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Pharmaceuticals
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Computational Predictions of Molecules with Potential Therapeutic Effects
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Computational Predictions of Molecules with Potential Therapeutic Effects

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 4733

Special Issue Editor

Dr. Whelton Miller

E-Mail Website
Guest Editor
Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
Interests: biophysics; bioengineering; chemistry; drug discovery; computer-aided drug design
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We invite submissions of original research, reviews, short communications, and perspectives on biophysics, medicinal chemistry, novel therapeutic agents, drug delivery systems, and computer-aided drug design (CADD) for our special issue. This issue also aims to highlight the latest advancements and innovative research driving the convergence of these fields, covering topics such as structural and functional studies of biomolecules, e.g., the identification of new proteins or protein targets, and integration of artificial intelligence (AI) & machine learning (ML) into the design and optimization of therapeutic agents, innovative drug delivery systems, and structure-activity relationships. We seek to disseminate cutting-edge research, promote interdisciplinary collaborations, and showcase practical applications in biomedical research, with a particular emphasis on advancing drug discovery and development. By showcasing expertise from diverse fields such as biophysics, medicinal chemistry, pharmacology, and computational biology, we aim to foster innovation and facilitate the translation of scientific discoveries into effective therapeutic strategies. Our goal is to highlight studies that not only contribute to the fundamental understanding of biological processes but also offer tangible solutions to current challenges in medicine. Manuscripts should be submitted through the online system per journal guidelines. Submission should contains validation studies. We look forward to your pioneering contributions.

Dr. Whelton Miller
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

  • biophysics
  • medicinal chemistry
  • drug discovery
  • molecular docking
  • molecular dynamics
  • structure-activity relationships
  • computer-aided drug design (CADD)

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Published Papers (3 papers)

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Research

27 pages, 12620 KiB  
Article
Insights into the Therapeutic Targets and Molecular Mechanisms of Eruca sativa Against Colorectal Cancer: An Integrated Approach Combining Network Pharmacology, Molecular Docking and Dynamics Simulation
by Humera Banu, Eyad Al-Shammari, Syed Shahanawaz, Faizul Azam, Mitesh Patel, Naif Abdulrahman Alarifi, Md Faruque Ahmad, Mohd Adnan and Syed Amir Ashraf
Pharmaceuticals 2025, 18(4), 453; https://doi.org/10.3390/ph18040453 - 24 Mar 2025
Cited by 1 | Viewed by 770
Abstract
Background/Objectives: This study presents a novel and comprehensive investigation into the anti-colorectal cancer (CRC) effects and underlying mechanisms of Eruca sativa (E. sativa) using an integrated approach combining network pharmacology, molecular docking and molecular dynamics simulation. Methods: Using an integrated approach, [...] Read more.
Background/Objectives: This study presents a novel and comprehensive investigation into the anti-colorectal cancer (CRC) effects and underlying mechanisms of Eruca sativa (E. sativa) using an integrated approach combining network pharmacology, molecular docking and molecular dynamics simulation. Methods: Using an integrated approach, six bioactive compounds and 40 potential targets were identified. A compound–target network was constructed, and enrichment analysis was performed to explore the key pathways influenced by E. sativa. Molecular docking analysis was used to evaluate the binding interactions between the identified compounds and key CRC-related targets (AKT1, PGR, MMP9, and PTGS2). Furthermore, molecular dynamics simulation was utilized to confirm the stability and reliability of these interactions. Results: The study found that E. sativa exhibits strong anticancer potential, particularly through major compounds such as β-ionone, 1-octanol, isorhamnetin, 2-hexenal, propionic acid, and quercetin. Molecular docking revealed favorable binding interactions between these compounds and key CRC targets, with quercetin and isorhamnetin showing the highest binding affinities. Additionally, molecular dynamics simulations validated the stability of these interactions, reinforcing their therapeutic relevance. Conclusions: This study provides valuable insights into the pharmacological mechanisms of E. sativa against CRC, highlighting its potential as a natural anticancer agent. These findings pave the way for future clinical studies to validate the efficacy and safety of E. sativa and its bioactive compounds, potentially contributing to the development of novel, plant-based therapeutic strategies for CRC treatment. Full article
(This article belongs to the Special Issue Computational Predictions of Molecules with Potential Therapeutic Effects)
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24 pages, 7028 KiB  
Article
Natural Product Identification and Molecular Docking Studies of Leishmania Major Pteridine Reductase Inhibitors
by Moses N. Arthur, George Hanson, Emmanuel Broni, Patrick O. Sakyi, Henrietta Mensah-Brown, Whelton A. Miller III and Samuel K. Kwofie
Pharmaceuticals 2025, 18(1), 6; https://doi.org/10.3390/ph18010006 - 24 Dec 2024
Cited by 2 | Viewed by 1546
Abstract
Background/Objectives: Pteridine reductase 1 (PTR1) has been one of the prime targets for discovering novel antileishmanial therapeutics in the fight against Leishmaniasis. This enzyme catalyzes the NADPH-dependent reduction of pterins to their tetrahydro forms. While chemotherapy remains the primary treatment, its effectiveness [...] Read more.
Background/Objectives: Pteridine reductase 1 (PTR1) has been one of the prime targets for discovering novel antileishmanial therapeutics in the fight against Leishmaniasis. This enzyme catalyzes the NADPH-dependent reduction of pterins to their tetrahydro forms. While chemotherapy remains the primary treatment, its effectiveness is constrained by drug resistance, unfavorable side effects, and substantial associated costs. Methods: This study addresses the urgent need for novel, cost-effective drugs by employing in silico techniques to identify potential lead compounds targeting the PTR1 enzyme. A library of 1463 natural compounds from AfroDb and NANPDB, prefiltered based on Lipinski’s rules, was used to screen against the LmPTR1 target. The X-ray structure of LmPTR1 complexed with NADP and dihydrobiopterin (Protein Data Bank ID: 1E92) was identified to contain the critical residues Arg17, Leu18, Ser111, Phe113, Pro224, Gly225, Ser227, Leu229, and Val230 including the triad of residues Asp181-Tyr194-Lys198, which are critical for the catalytic process involving the reduction of dihydrofolate to tetrahydrofolate. Results: The docking yielded 155 compounds meeting the stringent criteria of −8.9 kcal/mol instead of the widely used −7.0 kcal/mol. These compounds demonstrated binding affinities comparable to the known inhibitors; methotrexate (−9.5 kcal/mol), jatrorrhizine (−9.0 kcal/mol), pyrimethamine (−7.3 kcal/mol), hardwickiic acid (−8.1 kcal/mol), and columbamine (−8.6 kcal/mol). Protein–ligand interactions and molecular dynamics (MD) simulation revealed favorable hydrophobic and hydrogen bonding with critical residues, such as Lys198, Arg17, Ser111, Tyr194, Asp181, and Gly225. Crucial to the drug development, the compounds were physiochemically and pharmacologically profiled, narrowing the selection to eight compounds, excluding those with potential toxicities. The five selected compounds ZINC000095486253, ZINC000095486221, ZINC000095486249, 8alpha-hydroxy-13-epi-pimar-16-en-6,18-olide, and pachycladin D were predicted to be antiprotozoal (Leishmania) with Pa values of 0.642, 0.297, 0.543, 0.431, and 0.350, respectively. Conclusions: This study identified five lead compounds that showed substantial binding affinity against LmPTR1 as well as critical residue interactions. A 100 ns MD combined with molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculations confirmed the robust binding interactions and provided insights into the dynamics and stability of the protein–ligand complexes. Full article
(This article belongs to the Special Issue Computational Predictions of Molecules with Potential Therapeutic Effects)
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20 pages, 9396 KiB  
Article
Synthesis, Characterizations, Anti-Diabetic and Molecular Modeling Approaches of Hybrid Indole-Oxadiazole Linked Thiazolidinone Derivatives
by Shoaib Khan, Tayyiaba Iqbal, Rafaqat Hussain, Yousaf Khan, Zanib Fiaz, Fazal Rahim and Hany W. Darwish
Pharmaceuticals 2024, 17(11), 1428; https://doi.org/10.3390/ph17111428 - 24 Oct 2024
Cited by 2 | Viewed by 1658
Abstract
Objective: To synthesize hybrid compounds of indole and oxadiazole in search of highly effective anti-diabetic therapeutic agent. Methods: With the goal of advancing diabetes research, our group designed and synthesized a library of 15 compounds based on indole-derived oxadiazole bearing varied substituted thiazolidinone [...] Read more.
Objective: To synthesize hybrid compounds of indole and oxadiazole in search of highly effective anti-diabetic therapeutic agent. Methods: With the goal of advancing diabetes research, our group designed and synthesized a library of 15 compounds based on indole-derived oxadiazole bearing varied substituted thiazolidinone via a multistep synthetic route. 13C-NMR, 1H-NMR and HREI-MS were applied for the characterization of all the synthesized compounds. Their biological inhibitory activity against diabetic enzymes, i.e., α-amylase and α-glucosidase was also determined. Results: Compound 7, 9 and 15 exhibited excellent inhibition against α-amylase and α-glucosidase than the standard acarbose (IC50 = 8.50 ± 0.10 µM for α-amylase and 9.30 ± 0.30 µM for α-glucosidase. To ensure the inhibitory actions of these potent analogs in molecular docking, an in silico approach was used. To determine the drug likeness of the reported analogs, an ADMET investigation was also carried out to explore the nature of the designed compounds if used as a drug. Conclusion: Fluoro-substituted analog 15 has stronger inhibition profile against both enzymes. All the potent compounds can be used as effective anti-diabetic therapeutic agents in future. Full article
(This article belongs to the Special Issue Computational Predictions of Molecules with Potential Therapeutic Effects)
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