1
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Thorpe MP, Smith AN, Blackwell DJ, Hopkins CR, Knollmann BC, Akers WS, Johnston JN. The backbone constitution drives passive permeability independent of side chains in depsipeptide and peptide macrocycles inspired by ent-verticilide. Chem Sci 2024:d4sc02758b. [PMID: 39211739 PMCID: PMC11348715 DOI: 10.1039/d4sc02758b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
The number of peptide-like scaffolds found in late-stage drug development is increasing, but a critical unanswered question in the field is whether substituents (side chains) or the backbone drive passive permeability. The backbone is scrutinized in this study. Five series of macrocyclic peptidic compounds were prepared, and their passive permeability was determined (PAMPA, Caco-2), to delineate structure-permeability relationships. Each series was based on the cell-permeable antiarrhythmic compound ent-verticilide, a cyclic oligomeric depsipeptide (COD) containing repeating ester/N-Me amide didepsipeptide monomers. One key finding is that native lipophilic ester functionality can impart a favorable level of permeability, but ester content alone is not the final determinant - the analog with highest P app was discovered by a single ester-to-N-H amide replacement. Furthermore, the relative composition of esters and N-Me amides in a series had more nuanced permeability behavior. Overall, a systematic approach to structure-permeability correlations suggests that a combinatorial-like investigation of functionality in peptidic or peptide-like compounds could better identify leads with optimal passive permeability, perhaps prior to modification of side chains.
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Affiliation(s)
- Madelaine P Thorpe
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Abigail N Smith
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Corey R Hopkins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Bjorn C Knollmann
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Wendell S Akers
- Pharmaceutical Sciences Research Center, College of Pharmacy, Lipscomb University Nashville TN 37204 USA
| | - Jeffrey N Johnston
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
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2
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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3
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Ly HM, Desgagné M, Nguyen DT, Comeau C, Froehlich U, Marsault É, Boudreault PL. Insights on Structure-Passive Permeability Relationship in Pyrrole and Furan-Containing Macrocycles. J Med Chem 2024; 67:3711-3726. [PMID: 38417040 PMCID: PMC10946398 DOI: 10.1021/acs.jmedchem.3c02162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 03/01/2024]
Abstract
Macrocycles have recognized therapeutic potential, but their limited cellular permeability can hinder their development as oral drugs. To better understand the structure-permeability relationship of heterocycle-containing, semipeptidic macrocycles, a library was synthesized. These compounds were created by developing two novel reactions described herein: the reduction of activated oximes by LiBH4 and the aqueous reductive mono-N-alkylation of aldehydes using catalytic SmI2 and stoichiometric Zn. The permeability of the macrocycles was evaluated through a parallel artificial membrane permeability assay (PAMPA), and the results indicated that macrocycles with a furan incorporated into the structure have better passive permeability than those with a pyrrole moiety. Compounds bearing a 2,5-disubstituted pyrrole (endo orientation) were shown to be implicated in intramolecular H-bonds, enhancing their permeability. This study highlighted the impact of heterocycles moieties in semipeptides, creating highly permeable macrocycles, thus showing promising avenues for passive diffusion of drugs beyond the rule-of-five chemical space.
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Affiliation(s)
- Huy M Ly
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Michael Desgagné
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Duc Tai Nguyen
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Ulrike Froehlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
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4
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Tang X, Kokot J, Waibl F, Fernández-Quintero ML, Kamenik AS, Liedl KR. Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J Chem Inf Model 2023; 63:7107-7123. [PMID: 37943023 PMCID: PMC10685455 DOI: 10.1021/acs.jcim.3c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
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Affiliation(s)
- Xuechen Tang
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, 8093 Zürich, Switzerland
| | | | - Anna S. Kamenik
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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5
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L'Exact M, Comeau C, Bourhis A, Boisvert O, Fröhlich U, Létourneau D, Marsault É, Lavigne P, Grandbois M, Boudreault PL. Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184196. [PMID: 37400050 DOI: 10.1016/j.bbamem.2023.184196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.
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Affiliation(s)
- Marion L'Exact
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christian Comeau
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alix Bourhis
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olivier Boisvert
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Ulrike Fröhlich
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Danny Létourneau
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Éric Marsault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lavigne
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michel Grandbois
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Luc Boudreault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
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6
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Ferraro G, Voli A, Mozzicafreddo M, Pollastro F, Tosco A, Monti MC. Targeting phosphoglycerate kinases by tatridin A, a natural sesquiterpenoid endowed with anti-cancer activity, using a proteomic platform. Front Mol Biosci 2023; 10:1212541. [PMID: 37767160 PMCID: PMC10519794 DOI: 10.3389/fmolb.2023.1212541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/10/2023] [Indexed: 09/29/2023] Open
Abstract
Tatridin A (TatA) is a germacrane sesquiterpenoid containing one E-double bond and one Z-double bond in its 10-membered ring, which is fused to a 3-methylene-dihydrofuran-2-one moiety. Tatridin A bioactivity has been poorly investigated despite its interesting chemical structure. Here, a functional proteomic platform was adapted to disclose its most reliable targets in leukemia monocytic cells, and phosphoglycerate kinases were recognized as the most affine enzymes. Through a combination of limited proteolysis and molecular docking, it has been discovered that tatridin A interacts with the active domains of phosphoglycerate kinase 1, altering its hinge region, and it can be accountable for tatridin A inhibition potency on enzyme activity. A more detailed tatridin A biological profile showed that it is also fully active against gastric cancer cells, downregulating the mRNA levels of chemokine receptor 4 and β-catenin and inhibiting the invasiveness of living KATO III cells as a direct consequence of phosphoglycerate kinase 1 antagonism.
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Affiliation(s)
- Giusy Ferraro
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | - Antonia Voli
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Ancona, Italy
| | - Federica Pollastro
- Department of Pharmaceutical Sciences, Università Del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
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7
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Garcia Jimenez D, Vallaro M, Rossi Sebastiano M, Apprato G, D’Agostini G, Rossetti P, Ermondi G, Caron G. Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs. J Med Chem 2023; 66:10681-10693. [PMID: 37490408 PMCID: PMC10424176 DOI: 10.1021/acs.jmedchem.3c00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 07/27/2023]
Abstract
New chemical modalities in drug discovery include molecules belonging to the bRo5 chemical space. Because of their complex and flexible structure, bRo5 compounds often suffer from a poor solubility/permeability profile. Chameleonicity describes the capacity of a molecule to adapt to the environment through conformational changes; the design of molecular chameleons is a medicinal chemistry strategy simultaneously optimizing solubility and permeability. A default method to quantify chameleonicity in early drug discovery is still missing. Here we introduce Chamelogk, an automated, fast, and cheap chromatographic descriptor of chameleonicity. Moreover, we report measurements for 55 Ro5 and bRo5 compounds and validate our method with literature data. Then, selected case studies (macrocycles, nonmacrocyclic compounds, and PROTACs) are used to illustrate the application of Chamelogk in combination with lipophilicity (BRlogD) and polarity (Δ log kwIAM) descriptors. Overall, we show how Chamelogk deserves being included in property-based drug discovery strategies to design oral bioavailable bRo5 compounds.
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Affiliation(s)
- Diego Garcia Jimenez
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Apprato
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia D’Agostini
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Paolo Rossetti
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
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8
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Moxam J, Naylon S, Richaud AD, Zhao G, Padilla A, Roche SP. Passive Membrane Permeability of Sizable Acyclic β-Hairpin Peptides. ACS Med Chem Lett 2023; 14:278-284. [PMID: 36923919 PMCID: PMC10009788 DOI: 10.1021/acsmedchemlett.2c00486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The recent shift toward increasingly larger drug modalities has created a significant demand for novel classes of compounds with high membrane permeability that can inhibit intracellular protein-protein interactions (PPIs). While major advances have been made in the design of cell-permeable helices, stapled β-sheets, and cyclic peptides, the development of large acyclic β-hairpins lags far behind. Therefore, we investigated a series of 26 β-hairpins (MW > 1.6 kDa) belonging to a chemical space far beyond the Lipinski "rule of five" (fbRo5) and showed that, in addition to their innate plasticity, the lipophilicity of these peptides (log D 7.4 ≈ 0 ± 0.7) can be tuned to drastically improve the balance between aqueous solubility and passive membrane permeability.
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Affiliation(s)
- Jillene Moxam
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Sarah Naylon
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alexis D. Richaud
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alberto Padilla
- Department
of Natural Science, Keiser University, Fort Lauderdale, Florida 33309, United States
| | - Stéphane P. Roche
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
- Center
for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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9
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Colarusso E, Ceccacci S, Monti MC, Gazzillo E, Giordano A, Chini MG, Ferraro MG, Piccolo M, Ruggiero D, Irace C, Terracciano S, Bruno I, Bifulco G, Lauro G. Identification of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based small molecules as selective BRD9 binders. Eur J Med Chem 2023; 247:115018. [PMID: 36577218 DOI: 10.1016/j.ejmech.2022.115018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Targeting bromodomain-containing protein 9 (BRD9) represents a promising strategy for the development of new agents endowed with anticancer properties. With this aim, a set of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based compounds was investigated following a combined approach that relied on in silico studies, chemical synthesis, biophysical and biological evaluation of the most promising items. The protocol was initially based on molecular docking experiments, accounting a library of 1896 potentially synthesizable items tested in silico against the bromodomain of BRD9. A first set of 21 compounds (1-21) was selected and the binding on BDR9 was assessed through AlphaScreen assays. The obtained results disclosed compounds 17 and 20 able to bind BRD9 in the submicromolar range (IC50 = 0.35 ± 0.18 μM and IC50 = 0.14 ± 0.03 μM, respectively) showing a promising selectivity profile when tested against further nine bromodomains. Taking advantage of 3D structure-based pharmacophore models, additional 10 derivatives were selected in silico for the synthetic step and binding assessment, highlighting seven compounds (22, 23, 25, 26, 28, 29, 31) able to selectively bind BRD9 among different bromodomains. The ability of the identified BRD9 binders to cross artificial membranes in vitro was also assessed, revealing a very good passive permeability profile. Preliminary studies were carried out on a panel of healthy and cancer human cell lines to explore the biological behavior of the selected compounds, disclosing a moderate activity and significant selectivity profile towards leukaemia cells. These results highlighted the applicability of the reported multidisciplinary approach for accelerating the selection of promising items and for driving the chemical synthesis of novel selective BRD9 binders. Moreover, the low molecular weight of the reported 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based BRD9 binders suggests the possibility for further exploring the chemical space in order to obtain new analogues with improved potency.
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Affiliation(s)
- Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Sara Ceccacci
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale Delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Dafne Ruggiero
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy.
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10
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Cox B, Nicolaï J, Williamson B. The role of the efflux transporter, P-glycoprotein, at the blood-brain barrier in drug discovery. Biopharm Drug Dispos 2023; 44:113-126. [PMID: 36198662 DOI: 10.1002/bdd.2331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/08/2022]
Abstract
The blood-brain barrier (BBB) expresses a high abundance of transporters, particularly P-glycoprotein (P-gp), that regulate endogenous and exogenous molecule uptake and removal of waste. This review discusses key drug metabolism and pharmacokinetic considerations for the efflux transporter P-gp at the BBB in drug discovery and development. We highlight the differences in P-gp expression and protein levels across species but the limited observations of species-specific substrates. Given the impact of age and disease on BBB biology, we summarise the modulation of P-gp for several neurological disorders and ageing and exemplify several disease-specific hurdles or opportunities for drug exposure in the brain. Furthermore, the review includes observations of CNS-related drug-drug interactions due to the inhibition or induction of P-gp at the BBB in animal studies and humans and the need for continued evaluation especially for compounds with a narrow therapeutic window. This review focusses primarily on small molecules but also considers the impact of new chemical entities, particularly beyond Ro5 molecules and their potential to be recognised as P-gp substrates as well as advanced drug delivery systems which offer an alternative approach to achieve and sustain central nervous system exposure.
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Affiliation(s)
- Benoit Cox
- DMPK, Development Sciences, UCB Biopharma, Braine-l'Alleud, Belgium
| | - Johan Nicolaï
- DMPK, Janssen Pharmaceutical Companies of Johnson & Johnson, Janssen Research & Development, Beerse, Belgium
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11
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Nature-Derived Compounds as Potential Bioactive Leads against CDK9-Induced Cancer: Computational and Network Pharmacology Approaches. Processes (Basel) 2022. [DOI: 10.3390/pr10122512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Given the importance of cyclin-dependent kinases (CDKs) in the maintenance of cell development, gene transcription, and other essential biological operations, CDK blockers have been generated to manage a variety of disorders resulting from CDK irregularities. Furthermore, CDK9 has a crucial role in transcription by regulating short-lived anti-apoptotic genes necessary for cancer cell persistence. Addressing CDK9 with blockers has consequently emerged as a promising treatment for cancer. This study scrutinizes the effectiveness of nature-derived compounds (geniposidic acid, quercetin, geniposide, curcumin, and withanolide C) against CDK9 through computational approaches. A molecular docking study was performed after preparing the protein and the ligands. The selected blockers of the CDK9 exerted reliable binding affinities (−8.114 kcal/mol to −13.908 kcal/mol) against the selected protein, resulting in promising candidates compared to the co-crystallized ligand (LCI). The binding affinity of geniposidic acid (−13.908 kcal/mol) to CDK9 is higher than quercetin (−10.775 kcal/mol), geniposide (−9.969 kcal/mol), curcumin (−9.898 kcal/mol), withanolide C (−8.114 kcal/mol), and the co-crystallized ligand LCI (−11.425 kcal/mol). Therefore, geniposidic acid is a promising inhibitor of CDK9. Moreover, the molecular dynamics studies assessed the structure–function relationships and protein–ligand interactions. The network pharmacology study for the selected ligands demonstrated the auspicious compound–target–pathway signaling pathways vital in developing tumor, tumor cell growth, differentiation, and promoting tumor cell progression. Moreover, this study concluded by analyzing the computational approaches the natural-derived compounds that have potential interacting activities against CDK9 and, therefore, can be considered promising candidates for CKD9-induced cancer. To substantiate this study’s outcomes, in vivo research is recommended.
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12
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Ai Y, Sakamuru S, Imler G, Xia M, Xue F. Improving the solubility and antileukemia activity of Wnt/β-catenin signaling inhibitors by disrupting molecular planarity. Bioorg Med Chem 2022; 69:116890. [PMID: 35777269 PMCID: PMC9390976 DOI: 10.1016/j.bmc.2022.116890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Leukemia cells depend on the Wnt/β-catenin signaling pathway for their growth. Pyrvinium, a known Wnt signaling inhibitor, has demonstrated promising efficacy in the treatment of the aggressive blast phase chronic myeloid leukemia (BP-CML). We previously developed potent inhibitors 1-2 for the Wnt/β-catenin signaling pathway. However, the further application of these compounds as anti-leukemia agents is limited by their modest anti-leukemia activity in cells and poor aqueous solubility, due to the high molecular planarity of the chemical scaffold. Here, we reported our efforts in the synthesis and in vitro evaluation of 18 new compounds (4a-r) that have been designed to disrupt the molecular planarity of the chemical scaffold. Several compounds of the series showed significantly improved anti-leukemia activity and aqueous solubility. As a highlight, compounds 4c not only maintained excellent inhibitory potency (IC50 = 1.3 nM) for Wnt signaling but also demonstrated good anti-leukemia potency (IC50 = 0.9 µM) in the CML K562 cells. Moreover, compound 4c had an aqueous solubility of 5.9 µg/mL, which is over 50-fold enhanced compared to its parents 1-2.
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Affiliation(s)
- Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Srilatha Sakamuru
- 9800 Medical Center Drive, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, United States
| | - Greg Imler
- Naval Research Laboratory, Code 6930, 4555 Overlook Avenue, Washington, D.C. 20375, United States
| | - Menghang Xia
- 9800 Medical Center Drive, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States.
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13
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Ferraro G, Belvedere R, Petrella A, Tosco A, Stork B, Salamone S, Minassi A, Pollastro F, Morretta E, Monti MC. Drug affinity-responsive target stability unveils filamins as biological targets for artemetin, an anti-cancer flavonoid. Front Mol Biosci 2022; 9:964295. [PMID: 36090055 PMCID: PMC9452882 DOI: 10.3389/fmolb.2022.964295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Artemetin is a valuable 5-hydroxy-3,6,7,3′,4′-pentamethoxyflavone present in many different medicinal plants with very good oral bioavailability and drug-likeness values, owing to numerous bioactivities, such as anti-inflammatory and anti-cancer ones. Here, a multi-disciplinary plan has been settled and applied for identifying the artemetin target(s) to inspect its mechanism of action, based on drug affinity-responsive target stability and targeted limited proteolysis. Both approaches point to the disclosure of filamins A and B as direct artemetin targets in HeLa cell lysates, also giving detailed insights into the ligand/protein-binding sites. Interestingly, also 8-prenyl-artemetin, which is an artemetin more permeable semisynthetic analog, directly interacts with filamins A and B. Both compounds alter filamin conformation in living HeLa cells with an effect on cytoskeleton disassembly and on the disorganization of the F-actin filaments. Both the natural compound and its derivative are able to block cell migration, expectantly acting on tumor metastasis occurrence and development.
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Affiliation(s)
- Giusy Ferraro
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | | | | | | | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefano Salamone
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Alberto Minassi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Federica Pollastro
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Elva Morretta
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- *Correspondence: Maria Chiara Monti,
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14
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Wang S, König G, Roth HJ, Fouché M, Rodde S, Riniker S. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides. J Med Chem 2021; 64:12761-12773. [PMID: 34406766 DOI: 10.1021/acs.jmedchem.1c00775] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclic peptides have received increasing attention over the recent years as potential therapeutics for "undruggable" targets. One major obstacle is, however, their often relatively poor bioavailability. Here, we investigate the structure-permeability relationship of 24 cyclic decapeptides that share the same backbone N-methylation pattern but differ in their side chains. The peptides cover a large range of values for passive membrane permeability as well as lipophilicity and solubility. To rationalize the observed differences in permeability, we extracted for each peptide the population of the membrane-permeable conformation in water from extensive explicit-solvent molecular dynamics simulations and used this as a metric for conformational rigidity or "prefolding." The insights from the simulations together with lipophilicity measurements highlight the intricate interplay between polarity/lipophilicity and flexibility/rigidity and the possible compensating effects on permeability. The findings allow us to better understand the structure-permeability relationship of cyclic peptides and extract general guiding principles.
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Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gerhard König
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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15
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Seep L, Bonin A, Meier K, Diedam H, Göller AH. Ensemble completeness in conformer sampling: the case of small macrocycles. J Cheminform 2021; 13:55. [PMID: 34325738 PMCID: PMC8320181 DOI: 10.1186/s13321-021-00524-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/05/2021] [Indexed: 11/18/2022] Open
Abstract
In this study we compare the three algorithms for the generation of conformer ensembles Biovia BEST, Schrödinger Prime macrocycle sampling (PMM) and Conformator (CONF) form the University of Hamburg, with ensembles derived for exhaustive molecular dynamics simulations applied to a dataset of 7 small macrocycles in two charge states and three solvents. Ensemble completeness is a prerequisite to allow for the selection of relevant diverse conformers for many applications in computational chemistry. We apply conformation maps using principal component analysis based on ring torsions. Our major finding critical for all applications of conformer ensembles in any computational study is that maps derived from MD with explicit solvent are significantly distinct between macrocycles, charge states and solvents, whereas the maps for post-optimized conformers using implicit solvent models from all generator algorithms are very similar independent of the solvent. We apply three metrics for the quantification of the relative covered ensemble space, namely cluster overlap, variance statistics, and a novel metric, Mahalanobis distance, showing that post-optimized MD ensembles cover a significantly larger conformational space than the generator ensembles, with the ranking PMM > BEST >> CONF. Furthermore, we find that the distributions of 3D polar surface areas are very similar for all macrocycles independent of charge state and solvent, except for the smaller and more strained compound 7, and that there is also no obvious correlation between 3D PSA and intramolecular hydrogen bond count distributions.
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Affiliation(s)
- Lea Seep
- Pharmaceuticals R&D, Digital Technologies, Bayer AG, 42096, Wuppertal, Germany
| | - Anne Bonin
- Pharmaceuticals R&D, Digital Technologies, Bayer AG, 42096, Wuppertal, Germany
| | - Katharina Meier
- Pharmaceuticals R&D, Digital Technologies, Bayer AG, 42096, Wuppertal, Germany
| | - Holger Diedam
- Engineering & Technology, Applied Mathematics, Bayer AG, 51368, Leverkusen, Germany
| | - Andreas H Göller
- Pharmaceuticals R&D, Digital Technologies, Bayer AG, 42096, Wuppertal, Germany.
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16
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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17
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Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool. Mar Drugs 2021; 19:md19060311. [PMID: 34072121 PMCID: PMC8229464 DOI: 10.3390/md19060311] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.
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18
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Sarret P. Éric Marsault (1971-2021): A Legacy through the Prism of Relationship Chemistry. J Med Chem 2021; 64:5221-5224. [PMID: 33760613 DOI: 10.1021/acs.jmedchem.1c00481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Philippe Sarret
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
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19
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Comeau C, Ries B, Stadelmann T, Tremblay J, Poulet S, Fröhlich U, Côté J, Boudreault PL, Derbali RM, Sarret P, Grandbois M, Leclair G, Riniker S, Marsault É. Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties. J Med Chem 2021; 64:5365-5383. [PMID: 33750117 DOI: 10.1021/acs.jmedchem.0c02036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Incorporating small modifications to peptidic macrocycles can have a major influence on their properties. For instance, N-methylation has been shown to impact permeability. A better understanding of the relationship between permeability and structure is of key importance as peptidic drugs are often associated with unfavorable pharmacokinetic profiles. Starting from a semipeptidic macrocycle backbone composed of a tripeptide tethered head-to-tail with an alkyl linker, we investigated two small changes: peptide-to-peptoid substitution and various methyl placements on the nonpeptidic linker. Implementing these changes in parallel, we created a collection of 36 compounds. Their permeability was then assessed in parallel artificial membrane permeability assay (PAMPA) and Caco-2 assays. Our results show a systematic improvement in permeability associated with one peptoid position in the cycle, while the influence of methyl substitution varies on a case-by-case basis. Using a combination of molecular dynamics simulations and NMR measurements, we offer hypotheses to explain such behavior.
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Affiliation(s)
- Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Thomas Stadelmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jacob Tremblay
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Sylvain Poulet
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Ulrike Fröhlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Jérôme Côté
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Rabeb Mouna Derbali
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Philippe Sarret
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Michel Grandbois
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Grégoire Leclair
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
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20
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Kirk RD, Picard K, Christian JA, Johnson SL, DeBoef B, Bertin MJ. Unnarmicin D, an Anti-inflammatory Cyanobacterial Metabolite with δ and μ Opioid Binding Activity Discovered via a Pipeline Approach Designed to Target Neurotherapeutics. ACS Chem Neurosci 2020; 11:4478-4488. [PMID: 33284578 PMCID: PMC7811748 DOI: 10.1021/acschemneuro.0c00686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To combat the bottlenecks in drug discovery and development, a pipeline to identify neuropharmacological candidates using in silico, in vitro, and receptor specific assays was devised. The focus of this pipeline was to identify metabolites with the ability to reduce neuroinflammation, due to the implications that chronic neuroinflammation has in chronic pain and neurodegenerative diseases. A library of pure compounds isolated from the cyanobacterium Trichodesmium thiebautii was evaluated using this method. In silico analysis of drug likelihood and in vitro permeability analysis using the parallel artificial membrane permeability assay (PAMPA) highlighted multiple metabolites of interest from the library. Murine BV-2 microglia were used in conjunction with the Griess assay to determine if metabolites could reduce lipopolysaccharide induced neuroinflammation followed by analysis of pro-inflammatory cytokine concentrations in the supernatant of the treated cell cultures. The nontoxic metabolite unnarmicin D was further evaluated due to its moderate permeability in the PAMPA assay, promising ADME data, modulation of all cytokines tested, and prediction as an opioid receptor ligand. Molecular modeling of unnarmicin D to the μ and δ opioid receptors showed strong theoretical binding potential to the μ opioid receptor. In vitro binding assays validated this pipeline showing low micromolar binding affinity for the μ opioid receptor launching the potential for further analysis of unnarmicin D derivatives for the treatment of pain and neuroinflammation related diseases.
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Affiliation(s)
- Riley D. Kirk
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, United States
| | - Kassie Picard
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, United States
| | - Joseph A. Christian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, United States
| | - Shelby L. Johnson
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, United States
| | - Brenton DeBoef
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, United States
| | - Matthew J. Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, United States
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21
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Poongavanam V, Atilaw Y, Ye S, Wieske LHE, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Predicting the Permeability of Macrocycles from Conformational Sampling - Limitations of Molecular Flexibility. J Pharm Sci 2020; 110:301-313. [PMID: 33129836 DOI: 10.1016/j.xphs.2020.10.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Macrocycles constitute superior ligands for targets that have flat binding sites but often require long synthetic routes, emphasizing the need for property prediction prior to synthesis. We have investigated the scope and limitations of machine learning classification models and of regression models for predicting the cell permeability of a set of denovo-designed, drug-like macrocycles. 2D-Based classification models, which are fast to calculate, discriminated between macrocycles that had low-medium and high permeability and may be used as virtual filters in early drug discovery projects. Importantly, stereo- and regioisomer were correctly classified. QSPR studies of two small sets of comparator drugs suggested that use of 3D descriptors, calculated from biologically relevant conformations, would allow development of more precise regression models for late phase drug projects. However, a 3D permeability model could only be developed for a rigid series of macrocycles. Comparison of NMR based conformational analysis with in silico conformational sampling indicated that this shortcoming originates from the inability of the molecular mechanics force field to identify the relevant conformations for flexible macrocycles. We speculate that a Kier flexibility index of ≤10 constitutes a current upper limit for reasonably accurate 3D prediction of macrocycle cell permeability.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sofie Ye
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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22
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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