Tethering with extenders

Finding and Linking Fragments in One Step Tethering with Extenders... 

Fig. 9.6 Tethering with extenders. An extender is used to modify a residue in the protein the extender has some inherent affinity for the protein and also contains a thiol that can be used for Tethering. When complementary fragment is identified, this can be linked with binding elements from the extender to generate a potent inhibitor.

Fig. 9.7 Tethering with extenders on caspase-3. The extender (3) covalently modifies the protein and can then be deprotected to reveal a thiol for Tethering. One of the strongest hits is the salicylic acid derivative shown.

Fig. 9.8 Evolution of a fragment from Tethering with extenders to a potent caspase-3 inhibitor. Simple replacement of the disulfide linker with an alkyl linker resulted in a low micromolar inhibitor (4), and rigidification (5) and functionalization (6) of this linker led to increasingly potent inhibitors. The salicylic acid hit itself (7) had no detectable binding.

Tethering with extenders was also used to identify inhibitors to the antiinflammatory target caspase-1 [28, 29]. In this case, one of the same extenders previously designed for caspase-3 selected an entirely different set of fragments. This is consistent with different substrate peptide sequence preferences WEHD for caspase-1 vs DEVD for caspase-3 [30]. 

Fig. 9.10 Tethering with extenders to identify caspase-1 inhibitors. Two of the hits from tethering are shown, as are inhibitors derived from them.

A variant of Tethering with extenders, termed breakaway Tethering, has been developed for enzymes with catalytic sites that do not tolerate the insertion of a cysteine residue due to disruption of structural or functional integrity. Protein tyrosine phosphatases (PTPs)... 

Figure 2.19 Tethering with extenders approach (Figure reproduced in part from D.

Extending this methodology, Tamao and co-workers recently prepared a pentasilane, 4, containing a central trisilane unit constrained to the all-anti conformation by tethering with bis(tetramethylene) groups, as confirmed by single crystal X-ray diffraction.14... 

Figure 7.4 (a) Schematic illustration of the tethering with covalent extenders technique. Reprinted from Reference 43, with permission from Macmillan Publishers Ltd, Copyright (2003). (b) Schematic illustration of the site-specific DCC technique. Reprinted from Reference 27, with permission from Elsevier, Copyright (2008). 

Recently the investigation of the structure, molecular dynamics and action mechanism of enzymes revealed that protein globules of many enzymes consist of two tightly packed knots (matrix, domains, blocks) tethered with a relatively flexible spacer. (Lumry, 1995a,b, 2002 and references herein) (See also Section 4.1). The enzyme active sites are most commonly located in a cleft between these domains. Binding of substrates and inhibitors depends on the extend of matrix contraction (Fersht, 1999). 

In a different version of the same concept. Stork [67,68] and Bols [69-72] introduced silylene type tethering with glycosyl sulfoxide [67,68] or thioglycoside [69-72] donors. The silicon-tethered acceptor approach was also extended to the synthesis of a-D-gluco- [70,72] and a-D-galactopyranosyl linkages in oligosaccharides [70,72]. 

Figure 8.19. Stereo views of monomers of Complex III cytochrome bci complex of chicken with (A) and without (B) inhibitors. Protein in backbone representation with neutral residues in light gray, hydrophobics in gray, aromatics in black, and charged residues in white. (A) The tether is extended when the FeS is at Q site. (Prepared using the crystallographic results of Zhang et al. as obtained from...

Asao et al. conducted a systematic smdy of gold-catalyzed intramolecular reactions by designing two types of substrates one a top-down approach, in which a carbon chain is attached to the carbonyl group, and the other a bottom-up approach, in which a carbon tether is extended from the alkynyl terminus [37]. As the former case, benzannulation of 59 proceeded smoothly with an AuBrs catalyst, and the corresponding tricyclic compounds 60 were produced. On the other hand, the reaction of 61 gave dihydrophenanthrenone derivatives 62 as the latter case (Scheme 15.25). 

The utility of the Zincke reaction has been extended to the preparation of various NAD and NADH analogs. Holy and co-workers synthesized a series of NAD analogs containing nucleotide bases as a means to study through-space interaction between the pyridinium and base portions. Nicotinamide-derived Zincke salt 8 was used to link with various adenine derivatives via tethers that contained hydroxyl (105 —> 106, Scheme 8.4.35), phosphonate (107—>108, Scheme 8.4.36), and carboxylate "... 

Daoud and Cotton [10] pioneered this geometrical analysis of tethered layers with spherical symmetry, which was later extended by Zhulina et al. [36] and Wang et al. [37] to cylindrical layers. The subsequent analysis is purely geometrical and requires no free energy minimization. The tethered layer consists of a stratified array of blobs such that all blobs in a given sublayer are of equal size, E , but blobs in different layers differ in size. This corresponds to the uniform stretching assumption of the Alexander model. 

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