Classical and Quantum Molecular Simulations in Drug Design

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (20 June 2025) | Viewed by 5690

Special Issue Editor


E-Mail Website
Guest Editor
Center of Health Sciences, Laboratory of Molecular Modeling and Computational Structural Biology, Federal University of Rio de Janeiro, IPPN, Av. Carlos Chagas Filho 373, Bloco H, Rio de Janeiro 21941-599, Brazil
Interests: molecular modeling; computational and medicinal chemistry; molecular simulations; structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular simulation methods in drug design are computational techniques that use mathematical models and algorithms to study the structure, dynamics and interactions of molecules, such as proteins and drugs. It can help understand the molecular mechanisms of drug action, predict the binding affinity and selectivity of drug candidates, optimize drug properties and pharmacokinetics, and discover new drug targets and mechanisms. Some of the common molecular simulation methods in drug design are molecular docking, predicting the preferred orientation and conformation of a drug molecule when it binds to a target protein or receptor; molecular dynamics (MD), simulating the movement and behavior of atoms and molecules over time using Newtonian laws of motion and force fields; Monte Carlo (MC), that uses random sampling to approximate the behavior and outcomes of complex systems, such as drug design, and can help to explore the effects of uncertainty, variability and heterogeneity in drug design, and evaluate the performance and robustness of different design strategies; free energy calculations, estimating the thermodynamic quantity that determines the spontaneity and equilibrium of a molecular process, such as the binding of a drug to a biomolecular target; and quantum mechanics (QM), describing the electronic structure and properties of atoms and molecules using the principles of quantum physics and useful to model chemical reactions.

In this Special Issue, I aim to draw together research papers and reviews from experts in the field of molecular simulation that highlight traditional and new computational methods and strategies to discover and design new drugs.

Dr. Osvaldo Andrade Santos-Filho
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. Pharmaceuticals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). 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

  • molecular dynamics simulations
  • monte carlo simulations
  • docking simulations
  • free energy calculations
  • QM/MM modeling

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Review

25 pages, 2999 KiB  
Review
Computational Modeling of Pharmaceuticals with an Emphasis on Crossing the Blood–Brain Barrier
by Patrícia Alencar Alves, Luana Cristina Camargo, Gabriel Mendonça de Souza, Márcia Renata Mortari and Mauricio Homem-de-Mello
Pharmaceuticals 2025, 18(2), 217; https://doi.org/10.3390/ph18020217 - 6 Feb 2025
Cited by 2 | Viewed by 2617
Abstract
The discovery and development of new pharmaceutical drugs is a costly, time-consuming, and highly manual process, with significant challenges in ensuring drug bioavailability at target sites. Computational techniques are highly employed in drug design, particularly to predict the pharmacokinetic properties of molecules. One [...] Read more.
The discovery and development of new pharmaceutical drugs is a costly, time-consuming, and highly manual process, with significant challenges in ensuring drug bioavailability at target sites. Computational techniques are highly employed in drug design, particularly to predict the pharmacokinetic properties of molecules. One major kinetic challenge in central nervous system drug development is the permeation through the blood–brain barrier (BBB). Several different computational techniques are used to evaluate both BBB permeability and target delivery. Methods such as quantitative structure–activity relationships, machine learning models, molecular dynamics simulations, end-point free energy calculations, or transporter models have pros and cons for drug development, all contributing to a better understanding of a specific characteristic. Additionally, the design (assisted or not by computers) of prodrug and nanoparticle-based drug delivery systems can enhance BBB permeability by leveraging enzymatic activation and transporter-mediated uptake. Neuroactive peptide computational development is also a relevant field in drug design, since biopharmaceuticals are on the edge of drug discovery. By integrating these computational and formulation-based strategies, researchers can enhance the rational design of BBB-permeable drugs while minimizing off-target effects. This review is valuable for understanding BBB selectivity principles and the latest in silico and nanotechnological approaches for improving CNS drug delivery. Full article
(This article belongs to the Special Issue Classical and Quantum Molecular Simulations in Drug Design)
Show Figures

Graphical abstract

34 pages, 3761 KiB  
Review
ATP-Binding Cassette and Solute Carrier Transporters: Understanding Their Mechanisms and Drug Modulation Through Structural and Modeling Approaches
by Ahmad Elbahnsi, Balint Dudas, Isabelle Callebaut, Alexandre Hinzpeter and Maria A. Miteva
Pharmaceuticals 2024, 17(12), 1602; https://doi.org/10.3390/ph17121602 - 27 Nov 2024
Cited by 1 | Viewed by 2439
Abstract
The ATP-binding cassette (ABC) and solute carrier (SLC) transporters play pivotal roles in cellular transport mechanisms, influencing a wide range of physiological processes and impacting various medical conditions. Recent advancements in structural biology and computational modeling have provided significant insights into their function [...] Read more.
The ATP-binding cassette (ABC) and solute carrier (SLC) transporters play pivotal roles in cellular transport mechanisms, influencing a wide range of physiological processes and impacting various medical conditions. Recent advancements in structural biology and computational modeling have provided significant insights into their function and regulation. This review provides an overview of the current knowledge of human ABC and SLC transporters, emphasizing their structural and functional relationships, transport mechanisms, and the contribution of computational approaches to their understanding. Current challenges and promising future research and methodological directions are also discussed. Full article
(This article belongs to the Special Issue Classical and Quantum Molecular Simulations in Drug Design)
Show Figures

Figure 1

Back to TopTop