Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
4.7
4.6
Journals
Pharmaceuticals
Special Issues
The Role of Molecular Docking in the Design of Targeted...
share announcement

The Role of Molecular Docking in the Design of Targeted Therapeutic Entities and Nanomaterials

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

Deadline for manuscript submissions: 25 September 2024 | Viewed by 4938

Special Issue Editors

Prof. Mahmoud Elsabahy

E-Mail Website
Guest Editor
1. Department of Chemistry, Texas A&M University, College Station, TX, USA
2. Science Academy, Badr University in Cairo, Badr City, Egypt
Interests: nanotechnology; molecular docking; in silico; drug design; nanomaterials; nanodrugs; drug targeting
Dr. Noura G. Eissa

E-Mail Website
Guest Editor
1. Department of Pharmaceutics, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
2. Science Academy, Badr University in Cairo, Badr City, Cairo 11829, Egypt
Interests: nanotechnology; nanomaterials; drug targeting; drug delivery; cancer therapy; pharmaceutics

Special Issue Information

Dear Colleagues,

Molecular docking has become a useful computational technique for aiding in drug design by providing insights on interactions and dynamics of molecules and nanomaterials within biological systems. The docking of therapeutic entities and/or nanomaterials enables the prediction of preferred orientations and binding capacities of the developed therapeutics and nanostructures with the target site, thus, providing the capability to predict and achieve superior pharmacological activities. Given the wide variety of pharmacological targets and biomedical applications of nanoconstructs, this research area has received considerable interest. Accordingly, authors are invited to submit high-quality research articles regarding topics such as, but not limited to, molecular docking studies for designing novel compounds and/or nanomaterials for various biomedical applications. Review submissions highlighting the latest advances in the study of the design and biological interactions of novel active entities (i.e., active molecules and nanomaterials) with pharmacological targets are also encouraged.

Potential topics include, but are not limited to:

  • Molecular docking of small molecules
  • Molecular docking of nanomaterials
  • Computer-aided drug design
  • Targeted drug delivery
  • In silico modelling in pharmaceutical applications
  • Targeted nanoparticles
  • Molecular docking of natural compounds

Prof. Dr. Mahmoud Elsabahy
Dr. Noura G. G. Eissa
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.

Keywords

  • molecular docking
  • in silico
  • drug design
  • nanomaterials
  • nanodrugs
  • drug targeting
  • small molecules
  • natural compounds

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

19 pages, 3604 KiB  
Article
Synergistic Biomedical Potential and Molecular Docking Analyses of Coumarin–Triazole Hybrids as Tyrosinase Inhibitors: Design, Synthesis, In Vitro Profiling, and In Silico Studies
by Rukhsana Kausar, Ameer Fawad Zahoor, Hina Tabassum, Shagufta Kamal and Mashooq Ahmad Bhat
Pharmaceuticals 2024, 17(4), 532; https://doi.org/10.3390/ph17040532 - 20 Apr 2024
Viewed by 455
Abstract
The tyrosinase enzyme has a vital role in the browning of vegetables and fruits and the biosynthesis of melanin. In this work, we synthesized a diverse library of coumarin–triazole hybrids, and these compounds were characterized by using suitable analytical techniques. Our research work [...] Read more.
The tyrosinase enzyme has a vital role in the browning of vegetables and fruits and the biosynthesis of melanin. In this work, we synthesized a diverse library of coumarin–triazole hybrids, and these compounds were characterized by using suitable analytical techniques. Our research work extends beyond the synthetic effort to explore the therapeutic potential of these compounds. We put the synthesized compounds through meticulous in vitro screening against the tyrosinase enzyme, and these coumarin derivatives evinced good IC50 values in the range of 0.339 ± 0.25 µM to 14.06 ± 0.92 µM. In the library of synthesized compounds, six compounds were found to be more potent than standard ascorbic acid (IC50 = 11.5 ± 1.00), and among them, 17e and 17f, being the most active, exhibited remarkable anti-tyrosinase potential, with IC50 values of 0.339 ± 0.25 μM and 3.148 ± 0.23 μM, respectively. Furthermore, an in silico modeling study was carried out to determine the key interactions of these compounds with the tyrosinase protein (PDB ID: 2Y9X) and thus to authenticate our experimental findings. The quantitative SAR studies exhibited a good correlation between the synthesized derivatives of coumarin and their anti-tyrosinase activity. The docking studies verified the experimental results, and ligand 17e showed good interaction with the core residues of tyrosinase. This study not only expands the field of coumarin–triazole hybrid synthesis but also provides valuable insights for the development of novel tyrosinase inhibitors. Full article
(This article belongs to the Special Issue The Role of Molecular Docking in the Design of Targeted Therapeutic Entities and Nanomaterials)
►▼ Show Figures

Figure 1

21 pages, 5588 KiB  
Article
1,2,4-Triazole-Tethered Indolinones as New Cancer-Fighting Small Molecules Targeting VEGFR-2: Synthesis, Biological Evaluations and Molecular Docking
by Ahmed E. Elsawi, Mai I. Shahin, Hager A. Elbendary, Tarfah Al-Warhi, Fatma E. Hassan and Wagdy M. Eldehna
Pharmaceuticals 2024, 17(1), 81; https://doi.org/10.3390/ph17010081 - 8 Jan 2024
Viewed by 1130
Abstract
Targeting the VEGFR-2 signaling pathway is an inveterate approach toward combating pancreatic and hepatocellular cancers. Based on Sunitinib, the FDA-approved VEGFR-2 inhibitor, novel indolin-2-one-triazole hybrids were designed and synthesized as anti-hepatocellular and anti-pancreatic cancer agents with VEGFR-2 inhibitory activity. All the targeted compounds [...] Read more.
Targeting the VEGFR-2 signaling pathway is an inveterate approach toward combating pancreatic and hepatocellular cancers. Based on Sunitinib, the FDA-approved VEGFR-2 inhibitor, novel indolin-2-one-triazole hybrids were designed and synthesized as anti-hepatocellular and anti-pancreatic cancer agents with VEGFR-2 inhibitory activity. All the targeted compounds were assessed for their anti-cancer activity, revealing IC50 values extending from 0.17 to 4.29 µM for PANC1 and 0.58 to 4.49 µM for HepG2 cell lines. An extensive SAR study was conducted to explore the effect of different substituents along with N-alkylation. The potent anti-cancer analogs 11d, 11e, 11g, 11k and 14c were evaluated for their VEGFR-2 inhibitory actions, where their IC50 values ranged from 16.3 to 119.6 nM compared to Sorafenib, which revealed an IC50 of 29.7 nM, having compound 11d as the most active analog. An in silico ADME study was performed to confirm the drug-likeness of the synthesized compounds. Finally, molecular docking simulation was conducted for the most potent VEGFR-2 inhibitor (11d), demonstrating the strong binding with the vital amino acid residues of the VEGFR-2 ATP binding site. Full article
(This article belongs to the Special Issue The Role of Molecular Docking in the Design of Targeted Therapeutic Entities and Nanomaterials)
►▼ Show Figures

Graphical abstract

24 pages, 17799 KiB  
Article
Exploring Proteus mirabilis Methionine tRNA Synthetase Active Site: Homology Model Construction, Molecular Dynamics, Pharmacophore and Docking Validation
by Samar S. Elbaramawi, Ahmed G. Eissa, Nada A. Noureldin and Claire Simons
Pharmaceuticals 2023, 16(9), 1263; https://doi.org/10.3390/ph16091263 - 6 Sep 2023
Viewed by 1242
Abstract
Currently, the treatment of Proteus mirabilis infections is considered to be complicated as the organism has become resistant to numerous antibiotic classes. Therefore, new inhibitors should be developed, targeting bacterial molecular functions. Methionine tRNA synthetase (MetRS), a member of the aminoacyl-tRNA synthetase family, [...] Read more.
Currently, the treatment of Proteus mirabilis infections is considered to be complicated as the organism has become resistant to numerous antibiotic classes. Therefore, new inhibitors should be developed, targeting bacterial molecular functions. Methionine tRNA synthetase (MetRS), a member of the aminoacyl-tRNA synthetase family, is essential for protein biosynthesis offering a promising target for novel antibiotics discovery. In the context of computer-aided drug design (CADD), the current research presents the construction and analysis of a comparative homology model for P. mirabilis MetRS, enabling development of novel inhibitors with greater selectivity. Molecular Operating Environment (MOE) software was used to build a homology model for P. mirabilis MetRS using Escherichia coli MetRS as a template. The model was evaluated, and the active site of the target protein predicted from its sequence using conservation analysis. Molecular dynamic simulations were performed to evaluate the stability of the modeled protein structure. In order to evaluate the predicted active site interactions, methionine (the natural substrate of MetRS) and several inhibitors of bacterial MetRS were docked into the constructed model using MOE. After validation of the model, pharmacophore-based virtual screening for a systemically prepared dataset of compounds was performed to prove the feasibility of the proposed model, identifying possible parent compounds for further development of MetRS inhibitors against P. mirabilis. Full article
(This article belongs to the Special Issue The Role of Molecular Docking in the Design of Targeted Therapeutic Entities and Nanomaterials)
►▼ Show Figures

Figure 1

22 pages, 8290 KiB  
Article
Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening
by Marko Jukič, Sebastjan Kralj, Anja Kolarič and Urban Bren
Pharmaceuticals 2023, 16(8), 1170; https://doi.org/10.3390/ph16081170 - 17 Aug 2023
Cited by 1 | Viewed by 1290
Abstract
Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult [...] Read more.
Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries’ display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing. Full article
(This article belongs to the Special Issue The Role of Molecular Docking in the Design of Targeted Therapeutic Entities and Nanomaterials)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop