Abstract
Application of molecular dynamics simulation technique has become a conventional computational methodology to calculate significant processes at the molecular level. This computational methodology is particularly useful for analyzing the dynamics of proteinligand systems. Several uses of molecular dynamics simulation makes possible evaluation of important structural features found at interface between a ligand and a protein, such as intermolecular hydrogen bonds, contact area and binding energy. Considering structurebased virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligandbinding affinity. This information could be employed to select higher-affinity ligands obtained in screening processes. Many protein targets such as enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), and shikimate kinase have been submitted to these simulations and will be analyzed here. All command files used in this review are available for download at http://azevedolab.net/md_75.html.
Keywords: Molecular dynamics, computer simulations, enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), shikimate kinase, Mycobacterium tuberculosis, GROMACS, structure-based virtual screening, Protein Targets, hydrogen bonds
Current Medicinal Chemistry
Title: Molecular Dynamics Simulations of Protein Targets Identified in Mycobacterium tuberculosis
Volume: 18 Issue: 9
Author(s): W. F. de Azevedo
Affiliation:
Keywords: Molecular dynamics, computer simulations, enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), shikimate kinase, Mycobacterium tuberculosis, GROMACS, structure-based virtual screening, Protein Targets, hydrogen bonds
Abstract: Application of molecular dynamics simulation technique has become a conventional computational methodology to calculate significant processes at the molecular level. This computational methodology is particularly useful for analyzing the dynamics of proteinligand systems. Several uses of molecular dynamics simulation makes possible evaluation of important structural features found at interface between a ligand and a protein, such as intermolecular hydrogen bonds, contact area and binding energy. Considering structurebased virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligandbinding affinity. This information could be employed to select higher-affinity ligands obtained in screening processes. Many protein targets such as enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), and shikimate kinase have been submitted to these simulations and will be analyzed here. All command files used in this review are available for download at http://azevedolab.net/md_75.html.
Export Options
About this article
Cite this article as:
F. de Azevedo W., Molecular Dynamics Simulations of Protein Targets Identified in Mycobacterium tuberculosis, Current Medicinal Chemistry 2011; 18 (9) . https://dx.doi.org/10.2174/092986711795029519
DOI https://dx.doi.org/10.2174/092986711795029519 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
Call for Papers in Thematic Issues
Advances in Medicinal Chemistry: From Cancer to Chronic Diseases.
The broad spectrum of the issue will provide a comprehensive overview of emerging trends, novel therapeutic interventions, and translational insights that impact modern medicine. The primary focus will be diseases of global concern, including cancer, chronic pain, metabolic disorders, and autoimmune conditions, providing a broad overview of the advancements in ...read more
Approaches to the treatment of chronic inflammation
Chronic inflammation is a hallmark of numerous diseases, significantly impacting global health. Although chronic inflammation is a hot topic, not much has been written about approaches to its treatment. This thematic issue aims to showcase the latest advancements in chronic inflammation treatment and foster discussion on future directions in this ...read more
Cellular and Molecular Mechanisms of Non-Infectious Inflammatory Diseases: Focus on Clinical Implications
The Special Issue covers the results of the studies on cellular and molecular mechanisms of non-infectious inflammatory diseases, in particular, autoimmune rheumatic diseases, atherosclerotic cardiovascular disease and other age-related disorders such as type II diabetes, cancer, neurodegenerative disorders, etc. Review and research articles as well as methodology papers that summarize ...read more
Chalcogen-modified nucleic acid analogues
Chalcogen-modified nucleosides, nucleotides and oligonucleotides have been of great interest to scientific research for many years. The replacement of oxygen in the nucleobase, sugar or phosphate backbone by chalcogen atoms (sulfur, selenium, tellurium) gives these biomolecules unique properties resulting from their altered physical and chemical properties. The continuing interest in ...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
-
Dermatology and Global Health Meet Pharmacogenomics: Cutaneous Leishmaniasis
Current Pharmacogenomics and Personalized Medicine Bioactive Peptides from Marine Sources as Potential Anti-Inflammatory Therapeutics
Current Protein & Peptide Science Spirooxindoles as Potential Pharmacophores
Mini-Reviews in Medicinal Chemistry Burden of Bronchiectasis in Indigenous Peoples - How Can it be Improved?
Current Pediatric Reviews Accessing Highly-Halogenated Flavanones Using Protic Ionic Liquids and Microwave Irradiation
Current Organic Chemistry Biological Activities of Pyrazoline Derivatives -A Recent Development
Recent Patents on Anti-Infective Drug Discovery Natural Compounds Therapeutic Features in Brain Disorders by Experimental, Bioinformatics and Cheminformatics Methods
Current Medicinal Chemistry Targeting Toll-Like Receptor Signaling Pathways for Design of Novel Immune Therapeutics
Current Drug Discovery Technologies A Rational Approach to Identify Inhibitors of Mycobacterium tuberculosis Enoyl Acyl Carrier Protein Reductase
Current Pharmaceutical Design Trypanocidal Activity of Nitroaromatic Prodrugs: Current Treatments and Future Perspectives
Current Topics in Medicinal Chemistry Biochips for Detection of DNA Mutations
Current Analytical Chemistry Targeting TNF-Alpha in HIV-1 Infection
Current Drug Targets CT and CT-guided Percutaneous Needle Biopsy in Diagnosis of Primary Pulmonary Cryptococcosis in Immunocompetent Patients
Current Medical Imaging Blood Pressure Measurement: Lessons Learned from Our Ancestors
Current Pharmaceutical Design Toxicities of Immunosuppressive Treatment of Autoimmune Neurologic Diseases
Current Neuropharmacology Comparison of Pharmacokinetic Profiles of Moxifloxacin in Caesarean versus Non-Pregnant Sectioned Women by Fully Validated HPLC with Fluorescence Detection
Combinatorial Chemistry & High Throughput Screening Mass Spectrometry in the Elucidation of the Glycoproteome of Bacterial Pathogens
Current Proteomics Artificial Intelligence Approaches for Rational Drug Design and Discovery
Current Pharmaceutical Design Targeting the Formation of the Cell Wall Core of M. tuberculosis
Infectious Disorders - Drug Targets Vitamin D Deficiency in Tuberculosis and Diabetes Mellitus - A Cluster Analysis
Current Respiratory Medicine Reviews