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Torres-Carrillo N, Martínez-López E, Torres-Carrillo NM, López-Quintero A, Moreno-Ortiz JM, González-Mercado A, Gutiérrez-Hurtado IA. Pharmacomicrobiomics and Drug-Infection Interactions: The Impact of Commensal, Symbiotic and Pathogenic Microorganisms on a Host Response to Drug Therapy. Int J Mol Sci 2023; 24:17100. [PMID: 38069427 PMCID: PMC10707377 DOI: 10.3390/ijms242317100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Microorganisms have a close relationship with humans, whether it is commensal, symbiotic, or pathogenic. Recently, it has been documented that microorganisms may influence the response to drug therapy. Pharmacomicrobiomics is an emerging field that focuses on the study of how variations in the microbiome affect the disposition, action, and toxicity of drugs. Two additional sciences have been added to complement pharmacomicrobiomics, namely toxicomicrobiomics, which explores how the microbiome influences drug metabolism and toxicity, and pharmacoecology, which refers to modifications in the microbiome as a result of drug administration. In this context, we introduce the concept of "drug-infection interaction" to describe the influence of pathogenic microorganisms on drug response. This review analyzes the current state of knowledge regarding the relevance of microorganisms in the host's response to drugs. It also highlights promising areas for future research and proposes the term "drug-infection interaction" as an extension of pharmacomicrobiomics.
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Affiliation(s)
- Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Erika Martínez-López
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Nora Magdalena Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Andres López-Quintero
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - José Miguel Moreno-Ortiz
- Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.M.M.-O.); (A.G.-M.)
| | - Anahí González-Mercado
- Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.M.M.-O.); (A.G.-M.)
| | - Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico;
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2
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Hsu MH, Johnson EF. Differential Effects of Clotrimazole on X-Ray Crystal Structures of Human Cytochromes P450 3A5 and 3A4. Drug Metab Dispos 2023; 51:1642-1650. [PMID: 37770228 PMCID: PMC10658909 DOI: 10.1124/dmd.123.001464] [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: 07/21/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023] Open
Abstract
Cytochromes P450 CYP3A5 and CYP3A4 exhibit differential plasticity that underlies differences in drug metabolism and drug-drug interactions. To extend previous studies, CYP3A4 and CYP3A5 were cocrystallized with clotrimazole, a compact ligand that binds to the heme iron in the catalytic center of the active site. Binding studies indicate that clotrimazole exhibits tight binding to CYP3A5 with a binding affinity (Kd) of <0.01 μM like that of CYP3A4. A single clotrimazole is bound to the heme iron in CYP3A4 that triggers expansion of active site cavity that reflects a loss of aromatic interactions between phenylalanine sidechains in the distal active site and increased conformational entropy for the F-F' connector due to reorientation of Phe-304 to accommodate clotrimazole. In contrast to CYP3A4, the CYP3A5 Phe-304 exhibits an induced fit along with Phe-213 to form edge-to-face aromatic interactions with heme-bound clotrimazole. These aromatic interactions between aromatic amino acids propagate by induced fits with a second clotrimazole residing in the distal active site and a third clotrimazole bound in an expanded entrance channel as well as between the three clotrimazoles. The large, expanded entrance channel surrounded by the C-terminal loop and the F' and A' helices in CYP3A5 suggests conformational selection for the binding of clotrimazole due to its large girth, which may also cause the entrance channel to remain open after the binding of the first clotrimazole to the heme iron. The additional binding sites suggest a path for sequential binding of one molecule to reach and bind to the heme iron. SIGNIFICANCE STATEMENT: Clotrimazole binds to the heme iron of CYP3A5 and CYP3A4. In CYP3A5, two clotrimazoles also bind in the distal active site and in an expanded entrance channel. Aromatic interactions between clotrimazoles and phenylalanine sidechains including Phe-304 indicate induced fits for each clotrimazole. In contrast to CYP3A5, displacement of the CYP3A4 Phe-304 rotamer by clotrimazole leads to extensive disruption of phenylalanine interactions that limit the space above the heme, to an expanded active site cavity, and to increased CYP3A4 conformational heterogeneity.
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Affiliation(s)
- Mei-Hui Hsu
- Department of Molecular Medicine, Scripps Research, La Jolla, California
| | - Eric F Johnson
- Department of Molecular Medicine, Scripps Research, La Jolla, California
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3
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Suárez-García J, Cano-Herrera MA, María-Gaviria A, Osorio-Echeverri VM, Mendieta-Zerón H, Arias-Olivares D, Benavides-Melo J, García-Sánchez LC, García-Ortíz J, Becerra-Buitrago A, Valero-Rojas J, Rodríguez-González M, García-Eleno MA, Cuevas-Yañez E. Synthesis, characterization, in-vitro biological evaluation and theoretical studies of 1,2,3-triazoles derived from triclosan as Difenoconazole analogues. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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4
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Sun B, Liu Y, Fan H, An Y, Liu W, Wang Q, Han J. The discovery of novel antifungal phenylpyridines derivatives based on CYP53 binding model. Eur J Med Chem 2022; 242:114676. [PMID: 35994951 DOI: 10.1016/j.ejmech.2022.114676] [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: 04/13/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/15/2022]
Abstract
Benzoates as toxic intermediate are naturally produced by fungal intracellular metabolism, and CYP53 can specific transform the substrates. In the study, we constructed the CYP53 homology model and analyzed the corresponding active region. At the same time, the molecular docking and the structure-based pharmacophore model (SBP) were performed to explore the bind mode of representative CYP53 inhibitors. On the basis, a series of phenylpyridines derivatives were designed as novel CYP53 inhibitors, and their molecular structures were synthesized and evaluated. Compared with the positive control groups, their antifungal activity showed the obvious upward trend. In particular, target compounds (13a, 15b) possessed the excellent biological activity against pathogenic fungi and drug-resistant fungi in vivo and in vitro. The preliminary action mechanism has confirmed that target compounds could inhibit CYP53 activity, and block the metabolism of toxic intermediates (Benzoates). This further induced the accumulation of reactive oxygen species (ROS) through the pattern of mitochondrial depolarization, which eventually caused fungal lysis and death. In summary, the study provided the reasonable computational models, and effectively guided the generation of novel CYP53 antifungal inhibitors.
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Affiliation(s)
- Bin Sun
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China.
| | - Yating Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Haiyan Fan
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Yunfei An
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Wenxia Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Qingpeng Wang
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Jun Han
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
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5
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Desai SP, Zambri MT, Taylor MS. Borinic Acid Catalyzed Regioselective N-Alkylation of Azoles. J Org Chem 2022; 87:5385-5394. [PMID: 35385283 DOI: 10.1021/acs.joc.2c00281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method for regioselective N-alkylation of ambident, azole-type heterocycles with alkene or epoxide electrophiles is described. In the presence of diphenylborinic acid (Ph2BOH) and an amine cocatalyst, heterocyclic nucleophiles such as 1,2,3- and 1,2,4-triazoles, substituted tetrazoles, and purine are activated toward selective N-functionalization. The scope of electrophilic partners includes enones, 2-vinylpyridine, phenyl vinyl sulfone, a dehydroalanine derivative, and epoxides. Mechanistic studies, including in situ 11B NMR spectroscopy and kinetic analysis, are discussed.
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Affiliation(s)
- Shrey P Desai
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Matthew T Zambri
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mark S Taylor
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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6
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Mckenna A, P N Dubey S. Machine Learning Based Predictive Model for the Analysis of Sequence Activity Relationships Using Protein Spectra and Protein Descriptors. J Biomed Inform 2022; 128:104016. [PMID: 35143999 DOI: 10.1016/j.jbi.2022.104016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 11/26/2022]
Abstract
Accurately establishing the connection between a protein sequence and its function remains a focal point within the field of protein engineering, especially in the context of predicting the effects of mutations. From this, there has been a continued drive to build accurate and reliable predictive models via machine learning that allow for the virtual screening of many protein mutant sequences, measuring the relationship between sequence and 'fitness' or 'activity', commonly known as a Sequence-Activity-Relationship (SAR). An important preliminary stage in the building of these predictive models is the encoding of the chosen sequences. Evaluated in this work is a plethora of encoding strategies using the Amino Acid Index database, where the indices are transformed into their spectral form via Digital Signal Processing (DSP) techniques, as well as numerous protein structural and physiochemical descriptors. The encoding strategies are explored on a dataset curated to measure the thermostability of various mutants from a recombination library, designed from parental cytochrome P450s. In this work it was concluded that the implementation of protein spectra in concatenation with protein descriptors, together with the Partial Least Squares Regression (PLS) algorithm, gave the most noteworthy increase in the quality of the predictive models (as described in Encoding Strategy C), highlighting their utility in identifying an SAR. The accompanying software produced for this paper is termed pySAR (Python Sequence-Activity-Relationship), which allows for a user to find the optimal arrangement of structural and or physiochemical properties to encode their specific mutant library dataset; the source code is available at: https://github.com/amckenna41/pySAR.
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Affiliation(s)
- Adam Mckenna
- School of Electronics, Electrical Engineering and Computer Science, Queen's University of Belfast, University Road, BT7 1NN, Belfast, United Kingdom.
| | - Sandhya P N Dubey
- Department of Data Science and Computer Applications, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India.
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7
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Martín-Escolano R, Yiangou L, Kazana E, Robinson GK, Michaelis M, Tsaousis AD. Repurposing in vitro approaches for screening anti-parasitic drugs against the brain-eating amoeba Naegleria fowleri. Int J Parasitol Drugs Drug Resist 2021; 17:204-212. [PMID: 34875573 PMCID: PMC8652063 DOI: 10.1016/j.ijpddr.2021.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
Naegleria fowleri is both a pathogenic and a free-living microbial eukaryote, responsible for the development of primary amoebic meningoencephalitis (PAM) in humans. PAM is a rapid, severe and fatal underestimated infectious disease, which has been reported in countries with warmer climates. The major drawbacks with PAM are the lack of effective therapies and delay in diagnosis. The current frontline treatment presents a low rate of recovery (5%) and severe adverse effects. For example, many drug candidates lack efficacy, since they do not effectively cross the blood-brain-barrier. Consequently, more effective drugs are urgently needed. Herein, we report a new in vitro method suitable for medium- and high-throughput drug discovery assays, using the closely related Naegleria gruberi as a model. We have subsequently used this method to screen a library of 1175 Food and Drug Administration-approved drugs. As a result, we present three drugs (camptothecin, pyrimethamine, and terbinafine) that can be repurposed, and are anticipated to readily cross the blood-brain-barrier with activity against Naegleria species in therapeutically achievable concentrations. Successively, we integrated several in vitro assays that resulted in identifying fast-acting and high amoebicidal drugs. In conclusion, we present a new approach for the identification of anti-Naegleria drugs along with three potential drug candidates for further development for the treatment of PAM.
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Affiliation(s)
- Rubén Martín-Escolano
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Eleanna Kazana
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Gary K Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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8
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Prajapati J, Rao P, Poojara L, Goswami D, Acharya D, Patel SK, Rawal RM. Unravelling the antifungal mode of action of curcumin by potential inhibition of CYP51B: A computational study validated in vitro on mucormycosis agent, Rhizopus oryzae. Arch Biochem Biophys 2021; 712:109048. [PMID: 34600893 DOI: 10.1016/j.abb.2021.109048] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/09/2021] [Accepted: 09/29/2021] [Indexed: 11/28/2022]
Abstract
Like human, fungi too are known to share lot of structural similarities amongst their CYPs (Cytochrome P450 super family of enzymes) which allows antifungal 'azole' compounds to interact with CYPs of human. Clotrimazole, an 'azole' antifungal drug, is a known inhibitor of fungal CYP named CYP51B. Curcumin, a phytochemical obtained from Curcuma longa has the ability to interact with several different human CYPs to induce inhibition. The sequence and the structural similarities amongst both human and fungal CYPs suggest a strong possibility for curcumin to interact with fungal CYP51B to behave like an antifungal agent. To test this hypothesis a study was designed involving mucormycosis agent, Rhizopus oryzae. The ability of curcumin to interact with fungal CYP51B was analysed computationally through molecular docking, MM-GBSA and Molecular Dynamics (MD) simulation assessment. Further, interaction profile for fungal CYP51B-curcumin was compared with human CYP3A4-curcumin, as there are published evidence describing curcumin as an inhibitor of human CYPs. Additionally, to validate in silico findings, an in vitro assay was performed to examine the antifungal potentials of curcumin on the R. oryzae. Conclusive results allow us to determine a plausible mode of action of curcumin to act as an antifungal against a mucormycosis agent.
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Affiliation(s)
- Jignesh Prajapati
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Priyashi Rao
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Lipi Poojara
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Dhaval Acharya
- Department of Microbiology, B N Patel Institute of Paramedical and Sciences, Anand, 388001, Gujarat, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh M Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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9
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Nagao K, Ohmiya H. Carbocation Generation by Organophotoredox Catalysis. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kazunori Nagao
- Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University
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10
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Structure and inhibition of Cryptococcus neoformans sterylglucosidase to develop antifungal agents. Nat Commun 2021; 12:5885. [PMID: 34620873 PMCID: PMC8497620 DOI: 10.1038/s41467-021-26163-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 12/02/2022] Open
Abstract
Pathogenic fungi exhibit a heavy burden on medical care and new therapies are needed. Here, we develop the fungal specific enzyme sterylglucosidase 1 (Sgl1) as a therapeutic target. Sgl1 converts the immunomodulatory glycolipid ergosterol 3β-D-glucoside to ergosterol and glucose. Previously, we found that genetic deletion of Sgl1 in the pathogenic fungus Cryptococcus neoformans (Cn) results in ergosterol 3β-D-glucoside accumulation, renders Cn non-pathogenic, and immunizes mice against secondary infections by wild-type Cn, even in condition of CD4+ T cell deficiency. Here, we disclose two distinct chemical classes that inhibit Sgl1 function in vitro and in Cn cells. Pharmacological inhibition of Sgl1 phenocopies a growth defect of the Cn Δsgl1 mutant and prevents dissemination of wild-type Cn to the brain in a mouse model of infection. Crystal structures of Sgl1 alone and with inhibitors explain Sgl1’s substrate specificity and enable the rational design of antifungal agents targeting Sgl1. Sterylglucosidase 1 (Sgl1) is a virulence factor in Cryptococcus neoformans that modulates fungal pathogenesis and host response. Here, the authors characterize Sgl1 structurally, identify Sgl1 inhibitors, and demonstrate Sgl1 inhibition has efficacy in mouse models of infection.
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11
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Kobayashi R, Shibutani S, Nagao K, Ikeda Z, Wang J, Ibáñez I, Reynolds M, Sasaki Y, Ohmiya H. Decarboxylative N-Alkylation of Azoles through Visible-Light-Mediated Organophotoredox Catalysis. Org Lett 2021; 23:5415-5419. [PMID: 34139122 DOI: 10.1021/acs.orglett.1c01745] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An organophotoredox-catalyzed decarboxylative cross-coupling between azole nucleophiles and aliphatic carboxylic acid-derived redox-active esters is demonstrated. This protocol efficiently installs various tertiary or secondary alkyl fragments onto the nitrogen atom of azole nucleophiles under mild and transition-metal-free conditions. The pyridinium additive successfully inhibits the formation of elimination byproducts from the carbocation intermediate. This reaction is applicable to the synthesis of a protein-degrader-like molecule containing an azole and a thalidomide.
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Affiliation(s)
- Rino Kobayashi
- Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Shotaro Shibutani
- Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kazunori Nagao
- Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Zenichi Ikeda
- Research, Takeda Pharmaceutical Company Limited, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Junsi Wang
- Research, Takeda Pharmaceutical Company Limited, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Ignacio Ibáñez
- Research, Takeda Pharmaceutical Company Limited, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Matthew Reynolds
- Research, Takeda Pharmaceutical Company Limited, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusuke Sasaki
- Research, Takeda Pharmaceutical Company Limited, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Hirohisa Ohmiya
- Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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12
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Liu Y, Cong Y, Zhang C, Fang B, Pan Y, Li Q, You C, Gao B, Zhang JZH, Zhu T, Zhang L. Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement. RSC Adv 2021; 11:12036-12042. [PMID: 35423749 PMCID: PMC8696588 DOI: 10.1039/d1ra00352f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochrome P450 BM3 (BM3) is an important oxidoreductase that is widely used in drug synthesis, chemical synthesis, and other industries. However, as BM3 unquestionably increases costs by consuming a natural cofactor that unstably provides electrons, an alternative biomimetic cofactor with simpler structures represented by nicotinamide mononucleotide (NMNH) has been utilized. Currently, few reports exist on artificially modified BM3 enzymes using NMNH, especially regarding theoretical simulation and calculation. With the cognition of the mechanism in mind, we propose a strategy that optimizes and refines catalytic conformation. Based on constrained molecular dynamics simulation, the distance between N-5 of FAD flavin and C-4 of NMNH is used as a cue for the determination of improved conformation, and the potential positive mutants are subsequently screened virtually in accordance with binding free energy requirements. As a result, the Kcat/KM values of the favorable mutant S848R increased to 205.38% compared to the wild-type BM3 with NMNH. These data indicate that our strategy can be applied for the specific utilization of biomimetic cofactors by oxidoreductases represented by BM3. A rational design strategy was proposed to improve the efficient utilization of alternative biomimetic cofactor by P450 BM3 enzyme.![]()
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Affiliation(s)
- Yao Liu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Chuanxi Zhang
- School of Biotechnology, East China University of Science and Technology Shanghai 200237 China
| | - Bohuan Fang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Yue Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Qiangzi Li
- University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Chun You
- University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Bei Gao
- School of Biotechnology, East China University of Science and Technology Shanghai 200237 China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China.,Department of Chemistry, New York University New York New York 10003 USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
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13
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Lall MS, Bassyouni A, Bradow J, Brown M, Bundesmann M, Chen J, Ciszewski G, Hagen AE, Hyek D, Jenkinson S, Liu B, Obach RS, Pan S, Reilly U, Sach N, Smaltz DJ, Spracklin DK, Starr J, Wagenaar M, Walker GS. Late-Stage Lead Diversification Coupled with Quantitative Nuclear Magnetic Resonance Spectroscopy to Identify New Structure–Activity Relationship Vectors at Nanomole-Scale Synthesis: Application to Loratadine, a Human Histamine H1 Receptor Inverse Agonist. J Med Chem 2020; 63:7268-7292. [DOI: 10.1021/acs.jmedchem.0c00483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Manjinder S. Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Asser Bassyouni
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - James Bradow
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Maria Brown
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark Bundesmann
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jinshan Chen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory Ciszewski
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anne E. Hagen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dennis Hyek
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - Stephen Jenkinson
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Bo Liu
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - R. Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Senliang Pan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Usa Reilly
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Neal Sach
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Daniel J. Smaltz
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Douglas K. Spracklin
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeremy Starr
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Melissa Wagenaar
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory S. Walker
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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Beyzaei H, Malekraisi F, Aryan R, Ghasemi B. Green aqueous synthesis and antimicrobial evaluation of 3,5-disubstituted 1,2,4-triazoles. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02684-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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