Abstract
The study of protein-protein interactions (PPIs) has been growing for some years now, mainly as a result of easy access to high-throughput experimental data. Several computational approaches have been presented throughout the years as means to infer PPIs not only within the same species, but also between different species (e.g., host-pathogen interactions). The importance of unveiling the human protein interaction network is undeniable, particularly in the biological, biomedical and pharmacological research areas. Even though protein interaction networks evolve over time and can suffer spontaneous alterations, occasional shifts are often associated with disease conditions. These disorders may be caused by external pathogens, such as bacteria and viruses, or by intrinsic factors, such as auto-immune disorders and neurological impairment. Therefore, having the knowledge of how proteins interact with each other will provide a great opportunity to understand pathogenesis mechanisms, and subsequently support the development of drugs focused on very specific disease pathways and re-targeting already commercialized drugs to new gene products. Computational methods for PPI prediction have been highlighted as an interesting option for interactome mapping. In this paper we review the techniques and strategies used for both experimental identification and computational inference of PPIs. We will then discuss how this knowledge can be used to create protein interaction networks (PINs) and the various methodologies applied to characterize and predict the so-called “disease genes” and “disease networks”. This will be followed by an overview of the strategies employed to predict drug targets.
Keywords: Protein-Protein interaction, Disease networks, Drug targets, Drug design.
Current Topics in Medicinal Chemistry
Title:From Protein-Protein Interactions to Rational Drug Design: Are Computational Methods Up to the Challenge?
Volume: 13 Issue: 5
Author(s): Edgar D. Coelho, Joel P. Arrais and Jose Luis Oliveira
Affiliation:
Keywords: Protein-Protein interaction, Disease networks, Drug targets, Drug design.
Abstract: The study of protein-protein interactions (PPIs) has been growing for some years now, mainly as a result of easy access to high-throughput experimental data. Several computational approaches have been presented throughout the years as means to infer PPIs not only within the same species, but also between different species (e.g., host-pathogen interactions). The importance of unveiling the human protein interaction network is undeniable, particularly in the biological, biomedical and pharmacological research areas. Even though protein interaction networks evolve over time and can suffer spontaneous alterations, occasional shifts are often associated with disease conditions. These disorders may be caused by external pathogens, such as bacteria and viruses, or by intrinsic factors, such as auto-immune disorders and neurological impairment. Therefore, having the knowledge of how proteins interact with each other will provide a great opportunity to understand pathogenesis mechanisms, and subsequently support the development of drugs focused on very specific disease pathways and re-targeting already commercialized drugs to new gene products. Computational methods for PPI prediction have been highlighted as an interesting option for interactome mapping. In this paper we review the techniques and strategies used for both experimental identification and computational inference of PPIs. We will then discuss how this knowledge can be used to create protein interaction networks (PINs) and the various methodologies applied to characterize and predict the so-called “disease genes” and “disease networks”. This will be followed by an overview of the strategies employed to predict drug targets.
Export Options
About this article
Cite this article as:
D. Coelho Edgar, P. Arrais Joel and Luis Oliveira Jose, From Protein-Protein Interactions to Rational Drug Design: Are Computational Methods Up to the Challenge?, Current Topics in Medicinal Chemistry 2013; 13 (5) . https://dx.doi.org/10.2174/1568026611313050005
DOI https://dx.doi.org/10.2174/1568026611313050005 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
Call for Papers in Thematic Issues
Chemistry Based on Natural Products for Therapeutic Purposes
The development of new pharmaceuticals for a wide range of medical conditions has long relied on the identification of promising natural products (NPs). There are over sixty percent of cancer, infectious illness, and CNS disease medications that include an NP pharmacophore, according to the Food and Drug Administration. Since NP ...read more
Current Trends in Drug Discovery Based on Artificial Intelligence and Computer-Aided Drug Design
Drug development discovery has faced several challenges over the years. In fact, the evolution of classical approaches to modern methods using computational methods, or Computer-Aided Drug Design (CADD), has shown promising and essential results in any drug discovery campaign. Among these methods, molecular docking is one of the most notable ...read more
Drug Discovery in the Age of Artificial Intelligence
In the age of artificial intelligence (AI), we have witnessed a significant boom in AI techniques for drug discovery. AI techniques are increasingly integrated and accelerating the drug discovery process. These developments have not only attracted the attention of academia and industry but also raised important questions regarding the selection ...read more
From Biodiversity to Chemical Diversity: Focus of Flavonoids
Flavonoids are the largest group of polyphenols, plant secondary metabolites arising from the essential aromatic amino acid phenylalanine (or more rarely from tyrosine) via the phenylpropanoid pathway. The flavan nucleus is the basic 15-carbon skeleton of flavonoids (C6-C3-C6), which consists of two phenyl rings (A and B) and a heterocyclic ...read more
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
Patent Selections
Recent Patents on Biomarkers Determination of Binding Constant and Stoichiometry for Antibody-Antigen Interaction with Surface Plasmon Resonance
Current Proteomics Nanotechnology-Based Drug Delivery Systems for Treatment of Hyperproliferative Skin Diseases - A Review
Current Nanoscience Melanocortins and their Receptors and Antagonists
Current Drug Targets An Update on the Other Telomerase Inhibitors: Non-G-Quadruplex Interactive Agent, Non-Antisense, Non-Reverse Transcriptase Telomerase Inhibitors
Medicinal Chemistry Reviews - Online (Discontinued) Targeting Aurora Kinases in Cancer Treatment
Current Drug Targets Identification and Characterization of SNP Mutation in Genes Related to Non-small Cell Lung Cancer
Current Signal Transduction Therapy Patent Selections
Recent Patents on DNA & Gene Sequences Emerging Role and Targeting of Carcinoembryonic Antigen-related Cell Adhesion Molecule 6 (CEACAM6) in Human Malignancies
Clinical Cancer Drugs Advances in Anticancer Antibody-Drug Conjugates and Immunotoxins
Recent Patents on Anti-Cancer Drug Discovery Therapeutic Applications of Crocus sativus L. (Saffron): A Review
The Natural Products Journal Positron Emission Tomography for Neck Evaluation Following Definitive Treatment with Chemoradiotherapy for Locoregionally Advanced Head and Neck Squamous Cell Carcinoma
Reviews on Recent Clinical Trials COPD Management: Look Beyond the Airway Obstruction, Chronic Bronchitis and Emphysema
Current Respiratory Medicine Reviews Development of 96-microwell Plate Assay with Fluorescence Reader and HPLC Method with Fluorescence Detection for High-throughput Analysis of Linifanib in its Bulk and Dosage Forms
Current Pharmaceutical Analysis STAT Signaling and Cell Function
Current Genomics The Use of DNA Microarrays to Investigate the Pharmacogenomics of Drug Response in Living Systems
Current Topics in Medicinal Chemistry Cyclodextrins as Complexation Agents to Improve the Anti-inflammatory Drugs Profile: a Systematic Review and Meta-Analysis
Current Pharmaceutical Design Antiangiogenesis and Radiotherapy: What Is the Role of Combined Modality Treatment?
Current Medicinal Chemistry - Anti-Cancer Agents Proteomics in Computer-Aided Drug Design
Current Computer-Aided Drug Design Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma
Current Bioinformatics