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Keywords = 3D Pharmacophore

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35 pages, 3092 KB  
Article
Borylated Five-Membered Ring Iminosugars: Synthesis, Spectroscopic Analysis, and Biological Evaluation for Glycosidase Inhibition and Anticancer Properties for Application in Boron Neutron Capture Therapy (BNCT)—Part 1
by Kate Prichard, Suzuka Yamamoto, Yuna Shimadate, Kosuke Yoshimura, Barbara Bartholomew, Jayne Gilbert, Jennette Sakoff, Robert Nash, Atsushi Kato and Michela Simone
Pharmaceuticals 2025, 18(9), 1302; https://doi.org/10.3390/ph18091302 - 29 Aug 2025
Viewed by 548
Abstract
Background/Objectives: This article reports pyrrolidine iminosugars of L-gulose absolute stereochemical configuration that are functionalised via N-alkylation to bear boronate ester and boronic acid pharmacophores. Inclusion of boron pharmacophores has been shown to reduce toxicity profiles of drugs and can expand the [...] Read more.
Background/Objectives: This article reports pyrrolidine iminosugars of L-gulose absolute stereochemical configuration that are functionalised via N-alkylation to bear boronate ester and boronic acid pharmacophores. Inclusion of boron pharmacophores has been shown to reduce toxicity profiles of drugs and can expand the range of interactions between drugs and target enzymes. Methods: The synthetic development, detailed spectroscopic analysis, and biological investigation against glycosidase enzymes and cancer cell lines of these novel five-membered ring iminosugars are reported. Results: This family of iminosugars displays selective, moderate-to-weak inhibition (IC50s = 133–501 μM) of β-d-galactosidase (bovine liver) and emerging inhibition of β-d-glucosidases (almond) and (bovine liver). The boronic acid pharmacophore may be suitable for the management of lysosomal storage disorders to support the restoration of biological activity of mutant enzymes via the chaperone-mediated therapy approach. From a structure–activity perspective, the cancer screening revealed slight growth inhibition in a panel of cancer cell lines, with A2780 ovarian carcinoma cells showing the strongest response across all compounds. Beyond the growth inhibition capabilities, the real therapeutic potential of these borylated drugs lies in their switch-on/switch-off activation under BNCT radiotherapeutic conditions. Conclusions: This is an important novel family of drug leads capable of interacting with drug targets via intermolecular and intramolecular interactions, changing shape and electronics. Introduction of organic boron atoms to organic molecules presents significant synthetic and purification challenges, as well as analysis of the equilibria that arise in aqueous systems. We provide a methodology to achieve all this and introduce boron pharmacophores onto carbohydrate scaffolds in a systematic manner to facilitate a more widespread adoption of boron pharmacophores. Full article
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18 pages, 4256 KB  
Article
Multiscale Computational and Pharmacophore-Based Screening of ALK Inhibitors with Experimental Validation
by Ya-Kun Zhang, Jian-Bo Tong, Yue Sun and Yan-Rong Zeng
Pharmaceuticals 2025, 18(8), 1207; https://doi.org/10.3390/ph18081207 - 15 Aug 2025
Viewed by 597
Abstract
Background: Anaplastic lymphoma kinase (ALK) is a key receptor tyrosine kinase involved in regulating signaling pathways critical for cell proliferation, differentiation, and survival. Mutations or rearrangements of the ALK gene lead to aberrant kinase activation, driving tumorigenesis in various cancers. Although ALK inhibitors [...] Read more.
Background: Anaplastic lymphoma kinase (ALK) is a key receptor tyrosine kinase involved in regulating signaling pathways critical for cell proliferation, differentiation, and survival. Mutations or rearrangements of the ALK gene lead to aberrant kinase activation, driving tumorigenesis in various cancers. Although ALK inhibitors have shown clinical benefits, drug resistance remains a significant barrier to long-term efficacy. Developing novel ALK inhibitors capable of overcoming resistance is therefore essential. Methods: A structure-based pharmacophore model was constructed using the 3D structures of five approved ALK inhibitors. Systematic virtual screening of the Topscience drug-like database was performed incorporating PAINS filtering, ADMET prediction, and molecular docking to identify promising candidates. In vitro antiproliferative assays, molecular docking, molecular dynamics simulations, and MM/GBSA binding free energy calculations were used to evaluate biological activity and elucidate binding mechanisms. Results: Two candidates, F1739-0081 and F2571-0016, were identified. F1739-0081 exhibited moderate antiproliferative activity against the A549 cell line, suggesting potential for further optimization. Computational analyses revealed its probable binding modes and interactions with ALK, supporting the observed activity. Conclusions: This study successfully identified novel ALK inhibitor candidates with promising biological activity. The integrated computational and experimental approach provides valuable insights for the rational design of optimized ALK inhibitors to address drug resistance in cancer therapy. Full article
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14 pages, 3348 KB  
Article
In Silico Identification of Novel Compounds as Anthelmintics Against Haemonchus contortus Through Inhibiting β-Tubulin Isotype 1 and Glutathione S-Transferase
by Yaqian Jin, Sheikh Arslan Sehgal, Faizul Hassan and Guiqin Liu
Animals 2025, 15(13), 1846; https://doi.org/10.3390/ani15131846 - 23 Jun 2025
Cited by 2 | Viewed by 704
Abstract
Haemonchosis caused by the parasitic worm Haemonchus contortus is a major threat to cattle and other ruminants and imposes significant economic losses in the livestock industry. Different medications have been reported; however, these are not reliable now due to mass drug resistance. The [...] Read more.
Haemonchosis caused by the parasitic worm Haemonchus contortus is a major threat to cattle and other ruminants and imposes significant economic losses in the livestock industry. Different medications have been reported; however, these are not reliable now due to mass drug resistance. The current study investigates potential inhibitors of two H. contortus proteins: glutathione S-transferase (GST) and beta-tubulin isotype 1. GST helps the parasite to detoxify harmful substances, while beta-tubulin is essential for the cell division and structure. By using computational approaches, natural compounds were identified to inhibit the selected proteins. The 3D structures of GST and β-tubulin isotype 1 were prepared, and pharmacophore models were generated to search the Molport natural compound library. The lowest binding energy ranged from −6.7 to −10.4 Kcal/mol. Post-docking interactional analyses revealed that Glu45, Arg46, Cys126, Gln131, Lys252, Asn247, and Arg251 residues were the most common interacting residues in β-tubulin isotype 1. Similarly, in GST, Leu99, Asn100, Arg103, Lys107, Glu162, and Met163 were the most common interacting residues. In conclusion, extensive computational analyses including virtual screening, docking, and MD simulations revealed that the compound Molport-039-195-358 might have the ability to control haemonchosis by targeting GST and β-tubulin isotype 1. The in silico studies identified potent compounds by targeting GST and β-tubulin isotype 1 against Haemonchus contortus. The reported findings provide a foundation for the development of novel anthelmintic therapies. Full article
(This article belongs to the Special Issue Molecular Approaches to Control Intestinal Parasites in Animals)
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29 pages, 4906 KB  
Article
Ex Vivo Molecular Studies and In Silico Small Molecule Inhibition of Plasmodium falciparum Bromodomain Protein 1
by David O. Oladejo, Titilope M. Dokunmu, Gbolahan O. Oduselu, Daniel O. Oladejo, Olubanke O. Ogunlana and Emeka E. J. Iweala
Drugs Drug Candidates 2025, 4(3), 29; https://doi.org/10.3390/ddc4030029 - 21 Jun 2025
Viewed by 680
Abstract
Background: Malaria remains a significant global health burden, particularly in sub-Saharan Africa, accounting for high rates of illness and death. The growing resistance to frontline antimalarial therapies underscores the urgent need for novel drug targets and therapeutics. Bromodomain-containing proteins, which regulate gene expression [...] Read more.
Background: Malaria remains a significant global health burden, particularly in sub-Saharan Africa, accounting for high rates of illness and death. The growing resistance to frontline antimalarial therapies underscores the urgent need for novel drug targets and therapeutics. Bromodomain-containing proteins, which regulate gene expression through chromatin remodeling, have gained attention as potential targets. Plasmodium falciparum bromodomain protein 1 (PfBDP1), a 55 kDa nuclear protein, plays a key role in recognizing acetylated lysine residues and facilitating transcription during parasite development. Methods: This study investigated ex vivo PfBDP1 gene mutations and identified potential small molecule inhibitors using computational approaches. Malaria-positive blood samples were collected. Genomic DNA was extracted, assessed for quality, and amplified using PfBDP1-specific primers. DNA sequencing and alignment were performed to determine single-nucleotide polymorphism (SNP). Structural modeling used the PfBDP1 crystal structure (PDB ID: 7M97), and active site identification was conducted using CASTp 3.0. Virtual screening and pharmacophore modeling were performed using Pharmit and AutoDock Vina, followed by ADME/toxicity evaluations with SwissADME, OSIRIS, and Discovery Studio. GROMACS was used for 100 ns molecular dynamics simulations. Results: The malaria prevalence rate stood at 12.24%, and the sample size was 165. Sequencing results revealed conserved PfBDP1 gene sequences compared to the 3D7 reference strain. Virtual screening identified nine lead compounds with binding affinities ranging from −9.8 to −10.7 kcal/mol. Of these, CHEMBL2216838 had a binding affinity of −9.9 kcal/mol, with post-screening predictions of favorable drug-likeness (8.60), a high drug score (0.78), superior pharmacokinetics, and a low toxicity profile compared to chloroquine. Molecular dynamics simulations confirmed its stable interaction within the PfBDP1 active site. Conclusions: Overall, this study makes a significant contribution to the ongoing search for novel antimalarial drug targets by providing both molecular and computational evidence for PfBDP1 as a promising therapeutic target. The prediction of CHEMBL2216838 as a lead compound with favorable binding affinity, drug-likeness, and safety profile, surpassing those of existing drugs like chloroquine, sets the stage for preclinical validation and further structure-based drug design efforts. These findings are supported by prior experimental evidence showing significant parasite inhibition and gene suppression capability of predicted hits. Full article
(This article belongs to the Section In Silico Approaches in Drug Discovery)
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21 pages, 5296 KB  
Article
Exploring the Inhibitory Effects of Fucosylated Chondroitin Sulfate (FCS) Oligosaccharide Isolated from Stichopus horrens and the Derivatives on P-Selectin
by Caiyi Li, Huifang Sun, Xi Gu, Wen Long, Guangyu Zhu, Xiaolu Wu, Yu Wang, Pengfei Li, Le Sha, Jiali Zhang, Wenwu Sun, Na Gao, Zhili Zuo and Jinhua Zhao
Mar. Drugs 2025, 23(6), 236; https://doi.org/10.3390/md23060236 - 30 May 2025
Viewed by 838
Abstract
Unique fucosylated chondroitin sulfate (FCS) extracted from the sea cucumber Stichopus horrens was subjected to deacetylation and deaminative depolymerization to generate oligosaccharide fragments containing anTal-diol, which were further purified to obtain the trisaccharide ShFCS-3. Subsequently, the coupling of ShFCS-3 and 4-azidoaniline was achieved [...] Read more.
Unique fucosylated chondroitin sulfate (FCS) extracted from the sea cucumber Stichopus horrens was subjected to deacetylation and deaminative depolymerization to generate oligosaccharide fragments containing anTal-diol, which were further purified to obtain the trisaccharide ShFCS-3. Subsequently, the coupling of ShFCS-3 and 4-azidoaniline was achieved by reductive amination. After purification, the main product ShFCS-A1 and by-product ShFCS-A2 were obtained, which were identified as (N-(L-Fuc2S4S-α1,3-D-GlcA-β1,3-D-anTalA4S6S-1-)-4-azidoaniline) and (4S)-[2-(3-L-Fuc2S4S-α1)-D-GlcA-β1]-2,4,5-trihydroxy-5-sulfated-pent-2-enoic-acid) by 1D/2D NMR spectroscopy, respectively. ELISA experiments revealed that ShFCS-A1 exhibited P-selectin inhibition rates of 19.73% ± 9.60% at 1 μM, 96.28% ± 2.37% at 10 μM, and near-complete inhibition (99.92% ± 0.84%) at 100 μM. ShFCS-A2 demonstrated inhibition rates of 8.29% ± 3.00% at 1 μM, 74.02% ± 8.80% at 10 μM, and maximal inhibition approaching 100% at 100 μM. Cellular-level experiments revealed that ShFCS-A1 and ShFCS-A2 inhibited P-selectin binding to HL-60 cells by 92.72% ± 0.85% and 96.97% ± 1.16% at 100 μM, respectively. Molecular docking analysis indicated binding energies of −5.954 kcal/mol for ShFCS-A1 and −6.140 kcal/mol for ShFCS-A2 with P-selectin, confirming their potent inhibitory effects. These findings highlight the therapeutic potential of FCS oligosaccharides as pharmacophores and provide an important foundation for developing novel small-molecule P-selectin inhibitors. Full article
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26 pages, 7275 KB  
Article
Novel Potent and Selective Dopamine D4 Receptor Piperidine Antagonists as Potential Alternatives for the Treatment of Glioblastoma
by Federica Matteucci, Pegi Pavletić, Alessandro Bonifazi, Rian Garland, Hideaki Yano, Consuelo Amantini, Laura Zeppa, Emanuela Sabato, Giulio Vistoli, Valerio Mammoli, Loredana Cappellacci, Fabio Del Bello, Gianfabio Giorgioni, Riccardo Petrelli, Alessia Piergentili, Wilma Quaglia and Alessandro Piergentili
Pharmaceuticals 2025, 18(5), 739; https://doi.org/10.3390/ph18050739 - 17 May 2025
Viewed by 1584
Abstract
Background/Objectives: D4R antagonists have recently been suggested as potential therapeutic alternatives to the standard treatments of glioblastoma (GBM). In this study, new piperidine-based ligands, analogs of the potent and selective D4R compounds 77-LH-28-1 (7) and its 4-benzyl analog 8, [...] Read more.
Background/Objectives: D4R antagonists have recently been suggested as potential therapeutic alternatives to the standard treatments of glioblastoma (GBM). In this study, new piperidine-based ligands, analogs of the potent and selective D4R compounds 77-LH-28-1 (7) and its 4-benzyl analog 8, were synthesized and studied to investigate the effects produced by variations in the distances between the pharmacophoric features on the D4R affinity and selectivity. Methods: All the new compounds 9–20 were evaluated for their radioligand binding affinity at D2-like receptor subtypes and the results were rationalized by docking studies and molecular dynamics (MD) simulations. The functional profiles of the most interesting derivatives were assessed at D4R Go and Gi protein and β-arrestin by BRET assay and their potential anticancer activity was determined in GBM cell lines. Results: Radioligand binding results highlighted that the derivatives bearing a terminal butyl chain showed structure–activity relationships different from those with a benzyl terminal. From functional studies performed on the best derivatives 12 and 16, the response profiles of both compounds were more robust in antagonist mode, with derivative 16 showing higher antagonist potency than 12 across all three transducers. Interestingly, 12 and 16 dose-dependently decreased the cell viability of GBM cells, inducing cell death and cell cycle arrest, promoting an increase in ROS production, causing mitochondrial dysfunction, and significantly inhibiting colony formation. Conclusions: The promising biological profiles of 12 and 16 make them new lead candidates that warrant further investigation to gain a better understanding of the mechanism behind their antitumor activity and better evaluate their potential for GBM treatment. Full article
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18 pages, 1649 KB  
Article
Antiprotozoal Activity and Cytotoxicity Screening of Lippia adoensis (Hochst.) Extracts: Growth Inhibition of Plasmodium, Leishmania, and Trypanosoma Parasites
by Eugenie Aimée Madiesse Kemgne, Mariscal Brice Tchatat Tali, Darline Dize, Cyrille Armel Njanpa Ngansop, Boniface Pone Kamdem and Fabrice Fekam Boyom
J. Oman Med. Assoc. 2025, 2(1), 6; https://doi.org/10.3390/joma2010006 - 13 May 2025
Viewed by 720
Abstract
The serendipitous discovery of antiparasitic drugs, such as quinine and artemisinin, of plant origin reveals that searching new chemical pharmacophores from medicinal plants is valuable. The present study sought to explore the antiplasmodial, antileishmanial, and antitrypanosomal activities of Lippia adoensis extracts. Crude extracts [...] Read more.
The serendipitous discovery of antiparasitic drugs, such as quinine and artemisinin, of plant origin reveals that searching new chemical pharmacophores from medicinal plants is valuable. The present study sought to explore the antiplasmodial, antileishmanial, and antitrypanosomal activities of Lippia adoensis extracts. Crude extracts of L. adoensis leaves and twigs, which were obtained by extraction using 70% ethanol in water, were assayed for antiplasmodial activity against P. falciparum 3D7 and Dd2 through the SYBR green I-based fluorescence assay; and for antileishmanial, antitrypanosomal, and cytotoxic effects on Leishmania donovani, Trypanosoma brucei brucei, and Vero cells, respectively, using resazurin colorimetric assays. In vitro phytochemical analysis of L. adoensis extracts was performed using standard methods. Moreover, liquid chromatography–mass spectrometry (LC-MS) feature-based detection and molecular networking flow on Global Natural Product Social (GNPS) were also used for the phytochemical screening of L. adoensis extracts. Crude extracts from L. adoensis inhibited the growth of P. falciparum (3D7 and Dd2) (IC50s; (3D7): 10.00 and 97.46 μg/mL; (Dd2): 29.48 and 26.96 μg/mL), L. donovani (IC50s: 22.87–10.52 μg/mL), and T. brucei brucei (IC50s: 2.30–55.06 μg/mL). The extracts were found to be non-cytotoxic to Vero cells, thus yielding median cytotoxic concentrations (CC50s) above 100 μg/mL. In vitro phytochemical analysis of the crude extracts revealed the presence of alkaloids, terpenoids, phenolic compounds, and carbohydrates. The LC-MS tandem molecular networking flow predicted that the extracts contained valsafungin A and bacillamidin in the first cluster, and fatty acids, ketone, and aldehyde derivatives in the second cluster. Overall, the present study demonstrated the antiparasitic effects of L. adoensis extracts, thus justifying the use of this plant in the traditional treatment of fever and malaria conditions. Nevertheless, detailed metabolomic studies and antiparasitic mechanisms of action of the extracts are expected to unveil the potential antiparasitic hit compounds. Full article
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24 pages, 5400 KB  
Article
Design, Synthesis, Anticancer Evaluation and Molecular Docking of Pyrimidine, Pyrido[4,3-d]pyrimidine and 5,6,7,8-Tetrahydropyrido[3,4-d]pyrimidine Derivatives as Novel KRAS-G12D Inhibitors and PROTACs
by Hailong Yang, Lu Gan and Huabei Zhang
Pharmaceuticals 2025, 18(5), 696; https://doi.org/10.3390/ph18050696 - 8 May 2025
Viewed by 2582
Abstract
Background: KRAS-G12D mutations drive 20–50% of pancreatic/biliary cancers yet remain challenging to target due to GTP-pocket conservation and high cellular GTP levels. While allosteric inhibitors targeting the SWII pocket (e.g., MRTX1133) show promise, limited chemical diversity and paradoxical cellular/enzymatic activity relationships necessitate [...] Read more.
Background: KRAS-G12D mutations drive 20–50% of pancreatic/biliary cancers yet remain challenging to target due to GTP-pocket conservation and high cellular GTP levels. While allosteric inhibitors targeting the SWII pocket (e.g., MRTX1133) show promise, limited chemical diversity and paradoxical cellular/enzymatic activity relationships necessitate the exploration of novel scaffolds. This study aims to develop KRAS-G12D inhibitors and PROTACs to offer a selection of new chemical entities through systematic structure–activity optimization and evaluate their therapeutic potential through PROTAC derivatization. Methods: Eleven compounds featuring heterocyclic cores (pyrimidine/pyrido[4,3-d]pyrimidine/5,6,7,8-tetrahydroprodo[3,4-d]pyrimidine) were designed via structure-based drug design. Antiproliferative activity against KRAS-G12D (Panc1), KRAS-G13D (HCT116) and wild-type (A549) cells was assessed using the CCK-8 assay. KRAS-G12D enzymatic inhibition was measured using a GTPase activity assay. Molecular docking simulations (Sybyl 2.0; PDB:7RPZ) elucidated binding modes. Two PROTACs were synthesized from lead compounds by conjugating E3 ligase linkers. All the novel inhibitors and PROTACs were characterized by means of NMR or HRMS. Results: Compound 10c demonstrated selective anti-proliferation in Panc1 cells (IC50 = 1.40 μM) with 4.9-fold greater selectivity over wild-type cells, despite weak enzymatic inhibition (IC50 > 10 μM). Docking revealed critical hydrogen bonds between its protonated 3,8-diazabicyclo[3.2.1]octane moiety and Asp12/Gly60. The enzymatic inhibitor 10k showed potent KRAS-G12D inhibition (IC50 = 0.009 μM) through homopiperazine-mediated interactions with Glu92/His95. Derived PROTACs 26a/b exhibited reduced potency (IC50 = 3–5 μM vs. parental 10k: 2.22 μM), potentially due to impaired membrane permeability. Conclusions: Eleven novel KRAS-G12D inhibitors with a seven-membered ring pharmacophore were synthesized. Compound 10c showed strong anti-proliferative activity, while 10k exhibited potent enzymatic inhibition. Two PROTACs were designed but showed no clear advantage over 10k. This study provides valuable insights for KRAS-targeted drug development. Full article
(This article belongs to the Section Medicinal Chemistry)
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36 pages, 9116 KB  
Article
Computational Investigation of Montelukast and Its Structural Derivatives for Binding Affinity to Dopaminergic and Serotonergic Receptors: Insights from a Comprehensive Molecular Simulation
by Nasser Alotaiq and Doni Dermawan
Pharmaceuticals 2025, 18(4), 559; https://doi.org/10.3390/ph18040559 - 10 Apr 2025
Cited by 2 | Viewed by 1400
Abstract
Background/Objectives: Montelukast (MLK), a leukotriene receptor antagonist, has been associated with neuropsychiatric side effects. This study aimed to rationally modify MLK’s structure to reduce these risks by optimizing its interactions with dopamine D2 (DRD2) and serotonin 5-HT1A receptors using computational molecular simulation [...] Read more.
Background/Objectives: Montelukast (MLK), a leukotriene receptor antagonist, has been associated with neuropsychiatric side effects. This study aimed to rationally modify MLK’s structure to reduce these risks by optimizing its interactions with dopamine D2 (DRD2) and serotonin 5-HT1A receptors using computational molecular simulation techniques. Methods: A library of MLK derivatives was designed and screened using structural similarity analysis, molecular docking, molecular dynamics (MD) simulations, MM/PBSA binding free energy calculations, and ADME-Tox predictions. Structural similarity analysis, based on Tanimoto coefficient fingerprinting, compared MLK derivatives to known neuropsychiatric drugs. Docking was performed to assess initial receptor binding, followed by 100 ns MD simulations to evaluate binding stability. MM/PBSA calculations quantified binding affinities, while ADME-Tox profiling predicted pharmacokinetic and toxicity risks. Results: Several MLK derivatives showed enhanced DRD2 and 5-HT1A binding. MLK_MOD-42 and MLK_MOD-43 emerged as the most promising candidates, exhibiting MM/PBSA binding free energies of −31.92 ± 2.54 kcal/mol and −27.37 ± 2.22 kcal/mol for DRD2 and −30.22 ± 2.29 kcal/mol and −28.19 ± 2.14 kcal/mol for 5-HT1A, respectively. Structural similarity analysis confirmed that these derivatives share key pharmacophoric features with atypical antipsychotics and anxiolytics. However, off-target interactions were not assessed, which may influence their overall safety profile. ADME-Tox analysis predicted improved oral bioavailability and lower neurotoxicity risks. Conclusions: MLK_MOD-42 and MLK_MOD-43 exhibit optimized receptor interactions and enhanced pharmacokinetics, suggesting potential neuropsychiatric applications. However, their safety and efficacy remain to be validated through in vitro and in vivo studies. Until such validation is performed, these derivatives should be considered as promising candidates with optimized receptor binding rather than confirmed safer alternatives. Full article
(This article belongs to the Special Issue Application of 2D and 3D-QSAR Models in Drug Design)
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21 pages, 2096 KB  
Article
The Impact of Doxycycline as an Adjunctive Therapy on Prostate-Specific Antigen, Quality of Life, and Cognitive Function in Metastatic Prostate Cancer Patients: A Phase II Randomized Controlled Trial
by José Guzmán-Esquivel, Hossana S. Garcia-Garcia, Gustavo A. Hernández-Fuentes, Jesús Venegas-Ramírez, Carlos D. Barajas-Mejía, Idalia Garza-Veloz, Margarita L. Martinez-Fierro, Nancy E. Magaña-Vergara, José A. Guzmán-Solórzano, Patricia Calvo-Soto, Oscar N. Avila-Zamora, Mercedes Fuentes-Murguia, Gabriel Ceja-Espíritu and Iván Delgado-Enciso
Pharmaceutics 2025, 17(4), 404; https://doi.org/10.3390/pharmaceutics17040404 - 24 Mar 2025
Viewed by 2543
Abstract
Background/Objectives: Metastatic prostate cancer remains a major clinical challenge, with limited therapeutic options. Doxycycline, a tetracycline antibiotic with anti-inflammatory properties, has shown potential as an adjunctive therapy. This study aimed to evaluate its efficacy in reducing prostate-specific antigen (PSA) levels and improving quality [...] Read more.
Background/Objectives: Metastatic prostate cancer remains a major clinical challenge, with limited therapeutic options. Doxycycline, a tetracycline antibiotic with anti-inflammatory properties, has shown potential as an adjunctive therapy. This study aimed to evaluate its efficacy in reducing prostate-specific antigen (PSA) levels and improving quality of life in patients receiving standard treatment for metastatic prostate cancer. Methods: This phase II, double-blind, randomized controlled trial included 45 participants (aged 57–81 years) assigned to doxycycline (100 mg daily) or a placebo for six months. The primary outcome was the percentage change in PSA levels at 3 and 6 months. Secondary outcomes included quality of life (EQ-5D-5L), cognitive function (Mini-Mental State Examination), and glucose levels. Additionally, a structure–activity relationship (SAR) analysis was performed through an extensive bibliographic review to identify pharmacophores responsible for doxycycline’s biological activity, particularly its tetracyclic core. The SAR analysis included tetracyclines and derivatives, androgen-targeting agents, and other pharmacologically relevant molecules used in prostate cancer therapy. Statistical analysis was conducted using multivariate logistic regression. Results: At six months, the doxycycline group showed a median PSA reduction of 60% compared to 10% in the placebo group (p = 0.043). A ≥50% reduction in PSA levels was observed in 71.4% of patients receiving doxycycline versus 20.8% in the placebo group (p = 0.001), with an adjusted relative risk of 10.309 (95% CI: 2.359–45.055, p = 0.002). Quality of life improved, with 7.1% of doxycycline-treated patients reporting poor quality of life compared to 42.9% in the placebo group (p = 0.028). A slight improvement in cognitive function was also noted (p = 0.037). SAR analysis suggested that the tetracyclic ring of doxycycline may play a crucial role in its observed biological effects. Conclusions: Doxycycline demonstrates potential as an adjunctive therapy in metastatic prostate cancer by reducing PSA levels and improving quality of life. The SAR analysis supports the hypothesis that its tetracyclic structure may be responsible for its therapeutic effects. Further large-scale trials are warranted to confirm these findings. Full article
(This article belongs to the Special Issue Combination Therapy Approaches for Cancer Treatment)
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33 pages, 23877 KB  
Article
Improved Inhibitors Targeting the Thymidylate Kinase of Multidrug-Resistant Mycobacterium tuberculosis with Favorable Pharmacokinetics
by Souleymane Konate, Koffi N’Guessan Placide Gabin Allangba, Issouf Fofana, Raymond Kre N’Guessan, Eugene Megnassan, Stanislav Miertus and Vladimir Frecer
Life 2025, 15(2), 173; https://doi.org/10.3390/life15020173 - 25 Jan 2025
Viewed by 1358
Abstract
This study aims to design improved inhibitors targeting the thymidylate kinase (TMK) of Mycobacterium tuberculosis (Mtb), the causative agent of infectious disease tuberculosis that is associated with high morbidity and mortality in developing countries. TMK is an essential enzyme for the [...] Read more.
This study aims to design improved inhibitors targeting the thymidylate kinase (TMK) of Mycobacterium tuberculosis (Mtb), the causative agent of infectious disease tuberculosis that is associated with high morbidity and mortality in developing countries. TMK is an essential enzyme for the synthesis of bacterial DNA. We have performed computer-aided molecular design of MtbTMK inhibitors by modification of the reference crystal structures of the lead micromolar inhibitor TKI1 1-(1-((4-(3-Chlorophenoxy)quinolin-2-yl)methyl)piperidin-4-yl)-5-methylpyrimidine-2,4(1H,3H)-dione bound to TMK of Mtb strain H37Rv (PDB entries: 5NRN and 5NR7) using the computational approach MM-PBSA. A QSAR model was prepared for a training set of 31 MtbTMK inhibitors with published inhibitory potencies (IC50exp) and showed a significant correlation between the calculated relative Gibbs free energies of the MtbTMK–TKIx complex formation and the observed potencies. This model was able to explain approximately 95% of the variation in the in vitro inhibition data and validated our molecular model of MtbTMK inhibition for the subsequent design of new TKI analogs. Furthermore, we have confirmed the predictive capacity of this complexation QSAR model by generating a 3D QSAR PH4 pharmacophore-based model. A satisfactory correlation was also obtained for the validation PH4 model of MtbTMK inhibition (R2 = 0.84). We have extended the hydrophobic m-chloro-phenoxyquinolin-2-yl group of TKI1 that can occupy the entry into the thymidine binding cleft of MtbTMK by alternative larger hydrophobic groups. Analysis of residue interactions at the enzyme binding site made it possible to select suitable building blocks to be used in the preparation of a virtual combinatorial library of 28,900 analogs of TKI1. Structural information derived from the complexation model and the PH4 pharmacophore guided the in silico screening of the library of analogs and led to the identification of new potential MtbTMK inhibitors that were predicted to be effective in the low nanomolar concentration range. The QSAR complexation model predicted an inhibitory concentration IC50pre of 9.5 nM for the best new virtual inhibitor candidate TKI 13_1, which represents a significant improvement in estimated inhibitory potency compared to TKI1. Finally, the stability of the MtbTMK–inhibitor complexes and the flexibility of the active conformation of the inhibitors were assessed by molecular dynamics for five top-ranking analogs. This computational study resulted in the discovery of new MtbTMK inhibitors with predicted enhanced inhibitory potencies, which also showed favorable predicted pharmacokinetic profiles. Full article
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15 pages, 2179 KB  
Article
Stereoselective Synthesis and Biological Evaluation of Perhydroquinoxaline-Based κ Receptor Agonists
by Jonathan Hoffmann, Dirk Schepmann, Constantin Daniliuc, Marcel Bermudez and Bernhard Wünsch
Int. J. Mol. Sci. 2025, 26(3), 998; https://doi.org/10.3390/ijms26030998 - 24 Jan 2025
Viewed by 1077
Abstract
The hydroxylated perhydroquinoxaline 14 was designed by conformational restriction of the prototypical κ receptor agonist U-50,488 and the introduction of an additional polar group. The synthesis of 14 comprised ten reaction steps starting from diethyl 3-hydroxyglutarate (4). The first key step [...] Read more.
The hydroxylated perhydroquinoxaline 14 was designed by conformational restriction of the prototypical κ receptor agonist U-50,488 and the introduction of an additional polar group. The synthesis of 14 comprised ten reaction steps starting from diethyl 3-hydroxyglutarate (4). The first key step was the diastereoselective establishment of the tetrasubstituted cyclohexane 7 by the reaction of dialdehyde 6 with benzylamine and nitromethane. The piperazine ring was annulated by the reaction of silyloxy-substituted cyclohexanetriamine 8 with dimethyl oxalate. The pharmacophoric structural elements characteristic for κ receptor agonists were finally introduced by functional group modifications. The structure including the relative configuration of the tetrasubstituted cyclohexane derivative (2r,5s)-7a and the perhydroquinoxaline 9 was determined unequivocally by X-ray crystal structure analysis. The hydroxylated perhydroquinoxaline 14 showed moderate κ receptor affinity (Ki = 599 nM) and high selectivity over μ, δ, σ1, and σ2 receptors. An ionic interaction between the protonated pyrrolidine of 14 and D138 of κ receptor anchors 14 in the κ receptor binding pocket. Full article
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35 pages, 21863 KB  
Review
Perry Disease: Current Outlook and Advances in Drug Discovery Approach to Symptomatic Treatment
by Zbigniew Gajda, Magdalena Hawrylak, Jadwiga Handzlik and Kamil J. Kuder
Int. J. Mol. Sci. 2024, 25(19), 10652; https://doi.org/10.3390/ijms251910652 - 3 Oct 2024
Cited by 1 | Viewed by 2686
Abstract
Perry disease (PeD) is a rare, neurodegenerative, genetic disorder inherited in an autosomal dominant manner. The disease manifests as parkinsonism, with psychiatric symptoms on top, such as depression or sleep disorders, accompanied by unexpected weight loss, central hypoventilation, and aggregation of DNA-binding protein [...] Read more.
Perry disease (PeD) is a rare, neurodegenerative, genetic disorder inherited in an autosomal dominant manner. The disease manifests as parkinsonism, with psychiatric symptoms on top, such as depression or sleep disorders, accompanied by unexpected weight loss, central hypoventilation, and aggregation of DNA-binding protein (TDP-43) in the brain. Due to the genetic cause, no causal treatment for PeD is currently available. The only way to improve the quality of life of patients is through symptomatic therapy. This work aims to review the latest data on potential PeD treatment, specifically from the medicinal chemistry and computer-aided drug design (CADD) points of view. We select proteins that might represent therapeutic targets for symptomatic treatment of the disease: monoamine oxidase B (MAO-B), serotonin transporter (SERT), dopamine D2 (D2R), and serotonin 5-HT1A (5-HT1AR) receptors. We report on compounds that may be potential hits to develop symptomatic therapies for PeD and related neurodegenerative diseases and relieve its symptoms. We use Phase pharmacophore modeling software (version 2023.08) implemented in Schrödinger Maestro as a ligand selection tool. For each of the chosen targets, based on the resolved protein–ligand structures deposited in the Protein Data Bank (PDB) database, pharmacophore models are proposed. We review novel, active compounds that might serve as either hits for further optimization or candidates for further phases of studies, leading to potential use in the treatment of PeD. Full article
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14 pages, 4392 KB  
Article
Identification of Novel Bromodomain-Containing Protein 4 (BRD4) Binders through 3D Pharmacophore-Based Repositioning Screening Campaign
by Ester Colarusso, Erica Gazzillo, Eleonora Boccia, Stefania Terracciano, Ines Bruno, Giuseppe Bifulco, Maria Giovanna Chini and Gianluigi Lauro
Molecules 2024, 29(17), 4025; https://doi.org/10.3390/molecules29174025 - 26 Aug 2024
Cited by 1 | Viewed by 2221
Abstract
A 3D structure-based pharmacophore model built for bromodomain-containing protein 4 (BRD4) is reported here, specifically developed for investigating and identifying the key structural features of the (+)-JQ1 known inhibitor within the BRD4 binding site. Using this pharmacophore model, 273 synthesized and purchased compounds [...] Read more.
A 3D structure-based pharmacophore model built for bromodomain-containing protein 4 (BRD4) is reported here, specifically developed for investigating and identifying the key structural features of the (+)-JQ1 known inhibitor within the BRD4 binding site. Using this pharmacophore model, 273 synthesized and purchased compounds previously considered for other targets but yielding poor results were screened in a drug repositioning campaign. Subsequently, only six compounds showed potential as BRD4 binders and were subjected to further biophysical and biochemical assays. Compounds 2, 5, and 6 showed high affinity for BRD4, with IC50 values of 0.60 ± 0.25 µM, 3.46 ± 1.22 µM, and 4.66 ± 0.52 µM, respectively. Additionally, these compounds were tested against two other bromodomains, BRD3 and BRD9, and two of them showed high selectivity for BRD4. The reported 3D structure-based pharmacophore model proves to be a straightforward and useful tool for selecting novel BRD4 ligands. Full article
(This article belongs to the Special Issue Trends and Prospects in Computer-Aided Drug Design)
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20 pages, 4294 KB  
Article
In Silico Exploration of Novel EGFR Kinase Mutant-Selective Inhibitors Using a Hybrid Computational Approach
by Md Ali Asif Noor, Md Mazedul Haq, Md Arifur Rahman Chowdhury, Hilal Tayara, HyunJoo Shim and Kil To Chong
Pharmaceuticals 2024, 17(9), 1107; https://doi.org/10.3390/ph17091107 - 23 Aug 2024
Cited by 2 | Viewed by 3476
Abstract
Targeting epidermal growth factor receptor (EGFR) mutants is a promising strategy for treating non-small cell lung cancer (NSCLC). This study focused on the computational identification and characterization of potential EGFR mutant-selective inhibitors using pharmacophore design and validation by deep learning, virtual screening, ADMET [...] Read more.
Targeting epidermal growth factor receptor (EGFR) mutants is a promising strategy for treating non-small cell lung cancer (NSCLC). This study focused on the computational identification and characterization of potential EGFR mutant-selective inhibitors using pharmacophore design and validation by deep learning, virtual screening, ADMET (Absorption, distribution, metabolism, excretion and toxicity), and molecular docking-dynamics simulations. A pharmacophore model was generated using Pharmit based on the potent inhibitor JBJ-125, which targets the mutant EGFR (PDB 5D41) and is used for the virtual screening of the Zinc database. In total, 16 hits were retrieved from 13,127,550 molecules and 122,276,899 conformers. The pharmacophore model was validated via DeepCoy, generating 100 inactive decoy structures for each active molecule and ADMET tests were conducted using SWISS ADME and PROTOX 3.0. Filtered compounds underwent molecular docking studies using Glide, revealing promising interactions with the EGFR allosteric site along with better docking scores. Molecular dynamics (MD) simulations confirmed the stability of the docked conformations. These results bring out five novel compounds that can be evaluated as single agents or in combination with existing therapies, holding promise for treating the EGFR-mutant NSCLC. Full article
(This article belongs to the Special Issue Heterocyclic Compounds in Medicinal Chemistry)
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