR4 and CCR5. While CCR5 antagonists are well established, they do have potentially cytotoxic effects. As a result, the design of CXCR4 inhibitors could pose extremely useful in stoping HIV propagation. Recently, AMD3100 and AMD070 were identified as inhibitors of CXCR4 for blocking HIV-1 entry, but they showed cardio-toxic effects in vivo and/or lead to rapid heart beats. As a result, a new class of CXCR4 inhibitors is needed and could help to stop propagation of HIV-1.

My question is: What are potential inhibitors of CXCR4 and are they effective therapeutics to block HIV-1 propagation?

What I will need to do is some type of in silico study to identify potential antagonists and then verify in vitro which candidates are effective, run time course studies, cytopathic/cytotoxicity studies, dose-response analysis, etc. The work would take on a "working title" of CXCR4 antagonist design: identification and verification of in silico candidates as effective HIV-1 entry inhibitors.

I currently work in an HIV biology lab, but before I propose a project like this to my mentor, I need to have an idea of how to actually design the inhibitors and chose good inhibitor candidates in silico. I have understanding of protein database (PDB) files, PyMOL, jMOL, etc. as well as molecular biology but nothing in the line of pharmacology as this project would demand. Can anyone help me develop a project like this?

[deleted-132180]

Hello there,

To be honest, I don't know too much about designing small molecule inhibitors, but some questions came to mind as I read your post and perhaps you would like to keep these in mind as you develop your project ideas further. You mentioned that AMD3100 and AMD070 were recently identified as inhibitors of CXCR4 for blocking HIV-1 entry, but they showed cardio-toxic effects in vivo and/or lead to rapid heart beats. Is it known why these specific inhibitors have these effects (for example, do they triggering signaling pathways in cells that cause death or other toxic outcomes)? Is it due to general binding/blocking of CXCR4? Or is it a molecule-specific effect? Because if binding/blocking of CXCR4 in general is going to be toxic to cells, then I don't know whether designing other inhibitors that bind to CXCR4 will be the way to go. However, if the toxic effects are only specific to those two inhibitors, but not to other molecules that can bind to CXCR4, then it is possible that designing other potential inhibitors would work. I suggest you to actually talk to your mentor about wanting to design CXCR4 inhibitors because he/she would likely have a much better idea of whether this project is feasible and can provide lots of suggestions as to things you can try and things to avoid trying because they are likely not going to work. Once you have a more concrete idea of what your project is going to be like, then you can figure out the skill sets and programs you need in order to address your question.

Let us know if you have anymore questions.

Connie

[bionerd]

Yes, both the AMD inhibitors had agonist-specific cytotoxic effects, but it is conceivable that there could be a different, less toxic inhibitor

Is there a good way to start designing a small molecule inhibitor in silico?

-Reese

[bionerd]

Can anyone help me?

[SciB]

I would suggest that you try a college level or professional forum for your questions.

Sybee

[bionerd]

Hi SciB,

As a high school student, yes it has been challenging to find some help on such a specific project. Is there a specific forum (url) or place to go to do that?

Thanks!

[deleted-141593]

Hi Bionerd,

You can try the advanced forum: https://www.sciencebuddies.org/science- ... m.php?f=39

Also, this is a topic on which there is quite a bit of information: https://www.google.com/search?es_sm=122 ... S3ZM6Nig8A

Good example:
http://www.thno.org/v03p0047.htm

You can look a strategies other people have tried and see what makes sense to you. As an example, you can either try to mimic the structure of the natural chemokine ligands or the portion of HIV that binds CXCR4 (I think it's the gp120 V3 loop).

Also, how would you evaluate efficacy? Do you have recombinant HIV gp120? If not, you might only be able to evaluate binding of your inhibitor to CXCR4 and not inhibition of HIV protein engagement.

Do some reading and write back with your thoughts.

Cheers,
Colin