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Biomedicines
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Medicinal Chemistry in Drug Design and Discovery, 2nd Edition
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Medicinal Chemistry in Drug Design and Discovery, 2nd Edition

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 January 2026 | Viewed by 7291

Special Issue Editor

Dr. Małgorzata Jarończyk

E-Mail Website
Guest Editor
Department of Biomedical Research, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland
Interests: medicinal chemistry; drug design and discovery; in silico studies; docking; QSAR; molecular dynamics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will mainly focus on novel achievements in drug design and discovery and the elucidation of drug action and safety. Articles that emphasize research on structure–activity relationships, investigations of biochemical and pharmacological targets of drug action, and correlations of structures with the mode of action of biologically active compounds are sought.

The purpose of this Special Issue is to publish studies on the current developments in drug design, synthetic chemistry, virtual screening, combinatorial chemistry, drug targets, and the structure–activity relationship. Original research and review articles summarizing all aspects of medicinal chemistry using experimental and theoretical methods are welcome.

Dr. Małgorzata Jarończyk
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 250 words) can be sent to the Editorial Office for assessment.

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. Biomedicines 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 2600 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

  • design and synthesis of medicinal compounds
  • identification and characteristics of targets
  • mechanism of action
  • profiles of safety
  • structure–activity relationship
  • ligand–target interactions
  • drugs repurposing

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Related Special Issue

Published Papers (4 papers)

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Research

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27 pages, 4546 KB  
Article
New Insights into Complex PTSD Treatment: Focus on TAAR1 Agonists
by David-Mandl V. Tseilikman, Vadim E. Tseilikman, Vladislav A. Shatilov, Daria A. Obukhova, Ilya S. Zhukov, Ivan V. Yatsyk, Victoria A. Maistrenko, Vladimir A. Shipelin, Nikita V. Trusov, Marina N. Karpenko, Olga B. Tseilikman, Raul R. Gainetdinov and Jurica Novak
Biomedicines 2025, 13(12), 2972; https://doi.org/10.3390/biomedicines13122972 - 3 Dec 2025
Viewed by 27
Abstract
Background/Objectives: The therapeutic potential of selective trace amine-associated receptor 1 (TAAR1) agonists has been established in multiple animal models of depression and anxiety. PTSD is a debilitating psychiatric disorder frequently characterized by anxiety and often comorbid with major depressive disorder. Complex PTSD represents [...] Read more.
Background/Objectives: The therapeutic potential of selective trace amine-associated receptor 1 (TAAR1) agonists has been established in multiple animal models of depression and anxiety. PTSD is a debilitating psychiatric disorder frequently characterized by anxiety and often comorbid with major depressive disorder. Complex PTSD represents an even more severe clinical presentation, emerging from prolonged or repeated exposure to traumatic events. Recent studies indicate that TAAR1 agonists can attenuate anxiety-like behaviors in experimental models of PTSD; however, the molecular mechanisms underlying this effect remain poorly understood. In this study, we evaluated whether TAAR1 agonism modulates PTSD-related neurochemical and molecular changes within the hippocampus and striatum. Methods: Post-traumatic stress was modeled using predator stress, a validated experimental paradigm relevant to complex PTSD. Treatment consisted of intraperitoneal administration of the TAAR1 agonist LK00764. Monoamine neurotransmitters and their metabolites were quantified, and the expression of genes implicated in noradrenergic, dopaminergic, and serotonergic signaling pathways was assessed. In addition, gene network reconstruction was performed using artificial intelligence to identify TAAR1-dependent regulatory interactions. Results: Treatment with a TAAR1 agonist fully prevented behavioral abnormalities in the experimental model of complex PTSD. Neurochemical analyses revealed decreased 5-HT levels in the hippocampus and reduced dopamine and metabolite concentrations in the striatum following TAAR1 agonism. Moreover, TAAR1 activation was associated with increased expression of the neurotrophic factor BDNF in the striatum. Gene network reconstruction identified a distinct molecular hub within the PTSD network, comprising TAAR1-coexpressed genes, their encoded proteins, and interconnected signaling pathways, suggesting a tightly regulated feedback loop. Conclusions: These findings provide novel evidence that TAAR1 agonists exert protective effects against complex PTSD-related behavioral and neurochemical abnormalities. The reconstructed TAAR1-centered gene network offers mechanistic insight into receptor-dependent regulation of monoaminergic signaling and neuroplasticity, supporting further exploration of TAAR1 agonists as promising therapeutic candidates for PTSD. Full article
(This article belongs to the Special Issue Medicinal Chemistry in Drug Design and Discovery, 2nd Edition)
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39 pages, 7417 KB  
Article
Development of a Collagen–Cerium Oxide Nanohydrogel for Wound Healing: In Vitro and In Vivo Evaluation
by Ekaterina Vladimirovna Silina, Natalia Evgenievna Manturova, Victor Ivanovich Sevastianov, Nadezhda Victorovna Perova, Mikhail Petrovich Gladchenko, Alexey Anatolievich Kryukov, Aleksandr Victorovich Ivanov, Victor Tarasovich Dudka, Evgeniya Valerievna Prazdnova, Sergey Alexandrovich Emelyantsev, Evgenia Igorevna Kozhukhova, Vladimir Anatolievich Parfenov, Alexander Vladimirovich Ivanov, Mikhail Alexandrovich Popov and Victor Alexandrovich Stupin
Biomedicines 2025, 13(11), 2623; https://doi.org/10.3390/biomedicines13112623 - 26 Oct 2025
Viewed by 830
Abstract
Background: Effective regenerative therapeutics for acute and chronic wounds remain a critical unmet need in biomedicine. Objectives: This study aimed to develop novel collagen–cerium oxide nanoparticle hydrogels designed to enhance cellular metabolism, proliferation, and antioxidant/antimutagenic activity, accelerating wound regeneration in vivo. [...] Read more.
Background: Effective regenerative therapeutics for acute and chronic wounds remain a critical unmet need in biomedicine. Objectives: This study aimed to develop novel collagen–cerium oxide nanoparticle hydrogels designed to enhance cellular metabolism, proliferation, and antioxidant/antimutagenic activity, accelerating wound regeneration in vivo. Methods: Collagen–nanocerium composites were synthesized by combining a collagen extract with cerium oxide nanoparticles at defined concentrations. In vitro assays using human fibroblasts identified two formulations that enhanced proliferation and metabolic activity by 42–50%. FTIR spectroscopy confirmed chemical interactions within the composite matrix. Toxicity, antioxidant, and antigenotoxic effects were evaluated using Escherichia coli MG1655 lux-biosensors to assess their general toxicity, antioxidant and pro-oxidant activities, and antigenotoxic and promutagenic effects. In vivo efficacy was tested in Wistar rats with full-thickness skin wounds. Treated groups were compared to untreated controls and Dexpanthenol-treated positive controls. On days 3, 7, and 14, healing was assessed clinically, histologically, and morphometrically. Results: Biosensor analysis demonstrated non-toxicity and antigenotoxic activity of the nanocomposites, reduced DNA damage by up to 45%, providing 31–49% protection against H2O2 and 15–23% against O2− radicals. The animal study results demonstrated significantly accelerated healing with both nanocomposites versus control and comparison groups, evidenced by improved tissue regeneration, reduced inflammation, and increased fibroblast infiltration. Conclusions: The developed hydrogels exhibit promising pharmacological profiles, including antioxidant, antimutagenic, anti-inflammatory, and pro-regenerative effects validated across in vitro and in vivo models. Full article
(This article belongs to the Special Issue Medicinal Chemistry in Drug Design and Discovery, 2nd Edition)
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20 pages, 1433 KB  
Article
Betulinic Acid ω-Triphenylphosphonium Alkyl Esters: Antiproliferative Activities and In Silico Pharmacokinetic Profiles
by Cristian Suárez-Rozas, Claudia Duarte-Salinas, Javier Gajardo-De la Fuente, Paola Salgado-Figueroa, Julio Salas-Norambuena, Bruce K. Cassels, Cristina Theoduloz, José A. Jara, Sebastián Fuentes-Retamal, Paola R. Campodónico, Jorge Soto-Delgado and Mabel Catalán
Biomedicines 2025, 13(7), 1539; https://doi.org/10.3390/biomedicines13071539 - 24 Jun 2025
Cited by 1 | Viewed by 1172
Abstract
Background: Betulinic acid (BA) and some derivatives are well-known antiproliferative compounds. Literature precedents suggest that incorporating triphenylphosphonium (TPP+) salts on this triterpenoid scaffold enhances its biological activity. In the present study, we carried out a simple synthesis of [...] Read more.
Background: Betulinic acid (BA) and some derivatives are well-known antiproliferative compounds. Literature precedents suggest that incorporating triphenylphosphonium (TPP+) salts on this triterpenoid scaffold enhances its biological activity. In the present study, we carried out a simple synthesis of C-28 ester derivatives of this triterpenoid conjugated with TPP+ bromide salts through 4- to 6-carbon chains via nucleophilic substitution of the corresponding ω-TPP+bromoalkanes. Tests for antiproliferative activity in nine cancer cell lines and normal human fibroblasts showed that TPP+ incorporation enhanced the potency of BA by more than an order of magnitude, up to 100-fold. BA-C4-TPP+Br−, with a four-carbon chain separating the TPP+ moiety from the BA, showed remarkable antiproliferative effects, sometimes more potent than the reference drug (Etoposide). This compound exhibited the strongest mitochondrial uncoupling effect in human cancer cells. No significant LDH release was noted in colorectal carcinoma cells at low micromolar concentrations of BA-C4-TPP+Br−, and sub-micromolar concentrations were sufficient for inducing apoptosis. The in silico prediction of pharmacokinetic properties suggested high oral absorption (88%), as well as a non-inhibitor and non-substrate profile vs. cytochrome isoenzymes. These results point to this compound as a promising lead for the development of novel anticancer drugs. Full article
(This article belongs to the Special Issue Medicinal Chemistry in Drug Design and Discovery, 2nd Edition)
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Review

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38 pages, 6259 KB  
Review
Recent Advancements Towards the Use of Vitamin D Isoforms and the Development of Their Synthetic Analogues as New Therapeutics
by Rajiv Patel, Nandini, Harsha Kharkwal, Moumita Saha, Murugesan Sankaranarayanan, Saurabh Sharma and Subhash Chander
Biomedicines 2025, 13(4), 1002; https://doi.org/10.3390/biomedicines13041002 - 21 Apr 2025
Cited by 4 | Viewed by 4446
Abstract
Vitamin D and its metabolites are essential in various physiological processes, including muscle strength, metabolism, antifibrotic activity, and immune regulation. Researchers are focusing on developing vitamin D derivatives with optimized receptor selectivity and reduced systemic toxicity, enhancing their therapeutic efficacy against cancer, autoimmune [...] Read more.
Vitamin D and its metabolites are essential in various physiological processes, including muscle strength, metabolism, antifibrotic activity, and immune regulation. Researchers are focusing on developing vitamin D derivatives with optimized receptor selectivity and reduced systemic toxicity, enhancing their therapeutic efficacy against cancer, autoimmune disorders, and inflammatory diseases. Several analogues, such as alfacalcidol, paricalcitol, and falecalcitriol, are used for managing CKD-related bone disorders, while eldecalcitol is effective for osteoporosis, and calcipotriol against psoriasis. Recent studies have explored their impact on metabolic pathways, parathyroid hormone secretion, asthma, and liver fibrosis, revealing their broad clinical potential. Despite enormous efforts in the past decades, translations of vitamin D-drugs are disproportionately limited, mainly due to toxicity due to calcemic effects and undesirable metabolic profile. This review discusses structural modifications in vitamin D3, their influence on VDR binding, transcriptional activity, and calcium homeostasis, along with their role in targeting pathways like EGFR, KRAS, and Hedgehog in cancers. Advanced analytical techniques such as LC/ESI-MS/MS facilitate precise detection of vitamin D metabolites, further improving pharmacokinetic profiling. Future research may enable the clinical approval of novel vitamin D-based therapeutics with minimal disruption to calcium–phosphorus balance. Full article
(This article belongs to the Special Issue Medicinal Chemistry in Drug Design and Discovery, 2nd Edition)
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