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Diaz A, G S, Balaji S, Ramakrishnan J, Thamotharan S, Ramakrishnan V. Comprehensive screening of marine metabolites against class B1 metallo-β-lactamases of Klebsiella pneumoniae using two-pronged in silico approach. J Biomol Struct Dyn 2023; 41:10930-10943. [PMID: 36541935 DOI: 10.1080/07391102.2022.2159532] [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: 08/01/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The emergence of antibiotic resistance is one of the major global threats in healthcare. Metallo-β-Lactamases (MBL) are a class of enzymes in bacteria that cleave β-lactam antibiotics and confer resistance. MBLs are further divided into subclasses B1, B2 and B3. Of these, subclasses B1-MBLs (including NDM-1, VIM-2 and IMP-1) constitute the clinically prevalent lactamases conferring resistance. To date, no effective drugs are available clinically against MBLs. In this work, we aim to identify potent inhibitors for the B1 subclass of MBL from available marine metabolites in Comprehensive Marine Natural Product database through integrated in silico approaches. We have used two methods, namely, the high-throughput strategy and the pharmacophore-based strategy to identify potential inhibitors from marine metabolites. High-throughput virtual screening identified N-methyl mycosporine-Ser, which had the highest binding affinity to NDM-1. The pharmacophore-based approach based on co-crystallized ligands identified makaluvic acid and didymellamide with higher binding affinity across B1-MBLs. Taking into account of the advantage of a pharmacophore model-based approach with higher binding affinity, we conclude that both makaluvic acid and didymellamide show potential broad-spectrum effects by binding to all three B1-MBL receptors. The study also indicates the need to take multiple in silico approaches to screen and identify novel inhibitors. Together, our study reveals promising inhibitors that can be identified from marine systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aathithya Diaz
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shripushkar G
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shruti Balaji
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Subbiah Thamotharan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Vigneshwar Ramakrishnan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Derkach KV, Zakharova IO, Bakhtyukov AA, Sorokoumov VN, Kuznetsova VS, Shpakov AO. [Characterization and biological activity of new 4-oxo-1,4-dihydrocinnoline-based inhibitors of the tyrosine phosphatase PTP1B and TCPTP]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:427-436. [PMID: 36573409 DOI: 10.18097/pbmc20226806427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Functional disorders in obesity are largely due to a decrease in tissue sensitivity to insulin and leptin. One of the ways to restore it is inhibition of protein phosphotyrosine phosphatase 1B (PTP1B) and T-cell protein phosphotyrosine phosphatase (TCPTP), negative regulators of the insulin and leptin signaling. Despite progress in the development of inhibitors of these phosphatases, commercial preparations based on them have not been developed yet, and the mechanisms of action are poorly understood. The aim of the work was to study the effect of new derivatives of 4-oxo-1,4-dihydrocinnoline (PI04, PI06, PI07) on the activity of PTP1B and TCPTP, as well as to study the effect of their five-day administration (i.p., 10 mg/kg/day) to Wistar rats with diet-induced obesity on body weight and fat, metabolic and hormonal parameters, and gene expression of phosphatase and insulin and leptin receptors in the liver. It has been shown that PI04 is a mild, low selective inhibitor of both phosphatases (PTP1B, IC50=3.42(2.60-4.51) μM; TCPTP, IC50=4.16(3.49-4.95) μM), while PI06 and PI07 preferentially inhibit PTP1B (IC50=3.55 (2.63-4.78) μM) and TCPTP (IC50=1.45(1.18-1.78) μM), respectively. PI04 significantly reduced food intake, body weight and fat, attenuated hyperglycemia, normalized glucose tolerance, basal and glucose-stimulated levels of insulin and leptin, and insulin resistance index. Despite the anorexigenic effect, PI06 and PI07 were less effective, having little effect on glucose homeostasis and insulin sensitivity. PI04 significantly increased the expression of the PTP1B and TCPTP genes and decreased the expression of the insulin and leptin receptor genes. PI06 and PI07 had little effect on these indicators. Thus, PI04, the inhibitor of PTP1B and TCPTP phosphatases, restored metabolic and hormonal parameters in obese rats with greater efficiency than inhibitors of PTP1B (PI06) and TCPTP (PI07). This indicates the prospect of creating mixed PTP1B/TCPTP inhibitors for correction of metabolic disorders.
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Affiliation(s)
- K V Derkach
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - I O Zakharova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - A A Bakhtyukov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - V N Sorokoumov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - V S Kuznetsova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - A O Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia; Medical Faculty, St. Petersburg State University, St. Petersburg, Russia
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Wang YF, Fu Y, Ji YN, Shi NN, Lu XH, Gu YC, Shi QW, Huo CH. Sesquiterpene lactone dimers from the fruit of Carpesium abrotanoides L. PHYTOCHEMISTRY 2022; 203:113389. [PMID: 36007660 DOI: 10.1016/j.phytochem.2022.113389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/07/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Seven undescribed sesquiterpene lactone dimers (SLDs) (carpeabrodilactones A-G), one known SLD, and six known sesquiterpenes were isolated from the fruit of Carpesium abrotanoides L. Carpeabrodilactone A was a dimeric carabrane featuring a rare C-13-C-13' linkage. Carpeabrodilactones B and C are the first two SLDs to be described possessing a carabranolide unit and a guaianolide unit connected by an O-ether linkage. The structures of the SLDs were assigned based on HRESIMS, NMR analysis, 13C NMR calculation, ECD calculation, and modified Mosher's method. Four SLDs showed potent cytotoxicity against K562 and/or A549 cells, with IC50 values below 10 μM, but none inhibited protein tyrosine phosphatases at 40 μM, including PTP1B, SHP1, CD45, and TCPTP.
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Affiliation(s)
- Yu-Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yan Fu
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China; Core Facilities and Centers, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yan-Nan Ji
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China
| | - Ning-Ning Shi
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, Shijiazhuang, 050015, China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Qing-Wen Shi
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Chang-Hong Huo
- School of Pharmaceutical Sciences, Key Laboratory of Innovative Drug Development and Evaluation, Hebei Medical University, Shijiazhuang, 050017, China.
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Zhang D, Li S, Fan M, Zhao C. The Novel Compounds with Biological Activity Derived from Soil Fungi in the Past Decade. Drug Des Devel Ther 2022; 16:3493-3555. [PMID: 36248243 PMCID: PMC9553542 DOI: 10.2147/dddt.s377921] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022] Open
Abstract
The secondary metabolites isolated from soil fungi have received more and more attention, especially new compounds that exhibited good biological activities. In this review, a total of 546 new compounds are included in the relevant literature since 2011. The new compounds are isolated from soil fungi, We divided these compounds into seven categories, including alkaloids, terpenoids, steroids, ketones, phenylpropanoids, quinones, esters, lactones, etc. In addition, the biological activities and structure-activity relationships of these compounds have also been fully discussed. The activities of these compounds are roughly divided into eight categories, including anticancer activity, antimicrobial activity, anti-inflammatory activity, antioxidant activity, antiviral activity, antimalarial activity, immunosuppressive activity and other activities. Since natural products are an important source of new drugs, this review may have a positive guiding effect on drug screening.
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Affiliation(s)
- Danyu Zhang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Science, Beijing Normal University, Beijing, People’s Republic of China
| | - Shoujie Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Science, Beijing Normal University, Beijing, People’s Republic of China
| | - Mohan Fan
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Changqi Zhao
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Science, Beijing Normal University, Beijing, People’s Republic of China,Correspondence: Changqi Zhao, Tel +86-5880-5046, Email
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