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New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (15 December 2019) | Viewed by 41578

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Special Issue Editors

Dr. Martin Krátký

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Guest Editor

Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
Interests: antimicrobials; antimycobacterials; enzyme inhibitors; peptide carriers; prodrugs
Special Issues, Collections and Topics in MDPI journals

Dr. Jan Zitko

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Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
Interests: antimicrobial; antimycobacterial; heterocyclic chemistry; structure-based drug design; computer-aided drug design
Special Issues, Collections and Topics in MDPI journals

Dr. Radim Nencka

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Guest Editor

Institute of Organic Chemistry and Biochemistry of the CAS, Czech Republic
Interests: antiviral; computer-aided drug design; kinase inhibitors; medicinal chemistry

Special Issue Information

Dear Colleagues,

The 11^th Joint Meeting on Medicinal Chemistry 2019 (JMMC 2019) (https://www.jmmc2019.cz/) will take place in Prague, Czech Republic, on June 27–30, 2019. This year 2019 marks 20 years of history of this traditional Joint Meetings, founded in 1999 by Prof. G. Ronsivalle (Italy) together with Prof. A. Lipkowski (Poland) and Prof. G. Toth (Hungary). The main aim of the Joint Meetings is to promote Medicinal Chemistry, attract young scientists, and foster relationships between medicinal chemists of the participating countries. The success of last 10^th JMMC 2017 (249 participants from 28 countries) illustrates the importance of this kind of meetings. We are pleased to invite medicinal chemists from all over the world to come, stimulate discussion on drug discovery and development, and promote collaboration between medicinal chemistry scientists, both young and experienced.

The JMMC 2019 participants are cordially invited to contribute original research papers or reviews to this Special Issue of Biomolecules. We welcome submissions of previously unpublished original work within the broad scope of medicinal chemistry.

Assoc. Prof. Martin Krátký
Dr. Jan Zitko
Dr. Radim Nencka
Guest Editors

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. Biomolecules 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 2700 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

biological activity
computer-aided drug design
drug design and development
medicinal chemistry
screening

Published Papers (10 papers)

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Research

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20 pages, 6068 KiB

Open AccessArticle

Metallacarborane Complex Boosts the Rate of DNA Oligonucleotide Hydrolysis in the Reaction Catalyzed by Snake Venom Phosphodiesterase

by Damian Kaniowski, Katarzyna Kulik, Katarzyna Ebenryter-Olbińska, Ewelina Wielgus, Zbigniew Lesnikowski and Barbara Nawrot

Biomolecules 2020, 10(5), 718; https://doi.org/10.3390/biom10050718 - 05 May 2020

Cited by 12 | Viewed by 3122

Abstract

Antisense oligonucleotides conjugated with boron clusters (B-ASOs) have been described as potential gene expression inhibitors and carriers of boron for boron neutron capture therapy (BNCT), providing a dual-action therapeutic platform. In this study, we tested the nucleolytic stability of DNA oligonucleotides labeled with metallacarborane [(3,3’-iron-1,2,1’,2’-dicarbollide)(−1)]ate [Fe(C₂B₉H₁₁)₂] (FESAN) against snake venom phosphodiesterase (svPDE, 3’→5’-exonuclease). Contrary to the previously observed protective effect of carborane (C₂B₁₀H₁₂) modifications, the B-ASOs containing a metallacarborane moiety at the 5’-end of the oligonucleotide chain were hydrolyzed faster than their parent nonmodified oligomers. Interestingly, an enhancement in the hydrolysis rate was also observed in the presence of free metallacarborane, and this reaction was dependent on the concentration of the metallacarborane. Microscale thermophoresis (MST) analysis confirmed the high affinity (K_d nM range) of the binding of the metallacarborane to the proteins of crude snake venom and the moderate affinity (K_d µM range) between the metallacarborane and the short single-stranded DNA. We hypothesize that the metallacarborane complex covalently bound to B-ASO holds DNA molecules close to the protein surface, facilitating enzymatic cleavage. The addition of metallacarborane alone to the ASO/svPDE reaction mixture provides the interface to attract freely floating DNA molecules. In both cases, the local DNA concentration around the enzymes increases, giving rise to faster hydrolysis. It was experimentally shown that an allosteric effect, possibly attributable to the observed boost in the 3’→5’-exonucleolytic activity of snake venom phosphodiesterase, is much less plausible. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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19 pages, 3356 KiB

Open AccessArticle

N-(2-Hydroxyphenyl)-1-[3-(2-oxo-2,3-dihydro-1H- benzimidazol-1-yl)propyl]piperidine-4-Carboxamide (D2AAK4), a Multi-Target Ligand of Aminergic GPCRs, as a Potential Antipsychotic

by Agnieszka A. Kaczor, Katarzyna M. Targowska-Duda, Andrea G. Silva, Magda Kondej, Grażyna Biała and Marián Castro

Biomolecules 2020, 10(2), 349; https://doi.org/10.3390/biom10020349 - 24 Feb 2020

Cited by 13 | Viewed by 2912

Abstract

N-(2-hydroxyphenyl)-1-[3-(2-oxo-2,3-dihydro-1H-benzimidazol -1-yl)propyl]piperidine-4-carboxamide (D2AAK4) is a multitarget ligand of aminergic G protein-coupled receptors (GPCRs) identified in structure-based virtual screening. Here we present detailed in vitro, in silico and in vivo investigations of this virtual hit. D2AAK4 has an atypical antipsychotic profile and low affinity to off-targets. It interacts with aminergic GPCRs, forming an electrostatic interaction between its protonatable nitrogen atom and the conserved Asp 3.32 of the receptors. At the dose of 100 mg/kg D2AAK4 decreases amphetamine-induced hyperactivity predictive of antipsychotic activity, improves memory consolidation in passive avoidance test and has anxiogenic properties in elevated plus maze test (EPM). Further optimization of the virtual hit D2AAK4 will be aimed to balance its multitarget profile and to obtain analogs with anxiolytic activity. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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13 pages, 4260 KiB

Open AccessArticle

2,4-Dichlorophenoxyacetic Thiosemicarbazides as a New Class of Compounds against Stomach Cancer Potentially Intercalating with DNA

by Monika Pitucha, Agnieszka Korga-Plewko, Pawel Kozyra, Magdalena Iwan and Agnieszka A. Kaczor

Biomolecules 2020, 10(2), 296; https://doi.org/10.3390/biom10020296 - 13 Feb 2020

Cited by 14 | Viewed by 3297

Abstract

Thiosemicarbazide is a useful structural moiety that has the biological potential. Optimization of this structure can result in groundbreaking discovery of a new class of therapeutic agents. In the light of this, 1-(2,4-dichlorophenoxy)acetyl-4-(1-naphthyl)thiosemicarbazide (1) and 1,4-bis[(2,4-dichlorophenoxy)acetylthiosemicarbazide]phenyl (2) were synthesized and characterized by spectroscopic method. Cytotoxicity of obtained compounds was evaluated on MKN74 gastric cancer cell line and human skin fibroblast BJ based on methylthiazolyldiphenyl-tetrazolium bromide (MTT) test. The apoptosis/necrosis and cell cycle analysis were conducted using image cytometry. Additionally, in DNA of treated cells, abasic sites (AP) and double strands breaks (DSB) presence were measured. Intercalating properties of active compounds were evaluated using the UV–spectroscopic method. Among newly synthesized derivatives, compound 2 showed toxic effects on gastric cancer cells with simultaneous lack of toxicity to normal fibroblasts. Cell cycle analysis revealed that both compounds influence cell division mainly at the stage of replication. Simultaneously with DNA synthesis disorders, DNA damages like AP-sites and DSBs were observed. Spectroscopic studies revealed possible DNA intercalating properties of tested compounds. Obtained results indicate that the newly synthesized thiosemicarbazide derivatives are a promising group of compounds with potential anticancer activity resulted from interactions with DNA and cell cycle interrupt. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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17 pages, 9336 KiB

Open AccessArticle

Structural Changes of Sarco/Endoplasmic Reticulum Ca²⁺-ATPase Induced by Rutin Arachidonate: A Molecular Dynamics Study

by Yoel Rodríguez and Magdaléna Májeková

Biomolecules 2020, 10(2), 214; https://doi.org/10.3390/biom10020214 - 01 Feb 2020

Cited by 6 | Viewed by 3187

Abstract

Sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) maintains the level of calcium concentration in cells by pumping calcium ions from the cytoplasm to the lumen while undergoing substantial conformational changes, which can be stabilized or prevented by various compounds. Here we attempted to clarify the molecular mechanism of action of new inhibitor rutin arachidonate, one of the series of the acylated rutin derivatives. We performed molecular dynamics simulations of SERCA1a protein bound to rutin arachidonate positioned in a pure dipalmitoylphosphatidylcholine bilayer membrane. Our study predicted the molecular basis for the binding of rutin arachidonate towards SERCA1a in the vicinity of the binding site of calcium ions and near the location of the well-known inhibitor thapsigargin. The stable hydrogen bond between Glu771 and rutin arachidonate plays a key role in the binding. SERCA1a is kept in the E2 conformation preventing the formation of important salt bridges between the side chains of several residues, primarily Glu90 and Lys297. All in all, the structural changes induced by the binding of rutin arachidonate to SERCA1a may shift proton balance near the titrable residues Glu771 and Glu309 into neutral species, hence preventing the binding of calcium ions to the transmembrane binding sites and thus affecting calcium homeostasis. Our results could lead towards the design of new types of inhibitors, potential drug candidates for cancer treatment, which could be anchored to the transmembrane region of SERCA1a by a lipophilic fatty acid group. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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20 pages, 972 KiB

Open AccessArticle

4-Aminobenzoic Acid Derivatives: Converting Folate Precursor to Antimicrobial and Cytotoxic Agents

by Martin Krátký, Klára Konečná, Jiří Janoušek, Michaela Brablíková, Ondřej Janďourek, František Trejtnar, Jiřina Stolaříková and Jarmila Vinšová

Biomolecules 2020, 10(1), 9; https://doi.org/10.3390/biom10010009 - 19 Dec 2019

Cited by 45 | Viewed by 10185

Abstract

4-aminobenzoic acid (PABA), an essential nutrient for many human pathogens, but dispensable for humans, and its derivatives have exhibited various biological activities. In this study, we combined two pharmacophores using a molecular hybridization approach: this vitamin-like molecule and various aromatic aldehydes, including salicylaldehydes and 5-nitrofurfural, via imine bond in one-step reaction. Resulting Schiff bases were screened as potential antimicrobial and cytotoxic agents. The simple chemical modification of non-toxic PABA resulted in constitution of antibacterial activity including inhibition of methicillin-resistant Staphylococcus aureus (minimum inhibitory concentrations, MIC, from 15.62 µM), moderate antimycobacterial activity (MIC ≥ 62.5 µM) and potent broad-spectrum antifungal properties (MIC of ≥ 7.81 µM). Some of the Schiff bases also exhibited notable cytotoxicity for cancer HepG2 cell line (IC₅₀ ≥ 15.0 µM). Regarding aldehyde used for the derivatization of PABA, it is possible to tune up the particular activities and obtain derivatives with promising bioactivities. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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16 pages, 1958 KiB

Open AccessCommunication

2-Hydroxy-N-phenylbenzamides and Their Esters Inhibit Acetylcholinesterase and Butyrylcholinesterase

by Martin Krátký, Šárka Štěpánková, Neto-Honorius Houngbedji, Rudolf Vosátka, Katarína Vorčáková and Jarmila Vinšová

Biomolecules 2019, 9(11), 698; https://doi.org/10.3390/biom9110698 - 05 Nov 2019

Cited by 14 | Viewed by 2848

Abstract

The development of novel inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) represents a viable approach to alleviate Alzheimer’s disease. Thirty-six halogenated 2-hydroxy-N-phenylbenzamides (salicylanilides) with various substitution patterns and their esters with phosphorus-based acids were synthesized in yields of 72% to 92% and characterized. They were evaluated for in vitro inhibition of AChE from electric eel and BuChE from equine serum using modified Ellman’s spectrophotometric method. The benzamides exhibited a moderate inhibition of AChE with IC₅₀ values in a narrow concentration range from 33.1 to 85.8 µM. IC₅₀ values for BuChE were higher (53.5–228.4 µM). The majority of derivatives inhibit AChE more efficiently than BuChE and are comparable or superior to rivastigmine—an established cholinesterases inhibitor used in the treatment of Alzheimer’s disease. Phosphorus-based esters especially improved the activity against BuChE with 5-chloro-2-{[4-(trifluoromethyl)phenyl]carbamoyl}phenyl diethyl phosphite 5c superiority (IC₅₀ = 2.4 µM). This derivative was also the most selective inhibitor of BuChE. It caused a mixed inhibition of both cholinesterases and acted as a pseudo-irreversible inhibitor. Several structure-activity relationships were identified, e.g., favouring esters and benzamides obtained from 5-halogenosalicylic acids and polyhalogenated anilines. Both 2-hydroxy-N-phenylbenzamides and esters share convenient physicochemical properties for blood-brain-barrier penetration and thus central nervous system delivery. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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22 pages, 4375 KiB

Open AccessArticle

Synthesis of β-d-galactopyranoside-Presenting Glycoclusters, Investigation of Their Interactions with Pseudomonas aeruginosa Lectin A (PA-IL) and Evaluation of Their Anti-Adhesion Potential

by Lenka Malinovská, Son Thai Le, Mihály Herczeg, Michaela Vašková, Josef Houser, Eva Fujdiarová, Jan Komárek, Petr Hodek, Anikó Borbás, Michaela Wimmerová and Magdolna Csávás

Biomolecules 2019, 9(11), 686; https://doi.org/10.3390/biom9110686 - 01 Nov 2019

Cited by 9 | Viewed by 3030

Abstract

Pseudomonas aeruginosa is an opportunistic human pathogen associated with cystic fibrosis. This bacterium produces, among other virulence factors, a soluble d-galactose-specific lectin PA-IL (LecA). PA-IL plays an important role in the adhesion to the host cells and is also cytotoxic. Therefore, this protein is an interesting therapeutic target, suitable for inhibition by carbohydrate-based compounds. In the current study, β-d-galactopyranoside-containing tri- and tetravalent glycoclusters were synthesized. Methyl gallate and pentaerythritol equipped with propargyl groups were chosen as multivalent scaffolds and the galactoclusters were built from the above-mentioned cores by coupling ethylene or tetraethylene glycol-bridges and peracetylated propargyl β-d-galactosides using 1,3-dipolar azide-alkyne cycloaddition. The interaction between galactoside derivatives and PA-IL was investigated by several biophysical methods, including hemagglutination inhibition assay, isothermal titration calorimetry, analytical ultracentrifugation, and surface plasmon resonance. Their ability to inhibit the adhesion of P. aeruginosa to bronchial cells was determined by ex vivo assay. The newly synthesized multivalent galactoclusters proved to be significantly better ligands than simple d-galactose for lectin PA-IL and as a result, two representatives of the dendrimers were able to decrease adhesion of P. aeruginosa to bronchial cells to approximately 32% and 42%, respectively. The results may provide an opportunity to develop anti-adhesion therapy for the treatment of P. aeruginosa infection. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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20 pages, 3013 KiB

Open AccessArticle

Discovery of Orexant and Anorexant Agents with Indazole Scaffold Endowed with Peripheral Antiedema Activity

by Marilisa P. Dimmito, Azzurra Stefanucci, Stefano Pieretti, Paola Minosi, Szabolcs Dvorácskó, Csaba Tömböly, Gokhan Zengin and Adriano Mollica

Biomolecules 2019, 9(9), 492; https://doi.org/10.3390/biom9090492 - 16 Sep 2019

Cited by 19 | Viewed by 3360

Abstract

The endocannabinoid system represents an integrated neuronal network involved in the control of several organisms’ functions, such as feeding behavior. A series of hybrids of 5-(4-chlorophenyl)-1-(2,4-dichloro-phenyl)-4-methyl-N-(piperidin-1-yl)-1H-pyrazole-3-carboxamide (mimonabant), a well-known inverse agonist of the type-1 cannabinoid receptor (CB1), once used as an antiobesity drug, and the N-(2S)-substitutes of 1-[(4-fluorophenyl)methyl]indazole-3-carboxamide with 1-amino-3-methyl-1-oxobutane (AB-Fubinaca), 1-amino-3,3-dimethyl-1-oxobutane (ADB-Fubinaca), and 3-methylbutanoate (AMB-Fubinaca), endowed with potent agonistic activity towards cannabinoid receptors CB1 and CB2 were in solution as C-terminal amides, acids, methyl esters and N-methyl amides. These compounds have been studied by binding assays to cannabinoid receptors and by functional receptor assays, using rat brain membranes in vitro. The most active among them as an agonist, (S)-1-(2,4-dichlorobenzyl)-N-(3,3-dimethyl-1-(methylamino)-1-oxobutan-2-yl)-1H-indazole-3-carboxamide (LONI11), and an antagonist, (S)-2-(1-(2,4-dichlorobenzyl)-1H-indazole-3-carboxamido)-3-methylbutanoic acid (LONI4), were tested in vivo in mic, to evaluate their ability to stimulate or suppress feeding behavior after intraperitoneal (i.p.) administration. For a LONI11 formalin test and a tail flick test after an administration by the subcutaneous (s.c.) and intracerebroventricular (i.c.v.) routes, respectively, were also carried out in vivo in mice to investigate the antinociceptive property at the central and peripheral levesl. We observed a significant orexant effect for LONI11 and an intense anorexant effect for (S)-methyl 2-(1-(2,4-dichlorobenzyl)-1H-indazole-3-carboxamido)-3,3-dimethylbutanoate (LONI2) and LONI4. In zymosan-induced edema and hyperalgesia, LONI11 reduced the percent of paw volume increase and paw latency after s.c. administration, also suggesting a possible peripheral anti-inflammatory activity. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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29 pages, 7079 KiB

Open AccessArticle

New Thalidomide-Resembling Dicarboximides Target ABC50 Protein and Show Antileukemic and Immunomodulatory Activities

by Marcin Cieślak, Julia Kaźmierczak-Barańska, Karolina Królewska-Golińska, Mariola Napiórkowska, Iga Stukan, Urszula Wojda and Barbara Nawrot

Biomolecules 2019, 9(9), 446; https://doi.org/10.3390/biom9090446 - 04 Sep 2019

Cited by 10 | Viewed by 3993

Abstract

We identified novel dicarboximides that were selectively cytotoxic towards human leukemia cells. Using chemical and biological methods, we characterized the biological activity, identified cellular protein targets and defined the mechanism of action of the test dicarboximides. The reported IC₅₀ values (concentration required to reduce cell survival fraction to 50% of control) of selected dicarboximides were similar or lower than IC₅₀ of registered anticancer drugs, for example cytarabine, sorafenib, irinotecan. Test compounds induced apoptosis in chronic myelogenous (K562) and acute lymphoblastic (MOLT-4) leukemia cells by activation of receptor and mitochondrial apoptotic pathways and increased the expression of proapoptotic genes (BAX, NOXA, HTRA2, TNFRSF10B, ESRRBL1). Selected dicarboximides displayed immunomodulatory activity and downregulated IKZF1 and IKZF3 transcription factors in K562 and MOLT-4 leukemia cells. ATP-binding cassette protein 50 (ABC50) was identified as a target for dicarboximides. Cancer cells with knocked down ABC50 showed increased resistance to dicarboximides. Based on the structure of dicarboximides and thalidomide, novel proteolysis-targeting chimeras (PROTACs) were synthesized and used as tools to downregulate ABC50 in leukemia cells. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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Review

Jump to: Research

23 pages, 4762 KiB

Open AccessReview

Organometallic Compounds and Metal Complexes in Current and Future Treatments of Inflammatory Bowel Disease and Colorectal Cancer—a Critical Review

by Adrian Szczepaniak and Jakub Fichna

Biomolecules 2019, 9(9), 398; https://doi.org/10.3390/biom9090398 - 22 Aug 2019

Cited by 13 | Viewed by 4859

Abstract

In recent years, there has been a significant increase in the clinical use of organometallic compounds and metal complexes for therapeutic purposes including treatment of inflammatory bowel diseases (IBD). Their action is based on the inhibition of the inflow of pro-inflammatory cytokines, the elimination of free radicals or the modulation of intestinal microbiota. In addition, these compounds are intended for use in the diagnosis and treatment of colorectal cancer (CRC) which is often a consequence of IBD. The aim of this study is to critically discuss recent findings on the use of organometallic compounds and metal complexes in the treatment of IBD and CRC and suggest future trends in drug design. Full article

(This article belongs to the Special Issue New Molecules: Towards the Drugs of the Future - Selected Papers from JMMC 2019)

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