6491-83-4Relevant academic research and scientific papers
Additivity or cooperativity: Which model can predict the influence of simultaneous incorporation of two or more functionalities in a ligand molecule?
Nasief, Nader N.,Hangauer, David
, p. 897 - 915 (2015/05/27)
Predicting how binding affinity responds to ligand structural modifications in structure-activity relationship studies (SAR) is a major challenge in medicinal chemistry. This is particularly true when two or more of these modifications are carried out simultaneously. In this study, we present binding affinity data from several series of thermolysin inhibitors in which simultaneous structural modifications were investigated to determine whether they are cooperative or additive. Data revealed that, while additivity is at work in some cases, cooperativity is more commonly demonstrated. Cooperativity and additivity were then correlated with ligand descriptors, such as the spacing and the topological features of the modified groups, in a manner that may provide guidance as to when each model should be utilized. Cooperativity was particularly associated with contiguous groups and small unbranched hydrophobic side chain. Additivity, on the other hand, was associated with moderately distant hydrophobic group combinations and side chain branching. Such correlations can improve the predictability of SAR studies and can provide a starting point for additional investigations that may lead to further significant enhancements in the current scoring functions.
Influence of neighboring groups on the thermodynamics of hydrophobic binding: An added complex facet to the hydrophobic effect
Nasief, Nader N.,Hangauer, David
, p. 2315 - 2333 (2014/04/17)
The thermodynamic consequences of systematic modifications in a ligand side chain that binds in a shallow hydrophobic pocket, in the presence and absence of a neighboring ligand carboxylate group, were evaluated using isothermal titration calorimetry (ITC
Dissecting the hydrophobic effect on the molecular level: The role of water, enthalpy, and entropy in ligand binding to thermolysin
Biela, Adam,Nasief, Nader N.,Betz, Michael,Heine, Andreas,Hangauer, David,Klebe, Gerhard
, p. 1822 - 1828 (2013/04/23)
The hydrophobic effect is associated with the successive replacement of water molecules in the binding site of a protein by hydrophobic groups of the ligand. Although the hydrophobic effect is assumed to be entropy-driven, large changes in enthalpy and entropy are observed with the model system thermolysin. Structural changes in the binding features of the water molecules ultimately determine the thermodynamics of the hydrophobic effect. Copyright
Cyclic dipeptides exhibit potency for scavenging radicals
Furukawa, Tadashi,Akutagawa, Takashi,Funatani, Hitomi,Uchida, Toshikazu,Hotta, Yoshihiro,Niwa, Masatake,Takaya, Yoshiaki
, p. 2002 - 2009 (2012/05/04)
Twenty kinds of cyclic dipeptides containing l-leucine were synthesized, and their antioxidant activity against .OH and O2·- was investigated. Compounds possessing polar amino acid residues, such as Asp, Cys, Glu, Lys, Pro, Ser, and Trp, exhibited higher antioxidant activity against .OH than vitamin E. However, only cyclo(l-Cys-l-Leu) scavenged O2·-.
Syntheses of [12]aneN3-oligopeptide conjugates as effective DNA condensation agents
Li, Zhi-Fen,Guo, Zhi-Fo,Yan, Hao,Lu, Zhong-Lin,Wu, Da-Yong
supporting information; experimental part, p. 2897 - 2904 (2012/07/14)
With the aim to develop effective and low toxicity DNA condensation agents, a series of oligopeptide derived macrocyclic polyamine [12]aneN3 conjugates 7a-h·3HCl have been designed and synthesized through multi-step amidation reactions. Structu
Homochiral oligopeptides via a lattice-controlled polymerisation in racemic crystals of valine N-carboxyanhydride suspended in aqueous solutions
Eliash, Ran,Nery, Jose G.,Rubinstein, Irena,Clodic, Gilles,Bolbach, Gerard,Weissbuch, Isabelle,Lahav, Meir
, p. 10140 - 10151 (2008/09/18)
As part of our program on the biochirogenesis of homochiral peptides, we report the formation of racemic parallel (p) β sheets composed of alternating R and S chains of up to 14-15 repeat units of the same handedness through the polymerisation of (R,S)-valine N-carboxyanhydride (NCA) crystals suspended in aqueous solutions of a primary amine as the initiator. The occurrence of such a lattice-controlled reaction accompanied by a reduction in volume implies the operation of a mechanism that differs from that of the common solid-state polymerisation in vinyl systems. The topotacticity of the reaction is explained through the operation of a multistep nonlinear process comprising lattice control coupled with an asymmetric induction in the formation of homochiral short peptides followed by their self-assembly into racemic p β sheets, which operate as efficient templates in the ensuing process of enantioselective chain elongation at the polymer/crystal interface. The composition of the diastereoisomeric libraries of oligopeptides was determined by MALDI-TOF and MALDI-TOF-TOF MS analyses of the products obtained from monomers enantioselectively labelled with deuterium. The structure of the p β sheets could be determined by initiating the polymerisation reaction with water-soluble esters of enantiopure α-amino acids or short peptides. The same reaction performed with the monomer crystals suspended in hexane yielded a complex mixture of diastereoisomeric oligopeptides, thus highlighting the indispensable role played by water in controlling the stereoselectivity of the reaction. By contrast, polymerisation of (R,S)-leucine NCA crystals, with a different packing arrangement that presumably does not endorse the formation of periodic peptide templates, yielded, both in aqueous and hexane suspensions, libraries of peptides dominated by heterochiral diastereoisomers.
