Molecular recognition at the active site of catechol-O-methyltransferase (COMT): adenine replacements in bisubstrate inhibitors

L-Dopa, the standard therapeutic for Parkinson's disease, is inactivated by the enzyme catechol-O-methyltransferase (COMT). COMT catalyzes the transfer of an activated methyl group from S-adenosylmethionine (SAM) to its catechol substrates, such as L-dopa, in the presence of magnesium ions. The molecular recognition properties of the SAM-binding site of COMT have been investigated only sparsely. Here, we explore this site by structural alterations of the adenine moiety of bisubstrate inhibitors. The molecular recognition of adenine is of special interest due to the great abundance and importance of this nucleobase in biological systems. Novel bisubstrate inhibitors with adenine replacements were developed by structure-based design and synthesized using a nucleosidation protocol introduced by Vorbrüggen and co-workers. Key interactions of the adenine moiety with COMT were measured with a radiochemical assay. Several bisubstrate inhibitors, most notably the adenine replacements thiopyridine, purine, N-methyladenine, and 6-methylpurine, displayed nanomolar IC(50) values (median inhibitory concentration) for COMT down to 6 nM. A series of six cocrystal structures of the bisubstrate inhibitors in ternary complexes with COMT and Mg(2+) confirm our predicted binding mode of the adenine replacements. The cocrystal structure of an inhibitor bearing no nucleobase can be regarded as an intermediate along the reaction coordinate of bisubstrate inhibitor binding to COMT. Our studies show that solvation varies with the type of adenine replacement, whereas among the adenine derivatives, the nitrogen atom at position 1 is essential for high affinity, while the exocyclic amino group is most efficiently substituted by a methyl group.     

Selecting Agonists from Single Cells Infected with Combinatorial Antibody Libraries

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Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.     

An Unpredictable Reaction of <Emphasis Type="Italic">t</Emphasis>Bu<Subscript>2</Subscript>PHO·BCl<Subscript>3</Subscript> in the Presence of Water

Abstract  

When a benzene solution of tBu₂PHO·BCl₃ was exposed to air at room temperature, the phosphonium chloride [tBu₂PH₂]Cl was formed together with di-tert-butylphosphinic acid, tBu₂PO(OH). X-ray quality crystals of the hydrochloride [tBu₂PH₂]Cl·HCl were obtained from the reaction solution at room temperature. The hydrochloride [tBu₂PH₂]Cl·HCl crystallizes in the monoclinic space group P2₁ /m, a = 6.3012(7) ?, b = 6.8970(10) ?, c = 14.5011(15) ?, β = 99.376(9)°, V = 621.79(13) ?³, Z = 2, d _calcd = g cm⁻³ 1.165; R1 = 0.0510, wR2 = 0.1503 for 1,129 reflections with I > 2σ(I). The crystal was a non-merohedral twin with a contribution of 0.353(7) of the minor component. The structure is composed of discrete di-t-butylphosphonium cations and Cl anions. Both are located on a crystallographic mirror plane and are connected by P–H···Cl hydrogen bonds.     

The pentanuclear Fe(II) cluster [(C5H4)6Fe5]2-: bringing together ferrocene sandwiches and homoleptic Fe(II)-cyclopentadienyl sigma-complexes

Reaction of [(fc)3(Li)6.(TMEDA)2] with FeCl2 gives the pentanuclear iron complex [(fc)3(Fe)2(Li)2.(TMEDA)2] featuring two ferra[1]ferrocenophane moieties bridged by a 1,1'-ferrocenediyl unit; the non-ferrocene Fe(II) ions are tetra-coordinate and adopt a high-spin state.     

Manufacturing immunity to disease in a test tube: the magic bullet realized

Although it took over one hundred years, Ehrlich's concept of the magic bullet is now a reality. Today, therapeutic antibodies are, arguably, the most important class of new drugs for the treatment of illnesses ranging from Alzheimer's disease to cancer. The emergence of therapeutic antibodies had to wait for advances in immunochemistry that allowed construction of antibodies in vitro. The centerpiece of the new technology is the combinatorial antibody library, which essentially allows one to synthesize an artificial immune system with a diversity that exceeds that of the natural repertoire. The construction of such libraries was perceived to be difficult because, if the natural immune system was to be used as the starting material, construction of the libraries would entail protocols that are the opposite of usual cloning. In gene cloning one starts with complexity and reduces it to a singularity. In the generation of diversity by construction of combinatorial antibody libraries, one starts with a collection of clones, randomly expands their complexity, and then returns them to recoverable singularities. The methods developed to accomplish this seemingly formidable task now allow construction of antibodies in a test tube to any antigen. These synthetic antibodies may be qualitatively and quantitatively superior to those of nature.     

A polymorph of tetrakis(acetonitrile‐κN)copper(I) tetrafluoridoborate

A P2₁2₁2₁ polymorph of the title compound, [Cu(CH₃CN)₄]BF₄, is reported. The crystal structure is very similar to the structure of the Pna2₁ polymorph reported by Jones & Crespo [Acta Cryst. (1998), C 54 , 18–20]. The anions and one of the three independent cations occupy similar positions in both polymorphs. Two of the four symmetry‐related positions of the other two cations are also identical in the two polymorphs, and the other two positions are related by mirror symmetry. The crystal used for the structure determination contained a volume fraction of 0.088 (7) of the Pna2₁ polymorph.