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Di Micco S, Ciaglia T, Salviati E, Michela P, Kostrzewa M, Musella S, Schiano Moriello A, Di Sarno V, Smaldone G, Di Matteo F, Capolupo I, Infantino R, Bifulco G, Pepe G, Sommella EM, Kumar P, Basilicata MG, Allarà M, Sánchez-Fernández N, Aso E, Gomez-Monterrey IM, Campiglia P, Ostacolo C, Maione S, Ligresti A, Bertamino A. Novel pyrrole based CB2 agonists: New insights on CB2 receptor role in regulating neurotransmitters' tone. Eur J Med Chem 2024; 269:116298. [PMID: 38493727 DOI: 10.1016/j.ejmech.2024.116298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
The cannabinoid system is one of the most investigated neuromodulatory systems because of its involvement in multiple pathologies such as cancer, inflammation, and psychiatric diseases. Recently, the CB2 receptor has gained increased attention considering its crucial role in modulating neuroinflammation in several pathological conditions like neurodegenerative diseases. Here we describe the rational design of pyrrole-based analogues, which led to a potent and pharmacokinetically suitable CB2 full agonist particularly effective in improving cognitive functions in a scopolamine-induced amnesia murine model. Therefore, we extended our study by investigating the interconnection between CB2 activation and neurotransmission in this experimental paradigm. To this purpose, we performed a MALDI imaging analysis on mice brains, observing that the administration of our lead compound was able to revert the effect of scopolamine on different neurotransmitter tones, such as acetylcholine, serotonin, and GABA, shedding light on important networks not fully explored, so far.
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Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute (EBRIS), Via S. De Renzi 50, 84125, Salerno, Italy
| | - Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Emanuela Salviati
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Perrone Michela
- Department of Experimental Medicine, Pharmacology Division, University of Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Magdalena Kostrzewa
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Simona Musella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Aniello Schiano Moriello
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gerardina Smaldone
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Ilaria Capolupo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Rosmara Infantino
- Department of Experimental Medicine, Pharmacology Division, University of Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giacomo Pepe
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Eduardo M Sommella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Poulami Kumar
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | | | - Marco Allarà
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Nuria Sánchez-Fernández
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy; Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
| | - Ester Aso
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy; Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain
| | - Isabel M Gomez-Monterrey
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907, L'Hospitalet de Llobregat, Spain
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Sabatino Maione
- Department of Experimental Medicine, Pharmacology Division, University of Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Alessia Ligresti
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy; Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907, L'Hospitalet de Llobregat, Spain.
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
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Ciaglia T, Vestuto V, Di Sarno V, Musella S, Smaldone G, Di Matteo F, Napolitano V, Miranda MR, Pepe G, Basilicata MG, Novi S, Capolupo I, Bifulco G, Campiglia P, Gomez-Monterrey I, Snoeck R, Andrei G, Manfra M, Ostacolo C, Lauro G, Bertamino A. Peptidomimetics as potent dual SARS-CoV-2 cathepsin-L and main protease inhibitors: In silico design, synthesis and pharmacological characterization. Eur J Med Chem 2024; 266:116128. [PMID: 38232463 DOI: 10.1016/j.ejmech.2024.116128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
In this paper we present the design, synthesis, and biological evaluation of a new series of peptidomimetics acting as potent anti-SARS-CoV-2 agents. Starting from our previously described Main Protease (MPro) and Papain Like Protease (PLPro) dual inhibitor, CV11, here we disclose its high inhibitory activity against cathepsin L (CTSL) (IC50 = 19.80 ± 4.44 nM), an emerging target in SARS-CoV-2 infection machinery. An in silico design, inspired by the structure of CV11, led to the development of a library of peptidomimetics showing interesting activities against CTSL and Mpro, allowing us to trace the chemical requirements for the binding to both enzymes. The screening in Vero cells infected with 5 different SARS-CoV-2 variants of concerns, highlighted sub-micromolar activities for most of the synthesized compounds (13, 15, 16, 17 and 31) in agreement with the enzymatic inhibition assays results. The compounds showed lack of activity against several different RNA viruses except for the 229E and OC43 human coronavirus strains, also characterized by a cathepsin-L dependent release into the host cells. The most promising derivatives were also evaluated for their chemical and metabolic in-vitro stability, with derivatives 15 and 17 showing a suitable profile for further preclinical characterization.
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Affiliation(s)
- Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gerardina Smaldone
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Valeria Napolitano
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria Rosaria Miranda
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giacomo Pepe
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | | | - Sara Novi
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Ilaria Capolupo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy; European Biomedical Research Institute (EBRIS), Via S. De Renzi 50, 84125, Salerno, Italy
| | - Isabel Gomez-Monterrey
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy
| | - Robert Snoeck
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Michele Manfra
- Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
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Sehrawat R, Rathee P, Rathee P, Khatkar S, Akkol EK, Khatkar A, Sobarzo-Sánchez E. In silico design of novel bioactive molecules to treat breast cancer with chlorogenic acid derivatives: a computational and SAR approach. Front Pharmacol 2023; 14:1266833. [PMID: 38152692 PMCID: PMC10751932 DOI: 10.3389/fphar.2023.1266833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/19/2023] [Indexed: 12/29/2023] Open
Abstract
Introduction: Cancer is a vast group of diseases comprising abnormal cells that multiply and grow uncontrollably, and it is one of the top causes of death globally. Several types of cancers are diagnosed, but the incidence of breast cancer, especially in postmenopausal women, is increasing daily. Chemotherapeutic agents used to treat cancer are generally associated with severe side effects on host cells, which has led to a search for safe and potential alternatives. Therefore, the present research has been conducted to find novel bioactive molecules to treat breast cancer with chlorogenic acid and its derivatives. Chlorogenic acid was selected because of its known activity in the field. Methods: Several chlorogenic acid derivatives were subjected to computational studies such as molecular docking, determination of absorption, distribution, metabolism, and excretion (ADME), druglikeness, toxicity, and prediction of activity spectra for substances (PASS) to develop a potential inhibitor of breast cancer. The Protein Data Bank (PDB) IDs used for docking purposes were 7KCD, 3ERT, 6CHZ, 3HB5, and 1U72. Result: Exhaustive analysis of results has been conducted by considering various parameters, like docking score, binding energy, types of interaction with important amino acid residues in the binding pocket, ADME, and toxicity data of compounds. Among all the selected derivatives, CgE18, CgE11, CgAm13, CgE16, and CgE9 have astonishing interactions, excellent binding energy, and better stability in the active site of targeted proteins. The docking scores of compound CgE18 were -11.63 kcal/mol, -14.15 kcal/mol, and -12.90 kcal/mol against breast cancer PDB IDs 7KCD, 3HB5, and 1U72, respectively. The docking scores of compound CgE11 were -10.77 kcal/mol and -9.11 kcal/mol against breast cancer PDB IDs 3ERT and 6CHZ, respectively, whereas the docking scores of epirubicin hydrochloride were -3.85 kcal/mol, -6.4 kcal/mol, -8.76 kcal/mol, and -10.5 kcal/mol against PDB IDs 7KCD, 3ERT, 6CHZ, and 3HB5. The docking scores of 5-fluorouracil were found to be -5.25 kcal/mol, -3.43 kcal/mol, -3.73 kcal/mol, and -5.29 kcal/mol against PDB IDs 7KCD, 3ERT, 6CHZ, and 3HB5, which indicates the designed compounds have a better docking score than some standard drugs. Conclusion: Taking into account the results of molecular docking, drug likeness analysis, absorption, distribution, metabolism, excretion, and toxicity (ADMET) evaluation, and PASS, it can be concluded that chlorogenic acid derivatives hold promise as potent inhibitors for the treatment of breast cancer.
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Affiliation(s)
- Renu Sehrawat
- School of Medical and Allied Sciences, K. R. Mangalam University, Gurugram, Haryana, India
| | - Priyanka Rathee
- Faculty of Pharmaceutical Sciences, Baba Mastnath University, Rohtak, India
| | - Pooja Rathee
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Sarita Khatkar
- Vaish Institute of Pharmaceutical Education and Research, Rohtak, Haryana, India
| | - Esra Küpeli Akkol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara, Türkiye
| | - Anurag Khatkar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago, Chile
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
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Shi HL, Yuan SW, Xi XQ, Xie YL, Yue C, Zhang YJ, Yao LG, Xue C, Tang CD. Engineering of formate dehydrogenase for improving conversion potential of carbon dioxide to formate. World J Microbiol Biotechnol 2023; 39:352. [PMID: 37864750 DOI: 10.1007/s11274-023-03739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 10/23/2023]
Abstract
Formate dehydrogenase (FDH) is a D-2-hydroxy acid dehydrogenase, which can reversibly reduce CO2 to formate and thus act as non-photosynthetic CO2 reductase. In order to increase catalytic efficiency of formate dehydrogenase for CO2 reduction, two mutants V328I/F285W and V354G/F285W were obtained of which reduction activity was about two times more than the parent CbFDHM2, and the formate production from CO2 catalyzed by mutants were 2.9 and 2.7-fold higher than that of the parent CbFDHM2. The mutants had greater potential in CO2 reduction. The optimal temperature for V328I/F285W and V354G/F285W was 55 °C, and they showed increasement of relative activity under 45 °C to 55 °C compared with parent. The optimal pH for the mutants was 9.0, and they showed excellent stability in pH 4.0-11.5. The kcat/Km values of mutants were 1.75 times higher than that of the parent. Then the molecular basis for its improvement of biochemical characteristics were preliminarily elucidated by computer-aided methods. All of these results further established a solid foundation for molecular modification of formate dehydrogenase and CO2 reduction.
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Affiliation(s)
- Hong-Ling Shi
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, Liaoning, People's Republic of China
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Shu-Wei Yuan
- School of Chemistry and Chemical Engineering, Henan Normal University, 46 Jianshe East Road, Xinxiang, 453007, Henan, People's Republic of China
| | - Xiao-Qi Xi
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Yu-Li Xie
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Chao Yue
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Ying-Jun Zhang
- Henan Engineering Technology Research Center for Mushroom-based Foods, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116024, Liaoning, People's Republic of China.
| | - Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
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Fujita M, Tsuchiya K, Kurohara T, Fukuhara K, Misawa T, Demizu Y. In silico optimization of peptides that inhibit Wnt/β-catenin signaling. Bioorg Med Chem 2023; 84:117264. [PMID: 37003158 DOI: 10.1016/j.bmc.2023.117264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
The Wnt/β-catenin signaling pathway causes transcriptional activation through the interaction between β-catenin and T cell-specific transcription factor (TCF) and regulates a wide variety of cellular responses, including proliferation, differentiation and cell motility. Excessive transcriptional activation of the Wnt/β-catenin pathway is implicated in developing or exacerbating various cancers. We have recently reported that liver receptor homolog-1 (LRH-1)-derived peptides inhibit the β-catenin/TCF interaction. In addition, we developed a cell-penetrating peptide (CPP)-conjugated LRH-1-derived peptide that inhibits the growth of colon cancer cells and specifically inhibits the Wnt/β-catenin pathway. Nonetheless, the inhibitory activity of the CPP-conjugated LRH-1-derived peptide was unsatisfactory (ca. 20 μM), and improving the bioactivity of peptide inhibitors is required for their in vivo applications. In this study, we optimized the LRH-1-derived peptide using in silico design to enhance its activity further. The newly designed peptides showed binding affinity toward β-catenin comparable to the parent peptide. In addition, the CPP-conjugated stapled peptide, Penetratin-st6, showed excellent inhibition (ca. 5 μM). Thus, the combination of in silico design by MOE and MD calculations has revealed that logical molecular design of PPI inhibitory peptides targeting β-catenin is possible. This method can be also applied to the rational design of peptide-based inhibitors targeting other proteins.
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Affiliation(s)
- Minami Fujita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Kiyoshi Fukuhara
- Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
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Aghaie SM, Tabatabaei M, Nazarian S. Bioinformatics design of recombinant chimeric protein containing SipD and LptD immunogens and evaluation of its immunogenicity against Salmonella Typhimurium. Microb Pathog 2023; 175:105959. [PMID: 36581307 DOI: 10.1016/j.micpath.2022.105959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
The growing emergence of resistant bacteria is the current global concern for the humans and animals. Vaccination could be the desirable method to preventing such infectious diseases. Safe and effective vaccines are urgently needed to manage and prevent Salmonella contamination. Subunit vaccines are safe approaches for the protection against Salmonella spp. The bioinformatics methods were performed to determine the gene structure. Gene cassette (rLPSI) was ordered in pET28a (+), and cloned into E.coli BL21 (DE3), and the recombinant protein was expressed using IPTG (1 mM). Mice were immunized by subcutaneous administration of recombinant protein. Then, the mice were challenged by oral administration of 100LD50 of live S. Typhimurium. The Codon adaptation index of the chimeric gene was multiplied by 0.92. Validation results showed that >90% of residues lie in the desired or extra allowed area of the Ramachandran plot. The recombinant protein (65.9 kDa) was expressed in E.coli. Antibody titers in vaccinated mice were significantly different from those in the control groups. Recombinant protein immunization of the mice provided 90% and 70% protection against 10LD50 and 100LD50 of S. Typhimurium, respectively. In general, the results showed the high efficiency of rLPSI chimeric protein as a protective antigen against S. Typhimurium infection. The rLPSI chimeric protein could be an effective recombinant vaccine candidate against S. Typhimurium infection, but more research is needed.
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Affiliation(s)
- Seyed Mojtaba Aghaie
- Department of Pathobiology, Faculty of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mohammad Tabatabaei
- Department of Pathobiology, Faculty of Veterinary Medicine, Shiraz University, Shiraz, Iran.
| | - Shahram Nazarian
- Department of Biology, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran.
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Ardestani H, Nazarian S, Hajizadeh A, Sadeghi D, Kordbacheh E. In silico and in vivo approaches to recombinant multi-epitope immunogen of GroEL provides efficient cross protection against S. Typhimurium, S. flexneri, and S. dysenteriae. Mol Immunol 2022; 144:96-105. [PMID: 35217247 DOI: 10.1016/j.molimm.2022.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Stress or Heat Shock Proteins (HSPs) have been included in various operations like protein folding, autophagy, and apoptosis. HSP families recognize as protective antigens in a wide range of bacteria because they have been conserved through evolution. Due to their homology as well as antigenicity they are competent for applying in cross-protection against bacterial diseases. METHODS In the present study, bioinformatics approaches utilized to design epitope-based construction of Hsp60 (or GroEL) protein. In this regard, potential B-cell and T-cell epitopes except for allergenic sequences were selected by immunoinformatic tools. The structural and functional aspects of the DNA, RNA, and protein levels were assessed by bioinformatics software. Following in silico investigations, recombinant GroEL multi-epitope of Salmonella typhi was expressed, purified, and validated. Mouse groups were immunized with recombinant protein and humoral immune response was measured by enzyme linked immunosorbent assay (ELISA). Animal challenge against Salmonella Typhimurium, Shigella flexneri, and Shigella dysenteriae was evaluated. RESULTS recombinant protein expression and purification with 14.3 kilodaltons (kDa) was confirmed by SDS-PAGE and western blotting. After animal administration, the immunoglobulins evaluated increase after each immunization. Immunized antisera exhibited 80%, 40%, and 40% protection against the lethal dose infection by S. Typhimurium, S. flexneri, and S. dysenteriae respectively. Passive immunization conferred 50%, 30%, and 30% protection in mice against S. Typhimurium, S. flexneri and S. dysentery respectively. In addition, bacterial organ load had exhibited a significant decrease in colony forming unit (CFU) in the liver and spleen of the immunized mice compared to the control. CONCLUSION Our study demonstrates the efficacy of S. Typhi recombinant GroEL multi-epitope to consider as a universal immunogen candidate versus multiple bacterial pathogens.
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Affiliation(s)
- Hassan Ardestani
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran.
| | - Abbas Hajizadeh
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Davoud Sadeghi
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Emad Kordbacheh
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
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Pongsupasa V, Anuwan P, Maenpuen S, Wongnate T. Rational-Design Engineering to Improve Enzyme Thermostability. Methods Mol Biol 2022; 2397:159-78. [PMID: 34813064 DOI: 10.1007/978-1-0716-1826-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The fundamentals of thermostability engineering need to be carried out for proteins with low thermal stability to expand their utilization. Thus, comprehension of the thermal stability regulating factors of proteins is needful for the engineering of their thermostability. Protein engineering aims to overcome their natural limitations in tough conditions by refining protein stability and activity. Rational-design approach requires a crystal structure dataset along with the biophysical information, protein function, and sequence-based data, especially consensus sequence that is favorable for the protein folding during natural evolution. It can be attained by either single- or multiple-point mutation, by which amino acids are changed. In fact, these mutation approaches show several benefits. For example, the offered mutations are produced after an evaluation and design, which raise the chance to acquire favorable mutations. The rational-design engineering can improve the biochemical properties of enzymes, including the kinetic behaviors, substrate specificity, thermostability, and organic solvent tolerance. Moreover, this approach considerably reduces the library size, so less effort and time can be employed. Here, we apply the computational algorithms and programs with experiments to create thermostable enzymes that will be beneficial for future applications.
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9
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González CM, Gaikwad S, Lasanta G, Loureiro J, Nilsson N, Peluso-Iltis C, Rochel N, Mouriño A. Design, synthesis and evaluation of side-chain hydroxylated derivatives of lithocholic acid as potent agonists of the vitamin D receptor (VDR). Bioorg Chem 2021; 115:105202. [PMID: 34339974 DOI: 10.1016/j.bioorg.2021.105202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
A high number of biologically active and low-calcemic secosteroidal ligands of the vitamin D receptor (VDR) have been developed, some of which are already used clinically although with limited success in the treatment of hyperproliferative diseases because the required pharmaceutical dosages induce toxicity. We describe here the in silico design, synthesis, structural analysis and biological evaluation of two novel active lithocholic acid derivatives hydroxylated at the side chain as highly potent inhibitors of atopic dermatitis-relevant keratinocyte inflammation of potential therapeutic interest.
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Affiliation(s)
- Carmen M González
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Sunil Gaikwad
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Gonzalo Lasanta
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Julian Loureiro
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Niclas Nilsson
- LEO Pharma, Open Innovation, Industriparken 55, 2750 Ballerup, Denmark
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France.
| | - Antonio Mouriño
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain.
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10
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Ngo Hanna J, Nziko VDPN, Ntie-Kang F, Mbah JA, Toze FAA. The use of minimal topological differences to inspire the design of novel tetrahydroisoquinoline analogues with antimalarial activity. Heliyon 2021; 7:e07032. [PMID: 34095565 PMCID: PMC8165424 DOI: 10.1016/j.heliyon.2021.e07032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/18/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022] Open
Abstract
A quantitative structure-activity relationship (QSAR) study was conducted using nineteen previously synthesized, and tested 1-aryl-6-hydroxy-1,2,3,4-tetrahydroisoquinolines with proven in vitro activities against Plasmodium falciparum. In order to computationally design and screen potent antimalarial agents, these compounds with known biological activity ranging from 0.697 to 35.978 μM were geometry optimized at the B3LYP/6-311 + G(d,p) level of theory, using the Gaussian 09W software. To calculate the topological differences, the series of the nineteen compounds was superimposed and a hypermolecule obtained with s¯ = 17 and 20 vertices. Other molecular descriptors were considered in order to build a highly predictive QSAR model. These include the minimal topological differences (MTD), LogP, two dimensional polarity surface area (TDPSA), dipole moment (μ), chemical hardness (η), electrophilicity (ω), potential energy (Ep), electrostatic energy (Eele) and number of rotatable bonds (NRB). By using a training set composed of 15 randomly selected compounds from this series, several QSAR equations were derived. The QSAR equations obtained were then used to attempt to predict the IC50 values of 4 remaining compounds in a test (or validation) set. Ten analogues were proposed by a fragment search of a fragment library containing the pharmacophore model of the active compounds contained in the training set. The most active proposed analogue showed a predicted activity within the lower micromolar range.
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Affiliation(s)
- Joelleinsert Ngo Hanna
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon.,Department of Chemistry, Faculty of Science, University of Douala, P. O. Box 24157, Douala, Cameroon
| | | | - Fidele Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon.,Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Institute of Botany, Technical University University Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - James A Mbah
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Flavien A A Toze
- Department of Chemistry, Faculty of Science, University of Douala, P. O. Box 24157, Douala, Cameroon
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11
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Bahadori Z, Shabani AA, Minuchehr Z. Rational design of hyper-glycosylated human follicle-stimulating hormone analogs (a bioinformatics approach). J Biomol Struct Dyn 2021; 40:9114-9125. [PMID: 33998969 DOI: 10.1080/07391102.2021.1924268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-glycosylation is a complex mechanism in which the carbohydrate molecules bind to the Asn amino acid in the N-glycan consensus sequence (AsnXxxThr/Ser sequon, where Xxx is any residue, excluding Pro). Introduction of additional N-linked glycosylation site into proposed location in the protein causes to its hyper-glycosylation and can enhance the protein characteristics to provide promising prospects in treatment. Glycoengineering is a favorably used strategy to design and generate hyper-glycosylated variants. In this research, human follicle-stimulating hormone (HuFSH) was considered to identify appropriate positions for adding novel N-glycan sites. A rational computational strategy was applied to predict functional/structural variations induced through changes in polypeptide chain. We analyzed the amino acid chain of FSH to find out the proper locations to introduce asparagine and/or threonine for creating novel N-glycan positions. This analysis resulted in the recognition of 40 possible N-glycosylation positions, and then the eight adequate ones were chosen for additional investigation. The model validation techniques were used to examine 3-dimensional structures of the chosen mutant proteins. Finally, 2 mutants with a further glycan site were recommended as eligible FSH hyper-glycosylated analogs, which may be regarded for subsequent experimental studies. Our in silico approach may decrease tedious and time-wasting laboratory researches of the mutants.Communicated by Ramaswamy H. Sharma.
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Affiliation(s)
- Zohreh Bahadori
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Students Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Shabani
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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12
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Gaikwad S, González CM, Vilariño D, Lasanta G, Villaverde C, Mouriño A, Verlinden L, Verstuyf A, Peluso-Iltis C, Rochel N, Berkowska K, Marcinkowska E. Lithocholic acid-based design of noncalcemic vitamin D receptor agonists. Bioorg Chem 2021; 111:104878. [PMID: 33853023 DOI: 10.1016/j.bioorg.2021.104878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 12/19/2022]
Abstract
The hypercalcemic effects of the hormone 1α,25-dihydroxyvitamin D3 (calcitriol) and most of known vitamin D metabolites and analogs call for the development of non secosteroidal vitamin D receptor (VDR) ligands as new selective and noncalcemic agonists for treatment of hyperproliferative diseases. We report on the in silico design and stereoselective synthesis of six lithocholic acid derivatives as well as on the calcemic activity of a potent LCA derivative and its crystallographic structure in complex with zVDR LBD. The low calcemic activity of this compound in comparison with the native hormone makes it of potential therapeutic value. Structure-function relationships provide the basis for the development of even more potent and selective lithocholic acid-based VDR ligands.
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Affiliation(s)
- Sunil Gaikwad
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Carmen M González
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Daniel Vilariño
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Gonzalo Lasanta
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Carmen Villaverde
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Antonio Mouriño
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas, Universidad de Santiago de Compostela, Avda das Ciencias s/n, 15782 Santiago de Compostela, Spain.
| | - Lieve Verlinden
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Herestraat 49, bus, 9802, 3000 Leuven, Belgium
| | - Annemieke Verstuyf
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Herestraat 49, bus, 9802, 3000 Leuven, Belgium
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France; Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France.
| | - Klaudia Berkowska
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Ewa Marcinkowska
- Laboratory of Protein Biochemistry, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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13
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Dhiman P, Malik N, Khatkar A. Natural based piperine derivatives as potent monoamine oxidase inhibitors: an in silico ADMET analysis and molecular docking studies. BMC Chem 2020; 14:12. [PMID: 32099971 PMCID: PMC7027018 DOI: 10.1186/s13065-020-0661-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 01/18/2020] [Indexed: 11/10/2022] Open
Abstract
Neurodegenerative disorders follow numerous pathological ways concerning overexpression of monoamine oxidase and formation of reactive oxygen species. The computational design of the piperine derivatives has given the significant MAO inhibitors with considerable antioxidant potential. Molecular docking provided the mechanistic insight of the compounds within the hMAO active site. In the current study we have prepared a series of compounds related to piperine and investigated them through monoamine oxidase A and B assay and evaluated the free radical scavenging activity. The synthesized compounds were analyzed by using in silico techniques within the active site of MAO and the ADMET properties were also calculated. The results obtained in this study indicated the interesting therapeutic potential of some compounds such as 7and 17c as most promising hMAO-A inhibitors whereas compounds 15, 5 and 17b were found as hMAO-B inhibitors. Moreover, we assessed the antioxidant potential of the piperine analogues and compounds 5, 17b, and 7 showed very modest antioxidant activity against DPPH and H2O2 radicals. The outcome of the study indicating that the piperine related derivatives are found as considerable MAO inhibitors and antioxidants. Moreover, the SAR structure activity relationships are depicting the structural features required for the MAO inhibition. In case of MAO activity, good correlations were found among the calculated and experimental results.
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Affiliation(s)
- Priyanka Dhiman
- Department of Pharmaceutical Chemistry, Maharishi Markandeshwar College of Pharmacy, Maharishi Markandeshwar University, Mullana, Haryana 133203 India
| | - Neelam Malik
- Department of Pharmaceutical Chemistry, Maharishi Markandeshwar College of Pharmacy, Maharishi Markandeshwar University, Mullana, Haryana 133203 India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, 124001 India
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14
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Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI. In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice. J Biomol Struct Dyn 2020; 40:3196-3212. [PMID: 33222632 DOI: 10.1080/07391102.2020.1845978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The polyepitope strategy is promising approach for successfully creating a broadly protective flu vaccine, which targets T-lymphocytes (both CD4+ and CD8+) to recognise the most conserved epitopes of viral proteins. In this study, we employed a computer-aided approach to develop several artificial antigens potentially capable of evoking immune responses to different virus subtypes. These antigens included conservative T-cell epitopes of different influenza A virus proteins. To design epitope-based antigens we used experimentally verified information regarding influenza virus T-cell epitopes from the Immune Epitope Database (IEDB) (http://www.iedb.org). We constructed two "human" and two "murine" variants of polyepitope antigens. Amino acid sequences of target polyepitope antigens were designed using our original TEpredict/PolyCTLDesigner software. Immunogenic and protective features of DNA constructs encoding "murine" target T-cell immunogens were studied in BALB/c mice. We showed that mice groups immunised with a combination of computer-generated "murine" DNA immunogens had a 37.5% survival rate after receiving a lethal dose of either A/California/4/2009 (H1N1) virus or A/Aichi/2/68 (H3N2) virus, while immunisation with live flu H1N1 and H3N2 vaccine strains provided protection against homologous viruses and failed to protect against heterologous viruses. These results demonstrate that mechanisms of cross-protective immunity may be associated with the stimulation of specific T-cell responses. This study demonstrates that our computer-aided approach may be successfully used for rational designing artificial polyepitope antigens capable of inducing virus-specific T-lymphocyte responses and providing partial protection against two different influenza virus subtypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sergei I Bazhan
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Denis V Antonets
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Ekaterina V Starostina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N Ilyicheva
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga N Kaplina
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Yu Marchenko
- Department of zoonotic infections and Influenza, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Olga Yu Volkova
- Immunogenetics laboratory, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya Yu Bakulina
- Theoretical Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia.,Laboratory of structural bioinformatics and molecular modeling, Novosibirsk State University, Novosibirsk, Russia
| | - Larisa I Karpenko
- Bioengineering Department, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
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15
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Abstract
Despite diligent vaccination efforts, influenza virus infection remains a major cause for respiratory-related illness across the globe. The less-than-optimal immunity conferred by the currently prescribed seasonal vaccines and protracted production times warrant the development of novel vaccines. Induction of an epitope-focused antibody response targeting known neutralization epitopes is a viable strategy to enhance the breadth of protection against rapidly evolving infectious viruses. We report the development of a design framework to mimic the hemagglutinin (HA) head fragment of H1-subtype viruses by delineating the interaction network of invariant residues lining the receptor binding site (RBS); a site targeted by cross-reactive neutralizing antibodies. The incorporation of multiple sequence alignment information in our algorithm to fix the construct termini and engineer rational mutations facilitates the facile extension of the design to heterologous (subtype-specific) influenza strains. We evaluated our design protocol by generating head fragments from divergent influenza A H1N1 A/Puerto Rico/8/34 and pH1N1 A/California/07/2009 strains that share a sequence identity of only 74.4% within the HA1 subunit. The designed immunogens exhibited characteristics of a well-ordered protein, and bound conformation-specific RBS targeting antibodies with high affinity, a desirable feature for putative vaccine candidates. Additionally, the bacterial expression of these immunogens provides a low-cost, rapidly scalable alternative.
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Affiliation(s)
| | - Shiv Swaroop
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.,Department of Biochemistry, Central University of Rajasthan, Kishangarh, Ajmer, 305817, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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16
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Parmar GR, Shah AP, Sailor GU, Seth AK. In Silico Discovery of Novel Phytoconstituents of Amyris pinnata as a Mitotic Spindle Kinase Inhibitor. Curr Drug Res Rev 2020; 12:175-182. [PMID: 32077837 DOI: 10.2174/2589977512666200220122211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/13/2019] [Accepted: 01/08/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Despite many successes in the discovery of numerous cancer chemotherapeutic agents from natural sources, some of the moieties were dropped because of its inefficiency or serious toxicity. Mitosis is an ordered series of fundamentally mechanical events in which identical copies of the genome are moved to two discrete locations within the dividing cell. The crucial role of the mitotic spindle in cell division has identified, which is an important target in cancer chemotherapy. In the present study, we are reporting molecular docking studies and in silico pharmacokinetic profiles of selected phytoconstituents obtained from Amyris pinnata. METHODS Molecular docking studies of selected phytoconstituents were performed using iGEMDOCK. The crystal structure of the protein was exported from the protein data bank (PDB id: 4C4H). In silico pharmacokinetic profile of selected phytoconstituents was performed using the SWISSADME server. RESULTS Compound AMNP6 showed higher binding affinity as compared to the standard ligand. All the selected phytoconstituents have passed the Lipinski rule of five and shown no violations. CONCLUSION Good binding affinity and drug likeliness of the AMNP6 suggest that it can be further investigated and explored as mitotic spindle kinase inhibitor in cancer disease.
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Affiliation(s)
- Ghanshyam R Parmar
- Department of Pharmacy, Sumandeep Vidyapeeth, Vadodara-391760, Gujarat, India
| | - Ashish P Shah
- Department of Pharmacy, Sumandeep Vidyapeeth, Vadodara-391760, Gujarat, India
| | - Girish U Sailor
- Department of Pharmacy, Sumandeep Vidyapeeth, Vadodara-391760, Gujarat, India
| | - Avinash Kumar Seth
- Department of Pharmacy, Sumandeep Vidyapeeth, Vadodara-391760, Gujarat, India
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17
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Ma H, Qiu P, Harvey PJ, Li X, Zhang Z, Xu Q, Liang J, Kaas Q, Craik DJ, Yang J, Jiang T, Bi X, Yu R. In Silico Design of MDM2-Targeting Peptides from a Naturally Occurring Constrained Peptide. ChemMedChem 2019; 14:1710-1716. [PMID: 31444979 DOI: 10.1002/cmdc.201900366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/20/2019] [Indexed: 01/10/2023]
Abstract
Naturally occurring constrained peptides are frequently used as scaffolds for bioactive peptide grating due to their high stability. Here, we used in silico methods to design several constrained peptides comprising a scorpion toxin scaffold, a MDM2 binding epitope, and a cluster of positively charged residues. The designed peptides displayed varied binding affinity to MDM2 despite differing by only one or two residues. One of the peptides, SC426, had nanomolar binding affinity (KD =6.6±2.6 nm) to MDM2, and exhibited stronger inhibitory activity on the proliferation of HCT116 cells (p53-wild type) and SW480 cells (p53-mutant) than that of nutlin-3a. Binding mode analysis of the designed peptide at MDM2 suggests that the conserved "FWL" epitope was buried in the hydrophobic binding pocket, and the residues located at the periphery of the binding site contributed to the high binding affinity of SC426. Overall, in silico design of miniproteins with therapeutic potential through epitope grafting to the naturally occurring constrained peptide is an effective strategy.
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Affiliation(s)
- He Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Peiju Qiu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Peta J Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiao Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Zheyu Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Qingliang Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Jiazhen Liang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Xiaolin Bi
- Department of Nutrition, Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.,Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
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Ghaheh HS, Ganjalikhany MR, Yaghmaei P, Pourfarzam M, Mir Mohammad Sadeghi H. Improving the solubility, activity, and stability of reteplase using in silico design of new variants. Res Pharm Sci 2019; 14:359-368. [PMID: 31516513 PMCID: PMC6714118 DOI: 10.4103/1735-5362.263560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Reteplase (recombinant plasminogen activator, r-PA) is a thrombolytic agent recombined from tissue-type plasminogen activator (t-PA), which has several prominent features such as strong thrombolytic ability and E. coli expressibility. Despite these outstanding features, it demonstrates reduced fibrin binding affinity, reduced stimulation of protease activity, and lower solubility, hence higher aggregation propensity, compared to t-PA. The present study was devoted to design r-PA variants with comparable structural stability, enhanced biological activity, and high solubility. For this purpose, computational molecular modeling techniques were utilized. The supercharging technique was applied for r-PA to designing new species of the protein. Based on the results from in silico evaluation of selected mutations in comparison to the wild-type r-PA, the designed supercharged mutant (S7 variant) exhibited augmented stability, decreased solvation energy, as well as enhanced binding affinity to fibrin. The data also implied increased plasminogen cleavage activity of the new variant. These findings have implications to therapies which involve removal of intravascular blood clots, including the treatment of acute myocardial infarction.
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Affiliation(s)
| | | | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, I.R. Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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Finlay WJ, Lugovskoy AA. De novo discovery of antibody drugs - great promise demands scrutiny. MAbs 2019; 11:809-811. [PMID: 31122133 PMCID: PMC6601558 DOI: 10.1080/19420862.2019.1622926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/01/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023] Open
Abstract
We live in an era of rapidly advancing computing capacity and algorithmic sophistication. "Big data" and "artificial intelligence"find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts.
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Dhiman P, Malik N, Khatkar A. Lead optimization for promising monoamine oxidase inhibitor from eugenol for the treatment of neurological disorder: synthesis and in silico based study. BMC Chem 2019; 13:38. [PMID: 31384786 PMCID: PMC6661809 DOI: 10.1186/s13065-019-0552-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/08/2019] [Indexed: 01/30/2023] Open
Abstract
Natural based inhibitors of monoamine oxidase are promising drug candidates for the treatment of several neurodegenerative and neuropsychological disorders including depression, anxiety, Parkinson’s disease and Alzheimer’s disease. In the present study we designed and synthesized the eugenol based derivatives and investigated them for human MAO inhibitory potential as promising candidates for therapeutics of neurological disorders. Moreover, radical scavenging activity of designed derivatives was tested by and H2O2 and DPPH scavenging methods. Eugenol based derivatives were designed and synthesized for human MAO inhibitory action. The in silico and in vitro models were utilized for the evaluation of hMAO inhibition. The insight into molecular interactions among the compounds and both hMAO-A and hMAO-B active site was achieved by molecular docking studies. The two spectrophotometric titrations techniques were used to evaluate antioxidant potential. Compounds 5b and 16 were found as most active hMAO-A inhibitors with IC50 values of 5.989 ± 0.007 µM and 7.348 ± 0.027 µM respectively, through an appreciable selectivity index value of 0.19 and 0.14 respectively. In case of hMAO-B inhibition compounds 13a and 13b were found as most active hMAO-B inhibitors with IC50 values of 7.494 ± 0.014 µM and 9.183 ± 0.034 µM receptively and outstanding value of selectivity index of 5.14 and 5.72 respectively. Radical scavenging assay showed that compounds 5b, 5a, 9b, 9a were active antioxidants. The findings of present study indicated excellent correlation among dry lab and wet lab hMAO inhibitory experiments. Interestingly, the compounds exhibiting better MAO inhibition activity was also appeared as good antioxidant agents.
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Affiliation(s)
- Priyanka Dhiman
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana 124001 India
| | - Neelam Malik
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana 124001 India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana 124001 India
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Shafaghi M, Shabani AA, Minuchehr Z. Rational design of hyper-glycosylated human luteinizing hormone analogs (a bioinformatics approach). Comput Biol Chem 2019; 79:16-23. [PMID: 30708139 DOI: 10.1016/j.compbiolchem.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/29/2018] [Accepted: 01/02/2019] [Indexed: 01/09/2023]
Abstract
Glycoengineering is a recently used approach to extend serum half-life of valuable protein therapeutics. One aspect of glycoengineering is to introduce new N-glycosylation site (Asn-X-Thr/Ser, where X ≠ Pro) into desirable positions in the peptide backbone, resulting in the generation of hyper-glycosylated protein. In this study, human luteinizing hormone (LH) was considered for identification of the suitable positions for the addition of new N-linked glycosylation sites. A rational in silico approach was applied for prediction of structural and functional alterations caused by changes in amino acid sequence. As the first step, we explored the amino acid sequence of LH to find out desirable positions for introducing Asn or/and Thr to create new N-glycosylation sites. This exploration led to the identification of 38 potential N-glycan sites, and then the four acceptable ones were selected for further analysis. Three-dimensional (3D) structures of the selected analogs were generated and examined by the model evaluation methods. Finally, two analogs with one additional glycosylation site were suggested as the qualified analogs for hyper-glycosylation of the LH, which can be considered for further experimental investigations. Our computational strategy can reduce laborious and time-consuming experimental analyses of the analogs.
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Affiliation(s)
- Mona Shafaghi
- Dept. & Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran; Students Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Shabani
- Dept. & Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran.
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Pham LTM, Seo H, Kim KJ, Kim YH. In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin. Biotechnol Biofuels 2018; 11:325. [PMID: 30555531 PMCID: PMC6287364 DOI: 10.1186/s13068-018-1324-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/29/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND The lignin peroxidase isozyme H8 from the white-rot fungus Phanerochaete chrysosporium (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin. RESULTS The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from Phanerochaete chrysosporium and acid-stable manganese peroxidase isozyme 6 (MnP6) from Ceriporiopsis subvermispora. Effective salt bridges were probed by molecular dynamics simulation and changes to Gibbs free energy following mutagenesis were predicted, suggesting promising variants with higher stability under extremely acidic conditions. The rationally designed variant, A55R/N156E-H239E, demonstrated a 12.5-fold increased half-life under extremely acidic conditions, 9.9-fold increased catalytic efficiency toward veratryl alcohol, and a 7.8-fold enhanced lignin model dimer conversion efficiency compared to those of native LiPH8. Furthermore, the two constructed salt bridges in the variant A55R/N156E-H239E were experimentally confirmed to be identical to the intentionally designed LiPH8 variant using X-ray crystallography (PDB ID: 6A6Q). CONCLUSION Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.
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Affiliation(s)
- Le Thanh Mai Pham
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
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Dhiman P, Malik N, Khatkar A. Hybrid caffeic acid derivatives as monoamine oxidases inhibitors: synthesis, radical scavenging activity, molecular docking studies and in silico ADMET analysis. Chem Cent J 2018; 12:112. [PMID: 30413989 PMCID: PMC6768041 DOI: 10.1186/s13065-018-0481-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/01/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Monoamine oxidase has been implicated in numerous neurological disorders. Although synthetic monoamine oxidase inhibitors (MAOI) have emerged with many side effects, the aspiration of natural based MAOI has greatly increased. As they exhibit fewer side effects and food interaction along with improved neuropharmacological profile. RESULTS The in silico design of the caffeic acid derivatives led potent MAO inhibitors with remarkable antioxidant activity. The mechanistic insight of the compounds within the hMAO active site was achieved by molecular docking which led us to be more confident of the possible inhibition of MAO. CONCLUSIONS The synthesized eugenol based ester of caffeic acid compound 7 exhibited MAO-A inhibition with IC50 values of 07.03 ± 0.022 µM with good selectivity (SI = 0.291) towards MAO-A. Conversely, two anilides compounds 2 and 1, bearing chloro and nitro group at 2, 4 positions showed MAO-A inhibition with IC50 values of 08.51 ± 0.017 µM and 08.87 ± 0.005 µM, respectively. Only one compound 5 was found as a significant MAO-B inhibitor with the IC50 value of 10.80 ± 0.024 µM. Moreover, compounds 1, 2, 4 and 9 have profoundly appeared as potent antioxidants as evaluated in duel assay by scavenging DPPH and H2O2.
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Affiliation(s)
- Priyanka Dhiman
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana, 124001, India
| | - Neelam Malik
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana, 124001, India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, M. D. University, Rohtak, Haryana, 124001, India.
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Li XQ, Wu Q, Hu D, Wang R, Liu Y, Wu MC, Li JF. Improving the temperature characteristics and catalytic efficiency of a mesophilic xylanase from Aspergillus oryzae, AoXyn11A, by iterative mutagenesis based on in silico design. AMB Express 2017; 7:97. [PMID: 28508385 PMCID: PMC5432455 DOI: 10.1186/s13568-017-0399-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/02/2017] [Indexed: 11/10/2022] Open
Abstract
To improve the temperature characteristics and catalytic efficiency of a glycoside hydrolase family (GHF) 11 xylanase from Aspergillus oryzae (AoXyn11A), its variants were predicted based on in silico design. Firstly, Gly21 with the maximum B-factor value, which was confirmed by molecular dynamics (MD) simulation on the three-dimensional structure of AoXyn11A, was subjected to site-saturation mutagenesis. Thus, one variant with the highest thermostability, AoXyn11AG21I, was selected from the mutagenesis library, E. coli/Aoxyn11AG21X (X: any one of 20 amino acids). Secondly, based on the primary structure multiple alignment of AoXyn11A with seven thermophilic GHF11 xylanases, AoXyn11AY13F or AoXyn11AG21I–Y13F, was designed by replacing Tyr13 in AoXyn11A or AoXyn11AG21I with Phe. Finally, three variant-encoding genes, Aoxyn11AG21I, Aoxyn11AY13F and Aoxyn11AG21I–Y13F, were constructed by two-stage whole-plasmid PCR method, and expressed in Pichia pastoris GS115, respectively. The temperature optimum (Topt) of recombinant (re) AoXyn11AG21I–Y13F was 60 °C, being 5 °C higher than that of reAoXyn11AG21I or reAoXyn11AY13F, and 10 °C higher than that of reAoXyn11A. The thermal inactivation half-life (t1/2) of reAoXyn11AG21I–Y13F at 50 °C was 240 min, being 40-, 3.4- and 2.5-fold longer than those of reAoXyn11A, reAoXyn11AG21I and reAoXyn11AY13F. The melting temperature (Tm) values of reAoXyn11A, reAoXyn11AG21I, reAoXyn11AY13F and reAoXyn11AG21I–Y13F were 52.3, 56.5, 58.6 and 61.3 °C, respectively. These findings indicated that the iterative mutagenesis of both Gly21Ile and Tyr13Phe improved the temperature characteristics of AoXyn11A in a synergistic mode. Besides those, the catalytic efficiency (kcat/Km) of reAoXyn11AG21I–Y13F was 473.1 mL mg−1 s−1, which was 1.65-fold higher than that of reAoXyn11A.
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25
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Guida F, Battisti A, Gladich I, Buzzo M, Marangon E, Giodini L, Toffoli G, Laio A, Berti F. Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment. Biosens Bioelectron 2018; 100:298-303. [PMID: 28942212 DOI: 10.1016/j.bios.2017.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/29/2017] [Accepted: 09/10/2017] [Indexed: 01/16/2023]
Abstract
One of the main targets in current clinical oncology is the development of a cheap device capable of monitoring in real-time the concentration of a drug in the blood of a patient. This would allow fine-tuning the dosage according to the patient's metabolism, a key condition to reduce side effects. By using surface plasmon resonance and fluorescence spectroscopy we here show that short peptides designed in silico by a recently developed algorithm are capable of binding the anticancer drug irinotecan (CPT-11) with micromolar affinity. Importantly, the recognition takes place in the denaturating solution used in standard therapeutic drug monitoring to detach the drug from the proteins that are present in human plasma, and some of the peptides are capable of distinguishing CPT-11 from its metabolite SN-38. These results suggest that the in silico design of small artificial peptides is now a viable route for designing sensing units, opening a wide range of applications in diagnostic and clinical areas.
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26
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Gomes MN, Braga RC, Grzelak EM, Neves BJ, Muratov E, Ma R, Klein LL, Cho S, Oliveira GR, Franzblau SG, Andrade CH. QSAR-driven design, synthesis and discovery of potent chalcone derivatives with antitubercular activity. Eur J Med Chem 2017; 137:126-138. [PMID: 28582669 DOI: 10.1016/j.ejmech.2017.05.026] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
New anti-tuberculosis (anti-TB) drugs are urgently needed to battle drug-resistant Mycobacterium tuberculosis strains and to shorten the current 6-12-month treatment regimen. In this work, we have continued the efforts to develop chalcone-based anti-TB compounds by using an in silico design and QSAR-driven approach. Initially, we developed SAR rules and binary QSAR models using literature data for targeted design of new heteroaryl chalcone compounds with anti-TB activity. Using these models, we prioritized 33 compounds for synthesis and biological evaluation. As a result, 10 heteroaryl chalcone compounds (4, 8, 9, 11, 13, 17-20, and 23) were found to exhibit nanomolar activity against replicating mycobacteria, low micromolar activity against nonreplicating bacteria, and nanomolar and micromolar against rifampin (RMP) and isoniazid (INH) monoresistant strains (rRMP and rINH) (<1 μM and <10 μM, respectively). The series also show low activity against commensal bacteria and generally show good selectivity toward M. tuberculosis, with very low cytotoxicity against Vero cells (SI = 11-545). Our results suggest that our designed heteroaryl chalcone compounds, due to their high potency and selectivity, are promising anti-TB agents.
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Affiliation(s)
- Marcelo N Gomes
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Edyta M Grzelak
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil; Postgraduate Program of Society, Technology and Environment, University Center of Anápolis/UniEVANGELICA, Anápolis, Goiás, 75083-515, Brazil
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27955-7568, United States; Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Larry L Klein
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | | | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States.
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil.
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Uzuner U, Canakci S, Bektas KI, Sapmaz MT, Belduz AO. Redesigning pH optimum of Geobacillus sp. TF16 endoxylanase through in silico designed DNA swapping strategy. Biochimie 2017; 137:174-189. [PMID: 28351672 DOI: 10.1016/j.biochi.2017.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/23/2017] [Indexed: 12/27/2022]
Abstract
Thermoalkaliphilic xylanases are highly desired and of great importance due to their vast potential in paper pulp and bleaching processes. Here, we report rapid, cost-effective, and result-oriented combinatorial potential of in silico DNA swapping strategy to engineer the pH optimum of industrially crucial enzymes, particularly engineering of Geobacillus sp. TF16 endoxylanase for alkaline environments. The 3D structures of Geobacillus sp. TF16 and donor Bacillus halodurans C-125 endoxylanases were firstly predicted, analyzed, and compared for their similarities before any in silico design of mutants. Reasonably, to improve its alkaline pH tolerance, the corresponding regions in Geobacillus sp.TF16 endoxylanase were further engineered by swapping with negatively-charged amino acid-rich regions from B. halodurans C-125 endoxylanase. Through only two of four in silico-designed mutants, the optimum pH of GeoTF16 endoxylanase was improved from 8.5 to 10.0. Moreover, as compared to GeoTF16 parental enzyme, both GeoInt3 and GeoInt4 mutants revealed (i) enhanced biobleaching performance, (ii) improved adaptability to alkaline conditions, and (iii) better activity for broader pH range. Unlike GeoTF16 losing activity at pH 11.0 completely, GeoInt4 retained 60% and 40% of its activity at pH 11.0 and 12.0, respectively. Thus, GeoInt4 stands out as a more competent biocatalyst that is suitable for alkaline environments of diverse industrial applications. The current study represents an efficient protein engineering strategy to adapt industrial catalysts to diverse processing conditions. Further comprehensive and fine-tuned research efforts may result in biotechnologically more promising outcomes.
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Affiliation(s)
- Ugur Uzuner
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey; Institute for Plant Genomics and Biotechnology, Texas A&M University, 2123 TAMU, College Station, TX, 77840, USA.
| | - Sabriye Canakci
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Kadriye Inan Bektas
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Merve Tuncel Sapmaz
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Ali Osman Belduz
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
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Balagurunathan B, Jain VK, Tear CJY, Lim CY, Zhao H. In silico design of anaerobic growth-coupled product formation in Escherichia coli: experimental validation using a simple polyol, glycerol. Bioprocess Biosyst Eng 2016; 40:361-372. [PMID: 27796571 DOI: 10.1007/s00449-016-1703-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
Integrated approaches using in silico model-based design and advanced genetic tools have enabled efficient production of fuels, chemicals and functional ingredients using microbial cell factories. In this study, using a recently developed genome-scale metabolic model for Escherichia coli iJO1366, a mutant strain has been designed in silico for the anaerobic growth-coupled production of a simple polyol, glycerol. Computational complexity was significantly reduced by systematically reducing the target reactions used for knockout simulations. One promising penta knockout E. coli mutant (E. coli ΔadhE ΔldhA ΔfrdC ΔtpiA ΔmgsA) was selected from simulation study and was constructed experimentally by sequentially deleting five genes. The penta mutant E. coli bearing the Saccharomyces cerevisiae glycerol production pathway was able to grow anaerobically and produce glycerol as the major metabolite with up to 90% of theoretical yield along with stoichiometric quantities of acetate and formate. Using the penta mutant E. coli strain we have demonstrated that the ATP formation from the acetate pathway was essential for growth under anaerobic conditions. The general workflow developed can be easily applied to anaerobic production of other platform chemicals using E. coli as the cell factory.
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Affiliation(s)
- Balaji Balagurunathan
- Bioprocess Engineering Center, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Vishist Kumar Jain
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Crystal Jing Ying Tear
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Chan Yuen Lim
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Hua Zhao
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore.
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29
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Ghasemi F, Zomorodipour A, Karkhane AA, Khorramizadeh MR. In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. J Mol Graph Model 2016; 68:39-47. [PMID: 27356208 DOI: 10.1016/j.jmgm.2016.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 11/17/2022]
Abstract
N-glycosylation is a process during which a glycan moiety attaches to the asparagine residue in the N-glycosylation consensus sequence (Asn-Xxx-Ser/Thr), where Xxx can be any amino acid except proline. Introduction of a new N-glycosylation site into a protein backbone leads to its hyper-glycosylation, and may improve the protein properties such as solubility, folding, stability, and secretion. Glyco-engineering is an approach to facilitate the hyper-glycosylation of recombinant proteins by application of the site-directed mutagenesis methods. In this regard, selection of a suitable location on the surface of a protein for introduction of a new N-glycosylation site is a main concern. In this work, a computational approach was conducted to select suitable location(s) for introducing new N-glycosylation sites into the human coagulation factor IX (hFIX). With this aim, the first 45 residues of mature hFIX were explored to find out suitable positions for introducing either Asn or Ser/Thr residues, to create new N-glycosylation site(s). Our exploration lead to detection of five potential positions, for hyper-glycosylation. For each suggested position, an analog was defined and subjected for N-glycosylation efficiency prediction. After generation of three-dimensional structures, by homology-based modeling, the five designed analogs were examined by molecular dynamic (MD) simulations, to predict their stability levels and probable structural distortions caused by amino acid substitutions, relative to the native counterpart. Three out of five suggested analogs, namely; E15T, K22N, and R37N, reached equilibration state with relatively constant Root Mean Square Deviation values. Additional analysis on the data obtained during MD simulations, lead us to conclude that, R37N is the only qualified analog with the most similar structure and dynamic behavior to that of the native counterpart, to be considered for further experimental investigations.
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Affiliation(s)
- Fahimeh Ghasemi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Alireza Zomorodipour
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box: 14965/161, Tehran, Iran.
| | - Ali Asghar Karkhane
- Institute of Industrial and Environmental Biotechnology (IIEB), National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - M Reza Khorramizadeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences, 5th Fl., Dr. Shariati Hospital, North Karegar Ave., Tehran 1411413137, Iran.
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30
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Da Costa L, Roche M, Scheers E, Coluccia A, Neyts J, Terme T, Leyssen P, Silvestri R, Vanelle P. VP1 crystal structure-guided exploration and optimization of 4,5-dimethoxybenzene-based inhibitors of rhinovirus 14 infection. Eur J Med Chem 2016; 115:453-62. [PMID: 27049678 DOI: 10.1016/j.ejmech.2016.03.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 01/26/2023]
Abstract
Human rhinoviruses (HRV) are the predominant cause of common colds and flu-like illnesses, but are also responsible for virus-induced exacerbations of asthma and chronic obstructive pulmonary disease. However, to date, no drug has been approved yet for clinical use. In this study, we present the results of the structure-based lead optimization of a class of new small-molecule inhibitors that we previously reported to bind into the pocket beneath the canyon of the VP1 protein. A small series of analogues that we designed based on the available structure and interaction data were synthesized and evaluated for their potency to inhibit the replication of HRV serotype 14. 2-(4,5-Dimethoxy-2-nitrophenyl)-1-(4-(pyridin-4-yl)phenyl)ethanol (3v) was found to be a potent inhibitor exhibiting micromolar activity (EC50 = 3.4 ± 1.0 μM) with a toxicity for HeLa cells that was significantly lower than that of our previous hit (LPCRW_0005, CC50 = 104.0 ± 22.2 μM; 3v, CC50 > 263 μM).
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Affiliation(s)
- Laurène Da Costa
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Manon Roche
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Els Scheers
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Antonio Coluccia
- Institut Pasteur Italy, Department of Drug Chemistry and Technologies, Sapienza University, I-00185 Rome, Italy
| | - Johan Neyts
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium.
| | - Thierry Terme
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France
| | - Pieter Leyssen
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Romano Silvestri
- Institut Pasteur Italy, Department of Drug Chemistry and Technologies, Sapienza University, I-00185 Rome, Italy.
| | - Patrice Vanelle
- Aix-Marseille Université, Institut de Chimie Radicalaire, UMR 7273 CNRS, 27 Boulevard Jean Moulin, Marseille, France.
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31
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Golshani M, Rafati S, Jahanian-Najafabadi A, Nejati-Moheimani M, Siadat SD, Shahcheraghi F, Bouzari S. In silico design, cloning and high level expression of L7/L12-TOmp31 fusion protein of Brucella antigens. Res Pharm Sci 2015; 10:436-45. [PMID: 26752992 PMCID: PMC4691964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Globally, Brucella melitensis and B. abortus are the most common cause of human brucellosis. The outer membrane protein 31 (Omp31) and L7/L12 are immunodominant and protective antigens conserved in human Brucella pathogens which are considered as potential vaccine candidates. We aimed to design the fusion protein from Brucella L7/L12 and truncated Omp31proteins, in silico, clone the fusion in pET28a vector, and express it in Escherichia coli host. Two possible fusion forms, L7/L12-TOmp31 and TOmp31-L7/L12 were subjected to in silico modeling and analysis. Analysis and validation of the fusion proteins with three dimensional (3D) models showed that both models are in the range of native proteins. However, L7/L12-Tomp31 structure was more valid than the TOmp31-L7/L12 model and subjected to in vitro production. The major histocompatibility complex (MHC II) epitope mapping using IEDB database indicated that the model contained good MHC II binders. The L7/L12-TOmp31 coding sequence was cloned in pET28a vector. The integrity of the construct was confirmed by polymerase chain reaction, restriction enzyme mapping, and sequencing. The fusion was successfully expressed in E. coli BL21 (DE3) by induction with isopropyl β-D-thiogalactopyranoside. The rL7/L12-TOmp31 was purified with Ni-NTA column. The yield of the purified rL7/L12-TOmp31 was estimated by Bradford method and found to be 40 mg/L of the culture. Western blotting with anti-His antibody revealed a specific reactivity with purified rL7/L12-TOmp31 produced in E. coli and showed the functional expression in the prokaryotic system. In this study, a new protein vaccine candidate against brucellosis was constructed with the help of bioinformatics tools and the construct was expressed in the bacterial host. Studies evaluating the immunogenicity and cross-protection of this fusion protein against B. melitensis and B. abortus are underway.
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Affiliation(s)
- Maryam Golshani
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Sima Rafati
- Department of Molecular Immunology and Vaccine Research, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences and Isfahan Pharmaceutical Sciences Research center, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | | | - Seyed Davar Siadat
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, I.R. Iran
| | | | - Saeid Bouzari
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, I.R. Iran,Corresponding author: S. Bouzari Tel: 0098 21 66953311-20, Fax: 0098 21 66492619
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