Special Issue "Computer-Aided Molecular Modeling and Simulation in Drug Design"

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

Deadline for manuscript submissions: 31 December 2023 | Viewed by 1040

Special Issue Editors

Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Federal University of Pará, Belém 66075-110, Brazil
Interests: molecular modeling; drug design; computational enzymology; binding free energy methods
School of Chemistry, University of KwaZulu-Natal, Durban 4001, South Africa
Interests: chiral catalysis; cage chemistry; pharmaceutical applications of cage compounds
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Special Issue Information

Dear Colleagues,

Computer-aided molecular modeling and simulation has become an essential tool in drug design, allowing researchers to study and understand molecular interactions between a drug candidate and its target. This field combines principles from computational chemistry, bioinformatics, and biophysics to simulate and visualize the behavior of molecules at the atomic level.

Many computational methods are also used to predict the toxicity and pharmacokinetic properties of drug candidates. For example, QSAR (quantitative structure–activity relationship) models can be used to predict the activity of a drug candidate based on its chemical structure, while ADME (absorption, distribution, metabolism, and excretion) models can predict how the drug candidate will behave in a person’s body.

Overall, computer-aided molecular modeling and simulation techniques are important tools in modern drug design, allowing researchers to identify potential drug candidates more efficiently and accurately than traditional experimental methods can.

In this Special Issue, we aim to draw together research from experts in the field that highlight traditional and new computational methods and strategies to discover and design new drugs for clinical treatments.

Dr. José Rogério A. Silva
Prof. Dr. Gert Gert Kruger
Guest Editors

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.


  • computer-aided drug design
  • QSAR
  • molecular docking
  • molecular dynamics
  • free energy

Published Papers (1 paper)

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18 pages, 7105 KiB  
In-Silico Mining of the Toxins Database (T3DB) towards Hunting Prospective Candidates as ABCB1 Inhibitors: Integrated Molecular Docking and Lipid Bilayer-Enhanced Molecular Dynamics Study
Pharmaceuticals 2023, 16(7), 1019; https://doi.org/10.3390/ph16071019 - 18 Jul 2023
Viewed by 745
Multidrug resistance (MDR) is one of the most problematic issues in chemotherapeutic carcinoma therapy. The ABCB1 transporter, a drug efflux pump overexpressed in cancer cells, has been thoroughly investigated for its association with MDR. Thus, discovering ABCB1 inhibitors can reverse the MDR in [...] Read more.
Multidrug resistance (MDR) is one of the most problematic issues in chemotherapeutic carcinoma therapy. The ABCB1 transporter, a drug efflux pump overexpressed in cancer cells, has been thoroughly investigated for its association with MDR. Thus, discovering ABCB1 inhibitors can reverse the MDR in cancer cells. In the current work, a molecular docking technique was utilized for hunting the most prospective ABCB1 inhibitors from the Toxin and Toxin-Target Database (T3DB). Based on the docking computations, the most promising T3DB compounds complexed with the ABCB1 transporter were subjected to molecular dynamics (MD) simulations over 100 ns. Utilizing the MM-GBSA approach, the corresponding binding affinities were computed. Compared to ZQU (calc. −49.8 kcal/mol), Emamectin B1a (T3D1043), Emamectin B1b (T3D1044), Vincristine (T3D4016), Vinblastine (T3D4017), and Vindesine (T3D2479) complexed with ABCB1 transporter demonstrated outstanding binding affinities with ΔGbinding values of −93.0, −92.6, −93.8, −92.2, and −90.8 kcal/mol, respectively. The structural and energetic investigations confirmed the constancy of the identified T3DB compounds complexed with the ABCB1 transporter during the 100 ns MD course. To mimic the physiological conditions, MD simulations were conducted for those identified inhibitors complexed with ABCB1 transporter in the presence of a POPC membrane. These findings revealed that Emamectin B1a, Emamectin B1b, Vincristine, Vinblastine, and Vindesine are promising ABCB1 inhibitors that can reverse the MDR. Therefore, subjecting those compounds to further in-vitro and in-vivo investigations is worthwhile. Full article
(This article belongs to the Special Issue Computer-Aided Molecular Modeling and Simulation in Drug Design)
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