Wikipedia:Featured article candidates/Enzyme inhibitor

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Enzyme inhibitor[edit]

Self-nomination. This article tries to provide a reasonably complete account of the types of enzyme inhibitors, how they are investigated and why they are important. TimVickers 20:10, 17 September 2006 (UTC)[reply]

  • Comments again, nicely organized and well illustrated, but a few nitpicks:
  • The lead is arguably a little skimpy, and the last sentence could be clearer. Also it seems from the second paragraph that noncovalent bonding can't lead to (effectively) irreversible inhibition, which the text specifically mentions later.
Re-written last sentence, expanded the remainder of the intro, mentioning metabolic control. I was careful to say "Usually" when talking about irreversible inhibitors here, since I didn't want to give too much detail in the intro. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • There's only a brief mention of negative feedback inhibition in metabolic pathways. Considering how important a subject this is, it seems like there should be more discussion of it - maybe a paragraph about the major feedback loops in glyolysis, for example.
Yes, this was a major omission. New section on metabolic control replaced the brief mention of recreational drugs. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • Similarly, there should be a mention of protein inhibitors somewhere - such as the barnase/barstar system or the ribonuclease inhibitor.
I've put this in the metabolic control section. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • Both this article and the Lineweaver-Burk plot article are inconsistent in the spelling of "Burk" (which I thought was the correct spelling, but I could be wrong).
Burk is the correct spelling, how embarassing! TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • The Lineweaver-Burk plot image could use labels for the axis intercepts. (Might also be clearer labeled as "V-1".)
I tried adding these in, but to be large enough to be readable they made the plots look very cluttered. I've put this in the text.
I too found the old format a bit confusing at first glance (1/V and 1/S). I modified these a bit to make it more clear, I also changed it to [S] to denote substrate concentration. I made the most inhibited plot on the mixed graph more inclined since it was a bit cramped at the 1/Km intercept. I also changed the text to non-serif (Arial) since in my opinon it is clearer. I hope i was not too bold here. David D. (Talk) 21:50, 18 September 2006 (UTC)[reply]
Excellent figure. Much better. Thank you David. TimVickers 21:55, 18 September 2006 (UTC)[reply]
Linked next to kinetic scheme for reversible inhibitors. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • Couple of copyediting issues: "Sometimes in drug design it is important to take into consideration the concentrations of the substrates that enzymes are exposed to." (Just sometimes?),
Ah, yes, not exactly what I inteneded to say. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • "Natural enzyme inhibitors are often poisons that have evolved to defend a plant or animal against predators, these include some of the most poisonous compounds known." (a few comma splices in need of semicolons).
Split into 2 sentences. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • The paragraph about poisonous enzymes, while interesting, doesn't really fit with the theme of enzyme inhibition as written.
Good point, rewritten first part and removed second. TimVickers 21:53, 18 September 2006 (UTC)[reply]

Opabinia regalis 00:01, 18 September 2006 (UTC)[reply]

Looks good! Support. One other very minor comment: in the penicillin image, maybe render the actual penicillin molecule with fatter bonds? It's kind of hard to see against the black background. Opabinia regalis 02:55, 19 September 2006 (UTC)[reply]
I made a nicer one, anything to keep you happy. ;) TimVickers 03:34, 19 September 2006 (UTC)[reply]
Hmm, how about some chocolate then? :) But seriously, nice article. It's great to have the foundations of enzymology as well laid out as they are in your articles. Opabinia regalis 04:52, 20 September 2006 (UTC)[reply]
  • Comments:
  • "in the figure above left, an enzyme binds to its substrate S to form the enzyme-substrate complex ES. " - you meane right...
Corrected. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • in section Reversible inhibitors, images should change place
Moved images so they're next to the text referring to them. TimVickers 17:34, 18 September 2006 (UTC)[reply]
  • more external links?
Added some and removed linkspam. TimVickers 17:34, 18 September 2006 (UTC)[reply]
Good images. Stolen one - I thought the start of the article was a bit dry. TimVickers 17:34, 18 September 2006 (UTC)[reply]

Anyway, it's a perfectly referenced article, well-written, well-organised. Really great job! NCurse work 05:27, 18 September 2006 (UTC)[reply]

  • Support - thanks for your work TimVickers! NCurse work 06:18, 19 September 2006 (UTC)[reply]
  • Strong Support This is a wonderful article of top quality! This rivals many textbooks I have read, complete, without being too intimidating. Adenosine | Talk 09:40, 18 September 2006 (UTC)[reply]
  • Support. Comments. I'd support with a reduction of short, orphan paragraphs throughout wherever possible. Short paragraphs highlight areas that should either be expanded into a full idea, merged with related material or removed. Especially in the lead. The lead should be 3-4 full, cohesive, and well structured paragraphs — no fragmented ones. Otherwise the lead presents the material well, and is as accessible to a non technical reader as I imagine could be done for this topic. It's possible there's one orphan paragraph in the article that can't be fixed due to the technical nature of the topic, but see if you can eliminate them all. - Taxman Talk 22:51, 18 September 2006 (UTC)[reply]
I've done some more work on the introduction and merged several one-sentence paragraphs. TimVickers 23:55, 18 September 2006 (UTC)[reply]
Looks better. The rest certainly looks good, though I can't vouch for the content. Last thing is the 'Natural Poisons' section is choppy and doesn't flow well. Merging the first two para's into a cohesive one that's not redundant would work, or adding a transition that adds context about why the two ideas are different and need to be separate paras would help. I would have fixed it if I knew enough about the material to do it justice. Support now anyway, but see if you can't improve that. - Taxman Talk 13:46, 19 September 2006 (UTC)[reply]
  • Strong Support This is outstanding work! The only complaint I have is some white space in the Chemotherapy area, but even so it doesn't diminish my support for this article.--DaveOinSF 23:04, 18 September 2006 (UTC)[reply]
Thank you. What screen resolution are you using? I've laid this out for optimal viewing at 1024x768 pixels. TimVickers 02:27, 19 September 2006 (UTC)[reply]
I'm using 1024x768 as well. When I maximize the browser window, there is a large gap immediately below the "Chemotherapy" subheading. I see this both on my home computer and my one at work. I don't know why this is happening, but I'd like to know if other users do indeed see this as well. The methotrexate and folic acid graphic is immediately to the right of the large white space.--DaveOinSF 03:53, 19 September 2006 (UTC)[reply]
I can't see any space, is the Viagra structure figure displayed? TimVickers 04:17, 19 September 2006 (UTC)[reply]
I can't see a space either. David D. (Talk) 04:20, 19 September 2006 (UTC)[reply]
Ah! I can see it if I use Microsoft Internet Explorer. Strange. Any ideas David? TimVickers 04:23, 19 September 2006 (UTC)[reply]
I'm using a mac with safari. i don't have explorer here to check. i would suggest moving the figures around. I think that is the issue here becuase it is quite cramped. Maybe have all the figures in the same section, or in a table to ensure they stay together. David D. (Talk) 06:12, 19 September 2006 (UTC)[reply]
Thanks David, that's it fixed. TimVickers 13:50, 19 September 2006 (UTC)[reply]
Yes, fixed for me too.--DaveOinSF 17:02, 19 September 2006 (UTC)[reply]
  • Oppose for now. The kinetics section is very good, but I would have hoped to read more about the molecular basis of enzyme inhibition. Dr Zak 16:14, 19 September 2006 (UTC)[reply]
  • Support, now that the article has more of the underlying chemistry in it. Dr Zak 23:40, 19 September 2006 (UTC)[reply]
Do you want more detail on how ligands bind to proteins? There is a specialised page on this topic Ligand (biochemistry). I have added a link to this page in the introduction of article. TimVickers 16:42, 19 September 2006 (UTC)[reply]
This is a good point. At present there are different types of inhibitors mentioned but the idea is never really centralised. At present substrate and allosteric are covered in detail as is covalent vs non covalent binding of inhibitors. A distinction between protein and organic molecules is made. At the end you briefly mention posttranslation control with respect to ricin. While i had thought this was outside the scope of the article, I don't really think of this and an enzyme inhibitor, if we have a section on differnt type of inhibition it would be quite a suitable topic. Lastly regulation of gene expression is touched on in a few cases certainly this distinct could be more fully explained in a molecular mechanisms section. Sorry for rambling a bit here. I'll think on this some more. David D. (Talk) 16:54, 19 September 2006 (UTC)[reply]
First it would defintiely be a good idea to mention and link to the types of interactions. I think a discussion of substrate Kd vs inhibitor Ki values might be useful too. For example, often poisons are so toxic because they have a much lower Ki compared to the enzymes Km for normal substrates. If not competing, their toxicty is extreme due to their very low Ki values. David D. (Talk) 16:58, 19 September 2006 (UTC)[reply]
I just checked out the ligand link and at present it does not really mention molecular interactions. David D. (Talk) 17:03, 19 September 2006 (UTC)[reply]
Well, the article talks about DFP and how it phosphorylates the serine in the active site. If we had a couple more examples of enzyme inhibition on a molecular basis complete with structural formulas I'll change to support immediately. For example, eflornithine is mentioned briefly, but without formula and reaction mechanism, and we don't have a picture for the neuraminidase inhibitor either. Dr Zak 17:36, 19 September 2006 (UTC)[reply]
I have added a discussion of the practical meaning of Ki and I will add a reaction mechanism for DFMO and there is now an explanation of non-covalent interactions at the beginning of the section on reversible inhibitors. Thanks for raising this point, this was a serious omission. TimVickers 17:43, 19 September 2006 (UTC)[reply]
Cheers, brother! Any chance of you mentioning the antitrypsin? This protein has a very appealing structure! Dr Zak 17:50, 19 September 2006 (UTC)[reply]
It is mentioned in the metabolic control section, I could add a note that this is a natural transition state analogue if you wanted. TimVickers 17:57, 19 September 2006 (UTC)[reply]
Sorry, didn't notice! In my mind that protein is the prime, textbook example of a competitive inhibitor. Also, a graphic of that might make a more striking title picture than the current one as it is immediately obvious how the antitrypsin manages to inhibit trypsine activity. Dr Zak 18:09, 19 September 2006 (UTC)[reply]
I'm at risk of annoying an obvious and passionate antitrypsin fan! However, I think when most people think of enzyme inhibitors they think of drugs, and this is certainly their major practical application. This is why I discussed drugs first and concentrate the article on this subject. TimVickers 18:39, 19 September 2006 (UTC)[reply]
I snuck them back in. :-) Do revert me if you think that's over the top! The picture that was there before was of a fly agaric, which is known for muscarine, not for amanitin. The death cap mushroom does contain amanitin, but Image:3 types of lentil.jpg is nicer than Image:Amanita phalloides 1.JPG. Dr Zak 03:53, 20 September 2006 (UTC)[reply]
The "Natural toxins" section can actually do with improvement. Most of the compounds listed there are not enzyme inhibitors, and that includes taxol.
I have now added a new figure showing the mechanism of DFMO inhibition. TimVickers 22:37, 19 September 2006 (UTC)[reply]
Thanks! Dr Zak 23:40, 19 September 2006 (UTC)[reply]
  • Comment. Does sildenafil (Viagra) need to use the brandname as the main name? This hasn't been done with other pharmaceuticals eg ritonavir (Norvir). The article could do with a careful copyedit eg generic names should be lower case, figure legends are a mix of full stops/not, overuse of word 'since', some incorrect punctuation. I've fixed a few glitches, but I really don't have time to go through carefully. Espresso Addict 16:33, 19 September 2006 (UTC)[reply]

Replaced 4 uses of "since", added full stops to all figure legends and standardised on non-brand name designations for pharmaceuticals. TimVickers 17:35, 19 September 2006 (UTC)[reply]

I've made some minor changes (I hope I haven't introduced errors, my last acquaintance with biochemistry was over a decade ago), but I think more could be done if possible. Is there any consensus on using n-rules? I know that some onscreen characters can cause problems in some browsers, but enzyme–substrate, Michaelis–Menten & Lineweaver–Burk all grate a bit without. Espresso Addict 19:33, 19 September 2006 (UTC)[reply]

Good editing. No errors I can see, but I changed one to give plural usage on uses as drugs. What do you mean n-rule, is this different from a hyphen? TimVickers 19:42, 19 September 2006 (UTC)[reply]

It's a longer hyphen which is conventionally used typographically for number ranges and for joining two equal things, such as the examples I gave. Espresso Addict 19:48, 19 September 2006 (UTC)[reply]

It's discussed here Wikipedia:Manual of Style (dashes). What would be your recommendation? It's something I've never thought about before. TimVickers 20:11, 19 September 2006 (UTC)[reply]

The style guide seems to be going with the use of – as supported by most browsers, but inserted using the insert codes under the edit window (which I've only just noticed) to make it transparent for editing. Espresso Addict 22:34, 19 September 2006 (UTC)[reply]

Do you want to do this? Or are you happy for me to have a go at putting this character into the text? TimVickers 23:01, 19 September 2006 (UTC)[reply]

I'll have a go if you like -- but it's probably best to do it at a time when others aren't editing because edit conflicts would be boring. Espresso Addict 23:11, 19 September 2006 (UTC)[reply]

I'm off to my fiction-writing group, so I've finished with this article for the evening. If you have time tonight, thank you for the corrections. TimVickers 23:13, 19 September 2006 (UTC)[reply]

Done. I wasn't sure whether slow-tight and MALDI-TOF needed them; I've not encountered these terms. Espresso Addict 00:05, 20 September 2006 (UTC)[reply]

Comment: Tim, ref 23 looks a little dodgy. ;) David D. (Talk) 18:38, 20 September 2006 (UTC)[reply]

Not one of my best, but [irony]good enough for the likes of you.[/irony] TimVickers 18:56, 20 September 2006 (UTC)[reply]
On a more serious note, how do we define enzyme with respect to the natural poisons section. Clearly many of the well known examples are with respect to the channels, receptors and cyctoskeleton. This is a shade of gray area. Is taxol acting as an enzyme inhibitor? One could argue that it inhibits the GTPase activity. Are channels enzymes in the classical sense? Personally, i think they can be considered to have a function similar to enzymes and they definitely have the ability to move ions with michaelis mention kinetics. You get the idea. Since the article does tend to focus heavily on the more classical type of enzyme i wonder if this barrage of less conventional enzyme examples at the end is a little out of context. I tried to add a sentence to transition into this section. However, i think it still needs a little work possibly a general definition for enzyme nearer the front end of the article? David D. (Talk) 19:14, 20 September 2006 (UTC)[reply]
  • Agree that ion channels and the like aren't conventionally considered enzymes; if the definitions have changed, this section seems to need more explanation. Espresso Addict 19:34, 20 September 2006 (UTC)[reply]
This is a really tough area, since I would define an an enzyme as a protein that catalyses a chemical reaction. However, under this definition things like myosin or the Na+/K+ exchanger become enzymes, when they are never classed as such in common usage. I would like to stick to the common use of "enzyme" so perhaps we should replace some of these examples with more "enzyme" inhibitors.TimVickers 19:41, 20 September 2006 (UTC)[reply]
That was one of the reasons I introduced the glycoalkoloids. I think there is an interesting new perspective there too, with regard to some foods that we consider safe can be toxic. For example, green potaoes. Another embryonic idea I had is that since the body has to be efficient at removing natural toxins this can cause problems with respect to drug half lives. Possibly a mention of p450's and liver function since this article seems to focus on drugs towards the end. Probably not really part of this article but still a thought. David D. (Talk) 20:02, 20 September 2006 (UTC)[reply]

OK, I was bold and moved the majority of the material on ion channels to the talk page. It is too good to lose, so I'll add it to another article once I work out in which topic it best fits. TimVickers 20:12, 20 September 2006 (UTC)[reply]

  • Support, OK I'm on board now. This article is starting to look in great shape. Excellent job Tim. David D. (Talk) 00:16, 21 September 2006 (UTC)[reply]
  • NOTE to editors - Thank you all for your work on this article, it has been vastly improved by your efforts. A minor point is that this article uses < ref>citation</ref> notation and Pubmed formatting of journal, date, issue and page numbers: so please be consistent. TimVickers 15:04, 20 September 2006 (UTC)[reply]
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