The GP was talking about pharma. Proteins are not niche in pharma. Everything else may be niche in that domain, but proteins make up more than 95% of the targets of the pharmaceutical industry.
Also, it is likely important steps how to research and produce protein drugs, but the end target is to cure diseases, so you need lots of additional data about diseases of all types, symptoms, pathways, trials, etc.
Your sources are talking about the ratio of small molecule vs. large molecule drugs. Even if you're developing small molecule drugs you are likely targeting some aspect of protein signaling/gene expression.
People are being dismissive of your comments because to say that proteins are niche in the context of pharma is like saying advertising is niche in the context of Meta and Google.
> People are being dismissive of your comments because to say that proteins are niche in the context of pharma is like saying advertising is niche in the context of Meta and Google.
its all about how you define word "niche", for google, main revenue stream is supported by several pillars: search tech, infra tech, ads tech, ecosystem+network effect, human management. You remove one pillar, and everything is destroyed, so one can say ads is one of the niches in their food chain. I suspect with proteins it is about the same.
> in the context of pharma
there is no context of pharma. Post is about more broad bio-medical publications.
So the pathway to synthesize every protein is +/- the same: That's gene transcription[1] and translation[2]. If that's broken, you're in big trouble!
But if you mean in general if you're capable of looking at metabolic pathways where each protein catalyses a step in the pathway, that's definitely interesting. If a certain person has a flawed gene coding for protein X, that could indeed cause a problem.
To find valid answers, you might need to eg. track nodes and states in a graph, to figure all the consequences of a break. Not all types of storage systems/engines are equally good at that.
I read the post before I made any criticism of your comments. We're talking on a thread within the larger context of comments on the post. But more importantly, if you read the post, you will see there is a theme of industrial biochemistry (IE, pharma and biotech) running through it, because pharma/biotech is the primary consumer of these products, and the vast majority of the revenue stream.
that's one of the themes (and you are already working hard to stretch drugs pharma to "biochemistry"), if you can't see other themes in his examples and screenshots, I think this discussion is not interesting to me.
Hi there. Apologies for any confusion. I was clarifying the intent of the first comment in this thread. I will add some impressionistic comments below in case it helps your future service.
Even when a drug target is unknown, or remains mysterious, very high chances are that the target is a protein. DNA or RNA as targets are niche (DNA is often avoided as a target on purpose and it’s hard to be specific to it without DNA-like material, and RNA is still hard to target effectively, though things are improving). There is not much else of use in the cells (lipids, sugars, cofactors, and metabolites, some examples of which have been targeted by a couple drugs each over the long history of trials, often unintentionally.
Small molecules are an excellent modality for an eventual approved therapy. They almost always (so far) targets a protein. They are hard to design but when they are done well they expose the target to something nature hasn’t seen before in order to get a desired effect. Sometimes people don’t care about the target itself (think recreational drugs, or phenotypic drug discovery), but the target typically remains a protein.
Proteins make up the machinery of the cell. You jam or modify them to achieve desired effects.
Also, and totally minor: there are nowhere close to 19k different approved small molecules. The same drug can be included in multiple products or formulations bringing that number you mentioned to 19k marketed products. Each generic formulation of iboprofen increases the latter count by 1. Counting all the marketed products of pure orange juice may add up to a large number but it is still one ingredient.
No. The analysis in the paper above referred to molecules vs the snippet in the fda referred to products. More generally, other than marketing materials to doctors or patients or very rare exceptions talking about formulations etc, the scientific literature refers to the molecular entity as a drug not the particular named/branded product. I hope that the tool you are building will not mix up such concepts.
Yes that is the standard language in the field. It does not refer to the number of marketed products. Look up the number of novel drugs approved by the FDA per year. It only recently exceeded 40 per year, and the FDA has not existed for very long.
if we consider that you are not making things up(which I am very not confident), then your link is useless in this discussion, because it doesn't give a sense how many non-protein targeting drugs were approved by FDA.
and an increasing number of drugs- in the "old days" it was almost entirely small molecules, but they are starting to peter out (both because the low-hanging fruit has already been plucked, and also, small molecules are a usually a terrible way to modulate biological activity in specific ways.
