scholarly journals BH3-mimetics: recent developments in cancer therapy

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Paul A. Townsend ◽  
Maria V. Kozhevnikova ◽  
Olivier N. F. Cexus ◽  
Andrey A. Zamyatnin ◽  
Surinder M. Soond
Keyword(s):  
Protein Interactions ◽  
Tissue Homeostasis ◽  
Protein Protein Interactions ◽  
Delivery Methods ◽  
Apoptosis Pathway ◽  
Bh3 Mimetics ◽  
Treatment Regimens ◽  
Therapeutic Delivery ◽  
Pathological Conditions ◽  
Recent Developments

AbstractThe hopeful outcomes from 30 years of research in BH3-mimetics have indeed served a number of solid paradigms for targeting intermediates from the apoptosis pathway in a variety of diseased states. Not only have such rational approaches in drug design yielded several key therapeutics, such outputs have also offered insights into the integrated mechanistic aspects of basic and clinical research at the genetics level for the future. In no other area of medical research have the effects of such work been felt, than in cancer research, through targeting the BAX-Bcl-2 protein-protein interactions. With these promising outputs in mind, several mimetics, and their potential therapeutic applications, have also been developed for several other pathological conditions, such as cardiovascular disease and tissue fibrosis, thus highlighting the universal importance of the intrinsic arm of the apoptosis pathway and its input to general tissue homeostasis. Considering such recent developments, and in a field that has generated so much scientific interest, we take stock of how the broadening area of BH3-mimetics has developed and diversified, with a focus on their uses in single and combined cancer treatment regimens and recently explored therapeutic delivery methods that may aid the development of future therapeutics of this nature.

scholarly journals Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

2016 ◽  
Vol 113 (52) ◽  
pp. 15018-15023 ◽  
Author(s):  
Juan Rodriguez-Rivas ◽  
Simone Marsili ◽  
David Juan ◽  
Alfonso Valencia
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Accurate Information ◽  
Twilight Zone ◽  
Sequence Information ◽  
Protein Protein Interactions ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Protein Interfaces ◽  
Recent Developments

Protein–protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein–protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein–protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein–protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.

scholarly journals Where does axon guidance lead us?

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 78 ◽  
Author(s):  
Esther Stoeckli
Keyword(s):  
Axon Guidance ◽  
Protein Interactions ◽  
Neural Circuit ◽  
Surface Expression ◽  
Target Cells ◽  
Protein Protein Interactions ◽  
Guidance Receptors ◽  
Recent Developments ◽  
Genomic Studies ◽  
Circuit Formation

During neural circuit formation, axons need to navigate to their target cells in a complex, constantly changing environment. Although we most likely have identified most axon guidance cues and their receptors, we still cannot explain the molecular background of pathfinding for any subpopulation of axons. We lack mechanistic insight into the regulation of interactions between guidance receptors and their ligands. Recent developments in the field of axon guidance suggest that the regulation of surface expression of guidance receptors comprises transcriptional, translational, and post-translational mechanisms, such as trafficking of vesicles with specific cargos, protein-protein interactions, and specific proteolysis of guidance receptors. Not only axon guidance molecules but also the regulatory mechanisms that control their spatial and temporal expression are involved in synaptogenesis and synaptic plasticity. Therefore, it is not surprising that genes associated with axon guidance are frequently found in genetic and genomic studies of neurodevelopmental disorders.

α-Helix mimetics as inhibitors of protein–protein interactions

2008 ◽  
Vol 36 (6) ◽  
pp. 1414-1417 ◽  
Author(s):  
Ishu Saraogi ◽  
Andrew D. Hamilton
Keyword(s):  
Protein Interactions ◽  
First Generation ◽  
Side Chain ◽  
Protein Protein Interactions ◽  
Substitution Pattern ◽  
Pathological Conditions ◽  
Synthetic Accessibility ◽  
Helix Mimetics ◽  
Viable Approach ◽  
Α Helix

The inhibition of protein–protein interactions using small molecules is a viable approach for the treatment of a range of pathological conditions that result from a malfunctioning of these interactions. Our strategy for the design of such agents involves the mimicry of side-chain residues on one face of the α-helix; these residues frequently play a key role in mediating protein–protein interactions. The first-generation terphenyl scaffold, with a 3,2′,2″-substitution pattern, is able to successfully mimic key helix residues and disrupt therapeutically relevant interactions, including the Bcl-XL–Bak and the p53–hDM2 (human double minute 2) interactions that are implicated in cancer. The second- and third-generation scaffolds have resulted in greater synthetic accessibility and more drug-like character in these molecules.

scholarly journals Finding functional associations between prokaryotic virus orthologous groups: a proof of concept

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nikolaos Pappas ◽  
Bas E. Dutilh
Keyword(s):  
Protein Interactions ◽  
Systematic Evaluation ◽  
Proof Of Concept ◽  
Protein Protein Interactions ◽  
Viral Genomes ◽  
False Discovery ◽  
Machine Learning Approach ◽  
Recent Developments ◽  
Significant Step ◽  
Functional Context

Abstract Background The field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery. However, functional annotation of the increasing number of viral genomes is lagging behind. This is highlighted by the degree of annotation of the protein clusters in the prokaryotic Virus Orthologous Groups (pVOGs) database, with 83% of its current 9518 pVOGs having an unknown function. Results In this study we describe a machine learning approach to explore potential functional associations between pVOGs. We measure seven genomic features and use them as input to a Random Forest classifier to predict protein–protein interactions between pairs of pVOGs. After systematic evaluation of the model’s performance on 10 different datasets, we obtained a predictor with a mean accuracy of 0.77 and Area Under Receiving Operation Characteristic (AUROC) score of 0.83. Its application to a set of 2,133,027 pVOG-pVOG interactions allowed us to predict 267,265 putative interactions with a reported probability greater than 0.65. At an expected false discovery rate of 0.27, we placed 95.6% of the previously unannotated pVOGs in a functional context, by predicting their interaction with a pVOG that is functionally annotated. Conclusions We believe that this proof-of-concept methodology, wrapped in a reproducible and automated workflow, can represent a significant step towards obtaining a more complete picture of bacteriophage biology.

How Cancer Cells Resist Chemotherapy: Design and Development of Drugs Targeting Protein-Protein Interactions

2019 ◽  
Vol 19 (6) ◽  
pp. 394-412 ◽  
Author(s):  
Vadim V. Tarasov ◽  
Vladimir N. Chubarev ◽  
Ghulam Md Ashraf ◽  
Samira A. Dostdar ◽  
Alexander V. Sokolov ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Clinical Outcome ◽  
Cancer Cells ◽  
Protein Interactions ◽  
Resistance Mechanisms ◽  
Protein Protein Interactions ◽  
Treatment Regimens ◽  
Pubmed Search ◽  
Bona Fide ◽  
Improve Clinical Outcome

Background:Resistance toward chemotherapeutics is one of the main obstacles on the way to effective cancer treatment. Personalization of chemotherapy could improve clinical outcome. However, despite preclinical significance, most of the potential markers have failed to reach clinical practice partially due to the inability of numerous studies to estimate the marker’s impact on resistance properly.Objective:The analysis of drug resistance mechanisms to chemotherapy in cancer cells, and the proposal of study design to identify bona fide markers.Methods:A review of relevant papers in the field. A PubMed search with relevant keywords was used to gather the data. An example of a search request: drug resistance AND cancer AND paclitaxel.Results:We have described a number of drug resistance mechanisms to various chemotherapeutics, as well as markers to underlie the phenomenon. We also proposed a model of a rational-designed study, which could be useful in determining the most promising potential biomarkers.Conclusion:Taking into account the most reasonable biomarkers should dramatically improve clinical outcome by choosing the suitable treatment regimens. However, determining the leading biomarkers, as well as validating of the model, is a work for further investigations.

Mass Spectrometry for Structural Biology: Determining the Composition and Architecture of Protein Complexes

2011 ◽  
Vol 64 (6) ◽  
pp. 681 ◽  
Author(s):  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Protein Interactions ◽  
Structural Investigation ◽  
Protein Complexes ◽  
Individual Species ◽  
Protein Protein Interactions ◽  
Identify Protein Complex ◽  
Technological Advances ◽  
Recent Developments

Knowledge of protein structure and protein–protein interactions is vital for appreciating the elaborate biochemical pathways that underlie cellular function. While many techniques exist to probe the structure and complex interplay between functional proteins, none currently offer a complete picture. Mass spectrometry and associated methods provide complementary information to established structural biology tools, and with rapidly evolving technological advances, can in some cases even exceed other techniques by its diversity in application and information content. This is primarily because of the ability of mass spectrometry to precisely identify protein complex stoichiometry, detect individual species present in a mixture, and concomitantly offer conformational information. This review describes the attributes of mass spectrometry for the structural investigation of multiprotein assemblies in the context of recent developments and highlights in the field.

scholarly journals Fluorescence lifetime imaging microscopy (FLIM) to quantify protein–protein interactions inside cells

2006 ◽  
Vol 34 (5) ◽  
pp. 679-682 ◽  
Author(s):  
R.R. Duncan
Keyword(s):  
Spatial Resolution ◽  
Single Molecule ◽  
Protein Interactions ◽  
Single Photon ◽  
Imaging Spectroscopy ◽  
Living Cells ◽  
Fluorescence Lifetime Imaging ◽  
Protein Protein Interactions ◽  
Recent Developments

Recent developments in cellular imaging spectroscopy now permit the minimally invasive study of protein dynamics inside living cells. These advances are of interest to cell biologists, as proteins rarely act in isolation, but rather in concert with others in forming cellular machinery. Until recently, all protein interactions had to be determined in vitro using biochemical approaches: this biochemical legacy has provided cell biologists with the basis to test defined protein–protein interactions not only inside cells, but now also with high spatial resolution. These techniques can detect and quantify protein behaviours down to the single-molecule level, all inside living cells. More recent developments in TCSPC (time-correlated single-photon counting) imaging are now also driving towards being able to determine protein interaction rates with similar spatial resolution, and together, these experimental advances allow investigators to perform biochemical experiments inside living cells.

Methods to analyse composition and dynamics of macromolecular complexes

2013 ◽  
Vol 41 (5) ◽  
pp. 1235-1241 ◽  
Author(s):  
Heinrich Heide ◽  
Ilka Wittig
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Protein Biosynthesis ◽  
Biological Processes ◽  
Protein Protein Interactions ◽  
Macromolecular Complexes ◽  
Cellular Processes ◽  
Recent Developments ◽  
Dna Replication And Repair ◽  
Health And Disease

Macromolecular complexes are involved in a broad spectrum of cellular processes including protein biosynthesis, protein secretion and degradation, metabolism, DNA replication and repair, and signal transduction along with other important biological processes. The analysis of protein complexes in health and disease is important to gain insights into cellular physiology and pathophysiology. In the last few decades, research has focused on the identification and the dynamics of macromolecular complexes. Several techniques have been developed to isolate native protein complexes from cells and tissues to allow further characterization by microscopic and proteomic analysis. In the present paper, we provide a brief overview of proteomic methods that can be used to identify protein–protein interactions, focusing on recent developments to study the entire complexome of a biological sample.

scholarly journals Constrained Peptides as Miniature Protein Structures

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Hang Yin
Keyword(s):  
Protein Engineering ◽  
Protein Interactions ◽  
Protein Structures ◽  
Secondary Structures ◽  
Biological Functions ◽  
Protein Protein Interactions ◽  
Protein Secondary Structures ◽  
Recent Developments ◽  
Noncovalent Bonds ◽  
Constrained Peptides

This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.

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