Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer.

Background and Objectives: Breast cancer (BC) is one of the major causes of cancer-related death in women globally. Proper identification of BC-causing hub genes (HubGs) for prognosis, diagnosis, and therapies at an earlier stage may reduce such death rates. However, most of the previous studies detected HubGs through non-robust statistical approaches that are sensitive to outlying observations. Therefore, the main objectives of this study were to explore BC-causing potential HubGs from robustness viewpoints, highlighting their early prognostic, diagnostic, and therapeutic performance. Materials and Methods: Integrated robust statistics and bioinformatics methods and databases were used to obtain the required results. Results: We robustly identified 46 common differentially expressed genes (cDEGs) between BC and control samples from three microarrays (GSE26910, GSE42568, and GSE65194) and one scRNA-seq (GSE235168) dataset. Then, we identified eight cDEGs (COL11A1, COL10A1, CD36, ACACB, CD24, PLK1, UBE2C, and PDK4) as the BC-causing HubGs by the protein-protein interaction (PPI) network analysis of cDEGs. The performance of BC and survival probability prediction models with the expressions of HubGs from two independent datasets (GSE45827 and GSE54002) and the TCGA (The Cancer Genome Atlas) database showed that our proposed HubGs might be considered as diagnostic and prognostic biomarkers, where two genes, COL11A1 and CD24, exhibit better performance. The expression analysis of HubGs by Box plots with the TCGA database in different stages of BC progression indicated their early diagnosis and prognosis ability. The HubGs set enrichment analysis with GO (Gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways disclosed some BC-causing biological processes, molecular functions, and pathways. Finally, we suggested the top-ranked six drug molecules (Suramin, Rifaximin, Telmisartan, Tukysa Tucatinib, Lynparza Olaparib, and TG.02) for the treatment of BC by molecular docking analysis with the proposed HubGs-mediated receptors. Molecular docking analysis results also showed that these drug molecules may inhibit cancer-related post-translational modification (PTM) sites (Succinylation, phosphorylation, and ubiquitination) of hub proteins. Conclusions: This study's findings might be valuable resources for diagnosis, prognosis, and therapies at an earlier stage of BC.

Recent advances in the delivery and applications of nonviral CRISPR/Cas9 gene editing.

The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 genome editing system has been a major technological breakthrough that has brought revolutionary changes to genome editing for therapeutic and diagnostic purposes and precision medicine. With the advent of the CRISPR/Cas9 system, one of the critical limiting factors has been the safe and efficient delivery of this system to cells or tissues of interest. Several approaches have been investigated to find delivery systems that can attain tissue-targeted delivery, lowering the chances of off-target editing. While viral vectors have shown promise for in vitro, in vivo and ex vivo delivery of CRISPR/Cas9, their further clinical applications have been restricted due to shortcomings including limited cargo packaging capacity, difficulties with large-scale production, immunogenicity and insertional mutagenesis. Rapid progress in nonviral delivery vectors, including the use of lipid, polymer, peptides, and inorganic nanoparticle-based delivery systems, has established nonviral delivery approaches as a viable alternative to viral vectors. This review will introduce the molecular mechanisms of the CRISPR/Cas9 gene editing system, current strategies for delivering CRISPR/Cas9-based tools, an overview of strategies for overcoming off-target genome editing, and approaches for improving genome targeting and tissue targeting. We will also highlight current developments and recent clinical trials for the delivery of CRISPR/Cas9. Finally, future directions for overcoming the limitations and adaptation of this technology for clinical trials will be discussed.

Assessment of Drugs Toxicity and Associated Biomarker Genes Using Hierarchical Clustering.

Background and objectives: Assessment of drugs toxicity and associated biomarker genes is one of the most important tasks in the pre-clinical phase of drug development pipeline as well as in toxicogenomic studies. There are few statistical methods for the assessment of doses of drugs (DDs) toxicity and their associated biomarker genes. However, these methods consume more time for computation of the model parameters using the EM (expectation-maximization) based iterative approaches. To overcome this problem, in this paper, an attempt is made to propose an alternative approach based on hierarchical clustering (HC) for the same purpose. Methods and materials: There are several types of HC approaches whose performance depends on different similarity/distance measures. Therefore, we explored suitable combinations of distance measures and HC methods based on Japanese Toxicogenomics Project (TGP) datasets for better clustering/co-clustering between DDs and genes as well as to detect toxic DDs and their associated biomarker genes. Results: We observed that Word's HC method with each of Euclidean, Manhattan, and Minkowski distance measures produces better clustering/co-clustering results. For an example, in the case of the glutathione metabolism pathway (GMP) dataset LOC100359539/Rrm2, Gpx6, RGD1562107, Gstm4, Gstm3, G6pd, Gsta5, Gclc, Mgst2, Gsr, Gpx2, Gclm, Gstp1, LOC100912604/Srm, Gstm4, Odc1, Gsr, Gss are the biomarker genes and Acetaminophen_Middle, Acetaminophen_High, Methapyrilene_High, Nitrofurazone_High, Nitrofurazone_Middle, Isoniazid_Middle, Isoniazid_High are their regulatory (associated) DDs explored by our proposed co-clustering algorithm based on the distance and HC method combination Euclidean: Word. Similarly, for the peroxisome proliferator-activated receptor signaling pathway (PPAR-SP) dataset Cpt1a, Cyp8b1, Cyp4a3, Ehhadh, Plin5, Plin2, Fabp3, Me1, Fabp5, LOC100910385, Cpt2, Acaa1a, Cyp4a1, LOC100365047, Cpt1a, LOC100365047, Angptl4, Aqp7, Cpt1c, Cpt1b, Me1 are the biomarker genes and Aspirin_Low, Aspirin_Middle, Aspirin_High, Benzbromarone_Middle, Benzbromarone_High, Clofibrate_Middle, Clofibrate_High, WY14643_Low, WY14643_High, WY14643_Middle, Gemfibrozil_Middle, Gemfibrozil_High are their regulatory DDs. Conclusions: Overall, the methods proposed in this article, co-cluster the genes and DDs as well as detect biomarker genes and their regulatory DDs simultaneously consuming less time compared to other mentioned methods. The results produced by the proposed methods have been validated by the available literature and functional annotation.

Peptide-based targeted polymeric nanoparticles for siRNA delivery.

The development of polymer-based nanoparticulate delivery systems for siRNA is important for the clinical success of gene therapy. However, there are some major drawbacks that need to be overcome. Short interfering RNA (siRNA) has been investigated as a potential therapeutic drug to silence disease-associated genes, but its usage is limited due to the lack of effective and safe nanocarriers. In this study, DOPE-PEI, a nanoparticle consisting of the fusogenic lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) conjugated with low-molecular-weight, 600 Da, branched polyethylenimine (PEI) was produced and optimized for siRNA delivery. This delivery system was modified with other components such as 1,2-dioleoyl-sn-glycerol-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)2000] (DOPE-PEG2K), DOPE-PEG3.4K-bombesin and 1,2-dioleoyl-sn-glycerol-3-phosphoethanolamine/1,2-dioleoyl-3-trimethylammonium-propane (DOPE/DOTAP) and tested on PC-3 cells. The conjugation of DOPE to PEI polymer (DOPE-PEI) improved the efficiency of PEI to deliver siRNA into the cytosol and knockdown genes, but demonstrated high toxicity. The addition of DOPE-PEG2K reduced cellular toxicity by masking the surface positive charge of the DOPE-PEI/siRNA complex, with the incorporation of a gastrin-releasing peptide receptor (GRPR) targeting peptide and DOPE/DOTAP components improving the cellular uptake of siRNA into targeted cells and the siRNA knockdown efficiency.

Gastrin-releasing peptide receptor-targeted hybrid peptide/phospholipid pDNA/siRNA delivery systems.

Aim: To develop a peptide/phospholipid hybrid system for gastrin-releasing peptide receptor (GRPR)-targeted delivery of pDNA or siRNA. Materials & methods: A multifunctional GRPR-targeted peptide R9-K(GALA)-BBN(6-14) was combined with a phospholipid oligonucleotide delivery system (1:1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine and 1,2-dioleoyl-3-trimethylammonium-propane) and evaluated for pDNA and siRNA delivery in terms of complex size, toxicity, receptor-targeted delivery and gene expression or knockdown efficiency. Results: By combining peptide and phospholipid delivery systems, synergistic improvements in gene expression and knockdown were observed when compared with either system alone. The optimized formulation demonstrated high levels of EGFP expression and EGFP knockdown, GRPR-targeted delivery, enhanced endosomal release and minimal toxicity. Conclusion: The peptide/phospholipid hybrid system provides efficient GRPR-targeted DNA/siRNA delivery.

Advances in Targeted Gene Delivery.

Gene therapy has the potential to treat both acquired and inherited genetic diseases. Generally, two types of gene delivery vectors are used - viral vectors and non-viral vectors. Non-viral gene delivery systems have attracted significant interest (e.g. 115 gene therapies approved for clinical trials in 2018; clinicaltrials.gov) due to their lower toxicity, lack of immunogenicity and ease of production compared to viral vectors. To achieve the goal of maximal therapeutic efficacy with minimal adverse effects, the cell-specific targeting of non-viral gene delivery systems has attracted research interest. Targeting through cell surface receptors; the enhanced permeability and retention effect, or pH differences are potential means to target genes to specific organs, tissues, or cells. As for targeting moieties, receptorspecific ligand peptides, antibodies, aptamers and affibodies have been incorporated into synthetic nonviral gene delivery vectors to fulfill the requirement of active targeting. This review provides an overview of different potential targets and targeting moieties to target specific gene delivery systems.

Robust identification of significant interactions between toxicogenomic biomarkers and their regulatory chemical compounds using logistic moving range chart.

Identification of significant interactions between genes and chemical compounds/drugs is an important issue in toxicogenomic studies as well as in drug discovery and development. There are some online and offline computational tools for toxicogenomic data analysis to identify the biomarker genes and their regulatory chemical compounds/drugs. However, none of the researchers has considered yet the identification of significant interactions between genes and compounds. Therefore, in this paper, we have discussed two approaches namely moving range chart (MRC) and logistic moving range chart (LMRC) for the identification of significant up-regulatory (UpR) and down-regulatory (DnR) gene-compound interactions as well as toxicogenomic biomarkers and their regulatory chemical compounds/drugs. We have investigated the performance of both MRC and LMRC approaches using simulated datasets. Simulation results show that both approaches perform almost equally in absence of outliers. However, in presence of outliers, the LMRC shows much better performance than the MRC. In case of real life toxicogenomic data analysis, the proposed LMRC approach detected some important down-regulated biomarker genes those were not detected by other approaches. Therefore, in this paper, our proposal is to use LMRC for robust identification of significant interactions between genes and chemical compounds/drugs.

Robust Co-clustering to Discover Toxicogenomic Biomarkers and Their Regulatory Doses of Chemical Compounds Using Logistic Probabilistic Hidden Variable Model.

Detection of biomarker genes and their regulatory doses of chemical compounds (DCCs) is one of the most important tasks in toxicogenomic studies as well as in drug design and development. There is an online computational platform "Toxygates" to identify biomarker genes and their regulatory DCCs by co-clustering approach. Nevertheless, the algorithm of that platform based on hierarchical clustering (HC) does not share gene-DCC two-way information simultaneously during co-clustering between genes and DCCs. Also it is sensitive to outlying observations. Thus, this platform may produce misleading results in some cases. The probabilistic hidden variable model (PHVM) is a more effective co-clustering approach that share two-way information simultaneously, but it is also sensitive to outlying observations. Therefore, in this paper we have proposed logistic probabilistic hidden variable model (LPHVM) for robust co-clustering between genes and DCCs, since gene expression data are often contaminated by outlying observations. We have investigated the performance of the proposed LPHVM co-clustering approach in a comparison with the conventional PHVM and Toxygates co-clustering approaches using simulated and real life TGP gene expression datasets, respectively. Simulation results show that the proposed method improved the performance over the conventional PHVM in presence of outliers; otherwise, it keeps equal performance. In the case of real life TGP data analysis, three DCCs (glibenclamide-low, perhexilline-low, and hexachlorobenzene-medium) for glutathione metabolism pathway dataset as well as two DCCs (acetaminophen-medium and methapyrilene-low) for PPAR signaling pathway dataset were incorrectly co-clustered by the Toxygates online platform, while only one DCC (hexachlorobenzene-low) for glutathione metabolism pathway was incorrectly co-clustered by the proposed LPHVM approach. Our findings from the real data analysis are also supported by the other findings in the literature.

Toxic Dose prediction of Chemical Compounds to Biomarkers using an ANOVA based Gene Expression Analysis.

The aim of toxicogenomic studies is to optimize the toxic dose levels of chemical compounds (CCs) and their regulated biomarker genes. This is also crucial in drug discovery and development. There are popular online computational tools such as ToxDB and Toxygates to identify toxicogenomic biomarkers using t-test. However, they are not suitable for the identification of biomarker gene regulatory dose of corresponding CCs. Hence, we describe a one-way ANOVA model together with Tukey's HSD test for the identification of toxicogenomic biomarker genes and their influencing CC dose with improved efficiency. Glutathione metabolism pathway data analysis shows high and middle dose for acetaminophen, and nitrofurazone as well as high dose for methapyrilene as significant toxic CC dose. The corresponding regulated top seven toxicogenomic biomarker genes found in this analysis is Gstp1, Gsr, Mgst2, Gclm, G6pd, Gsta5 and Gclc.

A newly developed tool for measuring the availability of human resources for emergency obstetric and newborn care services: prospective analytic study in two district-level public facilities in Bangladesh.

BACKGROUND: In Bangladesh, while the infrastructure of public health facilities to provide maternal and newborn care services is adequate, services are not always available due to insufficient staffing. A human resource availability index for health facilities is needed for monitoring and advocacy. This study aimed to develop indices for measuring the availability of different types of human resources to provide round-the-clock emergency obstetric and newborn care (EmONC) service at district-level public facilities. METHODS: As part of a larger intervention study, 30 days of prospective observation of providers was done at a district hospital (DH) and a mother and child welfare centre (MCWC) in one district of Bangladesh using checklists. A scoring system was developed to create an index to quantify the availability of providers for maternal and newborn care. RESULTS: Based on the newly developed index, medical doctors in the emergency department of the DH were 100% available, but ranged from 27 to 41% availability in the obstetrics/gynecology (ob/gyn) and pediatric wards. In MCWC, the corresponding indices ranged from 32 to 36%. In the DH, the availability of nurses in the ob/gyn ward (96%) was relatively better than in the pediatric ward (65%) but that in operation theatre was only 31%. In the MCWC, the index for the presence of a paramedic or nursing aid was 82% in the ob/gyn ward and 63% in the operation theatre. However, the availability scores of facility support staff for maintenance and security were generally high (over 90%) in both facilities. CONCLUSIONS: Our newly developed index on availability of providers demonstrated huge gaps in availability of providers in evening and night shifts in most of the disciplines in the study facilities. This provider availability index is easy to create and can be used as a meaningful tool to quantify gaps in human resources by type in various types of district-level health facilities. Further studies are needed for adaptation of this tool in different types of health facilities and to assess its implication as an advocacy tool.

Bombesin/oligoarginine fusion peptides for gastrin releasing peptide receptor (GRPR) targeted gene delivery.

The development of non-viral gene delivery systems, with the capacity to overcome most of the biological barriers facing gene delivery, is challenging. We have developed peptide-based, multicomponent, non-viral delivery systems, incorporating: a bombesin peptide ligand (BBN(6-14)), to selectively target the gastrin releasing peptide receptor (GRPR); oligoarginine peptides (hexa- (R6) and nona-arginine (R9)), for plasmid DNA (pDNA) condensation; and GALA, to facilitate endosome escape. The uptake and endosome escape efficiency of bombesin/oligoarginine and bombesin/oligoarginine/GALA fusion peptides for oligonucleotide delivery was evaluated in terms of their complex size, cellular uptake, endosome escape, and cellular toxicity. Complex size and cell uptake studies demonstrated that the nona-arginine/bombesin delivery system was more efficient at condensing and delivering pDNA into PC-3 prostate cancer cells compared to the hexa-arginine/bombesin delivery system. Further, competition with free bombesin peptide, and comparative uptake studies in Caco-2 cells, which express GRPR at a lower level, suggested that GRPR contributes to the targeted uptake of this system. The addition of GALA into the nona-arginine/bombesin-based system further increased the pDNA cellular uptake at all tested N/P ratios; facilitated endosomal pDNA release; and had limited effects on cell viability. In conclusion, the delivery system combining BBN(6-14) with nona-arginine and GALA had optimal characteristics for the delivery of pDNA into the GRPR overexpressing cell line PC-3.

Robust Significance Analysis of Microarrays by Minimum ß-Divergence Method.

Identification of differentially expressed (DE) genes with two or more conditions is an important task for discovery of few biomarker genes. Significance Analysis of Microarrays (SAM) is a popular statistical approach for identification of DE genes for both small- and large-sample cases. However, it is sensitive to outlying gene expressions and produces low power in presence of outliers. Therefore, in this paper, an attempt is made to robustify the SAM approach using the minimum ß-divergence estimators instead of the maximum likelihood estimators of the parameters. We demonstrated the performance of the proposed method in a comparison of some other popular statistical methods such as ANOVA, SAM, LIMMA, KW, EBarrays, GaGa, and BRIDGE using both simulated and real gene expression datasets. We observe that all methods show good and almost equal performance in absence of outliers for the large-sample cases, while in the small-sample cases only three methods (SAM, LIMMA, and proposed) show almost equal and better performance than others with two or more conditions. However, in the presence of outliers, on an average, only the proposed method performs better than others for both small- and large-sample cases with each condition.

Investigation of bombesin peptide as a targeting ligand for the gastrin releasing peptide (GRP) receptor.

Gastrin releasing peptide (GRP) receptor (GRPR), a bombesin family receptor, is overexpressed in many cancers including breast, prostate, pancreatic and lung. The targeting of therapeutics to GRPR can be achieved using the full-length (14 amino acid) GRP analogue Bombesin (BBN) or the truncated BBN(6-14) sequence, both of which bind GRPR with high affinity and specificity. In this study, we have investigated the level of GRPR expression in various cancerous (Caco-2, HeLa, LNCap, MDA-MB-231, and PC-3) and non-cancerous (WPMY-1) cell lines using a western blotting approach. Such information is currently lacking in the literature, and is therefore of importance for the in vitro assessment of GRPR targeted therapeutics. Of the cell lines assessed, the PC-3 (prostate cancer) and Caco-2 (colon cancer) cell lines demonstrated the highest and lowest levels of GRPR expression respectively. Using this information, we further investigated the cellular uptake of carboxyfluorescein-labelled BBN and BBN(6-14) peptides by flow cytometry and confocal microscopy using cell lines that express GRPR (Caco-2, HeLa, PC-3). The uptake of each of these peptides was similar, suggesting that the shorter BBN(6-14) peptide is sufficient for GRPR targeting. Further, the uptake of these peptides could be inhibited by competition with unlabelled BBN peptides, suggesting their cellular uptake is GRPR-mediated, while the level of BBN uptake (as measured by flow cytometry) was found to be directly proportional to the level of GRPR expression. Overall, the information obtained from these studies provides useful information for the in vitro assessment of GRPR targeted therapeutics.

Market Assessment and Product Evaluation of Probiotic Containing Dietary Supplements Available in Bangladesh Market.

Probiotics containing food supplements available in Bangladesh market were identified and collected for assessment. To assess their label claim, they were resuspended into sterile distilled water. Then, series dilutions of each sample solution were prepared and immediately plated out, in duplicate, into De Man Rogosa Sharpe (MRS) agar. These plates were then incubated at 37°C for 48 hours and colonies were counted. Viable cell numbers stated on the labels were compared with actual viable cell numbers. To assess the viability of the probiotics included in the products, probiotic strains were isolated from each of the four products and screened for inhibitory activity against six indicator strains. It was surprisingly found that although the viable cell numbers of all supplements were three to four log cycles lower than label claim of the products, however, this problem did not affect the inhibitory activity of the probiotic strains against indicator strains according to in vitro assessment. Legislation and regulation regarding prebiotic-probiotic containing products should be built up in Bangladesh to ensure quality products supply to the consumers. Moreover, manufacturers of probiotic containing products should take the responsibility for providing the consumer with scientifically and legally correct information.

Role of early serum beta human chorionic gonadotropin measurement in predicting multiple pregnancy and pregnancy wastage in an in vitro ET fertilization cycle.

OBJECTIVE: This study was performed to assess the prognostic value of serum beta human chorionic gonadotropin (ßhCG), measured on day 14 post embryo transfer (ET) for predicting multiple gestation and pregnancy wastage in women undergoing in vitro fertilization ET (IVF-ET). MATERIALS AND METHODS: This retrospective study was performed between May 2009 and November 2012. Out of the 181 women who conceived, 168 were included and the remaining 13 were excluded as their pregnancy was biochemical. Serum ßhCG was measured using a chemiluminescent enzyme immunometric assay. The predictive values of serum ßhCG for establishing multiple pregnancy and pregnancy wastages were calculated by receiver operating characteristic (ROC) curve analysis. Median values of serum ßhCG and outcome of all pregnancies were compared. RESULTS: Out of the 168 patients who conceived after IVF treatment, 114 (68%) were viable pregnancies (delivered/ongoing). Among the viable pregnancies, 97 (85%) had a successful pregnancy outcome and the remaining 17 patients are ongoing pregnancies. Median values of ßhCG (625 IU/L) among viable pregnancies was significantly (P < 0.05) higher than that of nonviable pregnancies (174 IU/L). The median values of ßhCG for singleton (502 IU/L), twins (1093 IU/L), and triplets (2160 IU/L) was statistically significant (P < 0.05). Using ROC curve it was predicted that for a value of ßhCG at 375 IU/L, the sensitivity of viable pregnancy was 65% and specificity of viable pregnancy was also 65%, with positive and negative predictive values of 65 and 68%, respectively. Similarly for multiple pregnancy and pregnancy wastage the predictive values of ßhCG were 808 and 375 IU/L, respectively; while the sensitivity and specificity is more than 65% each. CONCLUSION: ßhCG cutoff values determined on day 14 post ET by ROC curve analysis are useful in discriminating between multiple pregnancy and pregnancy losses. The cutoff value might aid in the prognosis, clinical management, and counseling of the IVF patients.

Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity.

A mechanistic study of the essential allosteric activation of human pancreatic alpha-amylase by chloride ion has been conducted by exploring a wide range of anion substitutions through kinetic and structural experiments. Surprisingly, kinetic studies indicate that the majority of these alternative anions can induce some level of enzymatic activity despite very different atomic geometries, sizes, and polyatomic natures. These data and subsequent structural studies attest to the remarkable plasticity of the chloride binding site, even though earlier structural studies of wild-type human pancreatic alpha-amylase suggested this site would likely be restricted to chloride binding. Notably, no apparent relationship is observed between anion binding affinity and relative activity, emphasizing the complexity of the relationship between chloride binding parameters and the activation mechanism that facilitates catalysis. Of the anions studied, particularly intriguing in terms of observed trends in substrate kinetics and their novel atomic compositions were the nitrite, nitrate, and azide anions, the latter of which was found to enhance the relative activity of human pancreatic alpha-amylase by nearly 5-fold. Structural studies have provided considerable insight into the nature of the interactions formed in the chloride binding site by the nitrite and nitrate anions. To probe the role such interactions play in allosteric activation, further structural analyses were conducted in the presence of acarbose, which served as a sensitive reporter molecule of the catalytic ability of these modified enzymes to carry out its expected rearrangement by human pancreatic alpha-amylase. These studies show that the largest anion of this group, nitrate, can comfortably fit in the chloride binding pocket, making all the necessary hydrogen bonds. Further, this anion has nearly the same ability to activate human pancreatic alpha-amylase and leads to the production of the same acarbose product. In contrast, while nitrite considerably boosts the relative activity of human pancreatic alpha-amylase, its presence leads to changes in the electrostatic environment and active site conformations that substantially modify catalytic parameters and produce a novel acarbose rearrangement product. In particular, nitrite-substituted human pancreatic alpha-amylase demonstrates the unique ability to cleave acarbose into its acarviosine and maltose parts and carry out a previously unseen product elongation. In a completely unexpected turn of events, structural studies show that in azide-bound human pancreatic alpha-amylase, the normally resident chloride ion is retained in its binding site and an azide anion is found bound in an embedded side pocket in the substrate binding cleft. These results clearly indicate that azide enzymatic activation occurs via a mechanism distinct from that of the nitrite and nitrate anions.

Acarbose rearrangement mechanism implied by the kinetic and structural analysis of human pancreatic alpha-amylase in complex with analogues and their elongated counterparts.

A mechanistic study of the poorly understood pathway by which the inhibitor acarbose is enzymatically rearranged by human pancreatic alpha-amylase has been conducted by structurally examining the binding modes of the related inhibitors isoacarbose and acarviosine-glucose, and by novel kinetic measurements of all three inhibitors under conditions that demonstrate this rearrangement process. Unlike acarbose, isoacarbose has a unique terminal alpha-(1-6) linkage to glucose and is found to be resistant to enzymatic rearrangement. This terminal glucose unit is found to bind in the +3 subsite and for the first time reveals the interactions that occur in this part of the active site cleft with certainty. These results also suggest that the +3 binding subsite may be sufficiently flexible to bind the alpha-(1-6) branch points in polysaccharide substrates, and therefore may play a role in allowing efficient cleavage in the direct vicinity of such junctures. Also found to be resistant to enzymatic rearrangement was acarviosine-glucose, which has one fewer glucose unit than acarbose. Collectively, structural studies of all three inhibitors and the specific cleavage pattern of HPA make it possible to outline the simplest sequence of enzymatic reactions likely involved upon acarbose binding. Prominent features incorporated into the starting structure of acarbose to facilitate the synthesis of the final tightly bound pseudo-pentasaccharide product are the restricted availability of hydrolyzable bonds and the placement of the transition state-like acarviosine group. Additional "in situ" experiments designed to elongate and thereby optimize isoacarbose and acarviosine-glucose inhibition using the activated substrate alphaG3F demonstrate the feasibility of this approach and that the principles outlined for acarbose rearrangement can be used to predict the final products that were obtained.

Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.

The mechanism of allosteric activation of alpha-amylase by chloride has been studied through structural and kinetic experiments focusing on the chloride-dependent N298S variant of human pancreatic alpha-amylase (HPA) and a chloride-independent TAKA-amylase. Kinetic analysis of the HPA variant clearly demonstrates the pronounced activating effect of chloride ion binding on reaction rates and its effect on the pH-dependence of catalysis. Structural alterations observed in the N298S variant upon chloride ion binding suggest that the chloride ion plays a variety of roles that serve to promote catalysis. One of these is having a strong influence on the positioning of the acid/base catalyst residue E233. Absence of chloride ion results in multiple conformations for this residue and unexpected enzymatic products. Chloride ion and N298 also appear to stabilize a helical region of polypeptide chain from which projects the flexible substrate binding loop unique to chloride-dependent alpha-amylases. This structural feature also serves to properly orient the catalytically essential residue D300. Comparative analyses show that the chloride-independent alpha-amylases compensate for the absence of bound chloride by substituting a hydrophobic core, altering the manner in which substrate interactions are made and shifting the placement of N298. These evolutionary differences presumably arise in response to alternative operating environments or the advantage gained in a particular product profile. Attempts to engineer chloride-dependence into the chloride-independent TAKA-amylase point out the complexity of this system, and the fact that a multitude of factors play a role in binding chloride ion in the chloride-dependent alpha-amylases.

In situ extension as an approach for identifying novel alpha-amylase inhibitors.

A new approach for the discovery and subsequent structural elucidation of oligosaccharide-based inhibitors of alpha-amylases based upon autoglucosylation of known alpha-glucosidase inhibitors is presented. This concept, highly analogous to what is hypothesized to occur with acarbose, is demonstrated with the known alpha-glucosidase inhibitor, d-gluconohydroximino-1,5-lactam. This was transformed from an inhibitor of human pancreatic alpha-amylase with a K(i) value of 18 mm to a trisaccharide analogue with a K(i) value of 25 mum. The three-dimensional structure of this complex was determined by x-ray crystallography and represents the first such structure determined with this class of inhibitors in any alpha-glycosidase. This approach to the discovery and structural analysis of amylase inhibitors should be generally applicable to other endoglucosidases and readily adaptable to a high throughput format.