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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 17387

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Prof. Dr. Diego Muñoz-Torrero

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Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
Interests: multitarget anti-Alzheimer agents; hybrid compounds; cholinesterase inhibitors; amyloid anti-aggregating compounds; BACE-1 inhibitors; antiprotozoan compounds
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Prof. Dr. Mariana Spetea

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Institute of Pharmacy, Department of Pharmaceutical Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
Interests: opioid receptors; opioid pharmacology; pain research; CNS disorders; opioid drug discovery; structure-activity-relationships; GPCRs signalling
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Dr. Federica Belluti

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Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
Interests: medicinal chemistry; natural products; curcumin; drug design; multitarget drug discovery; bioactive compounds; neurodegeneration; cancer
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Dr. Panagiotis Zoumpoulakis

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Department of Food Science and Technology, University of West Attica, Athens, Greece
Interests: molecular design; bioanalysis; natural bioactive compounds; computational chemistry; analytical chemistry

Prof. Dr. Xinyong Liu

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Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, China
Interests: innovative drug research; antiviral drug; drug design; medicinal chemistry; antigout drug
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Molecules is dedicated to recent advances in medicinal chemistry research areas and comprises a diverse selection of exclusive papers from the Editorial Board Members (EBMs) of the Section Medicinal Chemistry. It focuses on highlighting recent interesting investigations conducted in the laboratories of our section’s EBMs and aims to represent our section as an attractive open-access publishing platform for medicinal chemistry research.

Dr. Diego Muñoz-Torrero
Prof. Dr. Mariana Spetea
Dr. Federica Belluti
Dr. Panagiotis Zoumpoulakis
Prof. Dr. Xinyong Liu
Guest Editors

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Published Papers (6 papers)

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Research

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12 pages, 3174 KiB

Open AccessArticle

Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA

by Chenyun Guo, Hao Xu, Xiao Li, Jiaxin Yu and Donghai Lin

Molecules 2023, 28(6), 2534; https://doi.org/10.3390/molecules28062534 - 10 Mar 2023

Cited by 6 | Viewed by 2062

Abstract

Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (K_d = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (K_d = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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34 pages, 7884 KiB

Open AccessArticle

Investigation into the Use of Encorafenib to Develop Potential PROTACs Directed against BRAF^V600E Protein

by Elisabetta Marini, Marco Marino, Giulia Gionfriddo, Federica Maione, Marta Pandini, Daniele Oddo, Marta Giorgis, Barbara Rolando, Federica Blua, Simone Gastaldi, Serena Marchiò, Sandra Kovachka, Francesca Spyrakis, Eleonora Gianquinto, Federica Di Nicolantonio and Massimo Bertinaria

Molecules 2022, 27(23), 8513; https://doi.org/10.3390/molecules27238513 - 3 Dec 2022

Cited by 8 | Viewed by 3725

Abstract

BRAF is a serine/threonine kinase frequently mutated in human cancers. BRAF^V600E mutated protein is targeted through the use of kinase inhibitors which are approved for the treatment of melanoma; however, their long-term efficacy is hampered by resistance mechanisms. The PROTAC-induced degradation of BRAF^V600E has been proposed as an alternative strategy to avoid the onset of resistance. In this study, we designed a series of compounds where the BRAF kinase inhibitor encorafenib was conjugated to pomalidomide through different linkers. The synthesized compounds maintained their ability to inhibit the kinase activity of mutated BRAF with IC₅₀ values in the 40–88 nM range. Selected compounds inhibited BRAF^V600E signaling and cellular proliferation of A375 and Colo205 tumor cell lines. Compounds 10 and 11, the most active of the series, were not able to induce degradation of mutated BRAF. Docking and molecular dynamic studies, conducted in comparison with the efficient BRAF degrader P5B, suggest that a different orientation of the linker bearing the pomalidomide substructure, together with a decreased mobility of the solvent-exposed part of the conjugates, could explain this behavior. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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14 pages, 2437 KiB

Open AccessArticle

Sirtuin 1-Activating Compounds: Discovery of a Class of Thiazole-Based Derivatives

by Giulia Bononi, Valentina Citi, Margherita Lapillo, Alma Martelli, Giulio Poli, Tiziano Tuccinardi, Carlotta Granchi, Lara Testai, Vincenzo Calderone and Filippo Minutolo

Molecules 2022, 27(19), 6535; https://doi.org/10.3390/molecules27196535 - 3 Oct 2022

Cited by 8 | Viewed by 3559

Abstract

Sirtuin 1 (SIRT1) is a NAD⁺-dependent deacetylase implicated in various biological and pathological processes, including cancer, diabetes, and cardiovascular diseases. In recent years, SIRT1-activating compounds have been demonstrated to exert cardioprotective effects. Therefore, this enzyme has become a feasible target to treat cardiovascular diseases, and many SIRT1 activators, of a natural or synthetic origin, have been identified. In the present work, we developed thiazole-based SIRT1 activators, which showed remarkably higher SIRT1 activation potencies compared with those of the reference compound resveratrol when tested in enzymatic assays. Thiazole 8, a representative compound of this series, was also subjected to further pharmacological investigations, where it was proven to reduce myocardial damage induced by an in vivo occlusion/reperfusion event, thus confirming its cardioprotective properties. In addition, the cardioprotective effect of compound 8 was significantly higher than that of resveratrol. Molecular modeling studies suggest the binding mode of these derivatives within SIRT1 in the presence of the p53-AMC peptide. These promising results could pave the way to further expand and optimize this chemical class of new and potent SIRT1 activators as potential cardioprotective agents. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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10 pages, 1608 KiB

Open AccessCommunication

Investigation on the Peroxidase-like Activity of Vitamin B6 and Its Applications in Colorimetric Detection of Hydrogen Peroxide and Total Antioxidant Capacity Evaluation

by Chun-Yan Zhang, Li-Jing Peng, Guo-Ying Chen, Hao Zhang and Feng-Qing Yang

Molecules 2022, 27(13), 4262; https://doi.org/10.3390/molecules27134262 - 1 Jul 2022

Cited by 5 | Viewed by 2757

Abstract

The peroxidase-like activity of vitamin B6 (VB6) was firstly demonstrated by catalyzing the peroxidase chromogenic substrate 3,3′,5,5′-tetramethylbenzidine (TMB) at the existence of H₂O₂. The influence of different factors on the catalytic property of VB6, including pH, temperature, VB6 concentration, and incubation time, were investigated. The steady-state kinetic study results indicate that VB6 possesses higher affinity to H₂O₂ than natural horseradish peroxidase and some other peroxidase mimics. Besides, the radical quenching experiment results confirm that hydroxyl radical (•OH) accounts for the catalytic process. Based on the excellent peroxidase-like catalytic activity of VB6, the colorimetric methods for H₂O₂ and gallic acid (GA) detection were developed by measuring the absorbance variance of the catalytic system. Under the optimal conditions, the linear ranges of the methods for H₂O₂ and GA determination with good selectivity are 50.0–600.0 μM and 10.0–50.0 μM, respectively. In addition, the developed method was applied in the detection of H₂O₂ in milk samples and evaluation of total antioxidant capacity of different tea infusions. This study may broaden the application prospect of VB6 in environmental and biomedical analysis fields, contribute to profound insight of the physiological functions of VB6, as well as lay foundation for further excavation of small-molecule peroxidase mimics. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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Review

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26 pages, 2847 KiB

Open AccessReview

Peripheralization Strategies Applied to Morphinans and Implications for Improved Treatment of Pain

by Helmut Schmidhammer, Mahmoud Al-Khrasani, Susanna Fürst and Mariana Spetea

Molecules 2023, 28(12), 4761; https://doi.org/10.3390/molecules28124761 - 14 Jun 2023

Cited by 3 | Viewed by 1982

Abstract

Opioids are considered the most effective analgesics for the treatment of moderate to severe acute and chronic pain. However, the inadequate benefit/risk ratio of currently available opioids, together with the current ‘opioid crisis’, warrant consideration on new opioid analgesic discovery strategies. Targeting peripheral opioid receptors as effective means of treating pain and avoiding the centrally mediated side effects represents a research area of substantial and continuous attention. Among clinically used analgesics, opioids from the class of morphinans (i.e., morphine and structurally related analogues) are of utmost clinical importance as analgesic drugs activating the mu-opioid receptor. In this review, we focus on peripheralization strategies applied to N-methylmorphinans to limit their ability to cross the blood–brain barrier, thus minimizing central exposure and the associated undesired side effects. Chemical modifications to the morphinan scaffold to increase hydrophilicity of known and new opioids, and nanocarrier-based approaches to selectively deliver opioids, such as morphine, to the peripheral tissue are discussed. The preclinical and clinical research activities have allowed for the characterization of a variety of compounds that show low central nervous system penetration, and therefore an improved side effect profile, yet maintaining the desired opioid-related antinociceptive activity. Such peripheral opioid analgesics may represent alternatives to presently available drugs for an efficient and safer pain therapy. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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Other

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9 pages, 1239 KiB

Open AccessBrief Report

Repurposing the Antiplatelet Agent Ticlopidine to Counteract the Acute Phase of ER Stress Condition: An Opportunity for Fighting Coronavirus Infections and Cancer

by Anna Tesei, Michela Cortesi, Martina Bedeschi, Noemi Marino, Giacomo Rossino, Roberta Listro, Daniela Rossi, Pasquale Linciano and Simona Collina

Molecules 2022, 27(14), 4327; https://doi.org/10.3390/molecules27144327 - 6 Jul 2022

Cited by 3 | Viewed by 2296

Abstract

Different pathological conditions, including viral infections and cancer, can have a massive impact on the endoplasmic reticulum (ER), causing severe damage to the cell and exacerbating the disease. In particular, coronavirus infections, including SARS coronavirus-2 (SARS-CoV-2), responsible for COVID-19, cause ER stress as a consequence of the enormous amounts of viral glycoproteins synthesized, the perturbation of ER homeostasis and the modification of ER membranes. Therefore, ER has a central role in the viral life cycle, thus representing one of the Achilles’ heels on which to focus therapeutic intervention. On the other hand, prolonged ER stress has been demonstrated to promote many pro-tumoral attributes in cancer cells, having a key role in tumor growth, metastasis and response to therapies. In this report, adopting a repurposing approach of approved drugs, we identified the antiplatelet agent ticlopidine as an interferent of the unfolded protein response (UPR) via sigma receptors (SRs) modulation. The promising results obtained suggest the potential use of ticlopidine to counteract ER stress induced by viral infections, such as COVID-19, and cancer. Full article

(This article belongs to the Special Issue Exclusive Papers from the Editorial Board Members (EBMs) of the Section “Medicinal Chemistry” of Molecules)

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