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Leconte A, Jacquin J, Duban M, Deweer C, Trapet P, Laruelle F, Farce A, Compère P, Sahmer K, Fiévet V, Hoste A, Siah A, Lounès-Hadj Sahraoui A, Jacques P, Coutte F, Deleu M, Muchembled J. Deciphering the mechanisms involved in reduced sensitivity to azoles and fengycin lipopeptide in Venturia inaequalis. Microbiol Res 2024; 286:127816. [PMID: 38964072 DOI: 10.1016/j.micres.2024.127816] [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: 04/23/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024]
Abstract
Apple scab, caused by the hemibiotrophic fungus Venturia inaequalis, is currently the most common and damaging disease in apple orchards. Two strains of V. inaequalis (S755 and Rs552) with different sensitivities to azole fungicides and the bacterial metabolite fengycin were compared to determine the mechanisms responsible for these differences. Antifungal activity tests showed that Rs552 had reduced sensitivity to tebuconazole and tetraconazole, as well as to fengycin alone or in a binary mixture with other lipopeptides (iturin A, pumilacidin, lichenysin). S755 was highly sensitive to fengycin, whose activity was close to that of tebuconazole. Unlike fengycin, lipopeptides from the iturin family (mycosubtilin, iturin A) had similar activity on both strains, while those from the surfactin family (lichenysin, pumilacidin) were not active, except in binary mixtures with fengycin. The activity of lipopeptides varies according to their family and structure. Analyses to determine the difference in sensitivity to azoles (which target the CYP51 enzyme involved in the ergosterol biosynthesis pathway) showed that the reduced sensitivity in Rs552 is linked to (i) a constitutive increased expression of the Cyp51A gene caused by insertions in the upstream region and (ii) greater efflux by membrane pumps with the involvement of ABC transporters. Microscopic observations revealed that fengycin, known to interact with plasma membranes, induced morphological and cytological changes in cells from both strains. Sterol and phospholipid analyses showed a higher level of ergosta-7,22-dien-3-ol and a lower level of PI(C16:0/C18:1) in Rs552 compared with S755. These differences could therefore influence the composition of the plasma membrane and explain the differential sensitivity of the strains to fengycin. However, the similar antifungal activities of mycosubtilin and iturin A in the two strains indirectly indicate that sterols are probably not involved in the fengycin resistance mechanism. This leads to the conclusion that different mechanisms are responsible for the difference in susceptibility to azoles or fengycin in the strains studied.
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Affiliation(s)
- Aline Leconte
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France; University of Lille, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, Charles Viollette Institute, Lille F-59000, France; University of Liège, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux B-5030, Belgium
| | - Justine Jacquin
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France
| | - Matthieu Duban
- University of Lille, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, Charles Viollette Institute, Lille F-59000, France
| | - Caroline Deweer
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France
| | - Pauline Trapet
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France
| | - Frédéric Laruelle
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d'Opale, CEDEX CS 80699, Calais 62228, France
| | - Amaury Farce
- Université Lille, Inserm, CHU Lille, U1286 - INFINITE - Institut de recherche translationnelle sur l'inflammation, Lille F-59000, France
| | - Philippe Compère
- Laboratoire de morphologie fonctionnelle et évolutive, UR FOCUS, and Centre de recherche appliquée et d'enseignement en microscopie (CAREM), Université de Liège, Liège, Belgium
| | - Karin Sahmer
- Université Lille, IMT Lille Douai, Univ. Artois, JUNIA, ULR 4515 - LGCgE, Laboratoire de Génie Civil et geo-Environnement, Lille F-59000, France
| | - Valentin Fiévet
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France
| | - Alexis Hoste
- University of Liège, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux B-5030, Belgium
| | - Ali Siah
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d'Opale, CEDEX CS 80699, Calais 62228, France
| | - Philippe Jacques
- University of Liège, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux B-5030, Belgium
| | - François Coutte
- University of Lille, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, Charles Viollette Institute, Lille F-59000, France
| | - Magali Deleu
- University of Liège, UMRt BioEcoAgro 1158-INRAE, Microbial Secondary Metabolites team, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux B-5030, Belgium
| | - Jérôme Muchembled
- JUNIA, UMRt BioEcoAgro 1158-INRAE, Plant Secondary Metabolites Team, Charles Viollette Institute, Lille F-59000, France.
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Zhang L, Calvo-Barreiro L, de Sousa Batista V, Świderek K, Gabr MT. Discovery of ICOS-targeted small molecules using affinity selection mass spectrometry screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.04.606538. [PMID: 39149231 PMCID: PMC11326138 DOI: 10.1101/2024.08.04.606538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Inducible T cell co-stimulator (ICOS) is a positive immune checkpoint receptor expressed on the surface of activated T cells, which could promote cell function after being stimulated with ICOS ligand (ICOS-L). Although clinical benefits have been reported in the ICOS modulation-based treatment for cancer and autoimmune disease, current modulators are restricted in biologics, whereas ICOS-targeted small molecules are lacking. To fill this gap, we performed an affinity selection mass spectrometry (ASMS) screening for ICOS binding using a library of 15,600 molecules. To the best of our knowledge, this is the first study that utilizes ASMS screening to discover small molecules targeting immune checkpoints. Compound 9 with a promising ICOS/ICOS-L inhibitory profile (IC50 = 29.38 ± 3.41 μM) was selected as the template for the modification. Following preliminary structure-activity relationship (SAR) study and molecular dynamic (MD) simulation revealed the critical role of the ortho-hydroxy group on compound 9 in the ICOS binding, as it could stabilize the interaction via the hydrogen bond formation with residuals on the glycan, and the depletion could lead to an activity lost. This work validates a promising inhibitor for the ICOS/ICOS-L interaction, and we anticipate future modifications could provide more potent modulators for this interaction.
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Affiliation(s)
- Longfei Zhang
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA
| | - Laura Calvo-Barreiro
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Katarzyna Świderek
- BioComp group, Institute of Advanced Materials (INAM), Universitat Jaume I, Spain
| | - Moustafa T Gabr
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA
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Rasheed HAM, Al-Majidi SMH. Synthesis, identification and evaluation of molecular docking and experimental anti-cancer and antioxidant activity of new spiro four membered ring derivatives bearing 5-nitro isatin. Nat Prod Res 2024; 38:2629-2636. [PMID: 36995026 DOI: 10.1080/14786419.2023.2195178] [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: 12/12/2022] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Spiro-5-nitro isatino aza-β-lactams were produced by a [2 + 2] cycloaddition of 5-nitro isatin Schiff bases [1-5] with different aromatic isocyanate and thioisocyanate. 1HNMR and 13CNMR as well as FTIR spectroscopies, were used to identify the structures of the obtained compounds. These spiro-5-nitro isatin aza- β-lactams interest to us due to their potential antioxidant and anticancer properties. The MTT assay was used to examine in vitro bioactivity testing against breast cancer (MCF-7) cell lines. From result data, compound 14 displayed IC50 values that were lower than those of the clinically used anticancer drug tamoxifen toward MCF-7 cells after 24 h while compound 9 after 48 h synthesized compounds [6-20] were evaluated for against antioxidant activity by using DPPH assay. In molecular docking, Promising compounds were used to reveal potential cytotoxic activity mechanisms.
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Affiliation(s)
| | - Suaad M H Al-Majidi
- Department of Chemistry, College of Science, University of Baghdad, Baghdad, Iraq
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Teixeira SC, de Souza G, Junior JPDL, Rosini AM, Martínez AFF, Fernandes TADM, Ambrósio SR, Veneziani RCS, Bastos JK, Martins CHG, Barbosa BF, Ferro EAV. Copaifera spp. oleoresins and two isolated compounds (ent-kaurenoic and ent-polyalthic acid) inhibit Toxoplasma gondii growth in vitro. Exp Parasitol 2024; 262:108771. [PMID: 38723847 DOI: 10.1016/j.exppara.2024.108771] [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: 10/23/2023] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Toxoplasmosis affects about one-third of the world's population. The disease treatment methods pose several side effects and do not efficiently eliminate the parasite, making the search for new therapeutic approaches necessary. We aimed to assess the anti-Toxoplasma gondii activity of four Copaifera oleoresins (ORs) and two isolated diterpene acids, named ent-kaurenoic and ent-polyalthic acid. We used HeLa cells as an experimental model of toxoplasmosis. Uninfected and infected HeLa cells were submitted to the treatments, and the parasite intracellular proliferation, cytokine levels and ROS production were measured. Also, tachyzoites were pre-treated and the parasite invasion was determined. Finally, an in silico analysis was performed to identify potential parasite targets. Our data show that the non-cytotoxic concentrations of ORs and diterpene acids controlled the invasion and proliferation of T. gondii in HeLa cells, thus highlighting the possible direct action on parasites. In addition, some compounds tested controlled parasite proliferation in an irreversible manner. An additional and non-exclusive mechanism of action involves the modulation of host cell components, by affecting the upregulation of the IL-6. Additionally, molecular docking suggested that ent-polyalthic acid has a high affinity for the active site of the TgCDPK1 protein. Copaifera ORs have great antiparasitic activity against T. gondii, and this effect can be partially explained by the presence of the isolated compounds ent-kaurenoic and ent-polyalthic acid.
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Affiliation(s)
- Samuel Cota Teixeira
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Guilherme de Souza
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Joed Pires de Lima Junior
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Alessandra Monteiro Rosini
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Aryani Felixa Fajardo Martínez
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | | | - Sergio Ricardo Ambrósio
- Nucleus of Research in Technological and Exact Sciences, Universidade de Franca, Franca, SP, Brazil
| | | | - Jairo Kenupp Bastos
- School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Carlos Henrique Gomes Martins
- Department of Microbiology, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Bellisa Freitas Barbosa
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Eloisa Amália Vieira Ferro
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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Diniz LP, Morgado J, Bergamo Araujo AP, da Silva Antônio LM, Mota-Araujo HP, de Sena Murteira Pinheiro P, Sagrillo FS, Cesar GV, Ferreira ST, Figueiredo CP, Manssour Fraga CA, Gomes FCA. Histone deacetylase inhibition mitigates cognitive deficits and astrocyte dysfunction induced by amyloid-β (Aβ) oligomers. Br J Pharmacol 2024. [PMID: 38936407 DOI: 10.1111/bph.16439] [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: 11/21/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND AND PURPOSE Inhibitors of histone deacetylases (iHDACs) are promising drugs for neurodegenerative diseases. We have evaluated the therapeutic potential of the new iHDAC LASSBio-1911 in Aβ oligomer (AβO) toxicity models and astrocytes, key players in neuroinflammation and Alzheimer's disease (AD). EXPERIMENTAL APPROACH Astrocyte phenotype and synapse density were evaluated by flow cytometry, Western blotting, immunofluorescence and qPCR, in vitro and in mice. Cognitive function was evaluated by behavioural assays using a mouse model of intracerebroventricular infusion of AβO. KEY RESULTS LASSBio-1911 modulates reactivity and synaptogenic potential of cultured astrocytes and improves synaptic markers in cultured neurons and in mice. It prevents AβO-triggered astrocytic reactivity in mice and enhances the neuroprotective potential of astrocytes. LASSBio-1911 improves behavioural performance and rescues synaptic and memory function in AβO-infused mice. CONCLUSION AND IMPLICATIONS These results contribute to unveiling the mechanisms underlying astrocyte role in AD and provide the rationale for using astrocytes as targets to new drugs for AD.
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Affiliation(s)
- Luan Pereira Diniz
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Morgado
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula Bergamo Araujo
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Savacini Sagrillo
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriele Vargas Cesar
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sérgio T Ferreira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávia Carvalho Alcantara Gomes
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Sahu D, Gupta C, Yennamalli RM, Sharma S, Roy S, Hasan S, Gupta P, Sharma VK, Kashyap S, Kumar S, Dwivedi VP, Zhao X, Panda AK, Das HR, Liu CJ. Novel peptide inhibitor of human tumor necrosis factor-α has antiarthritic activity. Sci Rep 2024; 14:12935. [PMID: 38839973 PMCID: PMC11153517 DOI: 10.1038/s41598-024-63790-6] [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: 01/20/2023] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
The inhibition of tumor necrosis factor (TNF)-α trimer formation renders it inactive for binding to its receptors, thus mitigating the vicious cycle of inflammation. We designed a peptide (PIYLGGVFQ) that simulates a sequence strand of human TNFα monomer using a series of in silico methods, such as active site finding (Acsite), protein-protein interaction (PPI), docking studies (GOLD and Flex-X) followed by molecular dynamics (MD) simulation studies. The MD studies confirmed the intermolecular interaction of the peptide with the TNFα. Fluorescence-activated cell sorting and fluorescence microscopy revealed that the peptide effectively inhibited the binding of TNF to the cell surface receptors. The cell culture assays showed that the peptide significantly inhibited the TNFα-mediated cell death. In addition, the nuclear translocation of the nuclear factor kappa B (NFκB) was significantly suppressed in the peptide-treated A549 cells, as observed in immunofluorescence and gel mobility-shift assays. Furthermore, the peptide protected against joint damage in the collagen-induced arthritis (CIA) mouse model, as revealed in the micro focal-CT scans. In conclusion, this TNFα antagonist would be helpful for the prevention and repair of inflammatory bone destruction and subsequent loss in the mouse model of CIA as well as human rheumatoid arthritis (RA) patients. This calls upon further clinical investigation to utilize its potential effect as an antiarthritic drug.
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Affiliation(s)
- Debasis Sahu
- Product Development Cell, National Institute of Immunology, New Delhi, India.
- Department of Orthopedics Surgery, New York University School of Medicine, New York, NY, USA.
- Science Habitat, Ubioquitos Inc, London, ON, Canada.
| | - Charu Gupta
- School of Biomedical Sciences, Galgotias University, Greater Noida, UP, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to Be University, Thanjavur, Tamil Nadu, India
| | - Shikha Sharma
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
- Science Habitat, Ubioquitos Inc, London, ON, Canada
| | - Saugata Roy
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Sadaf Hasan
- Department of Orthopedics Surgery, New York University School of Medicine, New York, NY, USA
| | - Pawan Gupta
- Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, India
| | - Vishnu Kumar Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Sujit Kashyap
- Division of Pediatric Rheumatology, University of California San Francisco, San Francisco, CA, USA
- Department of Genetics, University of Delhi, Delhi, India
| | - Santosh Kumar
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Xiangli Zhao
- Department of Orthopedics Surgery, New York University School of Medicine, New York, NY, USA
- Department of Orthopaedics and Rehabilitation, Yale University School of Medicine, New Haven, CT, USA
| | - Amulya Kumar Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Hasi Rani Das
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Chuan-Ju Liu
- Department of Orthopedics Surgery, New York University School of Medicine, New York, NY, USA
- Department of Orthopaedics and Rehabilitation, Yale University School of Medicine, New Haven, CT, USA
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Herbst C, Endres S, Würz R, Sotriffer C. Assessment of fragment docking and scoring with the endothiapepsin model system. Arch Pharm (Weinheim) 2024; 357:e2400061. [PMID: 38631672 DOI: 10.1002/ardp.202400061] [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: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases.
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Affiliation(s)
- Carina Herbst
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Sara Endres
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Rebecca Würz
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
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Farhat N, Khanam T, Noor S, Khan AU. Structural insight into the binding mode of cefotaxime and meropenem to TEM-1, SHV-1, KPC-2, and Amp-C type beta-lactamases. Cell Biochem Biophys 2024; 82:1299-1308. [PMID: 38730202 DOI: 10.1007/s12013-024-01284-y] [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] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Antimicrobial resistance is an emerging threat to public health around the world. The study employs computational and biophysical methods to investigate the properties of cefotaxime and meropenem's binding to various beta-lactamases like TEM-1, SHV-1, KPC-2, and Amp-C. The enzyme kinetics of purified proteins revealed an increase in Michaelis constant (Km) value in the presence of meropenem and cefotaxime, indicating a decrease in enzyme affinity for nitrocefin. Proteins interact with meropenem/cefotaxime, causing quenching through complex formation. All proteins have one binding site, and binding constant (Kb) values are 104, indicating strong interaction. The study found that meropenem and cefotaxime had high fitness scores for Amp-C, KPC-2,TEM-1 and SHV-1, with binding energy ranging from -7.4 to -7.8, and hydrogen bonds between them. Molecular Dynamic simulation of protein-ligand complexes revealed cefotaxime-binding proteins have slightly lower Root Mean Square Deviation(RMSD) than meropenem-binding proteins, indicating stable association antibiotics with these proteins.
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Affiliation(s)
- Nabeela Farhat
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Tasneem Khanam
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Saba Noor
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Istanbullu H, Coban G, Turunc E, Disel C, Debelec Butuner B. Discovery of selective TYK2 inhibitors: Design, synthesis, in vitro and in silico studies of promising hits with triazolopyrimidinone scaffold. Bioorg Chem 2024; 148:107430. [PMID: 38728909 DOI: 10.1016/j.bioorg.2024.107430] [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: 02/08/2024] [Revised: 04/26/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway mediates many cytokine and growth factor signals. Tyrosine kinase 2 (TYK2), one of the members of this pathway and the first described member of the JAK family. TYK2 associates with inflammatory and autoimmune diseases, cancer and diabetes. Here, we present novel compounds as selective inhibitors of the canonical kinase domain of TYK2 enzyme. These compounds were rationally designed and synthesized with appropriate reactions. Molecular modeling techniques were used to design and optimize the candidates for TYK2 inhibition and to determine the estimated binding orientations of them inside JAKs. Designed compounds potently inhibited TYK2 with good selectivity against other JAKs as determined by in vitro assays. In order to verify its selectivity properties, compound A8 was tested against 58 human kinases (KinaseProfiler™ assay). The effects of the selected seven compounds on the protein levels of members of the JAK/STAT family were also detected in THP-1 monocytes although the basal level of these proteins is poorly detectable. Therefore, their expression was induced by lipopolysaccharide treatment and compounds A8, A15, A18, and A19 were found to be potent inhibitors of the TYK2 enzyme, (9.7 nM, 6.0 nM, 5.0 nM and 10.3 nM, respectively), and have high selectivity index for the JAK1, JAK2, and JAK3 enzymes. These findings suggest that triazolo[1,5-a]pyrimidinone derivatives may be lead compounds for developing potent TYK2-selective inhibitors targeting enzymes' active site.
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Affiliation(s)
- Huseyin Istanbullu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Izmir Kâtip Celebi University, Cigli, Izmir, Turkey
| | - Gunes Coban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey.
| | - Ezgi Turunc
- Department of Biochemistry, Faculty of Pharmacy, Izmir Kâtip Celebi University, Cigli, Izmir, Turkey
| | - Cagla Disel
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Bilge Debelec Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
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Ţînţaş ML, Peauger L, Barré A, Papamicaël C, Besson T, Sopkovà-de Oliveira Santos J, Gembus V, Levacher V. Design, synthesis and preliminary biological evaluation of rivastigmine-INDY hybrids as multitarget ligands against Alzheimer's disease by targeting butyrylcholinesterase and DYRK1A/CLK1 kinases. RSC Med Chem 2024; 15:963-980. [PMID: 38516603 PMCID: PMC10953492 DOI: 10.1039/d3md00708a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Based on a multitarget approach implementing rivastigmine-INDY hybrids 1, we identified a set of pseudo-irreversible carbamate-type inhibitors of eqBuChE that, after carbamate transfer at the active site serine residue, released the corresponding INDY analogues 2 endowed with hDYRK1A/hCLK1 kinases inhibitory properties. A SAR study and molecular docking investigation of both series of compounds 1 and 2 revealed that appropriate structural modifications at the carbamate moiety and at the N-appendage of the benzothiazole core led to potent and selective eqBuChE inhibitors with IC50 up to 27 nM and potent hDYRK1A and hCLK1 inhibitors with IC50 up to 106 nM and 17 nM respectively. Pleasingly, identification of the matched pair of compounds 1b/2b with a good balance between inhibition of eqBuChE and hDYRK1A/hCLK1 kinases (IC50 = 68 nM and IC50 = 529/54 nM, respectively) further validated our multitarget approach based on a sequential mechanism of action. In addition, target compound 1b exhibited a suitable ADMET profile, including good brain permeability and high stability in PBS, encouraging further biological investigation as a drug candidate.
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Affiliation(s)
- Mihaela-Liliana Ţînţaş
- INSA Rouen Normandie, Univ Rouen Normandie, CNRS, COBRA UMR 6014, Normandie Univ INC3M FR 3038 F-76000 Rouen France
| | | | - Anaïs Barré
- INSA Rouen Normandie, Univ Rouen Normandie, CNRS, COBRA UMR 6014, Normandie Univ INC3M FR 3038 F-76000 Rouen France
| | - Cyril Papamicaël
- INSA Rouen Normandie, Univ Rouen Normandie, CNRS, COBRA UMR 6014, Normandie Univ INC3M FR 3038 F-76000 Rouen France
| | - Thierry Besson
- INSA Rouen Normandie, Univ Rouen Normandie, CNRS, COBRA UMR 6014, Normandie Univ INC3M FR 3038 F-76000 Rouen France
| | - Jana Sopkovà-de Oliveira Santos
- UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), Normandie Univ. Bd Becquerel F-14032 Caen France
| | - Vincent Gembus
- VFP Therapies 15 rue François Couperin 76000 Rouen France
| | - Vincent Levacher
- INSA Rouen Normandie, Univ Rouen Normandie, CNRS, COBRA UMR 6014, Normandie Univ INC3M FR 3038 F-76000 Rouen France
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11
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de Albuquerque KCO, da Veiga ADSS, Silveira FT, Campos MB, da Costa APL, Brito AKM, Melo PRDS, Percario S, de Molfetta FA, Dolabela MF. Anti-leishmanial activity of Eleutherine plicata Herb. and predictions of isoeleutherin and its analogues. Front Chem 2024; 12:1341172. [PMID: 38510811 PMCID: PMC10950963 DOI: 10.3389/fchem.2024.1341172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction: Leishmaniasis is caused by protozoa of the genus Leishmania, classified as tegumentary and visceral. The disease treatment is still a serious problem, due to the toxic effects of available drugs, the costly treatment and reports of parasitic resistance, making the search for therapeutic alternatives urgent. This study assessed the in vitro anti-leishmanial potential of the extract, fractions, and isoeleutherin from Eleutherine plicata, as well as the in silico interactions of isoeleutherin and its analogs with Trypanothione Reductase (TR), in addition to predicting pharmacokinetic parameters. Methods: From the ethanolic extract of E. plicata (EEEp) the dichloromethane fraction (FDEp) was obtained, and isoeleutherin isolated. All samples were tested against promastigotes, and parasite viability was evaluated. Isoeleutherin analogues were selected based on similarity in databases (ZINK and eMolecules) to verify the impact on structural change. Results and Discussion: The extract and its fractions were not active against the promastigote form (IC50 > 200 μg/mL), while isoeleutherin was active (IC50 = 25 μg/mL). All analogues have high intestinal absorption (HIA), cell permeability was moderate in Caco2 and low to moderate in MDCK. Structural changes interfered with plasma protein binding and blood-brain barrier permeability. Regarding metabolism, all molecules appear to be CYP3A4 metabolized and inhibited 2-3 CYPs. Molecular docking and molecular dynamics assessed the interactions between the most stable configurations of isoeleutherin, analogue compound 17, and quinacrine (control drug). Molecular dynamics simulations demonstrated stability and favorable interactions with TR. In summary, fractionation contributed to antileishmanial activity and isoleutherin seems to be promising. Structural alterations did not contribute to improve pharmacokinetic aspects and analogue 17 proved to be more promising than isoeleutherin, presenting better stabilization in TR.
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Affiliation(s)
| | | | | | | | - Ana Paula Lima da Costa
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | | | | | - Sandro Percario
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Maria Fâni Dolabela
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Innovation Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
- Faculty of Pharmacy, Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Sciences Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
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12
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Awuni E, Abdallah Musah R. Proposing lead compounds for the development of SARS-CoV-2 receptor-binding inhibitors. J Biomol Struct Dyn 2024; 42:2282-2297. [PMID: 37116068 DOI: 10.1080/07391102.2023.2204505] [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: 08/23/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
The COVID-19 pandemic has had deleterious effects on the world and demands urgent measures to find therapeutic agents to combat the current and related future outbreaks. The entry of SARS-CoV-2 into the host's cell is facilitated by the interaction between the viral spike receptor-binding domain (sRBD) and the human angiotensin-converting enzyme 2 (hACE2). Although the interface of sRBD involved in the sRBD-hACE2 interaction has been projected as a primary vaccine and drug target, currently no small-molecule drugs have been approved for covid-19 treatment targeting sRBD. Herein structure-based virtual screening and molecular dynamics (MD) simulation strategies were applied to identify novel potential small-molecule binders of the SARS-CoV-2 sRBD from an sRBD-targeted compound library as leads for the development of anti-COVID-19 drugs. The library was initially screened against sRBD by using the GOLD docking program whereby 19 compounds were shortlisted based on docking scores after using a control compound to set the selection cutoff. The stability of each compound in MD simulations was used as a further standard to select four hits namely T4S1820, T4589, E634-1449, and K784-7078. Analyses of simulations data showed that the four compounds remained stably bound to sRBD for ≥ 80 ns with reasonable affinities and interacted with pharmacologically important amino acid residues. The compounds exhibited fair solubility, lipophilicity, and toxicity-propensity characteristics that could be improved through lead optimization regimes. The overall results suggest that the scaffolds of T4S1820, E634-1449, and K784-7078 could serve as seeds for developing potent small-molecule inhibitors of SARS-CoV-2 receptor binding and cell entry.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
| | - Radiatu Abdallah Musah
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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13
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Huang YK, Cheng WC, Kuo TT, Yang JC, Wu YC, Wu HH, Lo CC, Hsieh CY, Wong SC, Lu CH, Wu WL, Liu SJ, Li YC, Lin CC, Shen CN, Hung MC, Lin JT, Yeh CC, Sher YP. Inhibition of ADAM9 promotes the selective degradation of KRAS and sensitizes pancreatic cancers to chemotherapy. NATURE CANCER 2024; 5:400-419. [PMID: 38267627 DOI: 10.1038/s43018-023-00720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/19/2023] [Indexed: 01/26/2024]
Abstract
Kirsten rat sarcoma virus (KRAS) signaling drives pancreatic ductal adenocarcinoma (PDAC) malignancy, which is an unmet clinical need. Here, we identify a disintegrin and metalloproteinase domain (ADAM)9 as a modulator of PDAC progression via stabilization of wild-type and mutant KRAS proteins. Mechanistically, ADAM9 loss increases the interaction of KRAS with plasminogen activator inhibitor 1 (PAI-1), which functions as a selective autophagy receptor in conjunction with light chain 3 (LC3), triggering lysosomal degradation of KRAS. Suppression of ADAM9 by a small-molecule inhibitor restricts disease progression in spontaneous models, and combination with gemcitabine elicits dramatic regression of patient-derived tumors. Our findings provide a promising strategy to target the KRAS signaling cascade and demonstrate a potential modality to enhance sensitivity to chemotherapy in PDAC.
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Affiliation(s)
- Yu-Kai Huang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan
| | - Ting-Ting Kuo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Juan-Cheng Yang
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Yang-Chang Wu
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Heng-Hsiung Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chia-Chien Lo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chih-Ying Hsieh
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Sze-Ching Wong
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chih-Hao Lu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wan-Ling Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Shih-Jen Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Chuan Li
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | - Ching-Chan Lin
- Division of Hematology and Oncology, China Medical University Hospital, Taichung, Taiwan
| | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Mien-Chie Hung
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jaw-Town Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, E-Da Hospital, Kaohsiung, Taiwan
| | - Chun-Chieh Yeh
- Department of Medicine, School of Medicine, China Medical University, Taichung, Taiwan.
- Department of Surgery, Organ Transplantation Center, China Medical University Hospital, Taichung, Taiwan.
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan.
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan.
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan.
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan.
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14
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Buttenschoen M, Morris GM, Deane CM. PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences. Chem Sci 2024; 15:3130-3139. [PMID: 38425520 PMCID: PMC10901501 DOI: 10.1039/d3sc04185a] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/17/2023] [Indexed: 03/02/2024] Open
Abstract
The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of crystallographic root-mean-square deviation (RMSD), upon closer inspection, it has become apparent that they often produce physically implausible molecular structures. It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode. It is vital, particularly for deep learning-based methods, that they are also evaluated on steric and energetic criteria. We present PoseBusters, a Python package that performs a series of standard quality checks using the well-established cheminformatics toolkit RDKit. The PoseBusters test suite validates chemical and geometric consistency of a ligand including its stereochemistry, and the physical plausibility of intra- and intermolecular measurements such as the planarity of aromatic rings, standard bond lengths, and protein-ligand clashes. Only methods that both pass these checks and predict native-like binding modes should be classed as having "state-of-the-art" performance. We use PoseBusters to compare five deep learning-based docking methods (DeepDock, DiffDock, EquiBind, TankBind, and Uni-Mol) and two well-established standard docking methods (AutoDock Vina and CCDC Gold) with and without an additional post-prediction energy minimisation step using a molecular mechanics force field. We show that both in terms of physical plausibility and the ability to generalise to examples that are distinct from the training data, no deep learning-based method yet outperforms classical docking tools. In addition, we find that molecular mechanics force fields contain docking-relevant physics missing from deep-learning methods. PoseBusters allows practitioners to assess docking and molecular generation methods and may inspire new inductive biases still required to improve deep learning-based methods, which will help drive the development of more accurate and more realistic predictions.
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15
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Liu J, Li Y, Wang P, Zhang Y, Tian Z. High-efficiency removal of pyrethroids using a redesigned odorant binding protein. JOURNAL OF HAZARDOUS MATERIALS 2024; 463:132856. [PMID: 37913660 DOI: 10.1016/j.jhazmat.2023.132856] [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: 07/14/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
Pyrethroids are ubiquitously present in environmental media and threaten both the ecosystem and human health. To explore effective ways to remove pyrethroids from the environment, an odorant binding protein (OBP) with affinity for various pyrethroids was investigated. Initially, the target OBP, Spodoptera littoralis pheromone binding protein 1 (SlitPBP1), underwent redesign to enhance its affinity for pyrethroids. The modified SlitPBP1E97ND106E demonstrated a substantially increased affinity for deltamethrin (DeltaM), with a dissociation constant of 0.77 ± 0.17 μM. The affinity of SlitPBP1E97ND106E for other pyrethroids also increased to varying extents. Consequently, SlitPBP1E97ND106E displayed a markedly enhanced capability to adsorb and remove pyrethroids. When exposed to free SlitPBP1E97ND106E in solution, the reduction in DeltaM surged from 16.78 ± 0.32% to 97.51 ± 0.56%. SlitPBP1E97ND106E was immobilized by coupling the protein to Ni2+-NTA agarose resin. Liquid chromatography results attested to the superior efficacy of immobilized SlitPBP1E97ND106E in removing pyrethroids, especially DeltaM. No significant differences in pyrethroid removal were detected across various water samples. Our findings introduce a potent tool for pyrethroid removal. A wider range of OBPs can similarly be optimized and applied to remove organic pollutants, including but not limited to pesticides.
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Affiliation(s)
- Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yifan Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Pei Wang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhen Tian
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
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16
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Arkless KL, Pan D, Shankar‐Hari M, Amison RT, Page CP, Rahman KM, Pitchford SC. Stimulation of platelet P2Y 1 receptors by different endogenous nucleotides leads to functional selectivity via biased signalling. Br J Pharmacol 2024; 181:564-579. [PMID: 36694432 PMCID: PMC10952403 DOI: 10.1111/bph.16039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/13/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND AND PURPOSE Platelet function during inflammation is dependent on activation by endogenous nucleotides. Non-canonical signalling via the P2Y1 receptor is important for these non-thrombotic functions of platelets. However, apart from ADP, the role of other endogenous nucleotides acting as agonists at P2Y1 receptors is unknown. This study compared the effects of ADP, Ap3A, NAD+ , ADP-ribose, and Up4A on platelet functions contributing to inflammation or haemostasis. EXPERIMENTAL APPROACH Platelets obtained from healthy human volunteers were incubated with ADP, Ap3A, NAD+ , ADP-ribose, or Up4A, with aggregation and fibrinogen binding measured (examples of function during haemostasis) or before exposure to fMLP to measure platelet chemotaxis (an inflammatory function). In silico molecular docking of these nucleotides to the binding pocket of P2Y1 receptors was then assessed. KEY RESULTS Platelet aggregation and binding to fibrinogen induced by ADP was not mimicked by NAD+ , ADP-ribose, and Up4A. However, these endogenous nucleotides induced P2Y1 -dependent platelet chemotaxis, an effect that required RhoA and Rac-1 activity, but not canonical PLC activity. Analysis of molecular docking of the P2Y1 receptor revealed distinct differences of amino acid interactions and depth of fit within the binding pocket for Ap3A, NAD+ , ADP-ribose, or Up4A compared with ADP. CONCLUSION AND IMPLICATIONS Platelet function (aggregation vs motility) can be differentially modulated by biased-agonist activation of P2Y1 receptors. This may be due to the character of the ligand-binding pocket interaction. This has implications for future therapeutic strategies aimed to suppress platelet activation during inflammation without affecting haemostasis as is the requirement of current ant-platelet drugs. LINKED ARTICLES This article is part of a themed issue on Platelet purinergic receptor and non-thrombotic disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.4/issuetoc.
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Affiliation(s)
- Kate L. Arkless
- Sackler Institute of Pulmonary PharmacologyInstitute of Pharmaceutical Science, King's College LondonLondonUK
| | - Dingxin Pan
- Sackler Institute of Pulmonary PharmacologyInstitute of Pharmaceutical Science, King's College LondonLondonUK
| | - Manu Shankar‐Hari
- School of Immunology and Microbial SciencesKing's College LondonLondonUK
- Centre for Inflammation ResearchThe University of EdinburghEdinburghUK
| | - Richard T. Amison
- Sackler Institute of Pulmonary PharmacologyInstitute of Pharmaceutical Science, King's College LondonLondonUK
| | - Clive P. Page
- Sackler Institute of Pulmonary PharmacologyInstitute of Pharmaceutical Science, King's College LondonLondonUK
| | - Khondaker Miraz Rahman
- Chemical Biology Group, Institute of Pharmaceutical ScienceKing's College LondonLondonUK
| | - Simon C. Pitchford
- Sackler Institute of Pulmonary PharmacologyInstitute of Pharmaceutical Science, King's College LondonLondonUK
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17
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Farhat N, Khan AU. Inhibitors against New Delhi metallo-betalactamase-1 (NDM-1) and its variants endemic in Indian settings along with the laboratory functional gain mutant of NDM-1. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04761-7. [PMID: 38278986 DOI: 10.1007/s10096-024-04761-7] [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: 05/11/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE The emergence of NDM-1 producing bacteria has become common in both hospital and community settings, but no inhibitor has yet been available for clinical treatment. Hence, demanding the urgent need of NDM-1 inhibitors, we initiated to screen broad spectrum inhibitors against NDM natural variants and laboratory mutant. METHODS We used docking and molecular dynamics simulations, in silico pharmacokinetic investigations, and density functional theory calculation to characterize molecules. Furthermore, an in vitro study, including MIC, kinetics, and fluorescence study were carried out to confirm the efficacies of the selected compounds. RESULTS According to the findings of the computational studies, three compounds were effective against NDM variants. Fourfold reduction in MIC of imipenem and meropenem was observed when combined with inhibitors (D2573, D2148, and D63) against blaNDM-1, blaNDM-4, blaNDM-6, and blaNDM-1Q123A, while twofold reduction in MIC of imipenem and meropenem was observed against blaNDM-5 and blaNDM-7. Similarly in the presence of inhibitors (D2573, D2148, and D63) the efficiency of nitrocefin hydrolysis by NDM-4, NDM-6, and Q123A decreases to much more extent as compared to NDM-5 and NDM-7. These results showed that the efficacy of these broad spectrum inhibitors decreases with increasing resistance of NDM variants. CONCLUSION This is the first time inhibitors were tested against different NDM natural variants which are endemic in Indian settings. Moreover, a functional gain laboratory mutant was also checked for their efficacies. We may propose these molecules for the pre-clinical trial to further translate.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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18
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_3] [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] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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19
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Gervasoni S, Manelfi C, Adobati S, Talarico C, Biswas AD, Pedretti A, Vistoli G, Beccari AR. Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative. Int J Mol Sci 2023; 25:450. [PMID: 38203621 PMCID: PMC10779154 DOI: 10.3390/ijms25010450] [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: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rarely employed. The present study aims to assess if multiple docking calculations can prove successful in target prediction. In detail, the docking simulations submitted to the MEDIATE initiative are utilized to predict the viral targets involved in the hits retrieved by a recently published cytopathic screening. Multiple docking results are combined by the EFO approach to develop target-specific consensus models. The combination of multiple docking simulations enhances the performances of the developed consensus models (average increases in EF1% value of 40% and 25% when combining three and two docking runs, respectively). These models are able to propose reliable targets for about half of the retrieved hits (31 out of 59). Thus, the study emphasizes that docking simulations might be effective in target identification and provide a convincing validation for the collaborative strategies that inspire the MEDIATE initiative. Disappointingly, cross-target and cross-program correlations suggest that common scoring functions are not specific enough for the simulated target.
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Affiliation(s)
- Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
- Department of Physics, Università di Cagliari, I-09042 Monserrato, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Sara Adobati
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Akash Deep Biswas
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
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20
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Farhat N, Mujahid S, Khan AU. Mechanistic Approach of Effective Combination of Antibiotics Against Clinical Bacterial Strains Having New Delhi Metallo-Beta-Lactamase Variants and Functional Gain Laboratory Mutant. Curr Microbiol 2023; 81:41. [PMID: 38108895 DOI: 10.1007/s00284-023-03553-0] [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: 07/03/2023] [Accepted: 11/05/2023] [Indexed: 12/19/2023]
Abstract
Antimicrobial resistance has emerged as a serious issue for physicians and health-care workers treating infections that could lead to the next pandemic. One of the key resistance mechanisms is beta-lactamases. Although several beta-lactamase inhibitors in combination with antibiotics have been created and are being utilized in clinical settings, resistance to these formulations has also been evolving in the bacterial population due to their distinct targets. In this study we used effective combination of antibiotic as an approach to inhibit multidrug resistance bacteria. We used four combinations and checked its efficacy against NDM (New Delhi Metallo-beta-lactamase) variants and functional gain laboratory mutant by employing FICI, enzyme kinetics, fluorescence and computational biology approaches (Docking and Molecular Dynamics Simulation). FICI values of all the combinations were either less than 0.5 or equal to 0.5. Binding features acquired by spectroscopic techniques showed important interaction and complex formation between drugs and enzymes with decreased ksv and kq values. In steady-state kinetics, a reduction in hydrolytic efficiency of enzymes was shown by cooperative binding behaviour when they were treated with different drugs. We have also tested functional gain laboratory mutant developed in our lab, keeping in view that if in future upcoming variants of this kind be emerged then these mutants could also be subsided by combinational therapy. This study identifies three other combinations better than fluoroquinolones effective against NDM variants and laboratory mutant.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Sameera Mujahid
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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21
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Pignatti E, Kollar J, Hafele E, Schuster D, Steele RE, Vogt B, Schumacher C, Groessl M. Structural and clinical characterization of CYP11B2 inhibition by dexfadrostat phosphate. J Steroid Biochem Mol Biol 2023; 235:106409. [PMID: 37827219 DOI: 10.1016/j.jsbmb.2023.106409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
Aldosterone synthase (CYP11B2) represents a promising drug target because its genetic dysregulation is causally associated with cardiovascular disease, its autonomous activity leads to primary aldosteronism, and its deficiency leads to salt wasting syndromes. The serendipitous discovery that the dextro-rotatory stereoisomer of the racemic aromatase (CYP19A1) inhibitor CGS16949A mediates potent CYP11B2 inhibition led to the purification and clinical development of dexfadrostat phosphate. To characterize the pharmacophore of dexfadrostat phosphate, structure-based enzyme coordination with CYP11B2, CYP11B1 and CYP19A1 was combined with steroid turnover upon in vitro and clinical treatment. Dexfadrostat, but not its 5S-enantiomer (5S-fadrozole), precisely coordinates with the catalytic heme moiety in the space of the CYP11B2 substrate binding pocket forming a tight and stable complex. Conversely, neither rigid nor flexible docking led to a plausible coordination geometry for dexfadrostat in steroid 11β-hydroxylase (CYP11B1 - orthologue to CYP11B2) or in CYP19A1. The inhibitory preference of dexfadrostat was confirmed in vitro using an adrenal cortex-derived cell line. Dexfadrostat phosphate treatment of healthy subjects in the context of a clinical phase 1 study led to a dose-dependent decrease in urinary aldosterone secretion, accompanied by an increase in urinary corticosterone and deoxycorticosterone metabolites. Increased urinary corticosterone metabolites are indicative of CYP11B2 (18-oxidase) inhibition with clinical features reminiscent of patients with inborn corticosterone methyloxidase type II deficiency. An off-target effect on CYP19A1 was not observed as indicated by no clinical changes in testosterone and estradiol levels. Therefore, dexfadrostat exhibits the ideal structural features for binding and catalytic inhibition of CYP11B2 but not CYP11B1. Clinically, treatment with dexfadrostat phosphate leads to suppression of aldosterone levels by inhibiting predominantly one or both final CYP11B2-mediated reactions.
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Affiliation(s)
- Emanuele Pignatti
- Department of Pediatric Endocrinology, Diabetology and Metabolism, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland.
| | - Jakub Kollar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Evelyn Hafele
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Daniela Schuster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Bruno Vogt
- Department of Nephrology and Hypertension, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
| | | | - Michael Groessl
- Department for BioMedical Research, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland; Department of Nephrology and Hypertension, University Hospital Inselspital, University of Bern, 3010 Bern, Switzerland
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22
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Alabdulraheem ZTJ, Durdagi S. Ab initio and comparative 3D modeling of FAM222A-encoded protein and target-driven-based virtual screening for the identification of novel therapeutics against Alzheimer's disease. J Mol Graph Model 2023; 125:108575. [PMID: 37552909 DOI: 10.1016/j.jmgm.2023.108575] [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: 01/29/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
The complex nature of Alzheimer's disease (AD) makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - the production of amyloid-beta plaques and tau tangles - are considered to be linked to AD. A genetic marker for brain atrophy, FAM222A, has been identified by the unique cross-phenotype meta-analysis of genetics imaging and the molecular features show an interaction between the protein aggregatin encoded by FAM222A and amyloid beta (Aβ)-peptide (1-42) via its N-terminal Aβ binding domain, thus increasing Aβ aggregation. Function of Aggregatin protein is unclear, and its 3D structure has not been investigated in experimental analysis, so far. Hence, in the present study, first time in literature, 3D models of FAM222A-encoded Aggregatin were systematically constructed by applying diverse homology modeling approaches and they were used as target structures at the virtual screening of FDA-approved drugs and drugs currently under research in clinical trials. Then, the identified hit molecules were chosen for further molecular dynamics (MD) simulations and post-MD analyses. Our integrated ligand-based and protein-driven-based virtual screening results show that Cefpiramide, Diniprofylline, Fostriecin, and Droperidol may target Aggregatin.
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Affiliation(s)
- Zeyad Tareq Jasim Alabdulraheem
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey; Molecular Therapy Laboratory, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul, Turkey; Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey.
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23
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Mandour YM, Refaat E, Hassanein HD. Anticancer activity, phytochemical investigation and molecular docking insights of Citrullus colocynthis (L.) fruits. Sci Rep 2023; 13:20038. [PMID: 37973959 PMCID: PMC10654702 DOI: 10.1038/s41598-023-46867-6] [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: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Cancer disease is regarded as one of the most significant public health issues, regardless of economic standards. Medicinal plants are now regarded as a natural source of anticancer medicines due to their antioxidant and anti-mutagenic actions. Cucurbitaceae is considered to be one of the most economically significant families. One family species is Citrullus colocynthis (L.), which has a high concentration of many active secondary chemical metabolites. Various C. colocynthis plant extracts showed cytotoxicity against some cancer cells. This study aims to identify the C. colocynthis fruit components and determine whether they have anticancer action against MIA PaCa-2 and A431 cells. High-Performance Liquid Chromatography/Quadrupole Time of Flight/Mass Spectrometry (HPLC/QTOF/MS); the technique was accustomed to investigate the compounds of the ethyl acetate (EtOAc) fruit extract. Anticancer activity was investigated on both MIAPaCa-2 and A-431 cell lines. DPPH assay for antioxidant activity was carried out. Molecular modelling was employed to help understand the molecular basis for the observed anticancer activity. 24 compounds were tentatively identified by comparing the extract's fragmentation pattern in positive mode against reference compounds spectra and literature. The EtOAc extract of C. colocynthis had effective positive results on cancer cells (MIAPaCa-2 and A-431) and was characterized by slight or no harmful effect on normal (healthy) cells. For the DPPH assay, EtOAc and BuOH extracts exhibited high antioxidant activity (86 and 76%, respectively) compared with the oxidative potential of the standard compound (Caffeic acid, 98%). One of the major cucurbitacin derivatives that LC/MS tentatively identified in the EtOAc extract was Cucurbita-5(10),6,23-triene-3β,25-diol. During this study, docking experiments and MD simulations were carried out, which suggested the anti-pancreatic cancer activity of C. colocynthis extract to be attributed to EGFR inhibition by Cucurbita-5(10),6,23-triene-3β,25-diol. Therefore, expansion of this type of research should be encouraged in the hope of obtaining natural therapeutics for cancerous tumors in the future, having the advantage of being cheaper, safer, and with fewer side effects.
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Affiliation(s)
- Yasmine M Mandour
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, 11578, Egypt
| | - Esraa Refaat
- Pharmacognosy Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Heba D Hassanein
- Chemistry of Medicinal Plant Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Giza, Egypt.
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24
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Kaboudi N, Krüger N, Hamzeh-Mivehroud M. Development of novel ligands against SARS-CoV-2 M pro enzyme: an in silico and in vitro Study. Mol Inform 2023; 42:e202300120. [PMID: 37590494 DOI: 10.1002/minf.202300120] [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: 05/31/2023] [Revised: 07/22/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Despite tremendous efforts made by scientific community during the outbreak of COVID-19 pandemic, this disease still remains as a public health concern. Although different types of vaccines were globally used to reduce the mortality, emergence of new variants of SARS-CoV-2 is a challenging issue in COVID-19 pharmacotherapy. In this context, target therapy of SARS-CoV-2 by small ligands is a promising strategy. METHODS In this investigation, we applied ligand-based virtual screening for finding novel molecules based on nirmatrelvir structure. Various criteria including drug-likeness, ADME, and toxicity properties were applied for filtering the compounds. The selected candidate molecules were subjected to molecular docking and dynamics simulation for predicting the binding mode and binding free energy, respectively. Then the molecules were experimentally evaluated in terms of antiviral activity against SARS-CoV-2 and toxicity assessment. RESULTS The results demonstrated that the identified compounds showed inhibitory activity towards SARS-CoV-2 Mpro . CONCLUSION In summary, the introduced compounds may provide novel scaffold for further structural modification and optimization with improved anti SARS-CoV-2 Mpro activity.
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Affiliation(s)
- Navid Kaboudi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nadine Krüger
- Platform Infection Models, German Primate Center-Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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25
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Farhat N, Khan AU. Repurposing FDA approved drug molecules against A B C classes of β-lactamases: a computational biology and molecular dynamics simulations study. J Biomol Struct Dyn 2023:1-15. [PMID: 37909541 DOI: 10.1080/07391102.2023.2276890] [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: 05/10/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
β-lactamase are the main resistance factor for β-lactam antibiotics in Gram-negative bacteria. Since β-lactam antibiotics are being utilised as an antimicrobial agents extensively for the past 70 years, a large number of β-lactam-inactivating β-lactamases have been produced by bacteria. Here, we employed a structure-based drug discovery approach to identify and assess the efficacy of a potential medication that might block the β-lactamases which hydrolyse antibiotics. The FDA-approved medications were subjected to virtual screening, molecular docking, molecular dynamics simulations, density functional theory, and covalent docking against the β-lactamases. We identified diosmin, hidrosmin, monoxuritin and solasulfone as β-lactamase inhibitors which are authorised for therapeutic use in humans. These medications interact in a remarkable variety of non-covalent ways with the conserved residues in the substrate-binding pocket of the β-lactamases. Diosmin has been identified as an inhibitor that binds covalently to the NDM-1 a class B metallo-betalactamase. After experimental validation and clinical demonstration, this study offers adequate evidence for the therapeutic use of these drugs for controlling multidrug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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26
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Rodrigues Dutra JV, Santos IA, Grosche VR, Jardim ACG, de Aguiar RS, Junior NN, José DP. L protein characterization and in silico screening of putative broad range target molecules for pathogenic mammarenaviruses from South America. J Biomol Struct Dyn 2023:1-19. [PMID: 37817533 DOI: 10.1080/07391102.2023.2268186] [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: 06/13/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
The genus Mammarenavirus belonging to the family Arenaviridae encompasses pathogenic viral species capable of triggering severe diseases in humans, causing concern for the health system due to the high fatality rate associated with them. Currently, there is a dearth of specific therapies against pathogens of the genus. Natural products isolated from plants have impacted the development of drugs against several diseases. The Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE) database offers several natural compounds with antimicrobial activities that can be used in the development of new antiviral drugs. In this context, here we modeled the arenavirus L protein, multifunctional machinery essential for the viral replicative cycle, making this enzyme a potential candidate for targeting the development of antivirals against genus pathogens. Using the modeled L protein, a virtual screening was performed, which suggested eleven molecules from the NuBBE database that binds to the active site of the L protein, which was promising in the in silico predictions of absorption and toxicity analysis. The NuBBE 1642 molecule proved to be the best candidate for four of the five species evaluated, acting as a possible broad-spectrum molecule. Additionally, our results showed that the L protein is highly conserved among species of the genus, as well as presenting close phylogenetic relationships between many of the species studied, strengthening its candidacy as a therapeutic target. The data presented here demonstrate that some NuBBE molecules are potential ligands for the L protein of arenaviruses, which may help to contain possible outbreaks.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- João Victor Rodrigues Dutra
- Federal University of Triângulo Mineiro, Iturama, Minas Gerais, Brazil
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Igor Andrade Santos
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Victória Riquena Grosche
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
- São Paulo State University, São José do Rio Preto, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
- São Paulo State University, São José do Rio Preto, Brazil
| | - Renato Santana de Aguiar
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nilson Nicolau Junior
- Laboratory of Molecular Modeling, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
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27
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Borges A, de Oliveira IP, Lescano CH, Parreira RLT, Orenha RP, da Silva de Laurentiz R. Molecular interaction analysis of the lignans from Piper cubeba in complex with Haemonchus contortus phosphomethyltransferase. Vet Parasitol 2023; 321:110001. [PMID: 37549491 DOI: 10.1016/j.vetpar.2023.110001] [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: 04/18/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
In vitro larvicidal assays carried out previously by our research group with cubebin, dihydrocubebin and hinokinin, lignans extracted from the fruits of Piper cubeba, against Haemonchus contortus larvae showed strong action larvicidal these compounds. Hinokinin was the most active (EC50 = 0.34 µg/mL) with strong action on the cuticle of the larvae as observed by scanning electron microscopy of the L3 stage. Therefore, to understand the mechanism of action of these compounds in silico studies were carried out using the enzyme phosphomethyltransferase of Haemonchus contortus that contain PMT-1 and PMT-2 di-domains responsible for phosphocholine synthesis, which is one of the main lipids in nematodes. This pathway is not found in mammals, so this enzyme is an important biological target for the development of new anthelmintics. Results of molecular docking, molecular dynamic and a density functional theory calculations studies with the three lignans show few interactions with PMT-1. However, hinokinin has important interactions with PMT-2, that can deactivate the enzyme and interrupt the phosphocholine synthesis, which is an essential compound for the development and maintenance of the nematode cuticle and its survive. Therefore, the previous results of the in vitro assay allied with in silico results, now realized; suggest that hinokinin may be a possible selective target for the development of new anthelmintics against Haemonchus contortus since the PMT-2 domain is present in this nematode.
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Affiliation(s)
- Alexandre Borges
- Universidade Estadual Paulista, Departamento de Física e Química, Faculdade de Engenharia de Ilha Solteira, Ilha Solteira, SP, Brazil; Faculdade de Medicina, Centro Universitário de Santa Fé do Sul - UNIFUNEC, Santa Fé do Sul, SP, Brazil
| | - Ivan Pires de Oliveira
- Universidade Federal de Minas Gerais, Instituto de Ciências Agrícolas, Montes Claros, MG, Brazil
| | | | | | - Renato Pereira Orenha
- Universidade de Franca, Centro de Pesquisas em Ciências Exatas e Tecnológicas, Franca, SP, Brazil
| | - Rosangela da Silva de Laurentiz
- Universidade Estadual Paulista, Departamento de Física e Química, Faculdade de Engenharia de Ilha Solteira, Ilha Solteira, SP, Brazil.
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28
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Mufti A, Feriani A, Ouchari W, Mandour YM, Tlili N, Ibrahim MA, Mahmoud MF, Sobeh M. Leonotis ocymifolia (Burm.f.) Iwarsson aerial parts aqueous extract mitigates cisplatin-induced nephrotoxicity via attenuation of inflammation, and DNA damage. Front Pharmacol 2023; 14:1221486. [PMID: 37593171 PMCID: PMC10428015 DOI: 10.3389/fphar.2023.1221486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Herein, we explored the protective effect of Leonotis ocymifolia (Burm.f.) Iwarsson aerial parts extract (LO) against cisplatin (CP)-induced nephrotoxicity in rats and profiled their phytocontents. A total of 31 compounds belonging to organic and phenolic acids and their glycosides as well as flavonoids and their O- and C-glycosides were identified through LC-MS/MS. The DPPH and FRAP assays revealed that the extract had powerful antioxidant properties. The in vivo results demonstrated that administering LO extract for 30 days (40 and 80 mg/kg b. w.) significantly improved the altered renal injury markers via reducing creatinine (high dose only) and uric acid levels compared to the Cp-group. The deleterious action of cisplatin on renal oxidative stress markers (GSH, MDA, SOD, and CAT) were also mitigated by LO-pretreatment. The reduction of the inflammatory marker (IL-6), and inhibition of DNA fragmentation, highlighted the prophylactic action of LO in kidney tissue. Molecular docking followed by a 100 ns molecular dynamic simulation analyses revealed that, amongst the 31 identified compounds in LO, chlorogenic and caffeoylmalic acids had the most stable binding to IL-6. The nephroprotective effects were further confirmed by histopathological observations, which showed improvement in ultrastructural changes induced by cisplatin. The observed findings reinforce the conclusion that L. ocymifolia extract exerts nephroprotective properties, which could be related to its antioxidant and anti-inflammatory activities. Further studies are required to determine the therapeutic doses and the proper administration time.
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Affiliation(s)
- Afoua Mufti
- Laboratory of Biotechnology and Biomonitoring of the Environment and Oasis Ecosystems, Faculty of Sciences of Gafsa, University of Gafsa, Gafsa, Tunisia
| | - Anouar Feriani
- Laboratory of Biotechnology and Biomonitoring of the Environment and Oasis Ecosystems, Faculty of Sciences of Gafsa, University of Gafsa, Gafsa, Tunisia
| | - Wafae Ouchari
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Yasmine M. Mandour
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Cairo, Egypt
| | - Nizar Tlili
- Institut Supérieur des Sciences et Technologies de L’Environnement, Université de Carthage, Carthage, Tunisia
| | | | - Mona F. Mahmoud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mansour Sobeh
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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29
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Sanram S, Aunkham A, Robinson R, Suginta W. Structural displacement model of chitooligosaccharide transport through chitoporin. J Biol Chem 2023; 299:105000. [PMID: 37394001 PMCID: PMC10406626 DOI: 10.1016/j.jbc.2023.105000] [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: 02/20/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023] Open
Abstract
VhChiP is a chitooligosaccharide-specific porin identified in the outer membrane of Vibrio campbellii type strain American Type Culture Collection BAA 1116. VhChiP contains three identical subunits, and in each subunit, the 19-amino acid N-terminal segment serves as a molecular plug (the "N-plug") that controls the closed/open dynamics of the neighboring pores. In this study, the crystal structures of VhChiP lacking the N-plug were determined in the absence and presence of chitohexaose. Binding studies of sugar-ligand interactions by single-channel recordings and isothermal microcalorimetry experiments suggested that the deletion of the N-plug peptide significantly weakened the sugar-binding affinity due to the loss of hydrogen bonds around the central affinity sites. Steered molecular dynamic simulations revealed that the movement of the sugar chain along the sugar passage triggered the ejection of the N-plug, while the H-bonds transiently formed between the reducing end GlcNAc units of the sugar chain with the N-plug peptide may help to facilitate sugar translocation. The findings enable us to propose the structural displacement model, which enables us to understand the molecular basis of chitooligosaccharide uptake by marine Vibrio bacteria.
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Affiliation(s)
- Surapoj Sanram
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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30
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Oyedele AQK, Ogunlana AT, Boyenle ID, Adeyemi AO, Rita TO, Adelusi TI, Abdul-Hammed M, Elegbeleye OE, Odunitan TT. Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices. Mol Divers 2023; 27:1879-1903. [PMID: 36057867 PMCID: PMC9441019 DOI: 10.1007/s11030-022-10523-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
The continuous approval of covalent drugs in recent years for the treatment of diseases has led to an increased search for covalent agents by medicinal chemists and computational scientists worldwide. In the computational parlance, molecular docking which is a popular tool to investigate the interaction of a ligand and a protein target, does not account for the formation of covalent bond, and the increasing application of these conventional programs to covalent targets in early drug discovery practice is a matter of utmost concern. Thus, in this comprehensive review, we sought to educate the docking community about the realization of covalent docking and the existence of suitable programs to make their future virtual-screening events on covalent targets worthwhile and scientifically rational. More interestingly, we went beyond the classical description of the functionality of covalent-docking programs down to selecting the 'best' program to consult with during a virtual-screening campaign based on receptor class and covalent warhead chemistry. In addition, we made a highlight on how covalent docking could be achieved using random conventional docking software. And lastly, we raised an alert on the growing erroneous molecular docking practices with covalent targets. Our aim is to guide scientists in the rational docking pursuit when dealing with covalent targets, as this will reduce false-positive results and also increase the reliability of their work for translational research.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Chemistry, University of New Haven, West Haven, CT, USA
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria.
- Department of Chemistry and Biochemsitry, University of Maryland, Maryland, USA.
- College of Health Sciences, Crescent University, Abeokuta, Nigeria.
| | | | - Temionu Oluwakemi Rita
- Department of Medical Laboratory Technology, Lagos State College of Health, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Misbaudeen Abdul-Hammed
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluwabamise Emmanuel Elegbeleye
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Tope Tunji Odunitan
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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Wegermann CA, Pirota V, Monzani E, Casella L, Costa LAS, Novato WTG, Machini MT, da Costa Ferreira AM. Interaction studies of oxindole-derivatives with β-amyloid peptides inhibiting its aggregation induced by metal ions. J Inorg Biochem 2023; 245:112227. [PMID: 37156056 DOI: 10.1016/j.jinorgbio.2023.112227] [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: 12/19/2022] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023]
Abstract
Some hydrazones and Schiff bases derived from isatin, an endogenous oxindole formed in the metabolism of tryptophan, were obtained to investigate their effects on in vitro aggregation of β-amyloid peptides (Aβ), macromolecules implicated in Alzheimer's disease. Some hydrazone ligands, prepared by condensation reactions of isatin with hydrazine derivatives, showed a large affinity binding to the synthetic peptides Aβ, particularly to Aβ1-16. Measurements by NMR spectroscopy indicated that those interactions occur mainly at the metal binding site of the peptide, involving His6, His13, and His14 residues, and that hydrazone E-diastereoisomer interacts preferentially with the amyloid peptides. Experimental results were consistent with simulations using a docking approach, where it is demonstrated that the amino acid residues Glu3, His6, His13, and His14 are those that mostly interact with the ligands. Further, these oxindole-derived ligands can efficiently chelate copper(II) and zinc(II) ions, forming moderate stable [ML] 1:1 species. The corresponding formation constants were determined by UV/Vis spectroscopy, by titrations of the ligands with increasing amounts of metal salts, and the obtained log K values were in the range 2.74 to 5.11. Both properties, good affinity for amyloid peptides, and reasonably good capacity of chelating biometal ions, like copper and zinc, can explain the efficient inhibition of Aβ fragments aggregation, as shown by experiments carried out with the oxindole derivatives in the presence of metal ions.
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Affiliation(s)
- Camila Anchau Wegermann
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Valentina Pirota
- Dipartimento di Chimica, Università degli Studi di Pavia, Pavia, Italy.
| | - Enrico Monzani
- Dipartimento di Chimica, Università degli Studi di Pavia, Pavia, Italy.
| | - Luigi Casella
- Dipartimento di Chimica, Università degli Studi di Pavia, Pavia, Italy.
| | - Luiz Antônio Sodré Costa
- NEQC - Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, MG, Brazil.
| | - Willian Tássio Gomes Novato
- NQTCM, Núcleo de Química Teórica e Computacional de Macaé, Instituto Multidisciplinar de Química, CM UFRJ Macaé, Universidade Federal do Rio de Janeiro, RJ, Brazil.
| | - M Teresa Machini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Ana Maria da Costa Ferreira
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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32
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Zaman N, Azam SS. Discrete Dynamics of Warhead Modulation on Covalent Inhibition of Oxyr: A QM/MM Study. J Phys Chem B 2023. [PMID: 37377002 DOI: 10.1021/acs.jpcb.2c07376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The bacterial transcriptional factor OxyR, a peroxide sensor conserved in bacterial virulence pathways, has the capability to exhibit exceptional reactivity toward hydrogen peroxide (H2O2). H2O2 is essential for oxidizing cysteine thiolates to maintain cellular redox homeostasis and is dispensable for bacterial growth that can potentially mitigate drug resistance, thus underlining OxyR as a valuable target. We employ quantum mechanics/molecular mechanics (QM/MM) umbrella sampling (US) simulations at the DFTB3/MM level of theory and propose a reaction mechanism with four potential covalent inhibitors. The potential of mean force reveals the direct role of intrinsic reactivity of inhibitors, for instance, benzothiophenes and modified experimental inhibitors with methyl oxo-enoate warhead-activated carbonyl samples in the first step of reaction, which shed light on the significance of proton transfer indispensable for full inhibition, whereas the nitrile inhibitor undergoes a stepwise mechanism with a small proton-transfer energy barrier and lower imaginary frequencies that materialize instantly after nucleophilic attack. To unveil the molecular determinants of respective binding affinities, transition states along the reaction path are optimized and characterized with B3LYP 6-31+G(d,p). Furthermore, the post-simulation analysis indicates the catalytic triad (His130/Cys199/Thr129), thermodynamically favored for inhibition, which restricts water molecules from acting as the potential source of protonation/deprotonation. This study thus serves as a preamble to add variation in the proposed structures and unveils the impact of functional groups lying in warheads that modulate the kinetics of proton transfer, which will certainly aid to design more selective and efficient irreversible inhibitors of OxyR.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
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33
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Sokouti B, Hamzeh-Mivehroud M. 6D-QSAR for predicting biological activity of human aldose reductase inhibitors using quasar receptor surface modeling. BMC Chem 2023; 17:63. [PMID: 37349775 DOI: 10.1186/s13065-023-00970-x] [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: 12/10/2022] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
The application of QSAR analysis dates back a half-century ago and is currently continuously employed in any rational drug design. The multi-dimensional QSAR modeling can be a promising tool for researchers to develop reliable predictive QSAR models for designing novel compounds. In the present work, we studied inhibitors of human aldose reductase (AR) to generate multi-dimensional QSAR models using 3D- and 6D-QSAR methods. For this purpose, Pentacle and Quasar's programs were used to produce the QSAR models using corresponding dissociation constant (Kd) values. By inspecting the performance metrics of the generated models, we achieved similar results with comparable internal validation statistics. However, considering the externally validated values, 6D-QSAR models provide significantly better prediction of endpoint values. The obtained results suggest that the higher the dimension of the QSAR model, the higher the performance of the generated model. However, more studies are required to verify these outcomes.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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34
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Mateev E, Georgieva M, Mateeva A, Zlatkov A, Ahmad S, Raza K, Azevedo V, Barh D. Structure-Based Design of Novel MAO-B Inhibitors: A Review. Molecules 2023; 28:4814. [PMID: 37375370 DOI: 10.3390/molecules28124814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
With the significant growth of patients suffering from neurodegenerative diseases (NDs), novel classes of compounds targeting monoamine oxidase type B (MAO-B) are promptly emerging as distinguished structures for the treatment of the latter. As a promising function of computer-aided drug design (CADD), structure-based virtual screening (SBVS) is being heavily applied in processes of drug discovery and development. The utilization of molecular docking, as a helping tool for SBVS, is providing essential data about the poses and the occurring interactions between ligands and target molecules. The current work presents a brief discussion of the role of MAOs in the treatment of NDs, insight into the advantages and drawbacks of docking simulations and docking software, and a look into the active sites of MAO-A and MAO-B and their main characteristics. Thereafter, we report new chemical classes of MAO-B inhibitors and the essential fragments required for stable interactions focusing mainly on papers published in the last five years. The reviewed cases are separated into several chemically distinct groups. Moreover, a modest table for rapid revision of the revised works including the structures of the reported inhibitors together with the utilized docking software and the PDB codes of the crystal targets applied in each study is provided. Our work could be beneficial for further investigations in the search for novel, effective, and selective MAO-B inhibitors.
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Affiliation(s)
- Emilio Mateev
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University-Sofia, 1000 Sofia, Bulgaria
| | - Maya Georgieva
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University-Sofia, 1000 Sofia, Bulgaria
| | - Alexandrina Mateeva
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University-Sofia, 1000 Sofia, Bulgaria
| | - Alexander Zlatkov
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University-Sofia, 1000 Sofia, Bulgaria
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Debmalya Barh
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India
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35
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Barzegar-Fallah A, Alimoradi H, Dunlop JL, Torbati E, Baird SK. Serotonin type-3 receptor antagonists selectively kill melanoma cells through classical apoptosis, microtubule depolymerisation, ERK activation, and NF-κB downregulation. Cell Biol Toxicol 2023; 39:1119-1135. [PMID: 34654991 DOI: 10.1007/s10565-021-09667-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/28/2021] [Indexed: 12/26/2022]
Abstract
Malignant melanoma is a highly metastatic tumour, resistant to treatment. Serotonin type-3 (5-HT3) receptor antagonists, such as tropisetron and ondansetron, are well-tolerated antiemetic drugs commonly used to prevent nausea caused by chemotherapy or radiotherapy. We investigated the anticancer effects of these drugs on melanoma cancer cell lines WM-266-4 and B16F10 with or without paclitaxel. We constructed IC50 curves and performed Chou-Talalay analysis, using data obtained with the MTT assay. Flow cytometry and fluorescent microscopy were used to examine characteristics of the cell cycle, cell death and cytoskeleton changes. Protein levels and activation were analysed by western blotting and molecular docking studies carried out. Data were analysed by one way ANOVA and post hoc testing. Ondansetron and tropisetron showed selective concentration-dependent cytotoxicity in melanoma cell lines WM-266-4 and B16F10. The effect in combination with paclitaxel was synergistic. The drugs did not cause cell cycle arrest but did promote characteristics of classical apoptosis, including accumulation of subG1 DNA, cleaved caspase-3, mitochondrial membrane permeability and phosphatidylserine exposure. As well, the cytosolic calcium level in the melanoma cells was enhanced, phosphorylated ERK1/2 induced and NF-κB inhibited. Finally, the formation of microtubules was shown to be impaired in melanoma cells treated with ondansetron or tropisetron. Docking studies were used to predict that these drugs could bind to the colchicine binding site on the tubulin molecule. Antiemetic drugs, already given in combination with chemotherapy, may enhance the cytotoxic effect of chemotherapy, following successful delivery to the tumour site.
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Affiliation(s)
- Anita Barzegar-Fallah
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand
| | - Houman Alimoradi
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand
| | - Jessica L Dunlop
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand
| | - Elham Torbati
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sarah K Baird
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, New Zealand.
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36
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Duay SS, Yap RCY, Gaitano AL, Santos JAA, Macalino SJY. Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs. Int J Mol Sci 2023; 24:ijms24119289. [PMID: 37298256 DOI: 10.3390/ijms24119289] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Malaria continues to be a global health threat, with approximately 247 million cases worldwide. Despite therapeutic interventions being available, patient compliance is a problem due to the length of treatment. Moreover, drug-resistant strains have emerged over the years, necessitating urgent identification of novel and more potent treatments. Given that traditional drug discovery often requires a great deal of time and resources, most drug discovery efforts now use computational methods. In silico techniques such as quantitative structure-activity relationship (QSAR), docking, and molecular dynamics (MD) can be used to study protein-ligand interactions and determine the potency and safety profile of a set of candidate compounds to help prioritize those tested using assays and animal models. This paper provides an overview of antimalarial drug discovery and the application of computational methods in identifying candidate inhibitors and elucidating their potential mechanisms of action. We conclude with the continued challenges and future perspectives in the field of antimalarial drug discovery.
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Affiliation(s)
- Searle S Duay
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Rianne Casey Y Yap
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Arturo L Gaitano
- Chemistry Department, Adamson University, Manila 1000, Philippines
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37
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Ondrová K, Zůvalová I, Vyhlídalová B, Krasulová K, Miková E, Vrzal R, Nádvorník P, Nepal B, Kortagere S, Kopečná M, Kopečný D, Šebela M, Rastinejad F, Pu H, Soural M, Rolfes KM, Haarmann-Stemmann T, Li H, Mani S, Dvořák Z. Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female mice. Nat Commun 2023; 14:2728. [PMID: 37169746 PMCID: PMC10174618 DOI: 10.1038/s41467-023-38478-6] [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: 11/27/2020] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
The human aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is a pivotal regulator of human physiology and pathophysiology. Allosteric inhibition of AhR was previously thought to be untenable. Here, we identify carvones as noncompetitive, insurmountable antagonists of AhR and characterize the structural and functional consequences of their binding. Carvones do not displace radiolabeled ligands from binding to AhR but instead bind allosterically within the bHLH/PAS-A region of AhR. Carvones do not influence the translocation of ligand-activated AhR into the nucleus but inhibit the heterodimerization of AhR with its canonical partner ARNT and subsequent binding of AhR to the promoter of CYP1A1. As a proof of concept, we demonstrate physiologically relevant Ahr-antagonism by carvones in vivo in female mice. These substances establish the molecular basis for selective targeting of AhR regardless of the type of ligand(s) present and provide opportunities for the treatment of disease processes modified by AhR.
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Affiliation(s)
- Karolína Ondrová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Iveta Zůvalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Barbora Vyhlídalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kristýna Krasulová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Eva Miková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Radim Vrzal
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petr Nádvorník
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Binod Nepal
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sandhya Kortagere
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Biochemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Fraydoon Rastinejad
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Hua Pu
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Miroslav Soural
- Department of Organic Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | | | - Hao Li
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sridhar Mani
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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38
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Jasilionis A, Plotka M, Wang L, Dorawa S, Lange J, Watzlawick H, van den Bergh T, Vroling B, Altenbuchner J, Kaczorowska A, Pohl E, Kaczorowski T, Nordberg Karlsson E, Freitag‐Pohl S. AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. Protein Sci 2023; 32:e4585. [PMID: 36721347 PMCID: PMC9929850 DOI: 10.1002/pro.4585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple-drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β-fold with multiple secondary structure elements omitted or shortened compared with protein structures of similar proteins. The functional characterization of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity toward thermophilic and mesophilic bacteria strains containing Orn-type or DAP-type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterized with a temperature optimum at 85°C. The extraordinary high melting temperature Tm 102.6°C confirms fold stability up to approximately 100°C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.
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Affiliation(s)
- Andrius Jasilionis
- Division of Biotechnology, Department of ChemistryLund UniversityLundSweden
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
| | - Lei Wang
- Institute of Biomedical GeneticsUniversity of StuttgartStuttgartGermany
| | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
| | | | | | | | | | | | - Anna‐Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of BiologyUniversity of GdanskGdanskPoland
| | - Ehmke Pohl
- Department of BiosciencesDurham UniversityDurhamUK
- Department of ChemistryDurham UniversityDurhamUK
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of BiologyUniversity of GdanskGdanskPoland
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39
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Nicolella HD, Ribeiro AB, Munari CC, Melo MR, Ozelin SD, da Silva LHD, Marquele-Oliveira F, Orenha RP, Veneziani RCS, Parreira RLT, Tavares DC. Antimelanoma effect of manool in 2D cell cultures and reconstructed human skin models. J Biochem Mol Toxicol 2023; 37:e23282. [PMID: 36541366 DOI: 10.1002/jbt.23282] [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: 03/28/2022] [Revised: 11/03/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Melanoma is the most aggressive and lethal type of skin cancer, characterized by therapeutic resistance. In this context, the present study aimed to investigate the cytotoxic potential of manool, a diterpene from Salvia officinalis L., in human (A375) and murine (B16F10) melanoma cell lines. The analysis of cytotoxicity using the XTT assay showed the lowest IC50 after 48 h of treatment with the manool, being 17.6 and 18.2 µg/ml for A375 and B16F10, respectively. A selective antiproliferative effect of manool was observed on the A375 cells based on the colony formation assay, showing an IC50 equivalent to 5.6 µg/ml. The manool treatments led to 43.5% inhibition of the A375 cell migration at a concentration of 5.0 µg/ml. However, it did not affect cell migration in the B16F10 cells. Cell cycle analysis revealed that the manool interfered in the cell cycle of the A375 cells, blocking the G2/M phase. No changes in the cell cycle were observed in the B16F10 cells. Interestingly, manool did not induce apoptosis in the A375 cells, but apoptosis was observed after treatment of the B16F10 cells. Additionally, manool showed an antimelanoma effect in a reconstructed human skin model. Furthermore, in silico studies, showed that manool is stabilized in the active sites of the tubulin dimer with comparable energy concerning taxol, indicating that both structures can inhibit the proliferation of cancer cells. Altogether, it is concluded that manool, through the modulation of the cell cycle, presents a selective antiproliferative activity and a potential antimelanoma effect.
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40
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You Q, Li C, Sun J, Palade V, Pan F. Entropy-based lamarckian quantum-behaved particle swarm optimization for flexible ligand docking. Mol Inform 2023; 42:e2200080. [PMID: 36720014 DOI: 10.1002/minf.202200080] [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: 04/14/2022] [Revised: 09/02/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
AutoDock is a widely used software for flexible ligand docking problems since it is open source and easy to be implemented. In this paper, a novel hybrid algorithm is proposed and applied in the docking environment of AutoDock version 4.2.6 in order to enhance the accuracy and the efficiency for dockings with flexible ligands. This search algorithm, called entropy-based Lamarckian quantum-behaved particle swarm optimization (ELQPSO), is a combination of the QPSO with an entropy-based update strategy and the Solis and Wet local search (SWLS) method. By using the PDBbind core set v.2016, the ELQPSO is compared with the Lamarckian genetic algorithm (LGA), Lamarckian particle swarm optimization (LPSO) and Lamarckian QPSO (LQPSO). The experimental results reveal that the corresponding docking program of ELQPSO, named as EQDOCK in this paper, has a competitive performance in dealing with the protein-ligand docking problems. Moreover, for the test cases with different number of torsions, the EQDOCK outperforms the other three docking programs in finding docking conformations with small root mean squared deviation (RMSD) values in most cases. In particular, it has an advantage of solving highly flexible ligand docking problems over the others.
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Affiliation(s)
- Qi You
- Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Wuxi, Jiangsu, PR China
| | - Chao Li
- Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Wuxi, Jiangsu, PR China
| | - Jun Sun
- Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Wuxi, Jiangsu, PR China
| | - Vasile Palade
- Centre for Computational Science and Mathematical Modelling, Coventry University, Coventry, UK
| | - Feng Pan
- Key Laboratory of Advanced Process Control for Light Industry (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, PR China
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Roldán-Martín L, Sodupe M, Maréchal JD. Computational assessment of the impact of Cu(II) and Al(III) on β-amyloid 42 fibrils: Binding sites, structural stability, and possible physiological implications. Front Neurosci 2023; 17:1110311. [PMID: 36814794 PMCID: PMC9940836 DOI: 10.3389/fnins.2023.1110311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/09/2023] Open
Abstract
One of Alzheimer's disease major hallmarks is the aggregation of β-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the β-amyloid (Aβ42) fibrillary structure. Through classical and Gaussian accelerated molecular dynamics, it has been observed that the metal-free fiber shows a hinge fan-like motion of the S-shaped structure, maintaining the general conformation. Upon metal coordination, distinctive patterns are observed depending on the metal. Cu(II) binds to the flexible N-terminal region and induces structural changes that could ultimately disrupt the fibrillary structure. In contrast, Al(III) binding takes place with the residues Glu22 and Asp23, and its binding reinforces the core stability of the system. These results give clues on the molecular impact of the interaction of metal ions with the aggregates and sustain their non-innocent roles in the evolution of the illness.
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Ribeiro AB, Nicolella HD, da Silva LHD, Mejía JAA, Tanimoto MH, Ambrósio SR, Bastos JK, Orenha RP, Parreira RLT, Tavares DC. Guttiferone E Displays Antineoplastic Activity Against Melanoma Cells. PLANTA MEDICA 2023; 89:158-167. [PMID: 36170858 DOI: 10.1055/a-1890-5446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Guttiferone E (GE) is a benzophenone found in Brazilian red propolis. In the present study, the effect of GE on human (A-375) and murine (B16-F10) melanoma cells was investigated. GE significantly reduced the cellular viability of melanoma cells in a time-dependent manner. In addition, GE demonstrated antiproliferative effect, with IC50 values equivalent to 9.0 and 6.6 µM for A-375 and B16-F10 cells, respectively. The treatment of A-375 cells with GE significantly increased cell populations in G0/G1 phase and decreased those in G2/M phase. Conversely, on B16-F10 cells, GE led to a significant decrease in the populations of cells in G0/G1 phase and concomitantly an increase in the population of cells in phase S. A significantly higher percentage of apoptotic cells was observed in A-375 (43.5%) and B16-F10 (49.9%) cultures after treatment with GE. Treatments with GE caused morphological changes and significant decrease to the melanoma cells' density. GE (10 µM) inhibited the migration of melanoma cells, with a higher rate of inhibition in B16-F10 cells (73.4%) observed. In addition, GE significantly reduced the adhesion of A375 cells, but showed no effect on B16-F10. Treatment with GE did not induce changes in P53 levels in A375 cultures. Molecular docking calculations showed that GE is stable in the active sites of the tubulin dimer with a similar energy to taxol chemotherapy. Taken together, the data suggest that GE has promising antineoplastic potential against melanoma.
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Affiliation(s)
| | | | | | | | - Matheus Hikaru Tanimoto
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Jairo Kenupp Bastos
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Renato Pereira Orenha
- University of Franca, Avenida Dr. Armando Salles Oliveira, Franca, São Paulo, Brazil
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Zangerl-Plessl EM, Wu W, Sanguinetti MC, Stary-Weinzinger A. Binding of RPR260243 at the intracellular side of the hERG1 channel pore domain slows closure of the helix bundle crossing gate. Front Mol Biosci 2023; 10:1137368. [PMID: 36911523 PMCID: PMC9996038 DOI: 10.3389/fmolb.2023.1137368] [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: 01/04/2023] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
The opening and closing of voltage-dependent potassium channels is dependent on a tight coupling between movement of the voltage sensing S4 segments and the activation gate. A specific interaction between intracellular amino- and carboxyl-termini is required for the characteristically slow rate of channel closure (deactivation) of hERG1 channels. Compounds that increase hERG1 channel currents represent a novel approach for prevention of arrhythmia associated with prolonged ventricular repolarization. RPR260243 (RPR), a quinoline oxo-propyl piperidine derivative, inhibits inactivation and dramatically slows the rate of hERG1 channel deactivation. Here we report that similar to its effect on wild-type channels, RPR greatly slows the deactivation rate of hERG1 channels missing their amino-termini, or of split channels lacking a covalent link between the voltage sensor domain and the pore domain. By contrast, RPR did not slow deactivation of C-terminal truncated hERG1 channels or D540K hERG1 mutant channels activated by hyperpolarization. Together, these findings indicate that ability of RPR to slow deactivation requires an intact C-terminus, does not slow deactivation by stabilizing an interaction involving the amino-terminus or require a covalent link between the voltage sensor and pore domains. All-atom molecular dynamics simulations using the cryo-EM structure of the hERG1 channel revealed that RPR binds to a pocket located at the intracellular ends of helices S5 and S6 of a single subunit. The slowing of channel deactivation by RPR may be mediated by disruption of normal S5-S6 interactions.
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Affiliation(s)
| | - Wei Wu
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research & Training Institute, Division of Cardiovascular Medicine, University of Utah, Salt Lake City, UT, United States
| | - Michael C Sanguinetti
- 3 Department of Internal Medicine, Division of Cardiovascular Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt LakeCity, UT, United States
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Evaluation of In Vitro and In Silico Anti-Alzheimer Potential of Nonpolar Extracts and Essential Oil from Mentha piperita. Foods 2023; 12:foods12010190. [PMID: 36613406 PMCID: PMC9818812 DOI: 10.3390/foods12010190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023] Open
Abstract
The anticholinesterase and antioxidant activities with chemical composition and molecular docking of essential oil and nonpolar extracts of Mentha piperita were evaluated using enzymatic and chemical methods. Molecular docking tools were used to explain the interaction of the major chemical constituents with the enzymes. GC/MS analyses revealed that the main compounds in M. piperita essential oil were l-menthone (43.601%) followed by pulegone (21.610%), linolenic acid (25.628%), and l-menthone (10.957%), representing the major compounds of the petroleum ether extract. Imidazoquinoline (7.767%) and 17-N-acetyl-oroidine (5.363%) were the major constituents of the chloroform extract. Linolenic acid (19.397%) and l-menthone (6.336%) were the most abundant compounds in the hexane extract. The M. piperita essential oil and nonpolar extracts showed moderate antioxidant activity. The essential oil showed the most promising anticholinesterase activity with IC50 = 10.66 ± 0.12 µg/mL and IC50 = 16.33 ± 0.03 µg/mL against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), respectively, close to galantamine in AChE and more active in BChE, followed by the interesting activity in the petroleum ether extract with IC50 = 23.42 ± 3.06 µg/mL in AChE and IC50 = 62.00 ± 3.22 µg/mL in BChE. The docking experiments showed that among the seven major identified compounds, N-acetyl-17-oroidine showed the highest binding score (63.01 in AChE and 63.68 in BChE). This compound was found to bind the catalytic and peripheral sites, resulting in more potent inhibitory activity than galantamine, which only binds to the catalytic site. These findings suggested the possible use of M. piperita essential oil and nonpolar extracts as a potential source of alternative natural anti-Alzheimer compounds.
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Ţînţaş ML, Peauger L, Alix F, Papamicaël C, Besson T, Sopková-de Oliveira Santos J, Gembus V, Levacher V. Straightforward Access to a New Class of Dual DYRK1A/CLK1 Inhibitors Possessing a Simple Dihydroquinoline Core. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010036. [PMID: 36615235 PMCID: PMC9822041 DOI: 10.3390/molecules28010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The DYRK (Dual-specificity tyrosine phosphorylation-regulated kinase) family of protein kinases is involved in the pathogenesis of several neurodegenerative diseases. Among them, the DYRK1A protein kinase is thought to be implicated in Alzheimer's disease (AD) and Down syndrome, and as such, has emerged as an appealing therapeutic target. DYRKs are a subset of the CMGC (CDK, MAPKK, GSK3 and CLK) group of kinases. Within this group of kinases, the CDC2-like kinases (CLKs), such as CLK1, are closely related to DYRKs and have also sparked great interest as potential therapeutic targets for AD. Based on inhibitors previously described in the literature (namely TG003 and INDY), we report in this work a new class of dihydroquinolines exhibiting inhibitory activities in the nanomolar range on hDYRK1A and hCLK1. Moreover, there is overwhelming evidence that oxidative stress plays an important role in AD. Pleasingly, the most potent dual kinase inhibitor 1p exhibited antioxidant and radical scavenging properties. Finally, drug-likeness and molecular docking studies of this new class of DYRK1A/CLK1 inhibitors are also discussed in this article.
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Affiliation(s)
- Mihaela-Liliana Ţînţaş
- INSA Rouen Normandie, Univ. Rouen Normandie, CNRS UMR 6014 COBRA, FR 3038, F-76000 Rouen, France
| | - Ludovic Peauger
- VFP Therapies, 15 rue François Couperin, 76000 Rouen, France
| | - Florent Alix
- VFP Therapies, 15 rue François Couperin, 76000 Rouen, France
| | - Cyril Papamicaël
- INSA Rouen Normandie, Univ. Rouen Normandie, CNRS UMR 6014 COBRA, FR 3038, F-76000 Rouen, France
- Correspondence: (C.P.); (V.G.); (V.L.); Tel.: +33-023-552-2485 (V.L.)
| | - Thierry Besson
- INSA Rouen Normandie, Univ. Rouen Normandie, CNRS UMR 6014 COBRA, FR 3038, F-76000 Rouen, France
| | - Jana Sopková-de Oliveira Santos
- UNICAEN, CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Normandie Univ., Bd Becquerel, F-14032 Caen, France
| | - Vincent Gembus
- VFP Therapies, 15 rue François Couperin, 76000 Rouen, France
- Correspondence: (C.P.); (V.G.); (V.L.); Tel.: +33-023-552-2485 (V.L.)
| | - Vincent Levacher
- INSA Rouen Normandie, Univ. Rouen Normandie, CNRS UMR 6014 COBRA, FR 3038, F-76000 Rouen, France
- Correspondence: (C.P.); (V.G.); (V.L.); Tel.: +33-023-552-2485 (V.L.)
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Nabi F, Ahmad O, Khan YA, Nabi A, Md Amiruddin H, Abul Qais F, Masroor A, Hisamuddin M, Uversky VN, Khan RH. Computational studies on phylogeny and drug designing using molecular simulations for COVID-19. J Biomol Struct Dyn 2022; 40:10753-10762. [PMID: 34278954 DOI: 10.1080/07391102.2021.1947895] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since the first appearance of a novel coronavirus pneumonia (NCP) caused by a novel human coronavirus, and especially after the infection started its rapid spread over the world causing the COVID-19 (coronavirus disease 2019) pandemics, a very substantial part of the scientific community is engaged in the intensive research dedicated to finding of the potential therapeutics to cure this disease. As repurposing of existing drugs represents the only instant solution for those infected with the virus, we have been working on utilization of the structure-based virtual screening method to find some potential medications. In this study, we screened a library of 646 FDA approved drugs against the receptor-binding domain of the SARS-CoV-2 spike (S) protein and the main protease of this virus. Scoring functions revealed that some of the anticancer drugs (such as Pazopanib, Irinotecan, and Imatinib), antipsychotic drug (Risperidone), and antiviral drug (Raltegravir) have a potential to interact with both targets with high efficiency. Further we performed molecular dynamics simulations to understand the evolution in protein upon interaction with drug. Also, we have performed a phylogenetic analysis of 43 different coronavirus strains infecting 12 different mammalian species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Yawar Ali Khan
- Department of Bioengeenering, Intergral University, Lucknow, India
| | - Anas Nabi
- Department of Computer Science, Vivekanand College of Technology and Management, Aligarh, India
| | - Hashmi Md Amiruddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Aiman Masroor
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia.,Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Li Y, Zhang L, Wang Y, Zou J, Yang R, Luo X, Wu C, Yang W, Tian C, Xu H, Wang F, Yang X, Li L, Yang S. Generative deep learning enables the discovery of a potent and selective RIPK1 inhibitor. Nat Commun 2022; 13:6891. [PMID: 36371441 PMCID: PMC9653409 DOI: 10.1038/s41467-022-34692-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
The retrieval of hit/lead compounds with novel scaffolds during early drug development is an important but challenging task. Various generative models have been proposed to create drug-like molecules. However, the capacity of these generative models to design wet-lab-validated and target-specific molecules with novel scaffolds has hardly been verified. We herein propose a generative deep learning (GDL) model, a distribution-learning conditional recurrent neural network (cRNN), to generate tailor-made virtual compound libraries for given biological targets. The GDL model is then applied to RIPK1. Virtual screening against the generated tailor-made compound library and subsequent bioactivity evaluation lead to the discovery of a potent and selective RIPK1 inhibitor with a previously unreported scaffold, RI-962. This compound displays potent in vitro activity in protecting cells from necroptosis, and good in vivo efficacy in two inflammatory models. Collectively, the findings prove the capacity of our GDL model in generating hit/lead compounds with unreported scaffolds, highlighting a great potential of deep learning in drug discovery.
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Affiliation(s)
- Yueshan Li
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Liting Zhang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Yifei Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jun Zou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Ruicheng Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xinling Luo
- grid.13291.380000 0001 0807 1581Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chengyong Wu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Wei Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chenyu Tian
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Haixing Xu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Falu Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xin Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Linli Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, 610041 Chengdu, Sichuan China
| | - Shengyong Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
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Ravi D, Sonyanaik B, Sakram B. Green design, synthesis of novel 2-methoxy-3-aryl-1,8-naphthyridines and their antimicrobial activity and molecular docking study. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Sivagami S, Kavitha R, Satanathan S, Rajesh J, Narenkumar J, Parthipan P, Muthusamy K, Alfarhan A. Multicomponent One-pot Synthesis, Characterization and Antimicrobial Screening of 2 Cyanoimino-6-aryl-4-(6-methoxynaphthalen-2-yl)-3,4-dihydro-1H-pyrimidines. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Niosomes: a novel targeted drug delivery system for cancer. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:240. [PMID: 36175809 DOI: 10.1007/s12032-022-01836-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 10/25/2022]
Abstract
Recently, nanotechnology is involved in various fields of science, of which medicine is one of the most obvious. The use of nanoparticles in the process of treating and diagnosing diseases has created a novel way of therapeutic strategies with effective mechanisms of action. Also, due to the remarkable progress of personalized medicine, the effort is to reduce the side effects of treatment paths as much as possible and to provide targeted treatments. Therefore, the targeted delivery of drugs is important in different diseases, especially in patients who receive combined drugs, because the delivery of different drug structures requires different systems so that there is no change in the drug and its effectiveness. Niosomes are polymeric nanoparticles that show favorable characteristics in drug delivery. In addition to biocompatibility and high absorption, these nanoparticles also provide the possibility of reducing the drug dosage and targeting the release of drugs, as well as the delivery of both hydrophilic and lipophilic drugs by Niosome vesicles. Since various factors such as components, preparation, and optimization methods are effective in the size and formation of niosomal structures, in this review, the characteristics related to niosome vesicles were first examined and then the in silico tools for designing, prediction, and optimization were explained. Finally, anticancer drugs delivered by niosomes were compared and discussed to be a suitable model for designing therapeutic strategies. In this research, it has been tried to examine all the aspects required for drug delivery engineering using niosomes and finally, by presenting clinical examples of the use of these nanocarriers in cancer, its clinical characteristics were also expressed.
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