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Gujjarlapudi M, Kotarya B, Mohanraj SS, Gupta D, Prasad ER, Kalle AM, Jaba J, Ponnusamy D, Padmasree K. Development of a rapid process for purification of Bowman-Birk and Kunitz inhibitors from legume seeds, and evaluation of their biophysical, insecticidal, and antimicrobial properties. Int J Biol Macromol 2023; 238:124050. [PMID: 36933601 DOI: 10.1016/j.ijbiomac.2023.124050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/02/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Bowman-Birk inhibitor (BBI ~10 kDa) and Kunitz inhibitor (KI ~20 kDa) are serine protease/proteinase inhibitor(s) [PI(s)] ubiquitously found in several Leguminous plant species with insecticidal and therapeutic properties. Due to narrow molecular mass differences, the separation of these inhibitors from a single seed variety is tedious. The present study is aimed to develop a rapid protocol (<24 h) for purifying BBI and KI from legume seeds using mild trichloroacetic acid (TCA) extraction followed by trypsin-affinity chromatography. The mature seeds of Vigna radiata and Cajanus platycarpus are used as a model to purify BBI and KI using this protocol. The BBI and KI purified from the seeds of V. radiata are labeled as VrBBI & VrKI, and C. platycarpus are labeled as CpBBI & CpKI, respectively. These PIs are confirmed by immunodetection and MALDI-TOF studies and further characterized for their structural (CD & fluorescence spectroscopy) and functional properties (temperature & DTT stability). BBI(s) purified using the above process are effective in the management of castor semi-looper 'Achaea janata', while KI(s) are effective in the management of pod borer 'Helicoverpa armigera'. Besides, both BBI(s) and KI(s) have significant potential in controlling the growth of methicillin-sensitive 'Staphylococcus aureus', a gram-positive pathogenic bacterium.
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Affiliation(s)
- Mariyamma Gujjarlapudi
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500 046, India
| | - Bharti Kotarya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500 046, India
| | | | - Deepali Gupta
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500 046, India
| | - Elaprolu R Prasad
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Arunasree M Kalle
- Department of Animal Biology, University of Hyderabad, Hyderabad 500 046, India
| | - Jagdish Jaba
- Entomology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502 324, India
| | - Duraimurugan Ponnusamy
- Crop Protection Section, ICAR-Indian Institute of Oilseeds Research, Hyderabad 500 030, India
| | - Kollipara Padmasree
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500 046, India.
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Pereira WA, Nascimento ÉCM, Martins JBL. Electronic and structural study of T315I mutated form in DFG-out conformation of BCR-ABL inhibitors. J Biomol Struct Dyn 2022; 40:9774-9788. [PMID: 34121617 DOI: 10.1080/07391102.2021.1935320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, the four main drugs for the treatment of chronic myeloid leukemia were analyzed, being imatinib, dasatinib, nilotinib and ponatinib followed by four derivative molecules of nilotinib and ponatinib. For these derivative molecules, the fluorine atoms were replaced by hydrogen and chlorine atoms in order to shade light to the structural effects on this set of inhibitors. Electronic studies were performed at density functional theory level with the B3LYP functional and 6-311+G(d,p) basis set. The frontier molecular orbitals, gap HOMO-LUMO, and NBO were analyzed and compared to docking studies for mutant T315I tyrosine kinase protein structure code 3IK3, in the DFG-out conformation. Structural similarities were pointed out, such as the presence of groups common to all inhibitors and modifications raised up on new generations of imatinib-based inhibitors. One of them is the trifluoromethyl group present in nilotinib and later included in ponatinib, in addition to the 1-methylpiperazin-1-ium group that is present in imatinib and ponatinib. The frontier molecular orbitals of imatinib and ponatinib are contributing to the same amino acid residues, and the ineffectiveness of imatinib against the T315I mutation was discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Washington A Pereira
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
| | - Érica C M Nascimento
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
| | - João B L Martins
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
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Gitlin-Domagalska A, Maciejewska A, Dębowski D. Bowman-Birk Inhibitors: Insights into Family of Multifunctional Proteins and Peptides with Potential Therapeutical Applications. Pharmaceuticals (Basel) 2020; 13:E421. [PMID: 33255583 PMCID: PMC7760496 DOI: 10.3390/ph13120421] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Bowman-Birk inhibitors (BBIs) are found primarily in seeds of legumes and in cereal grains. These canonical inhibitors share a highly conserved nine-amino acids binding loop motif CTP1SXPPXC (where P1 is the inhibitory active site, while X stands for various amino acids). They are natural controllers of plants' endogenous proteases, but they are also inhibitors of exogenous proteases present in microbials and insects. They are considered as plants' protective agents, as their elevated levels are observed during injury, presence of pathogens, or abiotic stress, i.a. Similar properties are observed for peptides isolated from amphibians' skin containing 11-amino acids disulfide-bridged loop CWTP1SXPPXPC. They are classified as Bowman-Birk like trypsin inhibitors (BBLTIs). These inhibitors are resistant to proteolysis and not toxic, and they are reported to be beneficial in the treatment of various pathological states. In this review, we summarize up-to-date research results regarding BBIs' and BBLTIs' inhibitory activity, immunomodulatory and anti-inflammatory activity, antimicrobial and insecticidal strength, as well as chemopreventive properties.
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Affiliation(s)
| | | | - Dawid Dębowski
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (A.G.-D.); (A.M.)
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de Freitas MAG, Amaral NO, Álvares ADCM, de Oliveira SA, Mehdad A, Honda DE, Bessa ASM, Ramada MHS, Naves LM, Pontes CNR, Castro CH, Pedrino GR, de Freitas SM. Blood pressure-lowering effects of a Bowman-Birk inhibitor and its derived peptides in normotensive and hypertensive rats. Sci Rep 2020; 10:11680. [PMID: 32669617 PMCID: PMC7363796 DOI: 10.1038/s41598-020-66624-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022] Open
Abstract
Bioactive plant peptides have received considerable interest as potential antihypertensive agents with potentially fewer side effects than antihypertensive drugs. Here, the blood pressure-lowering effects of the Bowman-Birk protease inhibitor, BTCI, and its derived peptides, PepChy and PepTry, were investigated using normotensive (Wistar-WR) and spontaneously hypertensive rats (SHR). BTCI inhibited the proteases trypsin and chymotrypsin, respectively, at 6 µM and 40 µM, a 10-fold greater inhibition than observed with PepTry (60 µM) and PepChy (400 µM). These molecules also inhibited angiotensin converting enzyme (ACE) with IC50 values of 54.6 ± 2.9; 24.7 ± 1.1; and 24.4 ± 1.1 µM, respectively, occluding its catalytic site, as indicated by molecular docking simulation, mainly for PepChy and PepTry. Gavage administration of BTCI and the peptides promoted a decrease of systolic and diastolic blood pressure and an increase of renal and aortic vascular conductance. These effects were more expressive in SHR than in WR. Additionally, BTCI, PepChy and PepTry promoted coronary vasodilation and negative inotropic effects in isolated perfused hearts. The nitric oxide synthase inhibitor blunted the BTCI and PepChy, with no cardiac effects on PepTry. The findings of this study indicate a therapeutic potential of BTCI and its related peptides in the treatment of hypertension.
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Affiliation(s)
- Maria Alzira Garcia de Freitas
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil
| | - Nathalia Oda Amaral
- Center of Neuroscience and Cardiovascular Physiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil
| | - Alice da Cunha Morales Álvares
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil
| | - Sandriele Aires de Oliveira
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil
| | - Azadeh Mehdad
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil
| | - Diego Elias Honda
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil
| | - Amanda Sá Martins Bessa
- Integrative Laboratory of Cardiovascular and Neurological Pathophysiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil
| | - Marcelo Henrique Soller Ramada
- Graduate Program in Genomic Science and Biotechnology, and Graduate Program in Gerontology, Catholic University of Brasília, Brasília, DF, 70790-160, Brazil
| | - Lara Marques Naves
- Center of Neuroscience and Cardiovascular Physiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil
| | - Carolina Nobre Ribeiro Pontes
- Integrative Laboratory of Cardiovascular and Neurological Pathophysiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil
| | - Carlos Henrique Castro
- Integrative Laboratory of Cardiovascular and Neurological Pathophysiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil
| | - Gustavo Rodrigues Pedrino
- Center of Neuroscience and Cardiovascular Physiology; Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, GO, 74690-900, Brazil.
| | - Sonia Maria de Freitas
- Biology Institute, Department of Cell Biology, Laboratory of Biophysics, University of Brasília (UnB), Quadra 604, Asa Norte, Bloco J 1° andar, Brasília, DF, 70910-900, Brazil.
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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