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Qin W, Xu L, Cheng K, Lu Y, Yang Z. Enhancing the imidase activity of BpIH toward 3-isobutyl glutarimide via semi-rational design. Appl Microbiol Biotechnol 2024; 108:474. [PMID: 39320489 PMCID: PMC11424739 DOI: 10.1007/s00253-024-13311-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 09/03/2024] [Accepted: 09/16/2024] [Indexed: 09/26/2024]
Abstract
(R)-3-Isobutylglutarate monoamide (R-IBM) is a key intermediate in the synthesis of the analgesic drug pregabalin. Recently, the imidase BpIH derived from Burkholderia phytofirmans was identified as a promising catalyst for the industrial production of R-IBM. Notably, this catalyst has the distinct advantage of achieving a 100% theoretical yield from 3-isobutyl glutarimide (IBI). In this study, homology modeling and structure alignment techniques were used to determine the substrate binding pocket of BpIH. Semi-rational design was used to analyze the amino acid residue conservation in the binding pocket region of BpIH. Interestingly, mutations of several low-conserved amino acid located 6-9 Å from the substrate significantly enhanced the catalytic activity of BpIH. Among them, the triple mutant Y37FH133NS226I (YHS-I) showed approximately a fivefold increase in enzyme activity and a significantly improved catalytic efficiency (kcat/Km). Under the same reaction time and conditions, YHS-I successfully converted IBI into R-IBM with a conversion rate of 88.87%, with an enantiomeric excess (ee) of the product exceeding 99.9%. In comparison, wild-type BpIH had a conversion rate of only 38.15%. Molecular dynamics and docking results indicated that YHS-I had higher rigidity around the mutation sites. The synergistic substitutions of Y37F, H133N, and S226I altered the interaction network within the mutation site, enhancing the protein's affinity for the substrate and improving catalytic efficiency. KEY POINTS: • 100% theoretical yield of R-IBM by BpIH compared with 50% by resolution • Semi-rational design of BpIH based on conservativity with homologous enzymes • Mutant with enzyme activity of sixfold and product ee value of 99.9.
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Affiliation(s)
- Wenping Qin
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Rd, Taizhou, 318000, China
- College of Life Sciences, Shanghai Normal University, 100 Guilin Rd, Shanghai, 200233, China
| | - Long Xu
- Taizhou Dachen Pharmaceutical Co., Ltd, 17 Fifth Avenue, Linhai Zone, Zhejiang National Chemical & Pharmaceutical Base, Taizhou, 317016, China
| | - Kun Cheng
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Rd, Taizhou, 318000, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 100 Guilin Rd, Shanghai, 200233, China.
| | - Zhongyi Yang
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Rd, Taizhou, 318000, China.
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Jitonnom J, Meelua W, Tue-Nguen P, Saparpakorn P, Hannongbua S, Chotpatiwetchkul W. 3D-QSAR and molecular docking studies of peptide-hybrids as dengue virus NS2B/NS3 protease inhibitors. Chem Biol Interact 2024; 396:111040. [PMID: 38735453 DOI: 10.1016/j.cbi.2024.111040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/11/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
Global warming and climate change have made dengue disease a global health issue. More than 50 % of the world's population is at danger of dengue virus (DENV) infection, according to the World Health Organization (WHO). Therefore, a clinically approved dengue fever vaccination and effective treatment are needed. Peptide medication development is new pharmaceutical research. Here we intend to recognize the structural features inhibiting the DENV NS2B/NS3 serine protease for a series of peptide-hybrid inhibitors (R1-R2-Lys-R3-NH2) by the 3D-QSAR technique. Comparative molecular field analysis (q2 = 0.613, r2 = 0.938, r2pred = 0.820) and comparative molecular similarity indices analysis (q2 = 0.640, r2 = 0.928, r2pred = 0.693) were established, revealing minor, electropositive, H-bond acceptor groups at the R1 position, minor, electropositive, H-bond donor groups at the R2 position, and bulky, hydrophobic groups at the R3 position for higher inhibitory activity. Docking studies revealed extensive H-bond and hydrophobic interactions in the binding of tripeptide analogues to the NS2B/NS3 protease. This study provides an insight into the key structural features for the design of peptide-based inhibitors of DENV NS2B/NS3 protease.
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Affiliation(s)
- Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand.
| | - Wijitra Meelua
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | - Panthip Tue-Nguen
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Program in Chemistry, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit, 53000, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Warot Chotpatiwetchkul
- Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
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Tue-Ngeun P, Rakitikul W, Thinkumrob N, Hannongbua S, Meelua W, Jitonnom J. Binding interactions and in silico ADME prediction of isoconessimine derivatives as potent acetylcholinesterase inhibitors. J Mol Graph Model 2024; 129:108746. [PMID: 38401250 DOI: 10.1016/j.jmgm.2024.108746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
In pursuit of new acetylcholinesterase (AChE) inhibitors for treating Alzheimer's disease (AD), a series of ten previously synthesized isoconessimine compounds (7a-7j) was in silico investigated for their binding interactions with AChE and pharmacokinetics based on absorption, distribution, metabolism, and excretion (ADME) properties using molecular docking, ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) method and SwissADME tools. Docking experiments showed that all compounds bind within the active site gorge of AChE (PDB entry 1C2B), posing its aryloxy-substitutional ethyl group to catalytic site and conessine skeleton to peripheral anionic site. ONIOM interaction energy was used as an ONIOM score to improve docking score, and it ranked 7b as the most potent AChE inhibitor, in agreement with previous experiment. Residues, ASP74, TRP86, GLY122, GLU202, TRP286, GLU292, SER293, ILE294, TYR337, TYR341, and HIS447 were identified as important for the binding of the AChE-isoconessimine complex. The SwissADME investigation suggested that four compounds (7a, 7c, 7d and 7f) agree with the rules of drug-likeness. The steric and electronic effects on the aryloxy-substitutional ethyl group as important factors in the AChE inhibition were also discussed, which brings a better understanding of Alzheimer's disease drug development.
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Affiliation(s)
- Panthip Tue-Ngeun
- Program in Chemistry, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit, 53000, Thailand; Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand
| | - Waleepan Rakitikul
- Program of Chemical Technology, Faculty of Science and Technology, Chiang Rai Rajabhat University, Chiang Rai, 57100, Thailand; Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand
| | - Natechanok Thinkumrob
- Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Wijitra Meelua
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand; Demonstration School, University of Phayao, Phayao, 56000, Thailand
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand.
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Morales-Quintana L, Monsalve L, Bernales M, Figueroa CR, Valdenegro M, Olivares A, Álvarez F, Cherian S, Fuentes L. Molecular dynamics simulation of the interaction of a raspberry polygalacturonase (RiPG) with a PG inhibiting protein (RiPGIP) isolated from ripening raspberry (Rubus idaeus cv. Heritage) fruit as a model to understand proteins interaction during fruit softening. J Mol Graph Model 2023; 122:108502. [PMID: 37116336 DOI: 10.1016/j.jmgm.2023.108502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Abstract
Polygalacturonase (PG) is an important hydrolytic enzyme involved in pectin disassembly and the subsequent textural changes during fruit ripening. Although the interaction of fungal PGs with other proteins has been documented, the interaction of plant PGs with other plant proteins has not yet been studied. In this study, the molecular mechanisms involved in raspberry fruit ripening, particularly the polygalacturonase (RiPG) interaction with polygalacturonase inhibiting protein (RiPGIP) and substrate, were investigated with a structural approach. The 3D model of RiPG2 and RiPGIP3 was built using a comparative modeling strategy and validated using molecular dynamics (MD) simulations. The RiPG2 model structure comprises 11 complete coils of right-handed parallel β-helix architecture, with an average of 27 amino acid residues per turn. The structural model of the RiPGIP3 displays a typical structure of LRR protein, with the right-handed superhelical fold with an extended parallel β-sheet. The conformational interaction between the RiPG2 protein and RiPGIP3 showed that RiPGIP3 could bind to the enzyme and thereby leave the active site cleft accessible to the substrate. All this evidence indicates that RiPG2 enzyme could interact with RiPGIP3 protein. It can be a helpful model for evaluating protein-protein interaction as a potential regulator mechanism of hydrolase activity during pectin disassembly in fruit ripening.
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Affiliation(s)
- Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Liliam Monsalve
- Centro Regional de Estudios en Alimentos Saludables (CREAS), CONICYT-Regional GORE Valparaíso Proyecto R17A10001, Avenida Universidad 330, Placilla, Curauma, Valparaíso, Chile
| | - Maricarmen Bernales
- Centro Regional de Estudios en Alimentos Saludables (CREAS), CONICYT-Regional GORE Valparaíso Proyecto R17A10001, Avenida Universidad 330, Placilla, Curauma, Valparaíso, Chile
| | - Carlos R Figueroa
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Universidad de Talca, Talca, Chile; Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, 8340755, Chile
| | - Mónika Valdenegro
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Calle San Francisco s/n, Quillota, Chile
| | - Araceli Olivares
- Centro Regional de Estudios en Alimentos Saludables (CREAS), CONICYT-Regional GORE Valparaíso Proyecto R17A10001, Avenida Universidad 330, Placilla, Curauma, Valparaíso, Chile
| | - Fernanda Álvarez
- Centro Regional de Estudios en Alimentos Saludables (CREAS), CONICYT-Regional GORE Valparaíso Proyecto R17A10001, Avenida Universidad 330, Placilla, Curauma, Valparaíso, Chile
| | - Sam Cherian
- Agrifarm Consultant, PWRA 68, Kakkand West PO, Kochi, 30, Kerala State, India
| | - Lida Fuentes
- Centro Regional de Estudios en Alimentos Saludables (CREAS), CONICYT-Regional GORE Valparaíso Proyecto R17A10001, Avenida Universidad 330, Placilla, Curauma, Valparaíso, Chile.
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Hemmati SA, Tabein S. Insect protease inhibitors; promising inhibitory compounds against SARS-CoV-2 main protease. Comput Biol Med 2022; 142:105228. [PMID: 35051855 PMCID: PMC8755557 DOI: 10.1016/j.compbiomed.2022.105228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/25/2021] [Accepted: 01/06/2022] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has adversely affected global health since its emergence in 2019. The lack of effective treatments prompted worldwide efforts to immediately develop therapeutic strategies against COVID-19. The main protease (Mpro) of SARS-CoV-2 plays a crucial role in viral replication, and therefore it serves as an attractive target for COVID-19-specific drug development. Due to the richness and diversity of insect protease inhibitors, we docked SARS-CoV-2 Mpro onto 25 publicly accessible insect-derived protease inhibitors using the ClusPro server, and the regions with high inhibitory potentials against Mpro were used to design peptides. Interactions of these inhibitory peptides with Mpro were further assessed by two directed docking programs, AutoDock and Haddock. AutoDock analysis predicted the highest binding energy (-9.39 kcal/mol) and the lowest inhibition constant (130 nM) for the peptide 1KJ0-7 derived from SGCI (Schistocerca gregaria chymotrypsin inhibitor). On the other hand, Haddock analysis resulted in the discovery of a different peptide designated 2ERW-9 from infestin, a serine protease inhibitor of Triatoma infestans, with the best docking score (-131), binding energy (-11.7 kcal/mol), and dissociation constant (2.6E-09 M) for Mpro. Furthermore, using molecular dynamic simulations, 1KJ0-7 and 2ERW-9 were demonstrated to form stable complexes with Mpro. The peptides also showed suitable drug-likeness properties compared to commercially available drugs based on Lipinski's rule. Our findings present two peptides with possible protease inhibitor activities against Mpro and further demonstrate the potential of insect-derived peptides and computer-aided methods for drug discovery.
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Affiliation(s)
- Seyed Ali Hemmati
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Saeid Tabein
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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6
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Inhibitory Potential of a Designed Peptide Inhibitor Based on Zymogen Structure of Trypsin from Spodoptera frugiperda: In Silico Insights. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10200-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Hemmati SA, Takalloo Z, Taghdir M, Mehrabadi M, Balalaei S, Moharramipour S, H Sajedi R. The trypsin inhibitor pro-peptide induces toxic effects in Indianmeal moth, Plodia interpunctella. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 171:104730. [PMID: 33357552 DOI: 10.1016/j.pestbp.2020.104730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/29/2020] [Accepted: 10/10/2020] [Indexed: 06/12/2023]
Abstract
The inhibitory potential of an inhibitor peptide based on the pro-region of trypsin zymogen was investigated in Indianmeal moth, P. interpunctella, which is a world-wide insect pest of stored food. Five peptides were designed based on molecular docking simulations. The designed peptide with the best score was selected and synthesized for further screening in vitro and in vivo. The peptide was characterized and its inhibitory effects towards the insect trypsin were evaluated and the kinetic analysis revealed a competitive type of inhibition against the target enzyme. The results showed that the peptide could successfully suppress the pest midgut trypsin, and more interestingly, it did not show considerable inhibitory effects on a mammalian trypsin. We also aimed to assess the effect of dietary insect meal treated with different concentrations of the peptide and observed a significant growth and development retardation in pupa and adult insects fed with the inhibitor peptide. The outcomes of the present study suggest an efficient inhibitor peptide that could specifically bind the P. interpunctella trypsin and inhibit its activity, which would be safe against human being health and environment. Notably, this is the first report on in vivo assessment of the direct effect of a pro-region as the specific inhibitor in development as well as survival of the pest insect. Furthermore, our findings could be a promising for future designed pesticides used in pest management.
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Affiliation(s)
- Seyed Ali Hemmati
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran; Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Zeinab Takalloo
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Saeed Balalaei
- Peptide Chemistry Research Center, K. N. Toosi University of Technology, Tehran, Iran
| | - Saeid Moharramipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Velasco J, Oliva B, Gonçalves AL, Lima AS, Ferreira G, França BA, Mulinari EJ, Gonçalves TA, Squina FM, Kadowaki MAS, Maiorano A, Polikarpov I, Oliveira LCD, Segato F. Functional characterization of a novel thermophilic exo-arabinanase from Thermothielavioides terrestris. Appl Microbiol Biotechnol 2020; 104:8309-8326. [PMID: 32813063 DOI: 10.1007/s00253-020-10806-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.
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Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Gislene Ferreira
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bruno Alves França
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Thiago Augusto Gonçalves
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Fábio Márcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Alfredo Maiorano
- Instituto de Pesquisas Tecnológicas do Estado de São Paulo, Diretoria de Operações e Negócios, Núcleo de Bionanomanufatura, São Paulo, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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Zhang H, Song T, Yang Y, Fu C, Li J. Exploring the Interaction Mechanism Between Cyclopeptide DC3 and Androgen Receptor Using Molecular Dynamics Simulations and Free Energy Calculations. Front Chem 2018; 6:119. [PMID: 29755968 PMCID: PMC5932393 DOI: 10.3389/fchem.2018.00119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/30/2018] [Indexed: 01/10/2023] Open
Abstract
Androgen receptor (AR) is a key target in the discovery of anti-PCa (Prostate Cancer) drugs. Recently, a novel cyclopeptide Diffusa Cyclotide-3 (DC3), isolated from Hedyotisdiffusa, has been experimentally demonstrated to inhibit the survival and growth of LNCap cells, which typically express T877A-mutated AR, the most frequently detected point mutation of AR in castration-resistant prostate cancer (CRPC). But the interaction mechanism between DC3 and AR is not clear. Here in this study we aim to explore the possible binding mode of DC3 to T877A-mutated AR from molecular perspective. Firstly, homology modeling was employed to construct the three-dimensional structure of the cyclopeptide DC3 using 2kux.1.A as the template. Then molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized Born surface area (MM-GBSA) methods were performed to determine the bind site and explore the detailed interaction mechanism of DC3-AR complex. The obtained results suggested that the site formed by H11, loop888-893, and H12 (site 2) was the most possible position of DC3 binding to AR. Besides, hydrogen bonds, hydrophobic, and electrostatic interactions play dominant roles in the recognition and combination of DC3-AR complex. The essential residues dominant in each interaction were specifically revealed. This work facilitates our understanding of the interaction mechanism of DC3 binding to AR at the molecular level and contributes to the rational cyclopeptide drug design for prostate cancer.
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Affiliation(s)
- Huimin Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Tianqing Song
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yizhao Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Chenggong Fu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Jiazhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
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10
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Nascimento JM, Oliveira MD, Franco OL, Migliolo L, de Melo CP, Andrade CA. Elucidation of mechanisms of interaction of a multifunctional peptide Pa-MAP with lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2899-909. [DOI: 10.1016/j.bbamem.2014.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/28/2014] [Accepted: 08/01/2014] [Indexed: 12/23/2022]
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11
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Functional and structural insights on self-assembled nanofiber-based novel antibacterial ointment from antimicrobial peptides, bacitracin and gramicidin S. J Antibiot (Tokyo) 2014; 67:771-5. [DOI: 10.1038/ja.2014.70] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 03/24/2014] [Accepted: 04/28/2014] [Indexed: 11/08/2022]
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12
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Mandal SM, Migliolo L, Franco OL. The use of MALDI-TOF-MS and in silico studies for determination of antimicrobial peptides' affinity to bacterial cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1939-1948. [PMID: 22926961 DOI: 10.1007/s13361-012-0453-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/28/2012] [Accepted: 07/18/2012] [Indexed: 06/01/2023]
Abstract
Several methods have been proposed for determining the binding affinity of antimicrobial peptides (AMPs) to bacterial cells. Here the utilization of MALDI-TOF-MS was proposed as a reliable and efficient method for high throughput AMP screening. The major advantage of the technique consists of finding AMPs that are selective and specific to a wide range of Gram-negative and -positive bacteria, providing a simple reliable screening tool to determine the potential candidates for broad spectrum antimicrobial drugs. As a prototype, amp-1 and -2 were used, showing highest activity toward Gram-negative and -positive membranes respectively. In addition, in silico molecular docking studies with both peptides were carried out for the membranes. In silico results indicated that both peptides presented affinity for DPPG and DPPE phospholipids, constructed in order to emulate an in vivo membrane bilayer. As a result, amp-1 showed a higher complementary surface for Gram-negative while amp-2 showed higher affinity to Gram-positive membranes, corroborating MS analyses. In summary, results here obtained suggested that in vitro methodology using MALDI-TOF-MS in addition to theoretical studies may be able to improve AMP screening quality.
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Affiliation(s)
- Santi M Mandal
- Mass Spectrometry and Proteomics Laboratory Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
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13
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Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1224-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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