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Computational Molecular Biology of Metabolic Pathways and Signal Transduction Pathways

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

Deadline for manuscript submissions: 30 August 2024 | Viewed by 598

Special Issue Editor


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Guest Editor
Herwig Laboratories, 80337 Munich, Germany
Interests: computational genomics; computational structural and molecular biology; molecular dynamics simulations; artificial intelligence; AI driven drug design and development; molecular modeling; computer aided drug design; computational proteomics; computational and theoretical chemistry and quantum mechanical and molecular mechanical modeling of bio-materials and larger bio-molecular systems

Special Issue Information

Dear Colleagues,

The regulation of metabolic pathways and the associated signal transduction has received immense therapeutic importance due to their key role in major neural disorders and tumor regulations and onco-metabolism. Furthermore, the metabolic pathways and signal transduction are entirely regulated through interactions of small bio-ligands, signaling molecules, neurotransmitters with receptors, proteins, and membrane bilayer proteins. The complete understanding of these interactions, their binding mode, and their associated biological function are dependent on how good we establish or understand the structure–activity relationship that actually helps in comprehension of these biological functions. Computational structural and molecular biology has emerged as an interdisciplinary discipline in combination with theoretical and computational chemistry and biophysics to explore the biological functions at molecular and atomistic levels. Since I have been working in the quoted areas with my colleague Dr. Khair Bux, thus, it would be a great pleasure to work as the Guest editor for this Special Issue of IJMS. I am very hopeful that my contribution will be quality-oriented and will help IJMS to report quality research in this discipline in the future.

Prof. Dr. Ralf Herwig
Guest Editor

Manuscript Submission Information

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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.

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Keywords

  • computational genomics
  • computational structural and molecular biology
  • molecular dynamics simulations
  • artificial intelligence
  • AI-driven drug design and development
  • molecular modeling
  • computer-aided drug design
  • computational proteomics
  • computational and theoretical chemistry

Published Papers (1 paper)

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Research

17 pages, 7214 KiB  
Article
Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1
by Zhuo Liu, Xueting Cao, Zhenyu Ma, Limei Xu, Lushan Wang, Jian Li, Min Xiao and Xukai Jiang
Int. J. Mol. Sci. 2024, 25(10), 5486; https://doi.org/10.3390/ijms25105486 - 17 May 2024
Viewed by 309
Abstract
Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains [...] Read more.
Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains largely unknown. Here, we employed all-atom molecular dynamics simulations, coupled to steered and umbrella sampling techniques, to examine the thermodynamics governing the transport of glucose and two glycoconjugate drugs (i.e., 6-D-glucose-conjugated methane sulfonate and 6-D-glucose chlorambucil) by GLUT1. We characterized the specific interactions between GLUT1 and substrates at different transport stages, including substrate recognition, transport, and releasing, and identified the key residues involved in these procedures. Importantly, our results described, for the first time, the free energy profiles of GLUT1-transporting glycoconjugate drugs, and demonstrated that H160 and W388 served as important gates to regulate their transport via GLUT1. These findings provide novel atomic-scale insights for understanding the transport mechanism of GLUT1, facilitating the discovery and rational design of GLUT1-targeted anticancer drugs. Full article
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