PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters

We introduce a protein–ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein–ligand crystal structures, enabling structure–thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein–ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein–ligand recognition and could be integrated into small molecule drug design

A Study of Brooks Law and the Surgical Team in regard to Open Source

Uppsatsens behandlar de speciella fördelar och nackdelar som uppstår när utvecklare släpper kod under öppen källkod. Framförallt studeras problematiken med Brooks lag som säger att när fler personer läggs till i ett försenat utvecklingsprojekt blir projektet ännu mer försenat. Denna problematik studeras utifrån ett öppet källkodsperspektiv där utvecklare utanför projektet kan sända in kod och förslag på förändringar när som helst under projektets gång. Uppsatsen försöker att utifrån utvecklingsmetoden kirurgteamet, formulerad av Fredrick Brooks, finna en lämplig metod där utvecklingsarbetet går så smidigt som möjligt utan att försaka de fördelar det innebär att kunna ta emot hjälp utifrån. Uppsatsen är framförallt en kvalitativ litteraturstudie där fokus ligger på att studera och sammanställa befintlig litteratur för att dra generella slutsatser utifrån denna

Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV

Membrane-associated carbonic anhydrase (CA) isoform IV participates in carbon metabolism and pH homeostasis and is implicated in the development of eye diseases such as retinitis pigmentosa and glaucoma. A series of substituted benzenesulfonamides were designed and their binding affinity to CA IV was determined by fluorescent thermal shift assay and isothermal titration calorimetry (ITC). Compound [(4-chloro-2-phenylsulfanyl-5-sulfamoyl-benzoyl)amino]propyl acetate (19) bound CA IV with the K d of 1.0 nM and exhibited significant selectivity over the remaining 11 human CA isoforms. The compound could be developed as a drug targeting CA IV. Various forms of recombinant CA IV were produced in Escherichia coli and mammalian cell cultures. Comparison of their temperature stability in various buffers and salt solutions demonstrated that CA IV is most stable at slightly alkaline conditions and at elevated sodium sulfate concentrations. High-resolution X-ray crystallographic structures of ortho-Cl and meta-thiazole-substituted benzene sulfonamide in complex with CA IV revealed the position of and interactions between the ligand and the protein. Sulfonamide inhibitor binding to CA IV is linked to several reactions—the deprotonation of the sulfonamide amino group, the protonation of CA–Zn(II)-bound hydroxide at the active site of CA IV, and the compensating reactions of the buffer. The dissection of binding-linked reactions yielded the intrinsic thermodynamic parameters, characterizing the interaction between CA IV and the sulfonamides in the binding-able protonation forms, including Gibbs energy, enthalpy, and entropy, that could be used for the characterization of binding to any CA in the process of drug design