Advances in Drug Discovery and Development: From Rational Design to Experimental Validation

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Drug Discovery, Development and Delivery".

Deadline for manuscript submissions: 31 March 2027 | Viewed by 3662

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Basque Center for Materials, Applications, and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain
Interests: AI-based drug design; molecular modeling; computational material; machine learning
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Special Issue Information

Dear Colleagues,

Drug discovery and development remain central to pharmaceutical research. Traditionally, experimental and computational methods were pursued separately, but recent studies highlight the advantages of combining them to improve the design of new medicines. Experimental approaches such as biochemical assays and structural biology, together with computational methods, have long provided important insights into the discovery of candidate compounds. In recent years, advances in machine learning and deep learning have further expanded these capabilities by enabling the analysis of complex datasets and identifying patterns that accelerate the discovery of promising therapeutic candidates. The synergy between established laboratory methods and modern computational innovations is transforming how drug candidates are discovered, refined, and advanced toward preclinical and clinical evaluation.

Recognizing this rapid progress and the growing need to integrate diverse approaches, this Special Issue aims to provide a platform for sharing recent advances and emerging strategies in drug discovery and development. Accordingly, we invite original research articles, reviews, and short communications that span the full discovery-to-development spectrum. The topics of interest include target identification and validation, drug–target interactions, computational toxicology, medicinal chemistry, biotechnology-based therapeutics, and translational studies that link preclinical findings with clinical research. Particular emphasis will be given to contributions that combine computational predictions with experimental validation, such as, for example, docking- or simulation-guided design followed by in vitro or in vivo testing using MIC assays, MTT cytotoxicity evaluation, cell culture studies, or Western blot analysis. By linking predictive modeling, laboratory validation, and translational insights, this Special Issue seeks to promote efficient strategies for developing safer and more effective next-generation therapies.

Dr. Vikas Kumar
Guest Editor

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Keywords

  • drug discovery
  • drug development
  • rational drug design
  • molecular docking
  • virtual screening
  • pharmacophore modeling
  • molecular dynamics simulations
  • machine learning in drug discovery
  • deep learning in drug discovery
  • experimental validation
  • structure–activity relationship
  • bioactive compounds

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Published Papers (2 papers)

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Research

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29 pages, 5278 KB  
Article
Synergistic Antitumor Effects of Rosmarinic Acid and Cisplatin in Retinoblastoma: Evidence from 2D and 3D Tumor Models
by Erkan Duman, Aydın Maçin, İlhan Özdemir, Şamil Öztürk and Mehmet Cudi Tuncer
Biomedicines 2026, 14(3), 602; https://doi.org/10.3390/biomedicines14030602 - 8 Mar 2026
Cited by 4 | Viewed by 708
Abstract
Background/Objectives: Retinoblastoma (RB) is the most common primary intraocular malignancy in children, with treatment limited by chemoresistance and therapy-related toxicity. Enhancing the efficacy of conventional chemotherapeutics while reducing dose-related adverse effects is crucial. This study investigates the chemosensitizing potential of rosmarinic acid [...] Read more.
Background/Objectives: Retinoblastoma (RB) is the most common primary intraocular malignancy in children, with treatment limited by chemoresistance and therapy-related toxicity. Enhancing the efficacy of conventional chemotherapeutics while reducing dose-related adverse effects is crucial. This study investigates the chemosensitizing potential of rosmarinic acid (RA), a natural polyphenolic compound, in combination with cisplatin (Cis) in RB models. Methods: The antiproliferative and synergistic effects of RA and Cis were evaluated in Y79 and WERI-Rb1 RB cell lines using MTT assays and Combination Index (CI) analysis. Apoptosis and oxidative stress were assessed by Annexin V-FITC/PI flow cytometry and intracellular reactive oxygen species (ROS) measurements, respectively. Three-dimensional (3D) tumor spheroids were generated from Y79 cells for in vitro validation using spheroid size analysis, ATP-based viability assays, and live/dead fluorescence staining. The ROS dependency of cytotoxicity was further examined using N-acetylcysteine (NAC) pretreatment. Cytokine secretion was analyzed by ELISA, and apoptosis-related gene expression was assessed by qRT-PCR. Results: RA and Cis reduced cell viability in a dose- and time-dependent manner, while their combination induced significantly enhanced cytotoxicity, confirmed by CI values < 1. Combined treatment increased apoptotic populations, elevated intracellular ROS, and upregulated Caspase-3 and Caspase-9. These effects were maintained in 3D spheroids, with reduced spheroid size and impaired integrity. NAC pretreatment attenuated ROS generation and partially rescued cell viability, indicating a ROS-dependent, but not exclusive, contribution to cytotoxicity. Conclusions: RA synergistically enhances cisplatin-induced anticancer effects in RB through oxidative stress, engagement of intrinsic (mitochondria-associated) apoptotic signaling, and reduction of tumor cell-derived inflammatory and angiogenic mediators. These findings highlight the potential of RA and Cis combination as a chemosensitizing strategy for RB therapy, warranting further in vivo evaluation. Full article
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Review

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12 pages, 432 KB  
Review
The Role of GLP-1 Analogues in the Treatment of Obesity-Related Asthma Phenotype
by Joanna Radzik-Zając
Biomedicines 2025, 13(11), 2610; https://doi.org/10.3390/biomedicines13112610 - 24 Oct 2025
Cited by 1 | Viewed by 2159
Abstract
Asthma and obesity are two common chronic diseases of growing clinical and social importance. One of the recognised phenotypes of asthma is obesity-related asthma, which is characterised by a more severe course, resistance to glucocorticosteroids, increased inflammation and poorer symptom control. This article [...] Read more.
Asthma and obesity are two common chronic diseases of growing clinical and social importance. One of the recognised phenotypes of asthma is obesity-related asthma, which is characterised by a more severe course, resistance to glucocorticosteroids, increased inflammation and poorer symptom control. This article discusses the complex pathophysiological mechanism of this phenotype, considering the role of chronic inflammation, immune dysregulation and metabolic disorders resulting from obesity. The potential role of glucagon-like peptide-1(GLP-1) receptor analogues as an innovative therapeutic option in the treatment of asthma in obese individuals, both with and without type 2 diabetes mellitus (T2DM), is also analysed. A literature review indicates that glucagon-like peptide-1 receptor analogue (GLP-1RA) drugs, in addition to their hypoglycaemic and weight-reducing effects, also exhibit anti-inflammatory activity in the respiratory system and may reduce the frequency of asthma exacerbations and improve asthma control. The article reviews current data from experimental and clinical studies, emphasising the need for further research on the use of GLP-1RA as an adjunct to conventional asthma therapy in the context of the obese asthma phenotype. Full article
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