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Co-solvent Simulations in Drug Design

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

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 44936

Special Issue Editor

Department of Pharmaceutical Sciences, Universitat Basel, Basel, Switzerland
Interests: molecular docking; molecular dynamics simulations; cytochrome P450; nuclear receptor; off-target binding; toxicity prediction; computer-aided / rational drug design; carbohydrate mimics

Special Issue Information

Dear Colleagues,

Molecular dynamics simulations have become the gold standard for studying structural and functional properties of biologically relevant molecules, finding numerous applications in modern structure-based drug design. Inspired by fragment-based design and X-ray crystallography, these simulations have been extended to include small, fragment-like molecules (co-solvents) in addition to natural solvent molecules (water). During simulation, these molecules tend to naturally concentrate at protein structures with matching interaction counterparts, thus demasking sites with increased propensity for ligand or protein binding. This offers many potential applications in rational drug design including druggability assessment and identification of cryptic pockets, induced-fit effects, or allosteric binding sites.

Original manuscripts and reviews dealing with further development, refinement, or application of co-solvent simulations with respect to drug design are welcome.

Dr. Martin Smiesko
Guest Editor

Manuscript Submission Information

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Keywords

  • co-solvent
  • molecular dynamics simulation
  • protein–protein interaction
  • binding site prediction
  • druggability assessment
  • cryptic pocket
  • induced fit
  • allosteric binding sites
  • structure-based drug design

Published Papers (1 paper)

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Review

35 pages, 1072 KiB  
Review
mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection
Int. J. Mol. Sci. 2020, 21(18), 6582; https://doi.org/10.3390/ijms21186582 - 09 Sep 2020
Cited by 172 | Viewed by 44506
Abstract
Messenger ribonucleic acid (mRNA)-based drugs, notably mRNA vaccines, have been widely proven as a promising treatment strategy in immune therapeutics. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have [...] Read more.
Messenger ribonucleic acid (mRNA)-based drugs, notably mRNA vaccines, have been widely proven as a promising treatment strategy in immune therapeutics. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have enabled them to become prevalent in pre-clinical and clinical trials against various infectious diseases and cancers. Recent technological advancements have alleviated some issues that hinder mRNA vaccine development, such as low efficiency that exist in both gene translation and in vivo deliveries. mRNA immunogenicity can also be greatly adjusted as a result of upgraded technologies. In this review, we have summarized details regarding the optimization of mRNA vaccines, and the underlying biological mechanisms of this form of vaccines. Applications of mRNA vaccines in some infectious diseases and cancers are introduced. It also includes our prospections for mRNA vaccine applications in diseases caused by bacterial pathogens, such as tuberculosis. At the same time, some suggestions for future mRNA vaccine development about storage methods, safety concerns, and personalized vaccine synthesis can be found in the context. Full article
(This article belongs to the Special Issue Co-solvent Simulations in Drug Design)
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