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Marques PH, Jaiswal AK, de Almeida FA, Pinto UM, Ferreira-Machado AB, Tiwari S, Soares SDC, Paiva AD. Lactic acid bacteria secreted proteins as potential Listeria monocytogenes quorum sensing inhibitors. Mol Divers 2023:10.1007/s11030-023-10722-7. [PMID: 37658910 DOI: 10.1007/s11030-023-10722-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
Listeria monocytogenes is an important human and animal pathogen able to cause an infection named listeriosis and is mainly transmitted through contaminated food. Among its virulence traits, the ability to form biofilms and to survive in harsh environments stand out and lead to the persistence of L. monocytogenes for long periods in food processing environments. Virulence and biofilm formation are phenotypes regulated by quorum sensing (QS) and, therefore, the control of L. monocytogenes through an anti-QS strategy is promising. This study aimed to identify, by in silico approaches, proteins secreted by lactic acid bacteria (LAB) potentially able to interfere with the agr QS system of L. monocytogenes. The genome mining of Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus NCFM revealed 151 predicted secreted proteins. Concomitantly, the three-dimensional (3D) structures of AgrB and AgrC proteins of L. monocytogenes were modeled and validated, and their active sites were predicted. Through protein-protein docking and molecular dynamic, Serine-type D-Ala-D-Ala carboxypeptidase and L,D-transpeptidase, potentially secreted by L. rhamnosus GG and L. acidophilus NCFM, respectively, were identified with high affinity to AgrB and AgrC proteins, respectively. By inhibiting the translocation of the cyclic autoinducer peptide (cyclic AIP) via AgrB, and its recognition in the active site of AgrC, these LAB proteins could disrupt L. monocytogenes communication by impairing the agr QS system. The application of the QS inhibitors predicted in this study can emerge as a promising strategy in controlling L. monocytogenes in food processing environment and as an adjunct to antibiotic therapy for the treatment of listeriosis.
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Affiliation(s)
- Pedro Henrique Marques
- Interunit Bioinformatics Graduate Program, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Arun Kumar Jaiswal
- Interunit Bioinformatics Graduate Program, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Alves de Almeida
- Instituto de Laticínios Cândido Tostes (ILCT), Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG), Juiz de Fora, Minas Gerais, Brazil
| | - Uelinton Manoel Pinto
- Food Research Center, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | | | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
| | - Siomar de Castro Soares
- Department of Microbiology, Immunology and Parasitology, Federal University of Triângulo Mineiro (UFTM), Uberaba, Minas Gerais, Brazil
| | - Aline Dias Paiva
- Department of Microbiology, Immunology and Parasitology, Federal University of Triângulo Mineiro (UFTM), Uberaba, Minas Gerais, Brazil.
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2
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Ibeji CU, Ukogu K, Kelani MT, Ani FE, Obasi NL, Ogundare SA, Maguire GE, Kruger HG. Synthesis, Crystal structure, photoluminescence properties and quantum mechanics studies of two schiff bases of 2-amino-p-cresol. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Identification of bioactive natural compounds as efficient inhibitors against Mycobacterium tuberculosis protein-targets: A molecular docking and molecular dynamics simulation study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117340] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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4
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Aliashkevich A, Cava F. LD-transpeptidases: the great unknown among the peptidoglycan cross-linkers. FEBS J 2021; 289:4718-4730. [PMID: 34109739 DOI: 10.1111/febs.16066] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/05/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
The peptidoglycan (PG) cell wall is an essential polymer for the shape and viability of bacteria. Its protective role is in great part provided by its mesh-like character. Therefore, PG-cross-linking enzymes like the penicillin-binding proteins (PBPs) are among the best targets for antibiotics. However, while PBPs have been in the spotlight for more than 50 years, another class of PG-cross-linking enzymes called LD-transpeptidases (LDTs) seemed to contribute less to PG synthesis and, thus, has kept an aura of mystery. In the last years, a number of studies have associated LDTs with cell wall adaptation to stress including β-lactam antibiotics, outer membrane stability, and toxin delivery, which has shed light onto the biological meaning of these proteins. Furthermore, as some species display a great abundance of LD-cross-links in their cell wall, it has been hypothesized that LDTs could also be the main synthetic PG-transpeptidases in some bacteria. In this review, we introduce these enzymes and their role in PG biosynthesis and we highlight the most recent advances in understanding their biological role in diverse species.
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Affiliation(s)
- Alena Aliashkevich
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Sweden
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5
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Yusuf T, Oladipo SD, Zamisa S, Kumalo HM, Lawal IA, Lawal MM, Mabuba N. Design of New Schiff-Base Copper(II) Complexes: Synthesis, Crystal Structures, DFT Study, and Binding Potency toward Cytochrome P450 3A4. ACS OMEGA 2021; 6:13704-13718. [PMID: 34095663 PMCID: PMC8173565 DOI: 10.1021/acsomega.1c00906] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 06/01/2023]
Abstract
We report the synthesis and crystal structures of three new copper(II) Schiff-base complexes. The complexes have been characterized by elemental analysis and Fourier transform infrared (FT-IR) and UV-visible spectroscopies. The X-ray diffraction (XRD) analysis reveals that complexes 1 and 3 crystallize in a monoclinic space group C2/c and 2 in a triclinic space group P1̅, each adopting a square planar geometry around the metal center. We use a density functional theory method to explore the quantum chemical properties of these complexes. The calculation proceeds with the three-dimensional (3D) crystal structure characterization of the complexes in which the calculated IR and UV-vis values are comparable to the experimental results. Charge distribution and molecular orbital analyses enabled quantum chemical property prediction of these complexes. We study the drug-likeness properties and binding potentials of the synthesized complexes. The in silico outcome showed that they could serve as permeability-glycoprotein (P-gp) and different cytochrome P450 substrates. Our calculations showed that the complexes significantly bind to cytochrome P450 3A4.
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Affiliation(s)
- Tunde
L. Yusuf
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
| | - Segun D. Oladipo
- Department
of Chemical Sciences, Olabisi Onabanjo University, P. M. B., 2002 Ago-Iwoye, Nigeria
| | - Sizwe Zamisa
- School
of Chemistry and Physics, University of
KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Isiaka A. Lawal
- Chemistry
Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus, Boulevard, 1900 Vanderbijlpark, South Africa
| | - Monsurat M. Lawal
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Nonhlangabezo Mabuba
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
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6
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Abrahams KA, Besra GS. Synthesis and recycling of the mycobacterial cell envelope. Curr Opin Microbiol 2021; 60:58-65. [PMID: 33610125 PMCID: PMC8035080 DOI: 10.1016/j.mib.2021.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of the disease tuberculosis, is a recognised global health concern. The efficacy of the current treatment regime is under threat due to the emergence of antibiotic resistance, directing an urgent requirement for the discovery of new anti-tubercular agents and drug targets. The mycobacterial cell wall is a well-validated drug target for Mtb and is composed of three adaptive macromolecular structures, peptidoglycan, arabinogalactan and mycolic acids, an array of complex lipids and carbohydrates. The majority of the enzymes involved in cell wall synthesis have been established, whilst studies directed towards the mechanisms of remodelling and recycling have been neglected. This review briefly describes mycobacterial cell wall synthesis, and focuses on aspects of remodelling and recycling, thus highlighting opportunities for future research.
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Tarui A, Karuo Y, Sato K, Kawai K, Omote M. Stereoselective Synthesis of Multisubstituted α-fluoro-β-lactams. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824666200221114707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
β-Lactams, found in β-lactam antibiotics, are the structurally distorted cyclic
compounds being subjected to nucleophilic acyl substitution reaction. α-Fluorination of β
-lactams is a simple and expedient approach to control the reactivity of β-lactam ring toward
nucleophilic attack, which would hopefully lead to the new design of future antibiotics.
From the viewpoint of obtaining multisubstituted α-fluoro-β-lactams, α-bromo-α-
fluoro-β-lactams are considered as key compounds for structure functionalization, including
nucleophilic substitution reaction, aldol-type reaction and metal-catalyzed crosscoupling
reaction. All the reactions can be conducted smoothly to afford a variety of multisubstituted
α-fluoro-β-lactams. During the course of the examination, chiral α,α-difluoro-
β-lactams and α -bromo-β-fluoro-α-lactams are successfully obtained, which are considered
potent precursors for making stereocontrolled multisubstituted α-fluoro-β-lactams.
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Affiliation(s)
- Atsushi Tarui
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Yukiko Karuo
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Kazuyuki Sato
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Masaaki Omote
- Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan
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Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase. Sci Rep 2020; 10:18925. [PMID: 33144641 PMCID: PMC7609661 DOI: 10.1038/s41598-020-75799-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/07/2020] [Indexed: 02/04/2023] Open
Abstract
Pulmonary tuberculosis, caused by Mycobacterium tuberculosis, is one of the most persistent diseases leading to death in humans. As one of the key targets during the latent/dormant stage of M. tuberculosis, isocitrate lyase (ICL) has been a subject of interest for new tuberculosis therapeutics. In this work, the cleavage of the isocitrate by M. tuberculosis ICL was studied using quantum mechanics/molecular mechanics method at M06-2X/6-31+G(d,p): AMBER level of theory. The electronic embedding approach was applied to provide a better depiction of electrostatic interactions between MM and QM regions. Two possible pathways (pathway I that involves Asp108 and pathway II that involves Glu182) that could lead to the metabolism of isocitrate was studied in this study. The results suggested that the core residues involved in isocitrate catalytic cleavage mechanism are Asp108, Cys191 and Arg228. A water molecule bonded to Mg2+ acts as the catalytic base for the deprotonation of isocitrate C(2)–OH group, while Cys191 acts as the catalytic acid. Our observation suggests that the shuttle proton from isocitrate hydroxyl group C(2) atom is favourably transferred to Asp108 instead of Glu182 with a lower activation energy of 6.2 kcal/mol. Natural bond analysis also demonstrated that pathway I involving the transfer of proton to Asp108 has a higher intermolecular interaction and charge transfer that were associated with higher stabilization energy. The QM/MM transition state stepwise catalytic mechanism of ICL agrees with the in vitro enzymatic assay whereby Asp108Ala and Cys191Ser ICL mutants lost their isocitrate cleavage activities.
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Adeowo FY, Ejalonibu MA, Elrashedy AA, Lawal MM, Kumalo HM. Multi-target approach for Alzheimer's disease treatment: computational biomolecular modeling of cholinesterase enzymes with a novel 4- N-phenylaminoquinoline derivative reveal promising potentials. J Biomol Struct Dyn 2020; 39:3825-3841. [PMID: 33030113 DOI: 10.1080/07391102.2020.1826129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The identification of dual inhibitors targeting the active sites of the cholinesterase enzymes, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), have lately surfaced as a multi-approach towards Alzheimer treatment. More recently, a novel series of 4-N-phenylaminoquinolines was synthesized and evaluated against AChE and BuChE in which one of the compounds displayed appreciable inhibition compared to the standard compound, galantamine. To provide a clearer picture of the inhibition mechanism of this potent compound at the molecular level, computational biomolecular modeling was carried out. The investigation was initiated with the exploration of the chemical properties of the identified compound 11 b and reference drug, galantamine. Density functional theory (DFT) calculations reveal some conceptual parameters that provide information on the stability and reactivity of the compounds as potential inhibitors. To unveil the binding mechanism, energetics and enzyme-ligand interactions, molecular dynamics (MD) simulations of six different systems were executed over a period. Calculated binding free energy values are in the same order with experimental IC50 data. Identification of the main residues driving optimum binding of the active compound 11 b to the binding region of both AChE and BuChE showed Trp81 and Trp110 as the most important, respectively. It was proposed that the studied compound could serve as a dual inhibitor for AChE and BuChE, therefore, would potentially be a promising moiety in a multi-target approach for the treatment of Alzheimer's disorder.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatima Y Adeowo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Murtala A Ejalonibu
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed A Elrashedy
- Molecular Bio-computational and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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Tsotetsi N, Amoako DG, Somboro AM, Khumalo HM, Khan RB. Molecular mechanisms underlying the renoprotective effects of 1,4,7-triazacyclononane: a βeta-lactamase inhibitor. Cytotechnology 2020; 72:785-796. [PMID: 32920746 DOI: 10.1007/s10616-020-00422-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
Broad-spectrum β-lactam antibiotics such as penicillin are routinely used against both Gram-negative and Gram-positive bacteria. However, bacteria that produce β-lactamase have developed resistance against these antibiotics by cleaving the β-lactam ring and rendering the antibiotic inactive. To combat this effect, 1,4,7- Triazacyclononane (TACN), a cyclic organic compound derived from cyclononanes has been shown to preserve the activity of β-lactam antibiotics by inhibiting β-lactamase. However, its cytotoxic effects require elucidation. Given that the cytotoxic target for many therapeutics is the kidney, this study investigated the effects of TACN on human embryonic kidney cells (Hek293) cells. Hek293 cells were treated with TACN (0-500 µM) for 24 h and the cytotoxicity was assessed (MTT and LDH assay). Apoptosis was luminometrically detected by measuring phosphatidylserine externalisation and caspase activity and fluorescently detecting necrosis. DNA fragmentation was visualised using fluorescent microscopy. Expression of the apoptosis-related protein were determined by western blot. The results generated indicate that TACN does not initiate necrosis as LDH was decreased. Likewise, decreased apoptosis was supported by the decreased phosphatidylserine, caspases, Bax, cleaved PARP, IAP and NF-kB. However, increased DNA fragmentation was associated with increased p53. Therefore, effects of TACN at the nucleus, produced a p53 response to initiate DNA repair and did not culminate in cell death. The findings show that TACN is not cytotoxic to Hek293 cells via the apoptotic route. Since TACN did not induce cell death, its potential as a metallo-β-lactamase inhibitor (MBLI) may be exploited to counteract the effect of MBL-producing bacteria. Restoring β-lactam activity will curb the global menace of antibiotic resistance.
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Affiliation(s)
- Nrateng Tsotetsi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Khumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rene B Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.
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Lawal MM, Lawal IA, Klink MJ, Tolufashe GF, Ndagi U, Kumalo HM. Density functional theory study of gold(III)-dithiocarbamate complexes with characteristic anticancer potentials. J Inorg Biochem 2020; 206:111044. [DOI: 10.1016/j.jinorgbio.2020.111044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/29/2020] [Accepted: 02/13/2020] [Indexed: 01/12/2023]
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12
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N-Phenyl substituent controlled diastereoselective synthesis of β-lactam-isatin conjugates. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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