Natural products and drug discovery: an evolutionary take

A question (of the nice variety) that students sometimes ask is about the relevance of natural products. The answer is a yes-and-no answer. I like to add to the usual arguments, an evolutionary take, which is two sided. A lot of secondary metabolites made by plants have been evolved to kill you (a mostly herbivore), but your liver has been evolved to be good at destroying them. For drug discovery, this has two opposite effects: the pro is a long list of antibacterial, antifungal and anticancer compounds to use or to adapt, the con is their ADME (absorption, distribution, metabolism, and excretion) properties have frustrated medchemists for decades and decades. Herein, the two faces of this coin are explored not by advocating for or against natural products, but exploring what they mean for medicinal chemistry.

Crossposting

 I have been rather quiet here, my personal blog, for a variety of reasons. As part of OPIG, I have written a few posts there (Blopig), some on requests (who would willingly write about fixing CUDA installations or exposing Jupyter notebooks in a compute node via reverse port forwarding?) and some out of personal choice. I have been involved in various projects, many of which I would like to write blog post about or people would like me to write about, so I am well behind on what I would like to post.

Custom carbon colours in py3Dmol

 Due to NGLView (the Python module) having a frozen older IPywidget version it breaks Colab and the major change for the latter library was a year ago (early 2023), so I am forced to revisit old code and switch to py3Dmol in my Colab demos. Today I figured out how to use custom carbon colours.

A possible BioB bipass route

Nearly a decade ago there was something bugging me and I believe I have figured it out —although it's pointless now. Namely, is another way of making biotin possible without using BioB, biotin synthase, an incredibly slow multistep radical SAM enzyme. 

Reading compressed molecular files on NFS

There are some tasks that make one feel like a failed door-to-door evangelist, one amongst these is proselyting about using compressed files on networked file systems. Namely, NFS are slower than local SSD drives, so most often it is actually quicker to read compressed files in memory rather than decompress them to disk. Here are two Python snippets for dealing with small molecule files.

A note on PLIP interactions

PLIP is a handy tool to enumerate the interactions of a given ligand. However, a few of tripping point I keep having is related to the fact the interactions are namedtuples. Here are some notes to circumvent the traps.

7 colour electronic paper

For Christmas I recieved a 5.65" seven-colour e-paper display, which is awesome. The catch as everything with a Raspberry Pi or Arduino is that beyond the gloss of the advert is something that is far from a flexible plug and play system. I enjoyed my voyage, but it was rather odd even if typical of a Raspberry Pi project.