MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'chem'. Sat, 03 Sep 2011 02:30:43 +0100 http://www.medworm.com/index.php?rid=1943574&cid=t_131139_136_f&fid=36032&url=http%3A%2F%2Fblog.healthtalk.com%2Fbreast-cancer%2Flife-with-breast-cancer%2Fchemo-brain-organization-and-add%2F Sister has been listening to me complain about what I call brain damage. After four years, I really believe that I am continuing to suffer from chemo brain. Every now and then, I go over the symptoms with Sister who feels they relate to ADD, so she got me a book on it. Having chemo brain, I seldom read a book from cover to cover starting on chapter one. Because this book is written for people with ADD it is not designed to be read conventionally anyway; this helped me to stick with it. Skimming through the chapters, I began to see how chemo-brain could be diagnosed as ADD. This isn’t so far fetched. Back in December of 2006, I was invited to participate in a Webcast on HealthTalk about chemo brain (worth listening to from the archives if you have the time). The other guest was a doct... Life with Breast Cancer blogs http://www.medworm.com/rss/comments.php?id=1943574 Sat, 08 Nov 2008 00:52:39 +0100 1943574 http://www.medworm.com/index.php?rid=1147437&cid=t_131139_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fsocial-chemistry-and-wikipedia.html As posted already are there still several problems with structure/substructure searches, and even the plain indexing of chemical structures within Wikipedia. Here are more details about it.==One==1.1. There are technical problems, because a SMILES code might contain characters reserved for the Wikipedia syntax.1.2. Some people dislike SMILES strings for large molecules1.3. It seems not to be easy to convince people about the relevance of unified chemical identifiers within Wikipedia, and subtructure and structure search link-outs. Especially the Wikipedia administration seems to be very skeptical and non-responsive.Substructure search in eMolecules and PubChem added I have added a SMILES based substructure search for eMolecules and PubChem. Please have a look at Cetirizine containing alrea... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147437 Wed, 12 Sep 2007 21:05:00 +0100 1147437 http://www.medworm.com/index.php?rid=865678&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F09%2F12%2Fzinc-mediated-inhibitors%2F “At pH 8.2 the inhibition constant (Ki) of BABIM for bovine trypsin in 1.0 mM EDTA, pH 8.2, is 19 uM. Addition of Zn²+ at concentration as low as 100 nM increases the affinity of BABIM for trypsin by 3,800 to Ki = 5.0 ± 0.3 nM. Zn²+ alone is a weak inhibitor of trypsin with a Ki of ~ 33 mM at pH 5.5, and ~ 1.0 mM at pH 7.0.” With such an opening statement, the dramatic plot of the story, was out even before you stepped into the theater. One minute you had no idea what to expect and the next, you knew the whole story and yet you said aloud, ‘what?’ The plot of the story is a novel way (in the days leading to the end of 20th century) to tackle serine based proteases from Arris Pharmaceuticals. In case you are wondering what BABIM is and how this acts at the active ... whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=865678 Wed, 12 Sep 2007 14:16:43 +0100 865678 http://www.medworm.com/index.php?rid=734921&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F07%2F14%2Fcrosslinking-serine-and-lysine%2F With many N’s and O’s in the written structure you could easily get mixed up, so i had to chemdraw it to get it right. Based on a central hydroxamate moiety, other formate and carbamate breakaway moieties are added to make the above structure, that is hydrolysed in aqueous buffer (pH = 7.5) to give benzyl N-hydroxycarbamate, the phenol and bicarbonate. When the class C beta lactamase of Enterobacter cloacae P99 was treated with these compounds, the activity of the enzyme was inhibited. The crystal structure revealed the inhibition to be due to the absence of the free serine and lysine residues at the active site. The probable sequence of events leading to this carbonyl crosslinking is depicted in the following scheme- the pdb structure and the paper. (Source: whistling in the... whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=734921 Sat, 14 Jul 2007 23:10:56 +0100 734921 http://www.medworm.com/index.php?rid=728553&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F06%2F17%2Fez-access-to-ez-in-indolin-2-ones%2F Tang et al. (SUGEN-1998) have synthesized various indolin-2-ones in their quest to inhibit kinases. Appropriate indolin-2-one is refluxed in ethanol/toulene with the aldehyde and piperidine to give the 3 substituted derivatives. With different aromatic aldehydes, they get different populations of E/Z isomers that were initially characterized usign nOe’s and later explained based on electronic and hydrogen bonding effects. A summary: Obviously, the presence of additional substitutions in the N1 of pyrrole or the relative pyrazole and other substitutions on the phenyl of the indolinone aromatic disrupts the peace of these E/Z isomers. (Source: whistling in the wind) whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=728553 Sun, 17 Jun 2007 22:21:50 +0100 728553 http://www.medworm.com/index.php?rid=728555&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F05%2F24%2Fsmall-molecules%2F Are these the signs of the coming times for small molecules inhibitors? (Source: whistling in the wind) whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=728555 Thu, 24 May 2007 03:38:46 +0100 728555 http://www.medworm.com/index.php?rid=728557&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F05%2F15%2Ftempo-not-just-for-oxidation%2F TEMPO, a nitroxide radical used for oxidation of alcohols, also finds an application in an interesting way. This paper describes the detection of a second site ligand by measuring the relaxation enhancement induced by spin labeled first ligand in case of Phosphatase of Yersinia pestis.   A few molecules containing both the salicylate and tempo groups having different linkages were synthesized. The most appropriate (based on cross family inhibition) first site binding ligand was the one that had the furan with the unsaturation in it. The salicylate moiety sits on the binding site of the enzyme and nitroxide radicals extends out. Screening this with various compouns gives the second site binding fragment. “The unpaired electron in TEMPO possesses a gyromagnetic ratio 657.4 times ... whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=728557 Tue, 15 May 2007 03:29:02 +0100 728557 http://www.medworm.com/index.php?rid=728558&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F04%2F25%2Fcation-pi-interactions-vs-salt-bridge%2F I usually find it difficult reading the computational papers and generally skip the details to reach the conclusions, however, these two(PNAS) papers(JACS) by Dougherty et al. gave me a pleasant reading time. The first one discusses the cation-Pi interactions of the aromatics with lys/arg in the context of protein structures. And the second discusses why a salt bridge though favourable in gas phase might not be so in water. Desolvation is a costly process while cation - pi is largely a hydrophobic interaction in comparision to a salt bridge. And obviously, again a perspective on why docking a guanidine against an acid might not be as appropriate as docking it with in a cation-pi interaction with a phenyl group, more so when the crystal struture of a related compound has already been deposi... whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=728558 Wed, 25 Apr 2007 22:26:12 +0100 728558 http://www.medworm.com/index.php?rid=568290&cid=t_131139_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F111755128%2F Jean-Claude Bradley has started his wiki experiment, where he will be presenting his work on a 4-Component Ugi reaction on a wiki. It will be interesting to note how this effort progresses. A number of people use ELNs, Wikis, etc to capture their experiments and research (I rolled my own html back in grad school), but using a wiki to publicly capture research that you want to publish is not that common. One of his students (at least I think it is his student) is also putting her research up on a wiki. Further reading: Peter Murray-Rust The onslaught against scientific publication Technorati Tags: Open science, Wiki, Useful Chem, Jean-Claude Bradley (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=568290 Wed, 25 Apr 2007 04:40:02 +0100 568290 http://www.medworm.com/index.php?rid=728560&cid=t_131139_149_f&fid=35789&url=http%3A%2F%2Fsanjayat.wordpress.com%2F2007%2F04%2F11%2Fis-drug-discovery-rational%2F Organic chemistry as taught in the undergraduate classes does seem to follow a logical sequence. However, when it comes to drug discovery, rationality often does take a flight of fancy. No doubt there are practitioners who almost convince you that rationality does exist in this field. I often tend to be one of them, and then there are papers like the one reviewed by ‘kyle’ and i take a few cautionary steps back. As listed in a previous post, thiol is a pretty zinc binder. One study, involving design of inhibitors for a zinc based enzyme, had this observation to make. The stereospecific amino group on the carbon adjacent to the one containing the thiol group displayed no interactions with enzyme residues when simulated. To avoid this painful stereocenter-inducing-scheme to get t... whistling in the wind blogs http://www.medworm.com/rss/comments.php?id=728560 Thu, 12 Apr 2007 01:55:08 +0100 728560 http://www.medworm.com/index.php?rid=728687&cid=t_131139_149_f&fid=35782&url=http%3A%2F%2Fsyntheticness.com%2Fblog%2F%3Fp%3D17 Im trying to get myself up to speed on some of the stetter methodology from some interesting groups. To do this, I am starting at the very beginnings - with the benzoin condensation. The reaction is a cyanide catalyzied coupling between aldehydes to form α-hydroxy ketones. Apparently, thiamine is now used as the activating catalyst rather than KCN. Looking into the mechanism, we can see the umpolung of the carbonyl results in the formation of the masked acyl anion upon nucleophilic attach by the cyanide and subsequent proton-shift: So, I guess that wraps that one up! Organic Syntheses, Coll. Vol. 1, p.94 (1941); Vol. 1, p.33 (1921). (Source: Syntheticness) Syntheticness blogs http://www.medworm.com/rss/comments.php?id=728687 Sat, 10 Mar 2007 05:28:30 +0100 728687