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Advance in Computational Protein Structural Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 2102

Special Issue Editor


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Guest Editor
Institute for Structural Biology, CNRS, University Grenoble Alpes, 38000 Grenoble, France
Interests: structural bioinformatic; molecular modelling; NMR spectroscopy; evolutionary couplings and sequence analysis; protein structures

Special Issue Information

Dear Colleagues,

One of the most fruitful combinations of experimental and computational methods is that of nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations, which has been successfully applied to obtain molecular information in many research areas, ranging from materials to biological systems.

Both NMR and MD simulations are used to study molecular structures, dynamics, and protein interactions at the atomic level. NMR is unique in its ability to provide information on three-dimensional structures as well as on the amplitude and rate of structure variations at the atomic level. MD has the unique ability to correlate different molecular states and mechanisms in time. When combined, these two techniques are highly complementary and allow for the comprehensive characterization of both structural and dynamical processes in protein complexes and interactions, which is critical for fully understanding the mechanisms behind many biological processes.

This Special Issue is focused on the symbiosis of these two techniques, used to understand, in detail, the key molecular mechanisms that cause infectious or transmissible diseases, the impact of computational structural biology on protein structure prediction methods, macromolecular functions and protein designs, and key methods in drug discovery.

Dr. Torsten Herrmann
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NMR spectroscopy
  • molecular dynamics simulation
  • infectious diseases
  • molecular architecture
  • protein dynamics
  • protein interactions
  • integrative structural biology
  • molecular modeling
  • protein structure prediction

Published Papers (1 paper)

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Research

15 pages, 6198 KiB  
Article
Structure-Guided Approach to Discover Tuberosin as a Potent Activator of Pyruvate Kinase M2, Targeting Cancer Therapy
by Mohd Adnan, Anas Shamsi, Abdelbaset Mohamed Elasbali, Arif Jamal Siddiqui, Mitesh Patel, Nawaf Alshammari, Salem Hussain Alharethi, Hassan H. Alhassan, Fevzi Bardakci and Md. Imtaiyaz Hassan
Int. J. Mol. Sci. 2022, 23(21), 13172; https://doi.org/10.3390/ijms232113172 - 29 Oct 2022
Cited by 11 | Viewed by 1758
Abstract
Metabolic reprogramming is a key attribute of cancer progression. An altered expression of pyruvate kinase M2 (PKM2), a phosphotyrosine-binding protein is observed in many human cancers. PKM2 plays a vital role in metabolic reprogramming, transcription and cell cycle progression and thus is deliberated [...] Read more.
Metabolic reprogramming is a key attribute of cancer progression. An altered expression of pyruvate kinase M2 (PKM2), a phosphotyrosine-binding protein is observed in many human cancers. PKM2 plays a vital role in metabolic reprogramming, transcription and cell cycle progression and thus is deliberated as an attractive target in anticancer drug development. The expression of PKM2 is essential for aerobic glycolysis and cell proliferation, especially in cancer cells, facilitating selective targeting of PKM2 in cell metabolism for cancer therapeutics. We have screened a virtual library of phytochemicals from the IMPPAT (Indian Medicinal Plants, Phytochemistry and Therapeutics) database of Indian medicinal plants to identify potential activators of PKM2. The initial screening was carried out for the physicochemical properties of the compounds, and then structure-based molecular docking was performed to select compounds based on their binding affinity towards PKM2. Subsequently, the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties, PAINS (Pan-assay interference compounds) patterns, and PASS evaluation were carried out to find more potent hits against PKM2. Here, Tuberosin was identified from the screening process bearing appreciable binding affinity toward the PKM2-binding pocket and showed a worthy set of drug-like properties. Finally, molecular dynamics simulation for 100 ns was performed, which showed decent stability of the protein-ligand complex and relatival conformational dynamics throughout the trajectory. The study suggests that modulating PKM2 with natural compounds is an attractive approach in treating human malignancy after required validation. Full article
(This article belongs to the Special Issue Advance in Computational Protein Structural Biology)
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