Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Small molecules as inhibitors of cyclin-dependent kinases

Cell division (mitosis) is one of the basic requirements for multicellular oranisms. The capability of a cell to replicate enables a complex assembly to be created. Faulty regulation of the control mechanism in the cell cycle leads to an excessive cell proliferation and is the cause of cancer. The key position of the cyclin-dependent kinases (CDKs) and their direct partners, as well as the fact that the majority of malign illnesses show defects in at least one of these key players of the cell cycle, is of great interest for the development of low-molecular-weight CDK inhibitors. In this Review an overview of the different structural classes of ATP-competitive inhibitors of CDKs are given, whose devlopment was aimed at battling cancer. The Review shows how far the development of selective CDK inhibitors has progressed and to what extent the expectations for such drugs have so far been fulfilled.     

Synthesis and characterization of Cu,Ni and Zn binding capability of some amino- and imidazole hydroxamic acids: Effects of substitution of side chain amino-N for imidazole-N or hydroxamic-N-H for -N-CH3 on metal complexation

Solution equilibrium studies on Cu(II)-, Ni(II)- and Zn(II)-N-Me-β-Alaninehydroxamic acid (N-Me-β-Alaha), -N-Me-α-alaninehydroxamic acid (N-Me-α-Alaha), -Imidazole-4-carbohydroxamic acid (Im-4-Cha), -N-Me-imidazole-4-carbohydroxamic acid (N-Me-Im-4-Cha) and -Imidazole-4-acetohydroxamic acid (Im-4-Aha) systems have been performed by pH-potentiometry, UV–Vis spectrophotometry, EPR, CD, ESI-MS and ¹H NMR methods. According to the results: (i) the amino-N atoms are more basic in N-Me-α-Alaha and N-Me-β-Alaha than the hydroxamate function, but the trend is just the opposite between the imidazole-N(3) and hydroxamate. (ii) The metal ion anchor is always the hydroxamate part in the amino acid derivatives, while it is always the imidazole-N(3) in the studied imidazolehydroxamic acids. (iii) The three studied N-Me derivatives do not form metallacrowns. Only hydroxamate type chelate is formed with N-Me-β-Alaha, but with N-Me-α-Alaha a new type of coordination mode (via amino-N and hydroxamate-O) also exists. N-Me-Im-4-Cha also forms a dinuclear complex, [M₂L₃], with Cu(II) and Ni(II) (but not with Zn(II)). In this complex, one of the three ligands might bridge the two metal ions (five-membered hydroxamate-(O,O) plus five-membered (N_im, O_carb) bridging bis-chelating mode), while each of the additional two ligands binds to one metal. (iv) The two studied N–H derivatives, having dissociable proton on the hydroxamic-N, are able to form metallacrown species. A pentanuclear complex, [M₅L₄H₋₄], is exclusively formed above pH 4 between Cu(II) and Im-4-Aha. Interestingly, this 12-metallacrown-4 type complex, although together with various mononuclear binding isomers, appears also with Ni(II) and Zn(II). Unfortunately, the complexes of Im-4-Cha are not soluble in water at physiological pH at all.     

Synthesis and biological activities of hydroxyl-protected fluorine-containing 4,4-dihydroxylmethyl-2-aryl-iminothiazolidines

Eight novel compounds were synthesized by a facile and mild method with high yields, and the structures of all the compounds were characterized by ¹H NMR IR mass and high resolution mass spectroscopy. Their inhibitory activity against insect-flight and trehalase in vitro were screened. Some target compounds have moderate inhibitory activity against trehalase, and show inhibition action to insect-flight.     

A microtiter plate assay for the detection of inhibitors of the Na +, K + -ATpase

A rapid microtiter plate assay for the detection of inhibitors of the Na⁺, K⁺-ATPase has been developed. The assay is based on the measurement of inorganic phosphate released from the substrate, ATP, and has been designed to be carried out in the individual wells of a microtiter plate. Since the production of inorganic phosphate is determined colorimetrically, multiple samples can be tested simultaneously using a microtiter plate reader. This microtiter plate assay is particularly useful for screening large numbers of samples, such as microbial culture supernatants.     

Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications

Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.     

The polysaccharide extracts from the fungi Coprinus comatus and Coprinellus truncorum do exhibit AChE inhibitory activity

The polysaccharide (PSH) extracts from the edible mushroom species Coprinus comatus and Coprinellus truncorum were screened in liquid for their acetylcholinesterase inhibitory (AChE) activity. Both extracts were found to display inhibition of the aforementioned enzyme reaching similar IC₅₀ values of 0.62 ± 0.07 and 0.61 ± 0.03 mg/mL, respectively. According to the means of FTIR spectroscopy, these PSH extracts mostly contained β-glucans. However, the presence of some proteins and polyphenolics as minor ingredients were also detected. Compared with existing literature data for anti-AChE activity of the sugar samples, the findings within this study may be treated as a profound bioactivity. Consequently, this study puts some light on the possible use of the screened macrofungi in the palliative treatment of Alzheimer’s disease.     

Homocoenzyme B12 and Bishomocoenzyme B12: Covalent Structural Mimics for Homolyzed,Enzyme‐Bound Coenzyme B12

Efficient electrochemical syntheses of “homocoenzyme B₁₂” ( 2 , Co_β‐(5′‐deoxy‐5′‐adenosyl‐methyl)‐cob(III )alamin) and “bishomocoenzyme B₁₂” ( 3 , Co_β‐[2‐(5′‐deoxy‐5′‐adenosyl)‐ethyl]‐cob(III )alamin) are reported here. These syntheses have provided crystalline samples of 2 and 3 in 94 and 77 % yield, respectively. In addition, in‐depth investigations of the structures of 2 and 3 in solution were carried out and a high‐resolution crystal structure of 2 was obtained. The two homologues of coenzyme B₁₂ ( 2 and 3 ) are suggested to function as covalent structural mimics of the hypothetical enzyme‐bound “activated” (that is, “stretched” or even homolytically cleaved) states of the B₁₂ cofactor. From crude molecular models, the crucial distances from the corrin‐bound cobalt center to the C5′ atom of the (homo)adenosine moieties in 2 and 3 were estimated to be about 3.0 and 4.4 Å, respectively. These values are roughly the same as those found in the two “activated” forms of coenzyme B₁₂ in the crystal structure of glutamate mutase. Indeed, in the crystal structure of 2 , the cobalt center was observed to be at a distance of 2.99 Å from the C5′ atom of the homoadenosine moiety and the latter was found to be present in the unusual syn conformation. In solution, the organometallic moieties of 2 and 3 were shown to be rather flexible and to be considerably more dynamic than the equivalent group in coenzyme B₁₂. The homoadenosine moiety of 2 was indicated to occur in both the syn and the anti conformations.     

Relative Abundance of Alpha-Amylase/Trypsin Inhibitors in Selected Sorghum Cultivars

Sorghum is of growing interest and considered as a safe food for wheat related disorders. Besides the gluten, α-amylase/trypsin-inhibitors (ATIs) have been identified as probable candidates for these disorders. Several studies focused on wheat-ATIs although there is still a lack of data referring to the relative abundance of sorghum-ATIs. The objective of this work was therefore to contribute to the characterization of sorghum ATI profiles by targeted proteomics tools. Fifteen sorghum cultivars from different regions were investigated with raw proteins ranging from 7.9 to 17.0 g/100 g. Ammonium bicarbonate buffer in combination with urea was applied for protein extraction, with concentration from 0.588 ± 0.047 to 4.140 ± 0.066 mg/mL. Corresponding electrophoresis data showed different protein profiles. UniProtKB data base research reveals two sorghum ATIs, {"type":"entrez-protein","attrs":{"text":"P81367","term_id":"3913899","term_text":"P81367"}}P81367 and {"type":"entrez-protein","attrs":{"text":"P81368","term_id":"3913900","term_text":"P81368"}}P81368; both reviewed and a targeted LC–MS/MS method was developed to analyze these. Quantifier peptides ELAAVPSR ({"type":"entrez-protein","attrs":{"text":"P81367","term_id":"3913899","term_text":"P81367"}}P81367) and TYMVR ({"type":"entrez-protein","attrs":{"text":"P81368","term_id":"3913900","term_text":"P81368"}}P81368) were identified and retained as biomarkers for relative quantification. Different reducing and alkylating agents were assessed and combination of tris (2 carboxyethyl) phosphine/iodoacetamide gave the best response. Linearity was demonstrated for the quantifier peptides with standard recovery between 92.2 and 107.6%. Nine sorghum cultivars presented up to 60 times lower ATI contents as compared to wheat samples. This data suggests that sorghum can effectively be considered as a good alternative to wheat.