Drug Targets in Cellular Processes of Cancer: From Nonclinical to Preclinical Models

Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid–liquid phase separations—which critically involve both intermolecular interactions between IDPs and their posttranslational modification—are analyzed to understand the potential of IDPs as new drug targets.

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Membrane proteins: always an insoluble problem?

Biochemical Society Transactions ◽

10.1042/bst20160025 ◽

2016 ◽

Vol 44 (3) ◽

pp. 790-795 ◽

Cited By ~ 25

Author(s):

Andrea E. Rawlings

Keyword(s):

Membrane Proteins ◽

Lipid Membranes ◽

Drug Targets ◽

Functional Characterization ◽

Water Soluble ◽

High Yield ◽

Cellular Processes ◽

Native Sequence ◽

Protein Research ◽

New Methodologies

Membrane proteins play crucial roles in cellular processes and are often important pharmacological drug targets. The hydrophobic properties of these proteins make full structural and functional characterization challenging because of the need to use detergents or other solubilizing agents when extracting them from their native lipid membranes. To aid membrane protein research, new methodologies are required to allow these proteins to be expressed and purified cheaply, easily, in high yield and to provide water soluble proteins for subsequent study. This mini review focuses on the relatively new area of water soluble membrane proteins and in particular two innovative approaches: the redesign of membrane proteins to yield water soluble variants and how adding solubilizing fusion proteins can help to overcome these challenges. This review also looks at naturally occurring membrane proteins, which are able to exist as stable, functional, water soluble assemblies with no alteration to their native sequence.

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A Human DUB Protein Array for Clarification of Linkage Specificity of Polyubiquitin Chain and Application to Evaluation of Its Inhibitors

Biomedicines ◽

10.3390/biomedicines8060152 ◽

2020 ◽

Vol 8 (6) ◽

pp. 152

Author(s):

Hirotaka Takahashi ◽

Satoshi Yamanaka ◽

Shohei Kuwada ◽

Kana Higaki ◽

Kohki Kido ◽

...

Keyword(s):

Drug Targets ◽

Protein Array ◽

Polyubiquitin Chain ◽

Deubiquitinating Enzymes ◽

Cellular Functions ◽

Cellular Processes ◽

Model Study ◽

Biochemical Analyses ◽

Almost All

Protein ubiquitinations play pivotal roles in many cellular processes, including homeostasis, responses to various stimulations, and progression of diseases. Deubiquitinating enzymes (DUBs) remove ubiquitin molecules from ubiquitinated proteins and cleave the polyubiquitin chain, thus negatively regulating numerous ubiquitin-dependent processes. Dysfunctions of many DUBs reportedly cause various diseases; therefore, DUBs are considered as important drug targets, although the biochemical characteristics and cellular functions of many DUBs are still unclear. Here, we established a human DUB protein array to detect the activity and linkage specificity of almost all human DUBs. Using a wheat cell-free protein synthesis system, 88 full-length recombinant human DUB proteins were prepared and termed the DUB array. In vitro DUB assays were performed with all of these recombinant DUBs, using eight linkage types of diubiquitins as substrates. As a result, 80 DUBs in the array showed DUB activities, and their linkage specificities were determined. These 80 DUBs included many biochemically uncharacterized DUBs in the past. In addition, taking advantage of these active DUB proteins, we applied the DUB array to evaluate the selectivities of DUB inhibitors. We successfully developed a high-throughput and semi-quantitative DUB assay based on AlphaScreen technology, and a model study using two commercially available DUB inhibitors revealed individual selectivities to 29 DUBs, as previously reported. In conclusion, the DUB array established here is a powerful tool for biochemical analyses and drug discovery for human DUBs.

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Small-Molecule Modulation of Lipid-Dependent Cellular Processes against Cancer: Fats on the Gunpoint

BioMed Research International ◽

10.1155/2018/6437371 ◽

2018 ◽

Vol 2018 ◽

pp. 1-17 ◽

Cited By ~ 7

Author(s):

Aswin T. Srivatsav ◽

Manjari Mishra ◽

Shobhna Kapoor

Keyword(s):

Small Molecule ◽

Drug Targets ◽

Membrane Lipids ◽

Membrane Microdomains ◽

Critical Function ◽

Future Directions ◽

Cellular Processes ◽

Cancer Phenotypes ◽

Critical Intervention ◽

Distinct Membrane

Lipid cell membrane composed of various distinct lipids and proteins act as a platform to assemble various signaling complexes regulating innumerous cellular processes which are strongly downregulated or altered in cancer cells emphasizing the still-underestimated critical function of lipid biomolecules in cancer initiation and progression. In this review, we outline the current understanding of how membrane lipids act as signaling hot spots by generating distinct membrane microdomains called rafts to initiate various cellular processes and their modulation in cancer phenotypes. We elucidate tangible drug targets and pathways all amenable to small-molecule perturbation. Ranging from targeting membrane rafts organization/reorganization to rewiring lipid metabolism and lipid sorting in cancer, the work summarized here represents critical intervention points being attempted for lipid-based anticancer therapy and future directions.

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Application of the Subtractive Genomics and Molecular Docking Analysis for the Identification of Novel Putative Drug Targets against Salmonella enterica subsp. enterica serovar Poona

BioMed Research International ◽

10.1155/2017/3783714 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 7

Author(s):

Tanvir Hossain ◽

Mohammad Kamruzzaman ◽

Talita Zahin Choudhury ◽

Hamida Nooreen Mahmood ◽

A. H. M. Nurun Nabi ◽

...

Keyword(s):

Molecular Docking ◽

Salmonella Enterica ◽

Drug Targets ◽

Subcellular Location ◽

Essential Genes ◽

Scoring Functions ◽

Essential Proteins ◽

Cellular Processes ◽

Subtractive Genomics ◽

Resistance Patterns

The emergence of novel pathogenic strains with increased antibacterial resistance patterns poses a significant threat to the management of infectious diseases. In this study, we aimed at utilizing the subtractive genomic approach to identify novel drug targets against Salmonella enterica subsp. enterica serovar Poona strain ATCC BAA-1673. We employed in silico bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted proteome was further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We carried out metabolic pathway and subcellular location analysis of the essential proteins of the pathogen to elucidate the involvement of these proteins in important cellular processes. We found 52 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we investigated these proteins in the DrugBank databases and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. Molecular docking analyses of the novel druggable targets with the drugs were carried out by AutoDock Vina option based on scoring functions. The results showed promising candidates for novel drugs against Salmonella infections.

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Regulatory effects of post-translational modifications on zDHHC S-acyltransferases

Journal of Biological Chemistry ◽

10.1074/jbc.rev120.014717 ◽

2020 ◽

Vol 295 (43) ◽

pp. 14640-14652

Author(s):

Filip Zmuda ◽

Luke H. Chamberlain

Keyword(s):

Drug Targets ◽

Acyl Chain ◽

Fatty Acyl ◽

Fatty Acyl Chain ◽

Physiological Importance ◽

Cellular Processes ◽

Cell Growth And Differentiation ◽

Regulatory Effects ◽

The Stability ◽

And Function

The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.

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Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of NAD synthetase from methicillin-resistantStaphylococcus aureus

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15007906 ◽

2015 ◽

Vol 71 (6) ◽

pp. 763-769 ◽

Cited By ~ 1

Author(s):

Gajanan Kashinathrao Arbade ◽

Sandeep Kumar Srivastava

Keyword(s):

Drug Targets ◽

Multidrug Resistant ◽

Community Settings ◽

X Ray Diffraction ◽

Pyrimidine Nucleotides ◽

Nad Metabolism ◽

Cellular Processes ◽

Wide Range ◽

Purine And Pyrimidine Nucleotides ◽

Nad Synthetase

Staphylococcus aureusis an important human and animal pathogen that causes a wide range of infections. The prevalence of multidrug-resistantS. aureusstrains in both hospital and community settings makes it imperative to characterize new drug targets to combatS. aureusinfections. In this context, enzymes involved in NAD metabolism and synthesis are significant drug targets as NAD is a central player in several cellular processes. NAD synthetase catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide, making it a crucial intermediate enzyme linked to the biosynthesis of several amino acids, purine and pyrimidine nucleotides, coenzymes and antibiotics.

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Invertebrate Models Untangle the Mechanism of Neurodegeneration in Parkinson’s Disease

Cells ◽

10.3390/cells10020407 ◽

2021 ◽

Vol 10 (2) ◽

pp. 407

Author(s):

Andrei Surguchov

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Drug Targets ◽

Brain Dysfunction ◽

Model Organisms ◽

Cellular Processes ◽

Neuronal Protein ◽

Major Player ◽

New Biomarkers ◽

Eukaryotic Organisms

Parkinson’s disease (PD) is the second most common neurodegenerative disease, afflicting ~10 million people worldwide. Although several genes linked to PD are currently identified, PD remains primarily an idiopathic disorder. Neuronal protein α-synuclein is a major player in disease progression of both genetic and idiopathic forms of PD. However, it cannot alone explain underlying pathological processes. Recent studies demonstrate that many other risk factors can accelerate or further worsen brain dysfunction in PD patients. Several PD models, including non-mammalian eukaryotic organisms, have been developed to identify and characterize these factors. This review discusses recent findings in three PD model organisms, i.e., yeast, Drosophila, and Caenorhabditis elegans, that opened new mechanisms and identified novel contributors to this disorder. These non-mammalian models share many conserved molecular pathways and cellular processes with humans. New players affecting PD pathogenesis include previously unknown genes/proteins, novel signaling pathways, and low molecular weight substances. These findings might respond to the urgent need to discover novel drug targets for PD treatment and new biomarkers for early diagnostics of this disease. Since the study of neurodegeneration using simple eukaryotic organisms brought a huge amount of information, we include only the most recent or the most important relevant data.

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Ligand Docking Methods to Recognize Allosteric Inhibitors for G-protein Coupled Receptors

10.20944/preprints202012.0085.v1 ◽

2020 ◽

Author(s):

K Harini ◽

S Jayashree ◽

Vikas Tiwari ◽

Sneha Vishwanath ◽

Ramanathan Sowdhamini

Keyword(s):

Binding Site ◽

G Protein ◽

Drug Targets ◽

G Protein Coupled Receptors ◽

Ligand Docking ◽

Computational Docking ◽

Cellular Processes ◽

Activation Mechanisms ◽

Approved Drugs ◽

G Protein Coupled

G-protein coupled receptors (GPCRs) are large protein families known to be important in many cellular processes. They are well known for their allosteric activation mechanisms. They are drug targets for several FDA-approved drugs. We have investigated the diversity of the ligand binding site for these class of proteins against their cognate ligands using computational docking, even if their structures are known in the ligand-complexed form. The cognate ligand of some of these receptors dock at allosteric binding site, with better score than the binding at the conservative site. Further, ligands obtained from GLASS database, which consists of experimentally verified GPCR ligands, also show allosteric binding to GPCRs. The allosteric binders show strong affinity to the binding site, though the residues at the binding site are not conserved across GPCR subfamilies.

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Overexpression or Deletion of Ergosterol Biosynthesis Genes Alters Doubling Time, Response to Stress Agents, and Drug Susceptibility inSaccharomyces cerevisiae

mBio ◽

10.1128/mbio.01291-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 36

Author(s):

Somanon Bhattacharya ◽

Brooke D. Esquivel ◽

Theodore C. White

Keyword(s):

Cell Wall ◽

Drug Targets ◽

Doubling Time ◽

Gene Deletion ◽

Drug Susceptibility ◽

Ergosterol Biosynthesis ◽

Gene Overexpression ◽

Content Type ◽

Cellular Processes ◽

Erg Genes

ABSTRACTErgosterol (ERG) is a critical sterol in the cell membranes of fungi, and its biosynthesis is tightly regulated by 25 known enzymes along the ERG production pathway. The effects of changes in expression of each ERG biosynthesis enzyme inSaccharomyces cerevisiaewere analyzed by the use of gene deletion or plasmid-borne overexpression constructs. The strains overexpressing the ERG pathway genes were examined for changes in doubling time and responses to a variety of stress agents. In addition, ERG gene overexpression strains and ERG gene deletion strains were tested for alterations in antifungal drug susceptibility. The data show that disruptions in ergosterol biosynthesis regulation can affect a diverse set of cellular processes and can cause numerous phenotypic effects. Some of the phenotypes observed include dramatic increases in doubling times, respiratory deficiencies on glycerol media, cell wall insufficiencies on Congo red media, and disrupted ion homeostasis under iron or calcium starvation conditions. Overexpression or deletion of specific enzymes in the ERG pathway causes altered susceptibilities to a variety of classes of antifungal ergosterol inhibitors, including fluconazole, fenpropimorph, lovastatin, nystatin, amphotericin B, and terbinafine. This analysis of the effect of perturbations to the ERG pathway caused by systematic overexpression of each of the ERG pathway genes contributes significantly to the understanding of the ergosterol biosynthetic pathway and its relationship to stress response and basic biological processes. The data indicate that precise regulation of ERG genes is essential for cellular homeostasis and identify several ERG genes that could be exploited in future antifungal development efforts.IMPORTANCEA common target of antifungal drug treatment is the fungal ergosterol biosynthesis pathway. This report helps to identify ergosterol biosynthesis enzymes that have not previously been appreciated as drug targets. The effects of overexpression of each of the 25 ERG genes inS. cerevisiaewere analyzed in the presence of six stress agents that target essential cellular processes (cell wall biosynthesis, protein translation, respiration, osmotic/ionic stress, and iron and calcium homeostasis), as well as six antifungal inhibitors that target ergosterol biosynthesis. The importance of identifying cell perturbations caused by gene overexpression or deletion is emphasized by the prevalence of gene expression alterations in many pathogenic and drug-resistant clinical isolates. Genes whose altered expression causes the most extensive phenotypic alterations in the presence of stressors or inhibitors have the potential to be drug targets.

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