Structural Insights into the Role of the Cyclic Backbone in a Squash Trypsin Inhibitor

: Tuberculosis is one of the leading cause for deaths due to infectious disease worldwide. There is an urgent need for developing new drugs due to the rising incidents of drug resistance. Triazoles have previously been reported to show antitubercular activity. Various computational tools pave the way for a rational approach in understanding the structural importance of these compounds in inhibiting Mycobacterium tuberculosis growth. The aim of this study is to develop and compare two different QSAR models based on a set of previously reported molecules and use the best one for gaining structural insights in to the Triazole molecules. In the current study, two separate models were generated with CoMFA and CoMSIA descriptors respectively based on a dataset of triazole molecules showing antitubercular activity. Several one dimensional (1D) descriptors were added to each of the models and the validation results and the contour data generated from them were compared. The best model was studied to give a detailed understanding of the triazole molecules and their role in the antitubercular activity.The r2, q2, predicted r2 and SEP (Standard error of prediction) for the CoMFA model were 0.866, 0.573, 0.119 and 0.736 respectively and for the CoMSIA model the r2, q2, predicted r2 and SEP were calculated to be 0.998, 0.634, 0.013 and 0.869 respectively. Although both the QSAR models produced acceptable internal and external validation scores but the CoMSIA results were significantly better. The CoMSIA contours also provided a better match than CoMFA with most of the features of the active compound 30b. Hence, the CoMSIA model was chosen and its contours were explored for gaining structural insights on the triazole molecules. The CoMSIA contours helped us to understand the role of several atoms and groups of the triazole molecules in their biological activity. The possibilities for substitution in the triazole compounds that would enhance the activity were also analysed. Thus, this study paves the way for designing new antitubercular drugs in future.

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Role of pancreatic secretory trypsin inhibitor (PSTI) in healing of chronic gastric ulcers in rats

Gastroenterology ◽

10.1016/s0016-5085(98)83621-4 ◽

1998 ◽

Vol 114 ◽

pp. A889

Author(s):

PC. Konturek ◽

T. Brzozowski ◽

SJ. Konturek ◽

S. Yagi ◽

G. Elia ◽

...

Keyword(s):

Trypsin Inhibitor ◽

Gastric Ulcers ◽

Pancreatic Secretory Trypsin Inhibitor

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Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

10.1101/2021.01.07.425261 ◽

2021 ◽

Author(s):

Pär Söderhjelm ◽

Mandar Kulkarni

Keyword(s):

Free Energy ◽

Trypsin Inhibitor ◽

Side Chain ◽

Side Chains ◽

Aromatic Residues ◽

Basic Pancreatic Trypsin Inhibitor ◽

Pancreatic Trypsin Inhibitor ◽

Energy Surfaces ◽

Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

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Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

Biochemical Journal ◽

10.1042/bj20110002 ◽

2011 ◽

Vol 436 (3) ◽

pp. 729-739 ◽

Cited By ~ 23

Author(s):

Marcio V. B. Dias ◽

William C. Snee ◽

Karen M. Bromfield ◽

Richard J. Payne ◽

Satheesh K. Palaninathan ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Drug Targets ◽

Structural Investigation ◽

Catalytic Mechanism ◽

Shikimate Pathway ◽

Structural Rearrangement ◽

Competitive Inhibitors ◽

Structural Insights ◽

Potential Drug Targets

The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analogue of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form π-stacking interactions with the catalytic Tyr24 have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19–24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.

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Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression

Scientific Reports ◽

10.1038/s41598-020-78882-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Debmalya Sengupta ◽

Gairika Bhattacharya ◽

Sayak Ganguli ◽

Mainak Sengupta

Keyword(s):

Lung Cancer ◽

Cancer Progression ◽

Structural Parameters ◽

Homology Modelling ◽

Missense Variants ◽

Potential Impact ◽

The Impact ◽

Structural Insights ◽

Rigid Docking

AbstractThe cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.

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Non-penetrance of the hereditary pancreatitis (HP) phenotype in a patient with the R122H mutation: The role of pancreatic secretory trypsin inhibitor (SPINK1/PSTI)

Gastroenterology ◽

10.1016/s0016-5085(08)81694-0 ◽

2001 ◽

Vol 120 (5) ◽

pp. A340

Author(s):

Asif Khalid ◽

Bryan S. Thompson

Keyword(s):

Trypsin Inhibitor ◽

Hereditary Pancreatitis ◽

Pancreatic Secretory Trypsin Inhibitor ◽

R122h Mutation

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Structural insights into the functional role of the Hcn sub-domain of the receptor-binding domain of the botulinum neurotoxin mosaic serotype C/D

Biochimie ◽

10.1016/j.biochi.2013.03.006 ◽

2013 ◽

Vol 95 (7) ◽

pp. 1379-1385 ◽

Cited By ~ 7

Author(s):

Yanfeng Zhang ◽

Anna S. Gardberg ◽

Thomas E. Edwards ◽

Banumathi Sankaran ◽

Howard Robinson ◽

...

Keyword(s):

Receptor Binding ◽

Functional Role ◽

Botulinum Neurotoxin ◽

Binding Domain ◽

Receptor Binding Domain ◽

Structural Insights

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Acid inhibition by intestinal nutrients mediated by CCK-A receptors but not plasma CCK

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.2001.281.4.g924 ◽

2001 ◽

Vol 281 (4) ◽

pp. G924-G930 ◽

Cited By ~ 5

Author(s):

K. C. Kent Lloyd ◽

Jiafang Wang ◽

Travis E. Solomon

Keyword(s):

Acid Secretion ◽

Gastric Acid ◽

Trypsin Inhibitor ◽

Acid Output ◽

Liquid Diet ◽

Acid Inhibition ◽

Soybean Trypsin Inhibitor ◽

The Individual

We examined the role of CCK-A receptors in acid inhibition by intestinal nutrients. Gastric acid and plasma CCK and gastrin levels were measured in rats with gastric and duodenal fistulas during intragastric 8% peptone and duodenal perfusion with saline, complete liquid diet (CLD; 20% carbohydrate, 6% fat, and 5% protein), and the individual components of CLD. Acid output was significantly inhibited (50–60%) by CLD, lipid, and dextrose. Plasma CCK was significantly increased by CLD (from 2.6 ± 0.3 to 4.8 ± 0.5 pM) and lipid (4.6 ± 0.5 pM). CCK levels 50-fold higher (218 ± 33 pM) were required to achieve similar acid inhibition by exogenous CCK-8 (10 nmol · kg−1 · h−1 iv). Intestinal soybean trypsin inhibitor elevated CCK (10.9 ± 2.5 pM) without inhibiting acid secretion. The CCK-A antagonist MK-329 (1 mg/kg iv) reversed acid inhibition caused by CLD, lipid, and dextrose. Peptone-stimulated gastrin (21.7 ± 1.9 pM) was significantly inhibited by CLD (14.5 ± 3.6 pM), lipid (12.3 ± 2.2 pM), and dextrose (11.9 ± 1.5 pM). Lipid and carbohydrate inhibit acid secretion by activating CCK-A receptors but not by altering plasma CCK concentrations.

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