scholarly journals Structural Modeling of the TMPRSS Subfamily of Host Cell Proteases Reveals Potential Binding Sites

2021 ◽  
Author(s):  
Diego E Escalante ◽  
Austin B Wang ◽  
David M Ferguson
Keyword(s):  
Binding Sites ◽  
Structural Data ◽  
Homology Model ◽  
Dynamic Simulations ◽  
Drug Candidates ◽  
Potential Binding ◽  
Wide Range ◽  
Range Of Functions ◽  
Atomic Coordinates ◽  
Homology Models

The transmembrane protease serine subfamily (TMPRSS) has at least eight members with known protein sequence: TMPRSS2, TMPRRS3, TMPRSS4, TMPRSS5, TMPRSS6, TMPRSS7, TMPRSS9, TMPRSS11, TMPRSS12 and TMPRSS13. A majority of these TMPRSS proteins have key roles in human hemostasis as well as promoting certain pathologies, including several types of cancer. In addition, TMPRSS proteins have been shown to facilitate the entrance of respiratory viruses into human cells, most notably TMPRSS2 and TMPRSS4 activate the spike protein of the SARS-CoV-2 virus. Despite the wide range of functions that these proteins have in the human body, none of them have been successfully crystallized. The lack of structural data has significantly hindered any efforts to identify potential drug candidates with high selectivity to these proteins. In this study, we present homology models for all members of the TMPRSS family including any known isoform (the homology model of TMPRSS2 is not included in this study as it has been previously published). The atomic coordinates for all homology models have been refined and equilibrated through molecular dynamic simulations. The structural data revealed potential binding sites for all TMPRSS as well as key amino acids that can be targeted for drug selectivity.

scholarly journals DNA Binding Site Selection of Dimeric and Tetrameric Stat5 Proteins Reveals a Large Repertoire of Divergent Tetrameric Stat5a Binding Sites

2000 ◽  
Vol 20 (1) ◽  
pp. 389-401 ◽  
Author(s):  
Elisabetta Soldaini ◽  
Susan John ◽  
Stefano Moro ◽  
Julie Bollenbacher ◽  
Ulrike Schindler ◽  
...  
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Site Selection ◽  
Binding Sites ◽  
Tetramer Binding ◽  
Dna Binding Site ◽  
Potential Binding ◽  
Wide Range ◽  
Large Repertoire ◽  
Selection Of

ABSTRACT We have defined the optimal binding sites for Stat5a and Stat5b homodimers and found that they share similar core TTC(T/C)N(G/A)GAA interferon gamma-activated sequence (GAS) motifs. Stat5a tetramers can bind to tandemly linked GAS motifs, but the binding site selection revealed that tetrameric binding also can be seen with a wide range of nonconsensus motifs, which in many cases did not allow Stat5a binding as a dimer. This indicates a greater degree of flexibility in the DNA sequences that allow binding of Stat5a tetramers than dimers. Indeed, in an oligonucleotide that could bind both dimers and tetramers, it was possible to design mutants that affected dimer binding without affecting tetramer binding. A spacing of 6 bp between the GAS sites was most frequently selected, demonstrating that this distance is favorable for Stat5a tetramer binding. These data provide insights into tetramer formation by Stat5a and indicate that the repertoire of potential binding sites for this transcription factor is broader than expected.

scholarly journals LuxS quorum sensing system, its protein modeling and active-binding sites and phylogenetic analysis from Aeromonas hydrophila

2017 ◽  
Author(s):  
Farman Ali ◽  
Zujie Yao ◽  
Wanxin Li ◽  
Sun Lina ◽  
Wenxiong Lin ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Binding Sites ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Zinc Ion ◽  
Dimensional Structure ◽  
Wide Range ◽  
Range Of Functions

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila.

scholarly journals The N2A region of titin has a unique structural configuration

2021 ◽  
Vol 153 (7) ◽  
Author(s):  
Chiara Stronczek ◽  
Stephan Lange ◽  
Belinda Bullard ◽  
Sebastian Wolniak ◽  
Emma Börgeson ◽  
...  
Keyword(s):  
Binding Sites ◽  
Force Production ◽  
Structural Data ◽  
Homology Model ◽  
Structural Configuration ◽  
C2c12 Myoblasts ◽  
X Ray ◽  
X Ray Crystallography ◽  
Processing Enzymes ◽  
Binding Partners

The N2A segment of titin is a main signaling hub in the sarcomeric I-band that recruits various signaling factors and processing enzymes. It has also been proposed to play a role in force production through its Ca2+-regulated association with actin. However, the molecular basis by which N2A performs these functions selectively within the repetitive and extensive titin chain remains poorly understood. Here, we analyze the structure of N2A components and their association with F-actin. Specifically, we characterized the structure of its Ig domains by elucidating the atomic structure of the I81-I83 tandem using x-ray crystallography and computing a homology model for I80. Structural data revealed these domains to present heterogeneous and divergent Ig folds, where I81 and I83 have unique loop structures. Notably, the I81-I83 tandem has a distinct rotational chain arrangement that confers it a unique multi-domain topography. However, we could not identify specific Ca2+-binding sites in these Ig domains, nor evidence of the association of titin N2A components with F-actin in transfected C2C12 myoblasts or C2C12-derived myotubes. In addition, F-actin cosedimentation assays failed to reveal binding to N2A. We conclude that N2A has a unique architecture that predictably supports its selective recruitment of binding partners in signaling, but that its mechanical role through interaction with F-actin awaits validation.

scholarly journals LuxS quorum sensing system, its protein modeling and active-binding sites and phylogenetic analysis from Aeromonas hydrophila

2017 ◽  
Author(s):  
Farman Ali ◽  
Zujie Yao ◽  
Wanxin Li ◽  
Sun Lina ◽  
Wenxiong Lin ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Binding Sites ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Zinc Ion ◽  
Dimensional Structure ◽  
Wide Range ◽  
Range Of Functions

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila.

scholarly journals Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity

2021 ◽  
Vol 17 (10) ◽  
pp. e1009470
Author(s):  
Daniel E. Mattox ◽  
Chris Bailey-Kellogg
Keyword(s):  
Protein Trafficking ◽  
Binding Sites ◽  
Lectin Binding ◽  
Structural Data ◽  
Novel Approach ◽  
Wide Range ◽  
Generalized Patterns ◽  
Lectin Specificity ◽  
Lectin Binding Sites

Lectin-glycan interactions facilitate inter- and intracellular communication in many processes including protein trafficking, host-pathogen recognition, and tumorigenesis promotion. Specific recognition of glycans by lectins is also the basis for a wide range of applications in areas including glycobiology research, cancer screening, and antiviral therapeutics. To provide a better understanding of the determinants of lectin-glycan interaction specificity and support such applications, this study comprehensively investigates specificity-conferring features of all available lectin-glycan complex structures. Systematic characterization, comparison, and predictive modeling of a set of 221 complementary physicochemical and geometric features representing these interactions highlighted specificity-conferring features with potential mechanistic insight. Univariable comparative analyses with weighted Wilcoxon-Mann-Whitney tests revealed strong statistical associations between binding site features and specificity that are conserved across unrelated lectin binding sites. Multivariable modeling with random forests demonstrated the utility of these features for predicting the identity of bound glycans based on generalized patterns learned from non-homologous lectins. These analyses revealed global determinants of lectin specificity, such as sialic acid glycan recognition in deep, concave binding sites enriched for positively charged residues, in contrast to high mannose glycan recognition in fairly shallow but well-defined pockets enriched for non-polar residues. Focused fine specificity analysis of hemagglutinin interactions with human-like and avian-like glycans uncovered features representing both known and novel mutations related to shifts in influenza tropism from avian to human tissues. As the approach presented here relies on co-crystallized lectin-glycan pairs for studying specificity, it is limited in its inferences by the quantity, quality, and diversity of the structural data available. Regardless, the systematic characterization of lectin binding sites presented here provides a novel approach to studying lectin specificity and is a step towards confidently predicting new lectin-glycan interactions.

Privileged Structures in the Design of Potential Drug Candidates for Neglected Diseases

2019 ◽  
Vol 26 (23) ◽  
pp. 4323-4354 ◽  
Author(s):  
Ana Cristina Lima Leite ◽  
José Wanderlan Pontes Espíndola ◽  
Marcos Veríssimo de Oliveira Cardoso ◽  
Gevanio Bezerra de Oliveira Filho
Keyword(s):  
Biologically Active ◽  
Neglected Diseases ◽  
Financial Return ◽  
Drug Candidates ◽  
Lead Compounds ◽  
Wide Range ◽  
Methods Of Synthesis ◽  
Current Therapies ◽  
Resistant Strains ◽  
Privileged Structures

Background: Privileged motifs are recurring in a wide range of biologically active compounds that reach different pharmaceutical targets and pathways and could represent a suitable start point to access potential candidates in the neglected diseases field. The current therapies to treat these diseases are based in drugs that lack of the desired effectiveness, affordable methods of synthesis and allow a way to emergence of resistant strains. Due the lack of financial return, only few pharmaceutical companies have been investing in research for new therapeutics for neglected diseases (ND). Methods: Based on the literature search from 2002 to 2016, we discuss how six privileged motifs, focusing phthalimide, isatin, indole, thiosemicarbazone, thiazole, and thiazolidinone are particularly recurrent in compounds active against some of neglected diseases. Results: It was observed that attention was paid particularly for Chagas disease, malaria, tuberculosis, schistosomiasis, leishmaniasis, dengue, African sleeping sickness (Human African Trypanosomiasis - HAT) and toxoplasmosis. It was possible to verify that, among the ND, antitrypanosomal and antiplasmodial activities were between the most searched. Besides, thiosemicarbazone moiety seems to be the most versatile and frequently explored scaffold. As well, phthalimide, isatin, thiazole, and thiazolidone nucleus have been also explored in the ND field. Conclusion: Some described compounds, appear to be promising drug candidates, while others could represent a valuable inspiration in the research for new lead compounds.

Cucurbitacins as Anticancer Agents: A Patent Review

2019 ◽  
Vol 14 (2) ◽  
pp. 133-143 ◽  
Author(s):  
Hidayat Hussain ◽  
Ivan R. Green ◽  
Muhammad Saleem ◽  
Khanzadi F. Khattak ◽  
Muhammad Irshad ◽  
...  
Keyword(s):  
Anticancer Agents ◽  
Wide Spectrum ◽  
Biological Effects ◽  
Therapeutic Effects ◽  
Cytotoxic Effects ◽  
Natural Sources ◽  
Oh Groups ◽  
Drug Candidates ◽  
The Past ◽  
Wide Range

Background: Cucurbitacins belong to a group of tetracyclic triterpenoids that display a wide range of biological effects. In the past, numerous cucurbitacins have been isolated from natural sources and many active compounds have been synthesized using the privileged scaffold in order to enhance its cytotoxic effects. Objective: his review covers patents on the therapeutic effects of natural cucurbitacins and their synthetic analogs published during the past decade. By far, the majority of patents published are related to cancer and Structure-Activity Relationships (SAR) of these compounds are included to lend gravitas to this important class of natural products. Methods: The date about the published patents was downloaded via online open access patent databases. Results: Cucurbitacins display significant cytotoxic properties, in particular cucurbitacins B and D which possess very potent effects towards a number of cancer cells. Numerous cucurbitacins isolated from natural sources have been derivatized through chemical modification at the C(2)-OH and C(25)- OH groups. Most importantly, an acyl ester of the C(25)-OH and, iso-propyl, n-propyl and ethyl ether groups of the C(2)-OH demonstrated the most increased cytotoxic activity. Conclusion: The significant cytotoxic effects of natural and semi-synthetic cucurbitacins make them attractive as new drug candidates. Moreover, cucurbitacins have the capability to form conjugates with other anticancer drugs which will synergistically enhance their anticancer effects. The authors believe that in order to get lead compounds, there should be a greater focus on the synthesis of homodimers, heterodimers, and halo derivatives of cucurbitacins. In the opinion of the authors the analysis of the published patents on the cucurbitacins indicates that these compounds can be developed into a regimen to treat a wide spectrum of cancers.

Structure, Function and Interactions of Tau: Particular Focus on Potential Drug Targets for the Treatment of Tauopathies

2018 ◽  
Vol 17 (5) ◽  
pp. 325-337 ◽  
Author(s):  
Hojjat Borna ◽  
Kasim Assadoulahei ◽  
Gholamhossein Riazi ◽  
Asghar Beigi Harchegani ◽  
Alireza Shahriary
Keyword(s):  
Tau Protein ◽  
Drug Targets ◽  
Brain Injuries ◽  
Potential Drug ◽  
Microtubule Network ◽  
Wide Range ◽  
Potential Risk Factors ◽  
Range Of Functions ◽  
Potential Drug Targets

Background & Objective: Neurodegenrative diseases are among the most widespread lifethreatening disorders around the world in elderly ages. The common feature of a group of neurodegenerative disorders, called tauopathies, is an accumulation of microtubule associated protein tau inside the neurons. The exact mechanism underlying tauopathies is not well-understood but several factors such as traumatic brain injuries and genetics are considered as potential risk factors. Although tau protein is well-known for its key role in stabilizing and organization of axonal microtubule network, it bears a broad range of functions including DNA protection and participation in signaling pathways. Moreover, the flexible unfolded structure of tau facilitates modification of tau by a wide range of intracellular enzymes which in turn broadens tau function and interaction spectrum. The distinctive properties of tau protein concomitant with the crucial role of tau interaction partners in the progression of neurodegeneration suggest tau and its binding partners as potential drug targets for the treatment of neurodegenerative diseases. Conclusion: This review aims to give a detailed description of structure, functions and interactions of tau protein in order to provide insight into potential therapeutic targets for treatment of tauopathies.

scholarly journals Modern Synthetic Methods for the Stereoselective Construction of 1,3-Dienes

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 249
Author(s):  
Raquel G. Soengas ◽  
Humberto Rodríguez-Solla
Keyword(s):  
Organic Chemistry ◽  
Natural Products ◽  
Functional Group ◽  
Biological Activities ◽  
Synthetic Methods ◽  
Bond Forming ◽  
Drug Candidates ◽  
The Past ◽  
Wide Range

The 1,3-butadiene motif is widely found in many natural products and drug candidates with relevant biological activities. Moreover, dienes are important targets for synthetic chemists, due to their ability to give access to a wide range of functional group transformations, including a broad range of C-C bond-forming processes. Therefore, the stereoselective preparation of dienes have attracted much attention over the past decades, and the search for new synthetic protocols continues unabated. The aim of this review is to give an overview of the diverse methodologies that have emerged in the last decade, with a focus on the synthetic processes that meet the requirements of efficiency and sustainability of modern organic chemistry.

scholarly journals Ways into Understanding HIF Inhibition

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 159
Author(s):  
Tina Schönberger ◽  
Joachim Fandrey ◽  
Katrin Prost-Fingerle
Keyword(s):  
Protein Interactions ◽  
Target Genes ◽  
Protein Protein Interactions ◽  
Low Oxygen ◽  
Drug Candidates ◽  
Open Questions ◽  
Wide Range ◽  
Hif Pathway

Hypoxia is a key characteristic of tumor tissue. Cancer cells adapt to low oxygen by activating hypoxia-inducible factors (HIFs), ensuring their survival and continued growth despite this hostile environment. Therefore, the inhibition of HIFs and their target genes is a promising and emerging field of cancer research. Several drug candidates target protein–protein interactions or transcription mechanisms of the HIF pathway in order to interfere with activation of this pathway, which is deregulated in a wide range of solid and liquid cancers. Although some inhibitors are already in clinical trials, open questions remain with respect to their modes of action. New imaging technologies using luminescent and fluorescent methods or nanobodies to complement widely used approaches such as chromatin immunoprecipitation may help to answer some of these questions. In this review, we aim to summarize current inhibitor classes targeting the HIF pathway and to provide an overview of in vitro and in vivo techniques that could improve the understanding of inhibitor mechanisms. Unravelling the distinct principles regarding how inhibitors work is an indispensable step for efficient clinical applications and safety of anticancer compounds.

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