Penicillin-binding protein (PBP) inhibitor development: A 10-year chemical perspective.

Bacterial cell wall formation is essential for cellular survival and morphogenesis. The peptidoglycan (PG), a heteropolymer that surrounds the bacterial membrane, is a key component of the cell wall, and its multistep biosynthetic process is an attractive antibacterial development target. Penicillin-binding proteins (PBPs) are responsible for cross-linking PG stem peptides, and their central role in bacterial cell wall synthesis has made them the target of successful antibiotics, including ß-lactams, that have been used worldwide for decades. Following the discovery of penicillin, several other compounds with antibiotic activity have been discovered and, since then, have saved millions of lives. However, since pathogens inevitably become resistant to antibiotics, the search for new active compounds is continuous. The present review highlights the ongoing development of inhibitors acting mainly in the transpeptidase domain of PBPs with potential therapeutic applications for the development of new antibiotic agents. Both the critical aspects of the strategy, design, and structure-activity relationships (SAR) are discussed, covering the main published articles over the last 10 years. Some of the molecules described display activities against main bacterial pathogens and could open avenues toward the development of new, efficient antibacterial drugs.

Structural insights into functional overlapping and differentiation among myosin V motors.

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.

Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding.

Nucleoside diphosphate kinases play a crucial role in the purine-salvage pathway of trypanosomatid protozoa and have been found in the secretome of Leishmania sp., suggesting a function related to host-cell integrity for the benefit of the parasite. Due to their importance for housekeeping functions in the parasite and by prolonging the life of host cells in infection, they become an attractive target for drug discovery and design. In this work, we describe the first structural characterization of nucleoside diphosphate kinases b from trypanosomatid parasites (tNDKbs) providing insights into their oligomerization, stability and structural determinants for nucleotide binding. Crystallographic studies of LmNDKb when complexed with phosphate, AMP and ADP showed that the crucial hydrogen-bonding residues involved in the nucleotide interaction are fully conserved in tNDKbs. Depending on the nature of the ligand, the nucleotide-binding pocket undergoes conformational changes, which leads to different cavity volumes. SAXS experiments showed that tNDKbs, like other eukaryotic NDKs, form a hexamer in solution and their oligomeric state does not rely on the presence of nucleotides or mimetics. Fluorescence-based thermal-shift assays demonstrated slightly higher stability of tNDKbs compared to human NDKb (HsNDKb), which is in agreement with the fact that tNDKbs are secreted and subjected to variations of temperature in the host cells during infection and disease development. Moreover, tNDKbs were stabilized upon nucleotide binding, whereas HsNDKb was not influenced. Contrasts on the surface electrostatic potential around the nucleotide-binding pocket might be a determinant for nucleotide affinity and protein stability differentiation. All these together demonstrated the molecular adaptation of parasite NDKbs in order to exert their biological functions intra-parasite and when secreted by regulating ATP levels of host cells.

Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.

Branching enzymes (BEs) catalyze the formation of branch points in glycogen and amylopectin by cleavage of α-1,4 glycosidic bonds and subsequent transfer to a new α-1,6 position. BEs generally belong to glycoside hydrolase family 13 (GH13); however TK1436, isolated from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, is the first GH57 member, which possesses BE activity. To date, the only BE structure that had been determined is a GH13-type from Escherichia coli. Herein, we have determined the crystal structure of TK1436 in the native state and in complex with glucose and substrate mimetics that permitted mapping of the substrate-binding channel and identification of key residues for glucanotransferase activity. Its structure encompasses a distorted (ß/α)(7)-barrel juxtaposed to a C-terminal α-helical domain, which also participates in the formation of the active-site cleft. The active site comprises two acidic catalytic residues (Glu183 and Asp354), the polarizer His10, aromatic gate-keepers (Trp28, Trp270, Trp407, and Trp416) and the residue Tyr233, which is fully conserved among GH13- and GH57-type BEs. Despite TK1436 displaying a completely different fold and domain organization when compared to E. coli BE, they share the same structural determinants for BE activity. Structural comparison with AmyC, a GH57 α-amylase devoid of BE activity, revealed that the catalytic loop involved in substrate recognition and binding, is shortened in AmyC structure and it has been addressed as a key feature for its inability for glucanotransferase activity. The oligomerization has also been pointed out as a possible determinant for functional differentiation among GH57 members.

Low-resolution structural studies of human Stanniocalcin-1.

BACKGROUND: Stanniocalcins (STCs) represent small glycoprotein hormones, found in all vertebrates, which have been functionally implicated in Calcium homeostasis. However, recent data from mammalian systems indicated that they may be also involved in embryogenesis, tumorigenesis and in the context of the latter especially in angiogenesis. Human STC1 is a 247 amino acids protein with a predicted molecular mass of 27 kDa, but preliminary data suggested its di- or multimerization. The latter in conjunction with alternative splicing and/or post-translational modification gives rise to forms described as STC50 and "big STC", which molecular weights range from 56 to 135 kDa. RESULTS: In this study we performed a biochemical and structural analysis of STC1 with the aim of obtaining low resolution structural information about the human STC1, since structural information in this protein family is scarce. We expressed STC1 in both E. coli and insect cells using the baculo virus system with a C-terminal 6 x His fusion tag. From the latter we obtained reasonable amounts of soluble protein. Circular dichroism analysis showed STC1 as a well structured protein with 52% of alpha-helical content. Mass spectroscopy analysis of the recombinant protein allowed to assign the five intramolecular disulfide bridges as well as the dimerization Cys202, thereby confirming the conservation of the disulfide pattern previously described for fish STC1. SAXS data also clearly demonstrated that STC1 adopts a dimeric, slightly elongated structure in solution. CONCLUSION: Our data reveal the first low resolution, structural information for human STC1. Theoretical predictions and circular dichroism spectroscopy both suggested that STC1 has a high content of alpha-helices and SAXS experiments revealed that STC1 is a dimer of slightly elongated shape in solution. The dimerization was confirmed by mass spectrometry as was the highly conserved disulfide pattern, which is identical to that found in fish STC1.

Over-expression of GFP-FEZ1 causes generation of multi-lobulated nuclei mediated by microtubules in HEK293 cells.

FEZ1 (Fasciculation and elongation protein zeta 1) is an ortholog of the Caenorhabditis elegans protein UNC-76, involved in neuronal development and axon outgrowth, in that worm. Mammalian FEZ1 has already been reported to cooperate with PKC-zeta in the differentiation and polarization of PC12 neuronal cells. Furthermore, FEZ1 is associated with kinesin 1 and JIP1 to form a cargo-complex responsible for microtubule based transport of mitochondria along axons. FEZ1 can also be classified as a hub protein, since it was reported to interact with over 40 different proteins in yeast two-hybrid screens, including at least nine nuclear proteins. Here, we transiently over-expressed GFP-FEZ1full in human HEK293 and HeLa cells in order to study the sub-cellular localization of GFP-FEZ1. We observed that over 40% of transiently transfected cells at 3 days post-transfection develop multi-lobulated nuclei, which are also called flower-like nuclei. We further demonstrated that GFP-FEZ1 localizes either to the cytoplasm or the nuclear fraction, and that the appearance of the flower-like nuclei depends on intact microtubule function. Finally, we show that FEZ1 co-localizes with both, alpha- and especially with gamma-tubulin, which localizes as a centrosome like structure at the center of the multiple lobules. In summary, our data suggest that FEZ1 has an important centrosomal function and supply new mechanistic insights to the formation of flower-like nuclei, which are a phenotypical hallmark of human leukemia cells.

Polimorfismo genético do fibrinogênio na doença arterial periférica / Genetic polymorphisms of fibrinogen in peripheral artery disease

O objetivo do presente estudo foi analisar freqüências alélicas e genotípicas para o gene codificador da cadeia beta do fibrinogênio em pacientes com doença arterial periférica (DAP). Foram estudados 44 pacientes caucasóides do sexo masculino com sintomas clínicos e comprovação angiográfica de DAP, com idade entre 38 e 79 anos (62±8,6 anos). Entre eles, 22 apresentaram obstrução aterosclerótica nas artérias ilíacas, femorais e/ou carótidas e 22 tinham aneurisma de aorta torácica, abdominal ou tóraco-abdominal. O grupo controle foi constituído por 56 indivíduos, sem história clínica de DAP ou alterações ao exame clínico, com idades variando de 43 a 80 anos (59±9,2 anos). Foram excluídos os indivíduos com doença renal, doença hepática ou diabetes mellitus. A análise do polimorfismo genético da cadeia do fibrinogênio foi realizada por PCR (polimerase chain reaction) e RFLP (restriction fragment lenght polimorphism) com a endonuclease Bcl I, identificando-se três genótipos: B1/B1, B1/B2 e B2/B2. A análise estatística incluiu teste exato de Fisher, calculo do odds ratio, teste de Kruskal Wallis e análise de variância (ANOVA). Admitiu-se erro a igual a 5 por cento, com nível de significância para P<0,05. O alelo B1 foi o mais prevalente em pacientes e controles (0,819 e 0,857, respectivamente; P=0,5605), com prevalência do genótipo B1/B1 nos pacientes (65,9 por cento) e controles (71,4 por cento; P=0,6639), seguido de B1/B2 (31,8; 28,6 por cento, respectivamente; P=0,8268). Em conclusão, DAP, independente do tipo de lesão obstrutiva ou aneurismática, apresenta-se indiferente ao polimorfismo Bcl I do fibrinogênio, portanto, sem influência dos alelos B1 e B2 para fibrinogênio e seus respectivos genótipos na doença.

The objective of this study was to analyze the frequencies of thealleles and genotypes of the gene encoder of the fibrinogen bchainin patients suffering from peripheral artery disease. A totalof 62 male Caucasoid patients with ages varying from 38 to 79years old were studied. All the patients had clinical symptoms ofperipheral artery disease, which was later confirmed byangiography. Forty of the patients had atheroscleroticobstructions of the iliac, femoral or carotid arteries and 22 sufferedfrom aneurysms of the thoracic, abdominal or thoracoabdominalaortas. All the patients were submitted to surgery. A controlgroup was formed of 62 individuals, with ages ranging from 43to 80 years old, without clinical histories or alterations in theirclinical examinations of peripheral artery disease. Individualswith renal disease, liver disease or diabetes mellitus wereexcluded. Analysis of the fibrinogen b-chain was performed usingpolymerase chain reaction and restriction fragment lengthpolymorphism with Bcl I endonuclease. Three genotypes, B1/B1,B1/B2 and B2/B2 were identified. Statistical analysis was madeusing the Fisher Exact test, odds ratio, Kruskal-Wallis test andvariance analysis (ANOVA). A p-value = 0.05 was consideredsignificant. The B1 allele was the most prevalent in both patientsand the control group (0.819 and 0.857, respectively), withprevalence of the B1/B1 genotype in patients and controls (65.9%vs. 71.4% respectively), followed by B1/B2 (31.8% vs. 28.6%respectively). No significant difference was observed in relationto the Bcl I polymorphisms of the fibrinogen b-chain andobstructive and aneurysmal peripheral artery disease. Inconclusion, the B1 and B2 polymorphisms of the fibrinogen bchain and teir respective genotypes do not have any influence in peripheral artery disease.

Influence of the polymorphism of apolipoprotein E in cerebral vascular disease.

UNLABELLED: The genetic heterogeneity of apolipoprotein E (apo E) has been associated with lipid profile and atherothrombotic stroke, however this association remains inconclusive. OBJECTIVE: To evaluate the relationship between the isoforms of apo E and atherothrombotic stroke, by ascertaining the frequency of its alleles and genotypes associated with the lipid profile in patients with stroke. METHOD: A total of 207 individuals were divided into two groups, consisting of 107 patients with stroke and 100 individuals without clinical symptoms of the disease. Blood samples were taken from patients and controls for molecular investigation of the apo E (epsilon2, epsilon3 and epsilon4 alleles) for the analysis of the lipid profile. RESULTS: The epsilon3 allele was the most common and its prevalence was significantly higher in patients (0.93) compared to the controls (0.86; p=0.024). The epsilon2 allele was rarely seen specifically in patients (0.02 versus 0.05 in controls, p=0.191). The epsilon4 allele was not associated with stroke showing a reduced frequency in patients (0.05) when compared to controls (0.09; p=0.011). Although higher average levels of lipid profile were found in patients when compared to controls, with statistical significance for the values of total cholesterol (TC) (203.6 mg/dL +/- 57.98 and 181.9 mg/dL +/- 68.47 respectively; p=0.003) and low-density lipoprotein cholesterol (LDLc) (131.4mg/dL +/- 52.60 and 116 mg/dL +/- 56.38, respectively; p=0.014), these were independent of the presence of the epsilon4 allele. In control group the higher TC and LDLc values occurred in the absence of the epsilon4 allele, confirming the conflicting effect of the alleles of apo E on the plasmatic lipids and atherothrombotic stroke. CONCLUSION: The isoforms of apo E cannot be regarded as an isolated risk factor for stroke and do not show association with lipid profile in this study.

Influence of the polymorphism of apolipoprotein E in cerebral vascular disease

The genetic heterogeneity of apolipoprotein E (apo E) has been associated with lipid profile and atherothrombotic stroke, however this association remains inconclusive. OBJECTIVE: To evaluate the relationship between the isoforms of apo E and atherothrombotic stroke, by ascertaining the frequency of its alleles and genotypes associated with the lipid profile in patients with stroke. METHOD: A total of 207 individuals were divided into two groups, consisting of 107 patients with stroke and 100 individuals without clinical symptoms of the disease. Blood samples were taken from patients and controls for molecular investigation of the apo E (epsilon2, epsilon3 and epsilon4 alleles) for the analysis of the lipid profile. RESULTS: The epsilon3 allele was the most common and its prevalence was significantly higher in patients (0.93) compared to the controls (0.86; p=0.024). The epsilon2 allele was rarely seen specifically in patients (0.02 versus 0.05 in controls, p=0.191). The epsilon4 allele was not associated with stroke showing a reduced frequency in patients (0.05) when compared to controls (0.09; p=0.011). Although higher average levels of lipid profile were found in patients when compared to controls, with statistical significance for the values of total cholesterol (TC) (203.6mg/dL±57.98 and 181.9mg/dL±68.47 respectively; p=0.003) and low-density lipoprotein cholesterol (LDLc) (131.4mg/dL±52.60 and 116mg/dL±56.38, respectively; p=0.014), these were independent of the presence of the epsilon4 allele. In control group the higher TC and LDLc values occurred in the absence of the epsilon4 allele, confirming the conflicting effect of the alleles of apo E on the plasmatic lipids and atherothrombotic stroke. CONCLUSION: The isoforms of apo E cannot be regarded as an isolated risk factor for stroke and do not show association with lipid profile in this study