The multiple roles of computational chemistry in fragment-based drug design

Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.     

Pyrimidinyl nitronyl nitroxides

The chemistry of 2,2,4,4-substituted pentane derivatives has been investigated with the aim of providing a flexible and versatile synthetic route to pyrimidinyl nitronyl nitroxides, in which the bis-N-oxy fragment is incorporated in a six-membered ring. The synthesis of 2,4-diamino-2,4-dimethylpentane and 2,4-bis(hydroxylamino)-2,4-dimethylpentane, convenient precursors of these nitroxides, is described and full characterization of a series of pyrimidinyl nitronyl nitroxides is reported, along with a preliminary study of their coordination properties.     

Homochiral and heterochiral coordination polymers and networks of silver(I)

The self-assembly of racemic and enantiopure binaphthylbis(amidopyridyl) ligands 1,1'-C(20)H(12){NHC(O)-4-C(5)H(4)N}(2), 1, and 1,1'-C(20)H(12){NHC(O)-3-C(5)H(4)N}(2), 2, with silver(I) salts (AgX; X = CF(3)CO(2), CF(3)SO(3), NO(3)) to form extended metal-containing arrays is described. It is shown that the self-assembly with racemic ligands can lead to homochiral or heterochiral polymers, through self-recognition or self-discrimination of the ligand units. The primary polymeric materials adopt helical conformations (secondary structure), and they undergo further self-assembly to form sheets or networks (tertiary structure). These secondary and tertiary structures are controlled through secondary bonding interactions between pairs of silver(I) centers, between silver cations and counteranions, or through hydrogen bonding involving amide NH groups. The self-assembly of the enantiopure ligand R-1 with silver trifluoroacetate gave a remarkable three-dimensional chiral, knitted network composed of polymer chains in four different supramolecular isomeric forms.     

Group 6 metal carbonyl complexes of a bulky phosphine: The crystal structures of tris(trimethylsilyl)phosphine-M(0)pentacarbonyl, M = chromium, molybdenum, and tungsten

The crystal structures of M(P{Si(CH₃)₃}₃)(CO)₅, M = Cr (1), Mo (2), and W (3), have been determined. Crystal data for 1, trigonal crystal system, space group = P3₁, a, b = 9.2118(6) ?, c = 22.416(3) ?, V = 1647.3(2) ?³, Z = 3; for 2, trigonal crystal system, space group = P3₂, a, b = 9.3394(3) ?, c = 22.7375(12) ?, V = 1717.56(12) ?³, Z = 3; trigonal crystal system, space group = P3₂, a, b = 9.3147(5) ?, c = 22.6955(16) ?, V = 1705.33(18) ?³, Z = 3. All three structures show distorted octahedral coordination environments around the metal center and exhibit especially long M–P bond distances, illustrating the unique steric and electronic properties of this bulky phosphine ligand. The ³¹P{¹H} NMR spectra of the compounds are also reported.     

Torsion in the full orbifold <Emphasis Type="Italic">K</Emphasis>-theory of abelian symplectic quotients

Let (M, ω, Φ) be a Hamiltonian T-space and let H í T{H\subseteq T} be a closed Lie subtorus. Under some technical hypotheses on the moment map Φ, we prove that there is no additive torsion in the integral full orbifold K-theory of the orbifold symplectic quotient [M//H]. Our main technical tool is an extension to the case of moment map level sets the well-known result that components of the moment map of a Hamiltonian T-space M are Morse-Bott functions on M. As first applications, we conclude that a large class of symplectic toric orbifolds, as well as certain S ¹-quotients of GKM spaces, have integral full orbifold K-theory that is free of additive torsion. Finally, we introduce the notion of semilocally Delzant which allows us to formulate sufficient conditions under which the hypotheses of the main theorem hold. We illustrate our results using low-rank coadjoint orbits of type A and B.     

Degradation of Poly(methyl methacrylate) Model Compounds at Constant Elevated Temperature Studied via High Resolution Electrospray Ionization Mass Spectrometry (ESI‐MS)

The products of the thermal degradation at 95 °C over 10 months of ω‐saturated and non‐saturated poly(methyl methacrylate) (pMMA) model compounds were identified with high accuracy via quadrupole ion trap and quadrupole ion trap‐time of flight (Q‐ToF) mass spectrometry. Analysis of the samples taken via these techniques indicated that degradation of vinyl terminated pMMA proceeds via the incorporation of oxygen via the formation of ethylene oxide type end groups, which subsequently rearrange under the expulsion of formaldehyde and 2‐oxo‐propionic acid methyl ester. The corresponding saturated model compounds were demonstrated to be stable over the same time period. The present findings highlight for the first time that poly(methyl methacrylate) degradation does not necessarily and exclusively proceed via radical intermediates.

     

Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose as carbon source for microbial growth: 13C-labeled glucose and 13C-forskolin binding to the galactose-H+ symport protein GalP in Escherichia coli

Obtrusive 13C-backgrounds can be a problem in 13C NMR-based studies of ligand binding to bacterial membrane transport proteins in their natural state in inner membranes. This is largely solved for the bacterial galactose-H+ symport protein GalP by growing the producing organism Escherichia coli on 13C-depleted glucose (13C 相似文献   

First principle computational study on the full conformational space of L-proline diamides

Ab initio molecular orbital computations were carried out at three levels of theory: RHF/3-21G, RHF/6-31G(d), and B3LYP/6-31G(d), on four model systems of the amino acid proline, HCO-Pro-NH2 [I], HCO-Pro-NH-Me [II], MeCO-Pro-NH2 [III], and MeCO-Pro-NH-Me [IV], representing a systematic variation in the protecting N- and C-terminal groups. Three previously located backbone conformations, gammaL, epsilonL, and alphaL, were characterized together with two ring-puckered forms syn (gauche+ = g+) or "DOWN" and anti (gauche- = g-) or "UP", as well as trans-trans, trans-cis, cis-trans, and cis-cis peptide bond isomers. The topologies of the conformational potential energy cross-sections (PECS) of the potential energy hypersurfaces (PEHS) for compounds [I]-[IV] were explored and analyzed in terms of potential energy curves (PEC), and HCO-Pro-NH2 [I] was also analyzed in terms of potential energy surfaces (PESs). Thermodynamic functions were also calculated for HCO-Pro-NH2 [I] at the CBS-4M and G3MP2 levels of theory. The study confirms that the use of the simplest model, compound [I] with P(N) = P(C) = H, along with the RHF/3-21G level of theory, is an acceptable practice for the analysis of peptide models because only minor differences in geometry and stability are observed.