1
|
D’Orsi R, Funicello M, Laurita T, Lupattelli P, Berti F, Chiummiento L. The Pseudo-Symmetric N-benzyl Hydroxyethylamine Core in a New Series of Heteroarylcarboxyamide HIV-1 Pr Inhibitors: Synthesis, Molecular Modeling and Biological Evaluation. Biomolecules 2021; 11:biom11111584. [PMID: 34827582 PMCID: PMC8615997 DOI: 10.3390/biom11111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
Here, we report the synthesis, enzyme inhibition and structure–activity relationship studies of a new potent class of HIV-1 protease inhibitors, which contain a pseudo-symmetric hydroxyethylamine core and heteroarylcarboxyamide moieties. The simple synthetic pathway furnished nine compounds in a few steps with high yields. The compounds were designed taking into account our previous results on other series of inhibitors with different substituents at P’ and P’’ and different ways of linking them to the inhibitor core. Potent inhibitory activity was obtained with nanomolar IC50 values measured with a standard fluorimetric test in 100 mM MES buffer, pH 5.5, containing 400 mM NaCl, 1 mM EDTA, 1 mM DTT and 1 mg/ml BSA. Compounds 9a–c, containing the indole ring in P1, exhibited an HIV-1 protease inhibitory activity more powerful than darunavir in the same assay. To obtain molecular insight into the binding properties of these compounds, docking analysis was performed, and their binding properties were also compared.
Collapse
Affiliation(s)
- Rosarita D’Orsi
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Teresa Laurita
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Paolo Lupattelli
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
- Correspondence: (F.B.); (L.C.)
| | - Lucia Chiummiento
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
- Correspondence: (F.B.); (L.C.)
| |
Collapse
|
2
|
Mazzotta S, Berastegui-Cabrera J, Vega-Holm M, García-Lozano MDR, Carretero-Ledesma M, Aiello F, Vega-Pérez JM, Pachón J, Iglesias-Guerra F, Sánchez-Céspedes J. Design, synthesis and in vitro biological evaluation of a novel class of anti-adenovirus agents based on 3-amino-1,2-propanediol. Bioorg Chem 2021; 114:105095. [PMID: 34175724 DOI: 10.1016/j.bioorg.2021.105095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/09/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Nowadays there is not an effective drug for the treatment of infections caused by human adenovirus (HAdV) which supposes a clinical challenge, especially for paediatric and immunosuppressed patients. Here, we describe the design, synthesis and biological evaluation as anti-adenovirus agents of a new library (57 compounds) of diester, monoester and triazole derivatives based on 3-amino-1,2-propanediol skeleton. Seven compounds (17, 20, 26, 34, 44, 60 and 66) were selected based on their high anti-HAdV activity at low micromolar concentration (IC50 from 2.47 to 5.75 µM) and low cytotoxicity (CC50 from 28.70 to >200 µM). In addition, our mechanistic assays revealed that compounds 20 and 44 might be targeting specifically the HAdV DNA replication process, and compound 66 would be targeting HAdV E1A mRNA transcription. For compounds 17, 20, 34 and 60, the mechanism of action seems to be associated with later steps after HAdV DNA replication.
Collapse
Affiliation(s)
- Sarah Mazzotta
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende (CS), Italy; Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy
| | - Judith Berastegui-Cabrera
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - María Del Rosario García-Lozano
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; Institute of Biomedicine of Seville (IBiS), SeLiver Group, University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Marta Carretero-Ledesma
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | - Jerónimo Pachón
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain; Department of Medicine, University of Seville, E-41009 Seville, Spain
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - Javier Sánchez-Céspedes
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain.
| |
Collapse
|
3
|
Mazzotta S, Berastegui-Cabrera J, Carullo G, Vega-Holm M, Carretero-Ledesma M, Mendolia L, Aiello F, Iglesias-Guerra F, Pachón J, Vega-Pérez JM, Sánchez-Céspedes J. Serinol-Based Benzoic Acid Esters as New Scaffolds for the Development of Adenovirus Infection Inhibitors: Design, Synthesis, and In Vitro Biological Evaluation. ACS Infect Dis 2021; 7:1433-1444. [PMID: 33073569 DOI: 10.1021/acsinfecdis.0c00515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the years, human adenovirus (HAdV) has progressively been recognized as a significant viral pathogen. Traditionally associated with self-limited respiratory, gastrointestinal, and conjunctival infections, mainly in immunocompromised patients, HAdV is currently considered to be a pathogen presenting significant morbidity and mortality in both immunosuppressed and otherwise healthy individuals. Currently available therapeutic options are limited because of their lack of effectivity and related side effects. In this context, there is an urgent need to develop effective anti-HAdV drugs with suitable therapeutic indexes. In this work, we identified new serinol-derived benzoic acid esters as novel scaffolds for the inhibition of HAdV infections. A set of 38 compounds were designed and synthesized, and their antiviral activity and cytotoxicity were evaluated. Four compounds (13, 14, 27, and 32) inhibited HAdV infection at low micromolar concentrations (2.82-5.35 μM). Their half maximal inhibitory concentration (IC50) values were lower compared to that of cidofovir, the current drug of choice. All compounds significantly reduced the HAdV DNA replication process, while they did not block any step of the viral entry. Our results showed that compounds 13, 14, and 32 seem to be targeting the expression of the E1A early gene. Moreover, all four derivatives demonstrated a significant inhibition of human cytomegalovirus (HCMV) DNA replication. This new scaffold may represent a potential tool useful for the development of effective anti-HAdV drugs.
Collapse
Affiliation(s)
- Sarah Mazzotta
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, E-41071 Seville, Spain
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Judith Berastegui-Cabrera
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Gabriele Carullo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
- Department of Biotechnology, Chemistry and Pharmacy, DoE 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, E-41071 Seville, Spain
| | - Marta Carretero-Ledesma
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Lara Mendolia
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, E-41071 Seville, Spain
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, E-41071 Seville, Spain
| | - Jerónimo Pachón
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
- Department of Medicine, University of Seville, E-41009 Seville, Spain
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, E-41071 Seville, Spain
| | - Javier Sánchez-Céspedes
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| |
Collapse
|
4
|
Faouzi A, Arnaud A, Bancet A, Barette C, Preto J, Do CV, Jordheim LP, Bousfiha Z, Nguyen TTB, Verrière M, Farce A, Fauvarque MO, Barret R, Lomberget T. Combretastatin A-4 sulfur-containing heterocyclic derivatives: Synthesis, antiproliferative activities and molecular docking studies. Eur J Med Chem 2021; 215:113275. [PMID: 33618157 DOI: 10.1016/j.ejmech.2021.113275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/24/2022]
Abstract
Combretastatin A-4 inspired heterocyclic derivatives were synthesized and evaluated for their biological activities on tubulin polymerization and cell proliferation. Among the 19 described sulfur-containing compounds, derivatives (Z)-4h and (Z)-4j exhibited interesting in cellulo tubulin polymerization inhibition and antiproliferative activities with IC50 values for six different cell lines between 8 and 27 nM. Furthermore, in silico docking studies within the colchicine/CA-4 binding site of tubulin were carried out to understand the interactions of our products with the protein target. The effects on the cell cycle of follicular lymphoma cells were also investigated at 1-10 nM concentrations showing that apoptotic processes occurred.
Collapse
Affiliation(s)
- Abdelfattah Faouzi
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France; Present Address: Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandre Arnaud
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France
| | - Alexandre Bancet
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France
| | - Caroline Barette
- Univ. Grenoble Alpes, CEA, Inserm, BGE U1038, 38000, Grenoble, France
| | - Jordane Preto
- Université de Lyon, Université Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Cong Viet Do
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France; University of Science and Technology of HanoÏ USTH, 18 Hoang Quoc Viet, Hanoi, 100000, Viet Nam; Present Address: Faculty of Pharmacy, Dai Nam University, 56 Vu Trong Phung, Hanoi, Viet Nam
| | - Lars Petter Jordheim
- Université de Lyon, Université Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Zineb Bousfiha
- Université de Lyon, Université Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69008, France
| | - Thi Thanh Binh Nguyen
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France; Present Address: VNU School of Medicine and Pharmacy, 144 Xuan Thuy, Cau Giay, Hanoi, 100000, Viet Nam
| | - Marion Verrière
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France
| | - Amaury Farce
- Université de Lille, Inserm, CHU Lille, U995, LIRIC, Lille Inflammation Research International Center, F-59006 Lille Cedex, France
| | | | - Roland Barret
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France
| | - Thierry Lomberget
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373, Lyon Cedex 08, France; Université de Lyon, Université Lyon 1, CNRS UMR 5246 Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Faculté de Pharmacie, ISPB, 8, Avenue Rockefeller, F-69373, Lyon, Cedex 08, France.
| |
Collapse
|
5
|
Rist PA, Grainger RS, Davies PW. Gold-Catalyzed Intermolecular Alkyne Oxyarylation for C3 Functionalization of Benzothiophenes. Org Lett 2021; 23:642-646. [PMID: 33467857 DOI: 10.1021/acs.orglett.0c03596] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
C3-selective C-C bond formation on benzothiophenes is challenging, and few direct functionalization methods are available. A gold-catalyzed reaction of alkynes with benzothiophene S-oxides provides regioselective entry into C3-alkylated benzothiophenes with the C7-alkylated isomer as the minor product. This oxyarylation reaction works with alkyl and aryl alkynes and substituted and unsubstituted benzothiophenes. Mechanistic studies identify that sulfoxide inhibits the catalyst [DTBPAu(PhCN)]SbF6, which also degrades and forms the unreactive complex [(DTBP)2Au]SbF6.
Collapse
Affiliation(s)
- Paige A Rist
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Richard S Grainger
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Paul W Davies
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| |
Collapse
|
6
|
Bais J, Benedetti F, Berti F, Cerminara I, Drioli S, Funicello M, Regini G, Vidali M, Felluga F. One Pot Synthesis of Micromolar BACE-1 Inhibitors Based on the Dihydropyrimidinone Scaffold and Their Thia and Imino Analogues. Molecules 2020; 25:molecules25184152. [PMID: 32927879 PMCID: PMC7571164 DOI: 10.3390/molecules25184152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/05/2022] Open
Abstract
A library of dihydropyrimidinones was synthesized via a “one-pot” three component Biginelli reaction using different aldehydes in combination with β-dicarbonyl compounds and urea. Selected 2-thiooxo and 2-imino analogs were also obtained with the Biginelli reaction from thiourea and guanidine hydrochloride, respectively. The products were screened in vitro for their β-secretase inhibitory activity. The majority of the compounds resulted to be active, with IC50 in the range 100 nM–50 μM.
Collapse
Affiliation(s)
- Jessica Bais
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Fabio Benedetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Iole Cerminara
- Dipartimento di Scienze, Università della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (I.C.); (M.F.)
| | - Sara Drioli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (I.C.); (M.F.)
| | - Giorgia Regini
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Mattia Vidali
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Fulvia Felluga
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
- Correspondence:
| |
Collapse
|
7
|
Spelmezan CG, Bencze LC, Katona G, Irimie FD, Paizs C, Toșa MI. Efficient and Stable Magnetic Chitosan-Lipase B from Candida Antarctica Bioconjugates in the Enzymatic Kinetic Resolution of Racemic Heteroarylethanols. Molecules 2020; 25:molecules25020350. [PMID: 31952168 PMCID: PMC7024219 DOI: 10.3390/molecules25020350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/19/2023] Open
Abstract
Lipase B from Candida antarctica immobilized by covalent binding on sebacoyl-activated chitosan-coated magnetic nanoparticles proved to be an efficient biocatalyst (49.2-50% conversion in 3-16 h and >96% enantiomeric excess) for the enzymatic kinetic resolution of some racemic heteroarylethanols through transesterification with vinyl acetate. Under optimal conditions (vinyl acetate, n-hexane, 45 °C), the biocatalyst remains active after 10 cycles.
Collapse
|
8
|
Tramutola F, Armentano MF, Berti F, Chiummiento L, Lupattelli P, D'Orsi R, Miglionico R, Milella L, Bisaccia F, Funicello M. New heteroaryl carbamates: Synthesis and biological screening in vitro and in mammalian cells of wild-type and mutant HIV-protease inhibitors. Bioorg Med Chem 2019; 27:1863-1870. [DOI: 10.1016/j.bmc.2019.03.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 01/30/2023]
|
9
|
Li Y, Tian Y, Qin Z, Yan A. Classification of HIV-1 Protease Inhibitors by Machine Learning Methods. ACS OMEGA 2018; 3:15837-15849. [PMID: 30556015 PMCID: PMC6288788 DOI: 10.1021/acsomega.8b01843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/24/2018] [Indexed: 05/16/2023]
Abstract
HIV-1 protease plays an important role in the processing of virus infection. Protease is an effective therapeutic target for the treatment of HIV-1. Our data set is based on a selection of 4855 HIV-1 protease inhibitors (PIs) from ChEMBL. A series of 15 classification models for predicting the active inhibitors were built by machine learning methods, including k-nearest neighors (K-NN), decision tree (DT), random forest (RF), support vector machine (SVM), and deep neural network (DNN). The molecular structures were characterized by (1) fingerprint descriptors including MACCS fingerprints and PubChem fingerprints and (2) physicochemical descriptors calculated by CORINA Symphony. The prediction accuracies of all of the models are more than 70% on the test set; the best accuracy of 83.07% was obtained by model 4A, which was built by the SVM method based on MACCS fingerprint descriptors. Nine consensus models were built with three kinds of different descriptors, which combined all of the machine learning methods using the "consensus prediction". Model C3a developed with MACCS fingerprint descriptors showed the highest accuracy on both training set (91.96%) and test set (83.15%). An external validation set including 35 989 compounds from DUD database and 239 active inhibitors from the recent literature was used to verify the performance of our model. The best prediction accuracy of 98.37% was obtained by model 3C, which was built by RF based on CORINA Symphony descriptors. In addition, from the analysis of molecular descriptors, it shows that the aromatic system and atoms related to hydrogen bonding provide important contributions to the bioactivity of PIs.
Collapse
Affiliation(s)
- Yang Li
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- Institute
of Science and Technology, Shandong University
of Traditional Chinese Medicine, Ji’nan, Shandong 250355, China
| | - Yujia Tian
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Zijian Qin
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Aixia Yan
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- E-mail: . Phone: +86-10-64421335 (A.Y.)
| |
Collapse
|
10
|
Funicello M, Chiummiento L, Tramutola F, Armentano M, Bisaccia F, Miglionico R, Milella L, Benedetti F, Berti F, Lupattelli P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors. Bioorg Med Chem 2017; 25:4715-4722. [DOI: 10.1016/j.bmc.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
|
11
|
Keri RS, Chand K, Budagumpi S, Balappa Somappa S, Patil SA, Nagaraja BM. An overview of benzo[b]thiophene-based medicinal chemistry. Eur J Med Chem 2017; 138:1002-1033. [PMID: 28759875 DOI: 10.1016/j.ejmech.2017.07.038] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/15/2017] [Accepted: 07/20/2017] [Indexed: 01/16/2023]
Abstract
Among sulfur containing heterocycles, benzothiophene and its derivatives are at the focus as these candidates have structural similarities with active compounds to develop new potent lead molecules in drug design. Benzo[b]thiophene scaffold is one of the privileged structures in drug discovery as this core exhibits various biological activities allowing them to act as anti-microbial, anti-cancer, anti-inflammatory, anti-oxidant, anti-tubercular, anti-diabetic, anti-convulsant agents and many more. Further, numerous benzothiophene-based compounds as clinical drugs have been extensively used to treat various types of diseases with high therapeutic potency, which has led to their extensive developments. Due to the wide range of biological activities of benzothiophene, their structure activity relationships (SAR) have generated interest among medicinal chemists, and this has culminated in the discovery of several lead molecules against numerous diseases. The present review is endeavoring to highlight the progress in the various pharmacological activities of benzo[b]thiophene derivatives. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic benzothiophene-based medicinal drugs, as well as more effective diagnostic agents and pathologic probes. Also, SAR studies that highlight the chemical groups responsible for evoking the potential activities of benzothiophene derivatives are studied and compared.
Collapse
Affiliation(s)
- Rangappa S Keri
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Kanakapura, Ramanagaram, Bangalore 562112, India.
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Srinivasa Budagumpi
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Kanakapura, Ramanagaram, Bangalore 562112, India
| | - Sasidhar Balappa Somappa
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India; Organic Chemistry Section, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research (CSIR)-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram, India
| | - Siddappa A Patil
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Kanakapura, Ramanagaram, Bangalore 562112, India
| | - Bhari Mallanna Nagaraja
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Kanakapura, Ramanagaram, Bangalore 562112, India
| |
Collapse
|
12
|
Synthetic and structural routes for the rational conversion of peptides into small molecules. Methods Mol Biol 2015; 1268:159-93. [PMID: 25555725 DOI: 10.1007/978-1-4939-2285-7_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The demand for modified peptides with improved stability profiles and pharmacokinetic properties is driving extensive research effort in this field. The conversion of peptides into organic molecules, as traditional drugs, is a long and puzzled way. Many and versatile approaches have been described for designing peptide mimetics: the substitution of natural residues with modified amino acids and the rigidification and modification of the backbone are the main structural and chemical routes walked in medicinal chemistry. All of these strategies have been successfully applied to obtain active new compounds in molecular biology, drug discovery and design. Here we propose a panoramic review of the most common methods for the preparation of modified peptides and the most interesting findings of the last decade.
Collapse
|
13
|
Bonini C, Chiummiento L, Di Blasio N, Funicello M, Lupattelli P, Tramutola F, Berti F, Ostric A, Miertus S, Frecer V, Kong DX. Synthesis and biological evaluation of new simple indolic non peptidic HIV Protease inhibitors: The effect of different substitution patterns. Bioorg Med Chem 2014; 22:4792-802. [DOI: 10.1016/j.bmc.2014.06.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/30/2022]
|
14
|
Recent patents and emerging therapeutics for HIV infections: a focus on protease inhibitors. Pharm Pat Anal 2014; 2:513-38. [PMID: 24237127 DOI: 10.4155/ppa.13.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The inclusion of protease inhibitors (PIs) in highly active antiretroviral therapy has significantly improved clinical outcomes in HIV-1-infected patients. To date, PIs are considered to be the most important therapeutic agents for the treatment of HIV infections. Despite high anti-HIV-1 potency, poor oral bioavailability of PIs has been a major concern. For achieving therapeutic concentrations, large doses of PIs are administered, which results in unacceptable systemic toxicities. Such severe and long-term toxicities necessitate the development of safer and potentially promising PIs. Recently, considerable attention has been paid to the development of newer compounds capable of inhibiting wild-type and resistant HIV-1 protease. Some of these PIs have displayed potent HIV-1 protease inhibitory activity. In this review, we have made an attempt to provide an overview on clinically approved and newly developing PIs, and related recent patents in the development of novel PIs.
Collapse
|
15
|
Design and synthesis of condensed thienocoumarins by Suzuki–Miyaura reaction/lactonization tandem protocol. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
16
|
Chiummiento L, Funicello M, Lupattelli P, Tramutola F. Ligand-free Suzuki coupling of arylboronic acids with methyl (E)-4-bromobut-2-enoate: synthesis of unconventional cores of HIV-1 protease inhibitors. Org Lett 2012; 14:3928-31. [PMID: 22804107 DOI: 10.1021/ol3016786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An effective ligand-free Suzuki coupling protocol to unite methyl (E)-4-bromobut-2-enoate with several arylboronic acids has been accomplished. Thus, a number of variously functionalized methyl 4-arylcrotonates have been achieved in high to excellent yields under mild conditions. This method enables the preparation of diverse aryl-substituted cores of HIV-1 protease inhibitors.
Collapse
Affiliation(s)
- Lucia Chiummiento
- Dipartimento di Chimica Antonio Mario Tamburro, Università Degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | | | | | | |
Collapse
|
17
|
Heterocycles in peptidomimetics and pseudopeptides: design and synthesis. Pharmaceuticals (Basel) 2012; 5:297-316. [PMID: 24281380 PMCID: PMC3763636 DOI: 10.3390/ph5030297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/22/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022] Open
Abstract
This minireview provides a brief outline of the peculiar aspects of the preparation of peptidomimetic and pseudopeptidic structures containing heterocycles. In particular novel tricyclic structures are investigated as potential drugs.
Collapse
|