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Investigating the structure-activity relationship of marine polycyclic batzelladine alkaloids as promising inhibitors for SARS-CoV-2 main protease (Mpro). Comput Biol Med 2022; 147:105738. [PMID: 35777088 PMCID: PMC9212445 DOI: 10.1016/j.compbiomed.2022.105738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/04/2022] [Accepted: 06/11/2022] [Indexed: 11/24/2022]
Abstract
Over a span of two years ago, since the emergence of the first case of the novel coronavirus (SARS-CoV-2) in China, the pandemic has crossed borders causing serious health emergencies, immense economic crisis and impacting the daily life worldwide. Despite the discovery of numerous forms of precautionary vaccines along with other recently approved orally available drugs, yet effective antiviral therapeutics are necessarily needed to hunt this virus and its variants. Historically, naturally occurring chemicals have always been considered the primary source of beneficial medications. Considering the SARS-CoV-2 main protease (Mpro) as the duplicate key element of the viral cycle and its main target, in this paper, an extensive virtual screening for a focused chemical library of 15 batzelladine marine alkaloids, was virtually examined against SARS-CoV-2 main protease (Mpro) using an integrated set of modern computational tools including molecular docking (MDock), molecule dynamic (MD) simulations and structure-activity relationships (SARs) as well. The molecular docking predictions had disclosed four promising compounds including batzelladines H–I (8–9) and batzelladines F-G (6–7), respectively according to their prominent ligand-protein energy scores and relevant binding affinities with the (Mpro) pocket residues. The best two chemical hits, batzelladines H–I (8–9) were further investigated thermodynamically though studying their MD simulations at 100 ns, where they showed excellent stability within the accommodated (Mpro) pocket. Moreover, SARs studies imply the crucial roles of the fused tricyclic guanidinic moieties, its degree of unsaturation, position of the N–OH functionality and the length of the side chain as a spacer linking between two active sites, which disclosed fundamental structural and pharmacophoric features for efficient protein-ligand interaction. Such interesting findings are greatly highlighting further in vitro/vivo examinations regarding those marine natural products (MNPs) and their synthetic equivalents as promising antivirals.
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Babin V, Taran F, Audisio D. Late-Stage Carbon-14 Labeling and Isotope Exchange: Emerging Opportunities and Future Challenges. JACS AU 2022; 2:1234-1251. [PMID: 35783167 PMCID: PMC9241029 DOI: 10.1021/jacsau.2c00030] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 05/04/2023]
Abstract
Carbon-14 (14C) is a gold standard technology routinely utilized in pharmaceutical and agrochemical industries for tracking synthetic organic molecules and providing their metabolic and safety profiles. While the state of the art has been dominated for decades by traditional multistep synthetic approaches, the recent emergence of late-stage carbon isotope labeling has provided new avenues to rapidly access carbon-14-labeled biologically relevant compounds. In particular, the development of carbon isotope exchange has represented a fundamental paradigm change, opening the way to unexplored synthetic transformations. In this Perspective, we discuss the recent developments in the field with a critical assessment of the literature. We subsequently discuss research directions and future challenges within this rapidly evolving field.
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Lombe BK, Winand L, Diettrich J, Töbermann M, Hiller W, Kaiser M, Nett M. Discovery, Biosynthetic Origin, and Heterologous Production of Massinidine, an Antiplasmodial Alkaloid. Org Lett 2022; 24:2935-2939. [PMID: 35412834 DOI: 10.1021/acs.orglett.2c00963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria of the genus Massilia represent an underexplored source of bioactive natural products. Here, we report the discovery of massinidine (1), a guanidine alkaloid with antiplasmodial activity, from these microbes. The unusual scaffold of massinidine is shown to originate from l-phenylalanine, acetate, and l-arginine. Massinidine biosynthesis genes were identified in the native producer and validated through heterologous expression in Myxococcus xanthus. Bioinformatic analyses indicate that the potential for massinidine biosynthesis is distributed in various proteobacteria.
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Affiliation(s)
- Blaise Kimbadi Lombe
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Lea Winand
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Jan Diettrich
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Melanie Töbermann
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Marcel Kaiser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
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Leblond A, Houari I, Beauxis Y, Leblanc K, Poupon E, Beniddir MA. Chemoinformatic Exploration of "Bioinspired Metabolomes" Illuminates Diacetyl Assembly Pathways Toward Nesteretal A-Like Cage Molecules. Org Lett 2022; 24:1247-1252. [PMID: 35112872 DOI: 10.1021/acs.orglett.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An appealing and challenging cage structure along with an unusual biosynthetic pathway prompted us to explore an expeditious bioinspired one-pot total synthesis of nesteretal A. An unconventional strategy was chosen, and a cascade reaction starting from diacetyl was studied. Under organocatalytic conditions mimicking an aldolase, nesteretal A and a related cage analogue were anticipated by in silico metabolization, detected, targeted, and characterized.
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Affiliation(s)
- Axel Leblond
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Inès Houari
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Yann Beauxis
- Université de Paris, CNRS, CiTCoM, F-75006 Paris, France
| | - Karine Leblanc
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Erwan Poupon
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
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5
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Wang CC, Wang XL, Zhang QL, Liu JT, Ma ZW, Liu Z, Chen YJ. Direct synthesis for N2-unprotected five-membered cyclic guanidines by regioselective [3+2] annulation of aziridines and cyanamides. Org Chem Front 2022. [DOI: 10.1039/d1qo01926k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel and efficient [3+2] annulation of 2-substituted aziridines and N-tosyl cyanamides via domino regioselective ring-opening/5-exo-dig cyclization procedure has been developed, allowing the direct preparation for N2-unprotected five-membered cyclic guanidines...
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Carroll AR, Copp BR, Davis RA, Keyzers RA, Prinsep MR. Marine natural products. Nat Prod Rep 2021; 38:362-413. [PMID: 33570537 DOI: 10.1039/d0np00089b] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review covers the literature published in 2019 for marine natural products (MNPs), with 719 citations (701 for the period January to December 2019) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1490 in 440 papers for 2019), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. Methods used to study marine fungi and their chemical diversity have also been discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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Gao Z, Li J, Song Y, Bi X, Meng X, Guo Y. Eight-step total synthesis of (+)-crambescin A. RSC Adv 2020; 10:39266-39270. [PMID: 35518432 PMCID: PMC9057376 DOI: 10.1039/d0ra08726b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/02/2022] Open
Abstract
(+)-Crambescin A belongs to the polycyclic guanidine natural product family and has been shown to possess various medically important properties. The chiral bicyclic guanidine structure of (+)-crambescin A presents a challenge for chemical synthesis. Here we implement a novel asymmetric Biginelli reaction strategy to achieve the enantiospecific total synthesis of (+)-crambescin A in only 8 steps from the abundant and inexpensive aliphatic aldehyde, urea and methyl 3-oxobutanoate. Here we implement a novel asymmetric Biginelli reaction strategy to achieve enantiospecific total synthesis of (+)-crambescin A in only 8 steps from the abundant and inexpensive aliphatic aldehyde, urea and methyl 3-oxobutanoate.![]()
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Affiliation(s)
- Zhenhua Gao
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
| | - Junchen Li
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
| | - Yunyang Song
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
| | - Xiaojing Bi
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
| | - Xiangyan Meng
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
| | - Yongbiao Guo
- State Key Laboratory of NBC Protection for Civilian Research Beijing 102205 P. R. China
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Berlinck RGS, Bernardi DI, Fill T, Fernandes AAG, Jurberg ID. The chemistry and biology of guanidine secondary metabolites. Nat Prod Rep 2020; 38:586-667. [PMID: 33021301 DOI: 10.1039/d0np00051e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2017-2019Guanidine natural products isolated from microorganisms, marine invertebrates and terrestrial plants, amphibians and spiders, represented by non-ribosomal peptides, guanidine-bearing polyketides, alkaloids, terpenoids and shikimic acid derived, are the subject of this review. The topics include the discovery of new metabolites, total synthesis of natural guanidine compounds, biological activity and mechanism-of-action, biosynthesis and ecological functions.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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Bian C, Wang J, Zhou X, Wu W, Guo R. Recent Advances on Marine Alkaloids from Sponges. Chem Biodivers 2020; 17:e2000186. [PMID: 32562510 DOI: 10.1002/cbdv.202000186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/19/2020] [Indexed: 12/19/2022]
Abstract
Alkaloids from marine secondary metabolites have received extensive attention from pharmacists in recent years. Miscellaneous alkaloids derived from marine sponges possessed various pharmacological activities including cytotoxicity, antimicrobial, antioxidant, and so on. Herein, we summarized 149 marine alkaloids from sponges based on their structures and bioactivities reported from 2015 to 2020 and analyzed the production environment of marine sponges with rich alkaloids. Moreover, we discussed biosynthesis routes of pyrrole and guanidine alkaloids from marine sponges Agelas and Monanchora. This article will be beneficial for future research on drugs from marine natural products.
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Affiliation(s)
- Changhao Bian
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Jiangming Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Xinyi Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Wenhui Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China.,Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, P. R. China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, P. R. China
| | - Ruihua Guo
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China.,Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, P. R. China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, P. R. China
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Rippel R, Pinheiro L, Lopes M, Lourenço A, Ferreira LM, Branco PS. Synthetic Approaches to a Challenging and Unusual Structure—An Amino-Pyrrolidine Guanine Core. Molecules 2020; 25:molecules25040797. [PMID: 32059504 PMCID: PMC7070370 DOI: 10.3390/molecules25040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022] Open
Abstract
The synthesis of an unreported 2-aminopyrrolidine-1-carboxamidine unit is here described for the first time. This unusual and promising structure was attained through the oxidative decarboxylation of amino acids using the pair of reagents, silver(I)/peroxydisulfate (Ag(I)/S2O82−) followed by intermolecular (in the case of l-proline derivative) and intramolecular trapping (in the case of acyl l-arginine) by N-nucleophiles. The l-proline approach has a broader scope for the synthesis of 2-aminopyrrolidine-1-carboxamidine derivatives, whereas the intramolecular cyclization afforded by the l-acylarginines, when applied, results in higher yields. The former allowed the first synthesis of cernumidine, a natural alkaloid isolated in 2011 from Solanum cernuum Vell, as its racemic form.
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