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Liu J, Cui T. Expression, Characterisation, Homology Modelling and Molecular Docking of a Novel M17 Family Leucyl-Aminopeptidase from Bacillus cereus CZ. Int J Mol Sci 2023; 24:15939. [PMID: 37958921 PMCID: PMC10649214 DOI: 10.3390/ijms242115939] [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: 09/28/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Leucyl-aminopeptidase (LAP), an important metallopeptidase, hydrolyses amino acid residues from the N-terminus of polypeptides and proteins, acting preferentially on the peptide bond formed by N-terminus leucine. A new leucyl-aminopeptidase was found in Bacillus cereus CZ. Its gene (bclap) contained a 1485 bp ORF encoding 494 amino acids with a molecular weight of 54 kDa. The bcLAP protein was successfully expressed in E. coli BL21(DE3). Optimal activity is obtained at pH 9.0 and 58 °C. The bcLAP displays a moderate thermostability and an alkaline pH adaptation range. Enzymatic activity is dramatically enhanced by Ni2+. EDTA significantly inhibits the enzymatic activity, and bestatin and SDS also show strong inhibition. The three-dimensional model of bcLAP monomer and homohexamer is simulated byPHYRE2 server and SWISS-MODEL server. The docking of bestatin, Leu-Trp, Asp-Trp and Ala-Ala-Gly to bcLAP is performed using AutoDock4.2.5, respectively. Molecular docking results show that the residues Lys260, Asp265, Lys272, Asp283, Asp342, Glu344, Arg346, Gly372 and His437 are involved in the hydrogen bonding with the ligands and zinc ions. There may be two nucleophilic catalytic mechanisms in bcLAP, one involving His 437 or Arg346 and the other involving His437 and Arg346. The bcLAP can hydrolyse the peptide bonds in Leu-Trp, Asp-Trp and Ala-Ala-Gly.
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Affiliation(s)
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
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Herwade AP, Barale SS, Sonawane KD, Pawar PK. In vivo developmental studies of Helicoverpa armigera and in silico molecular interactions with trypsin reveal the bio-insecticidal potential of trypsin inhibitor (SSTI) isolated from Solanum surattense. Int J Biol Macromol 2022; 223:335-345. [PMID: 36374713 DOI: 10.1016/j.ijbiomac.2022.10.226] [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: 08/25/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022]
Abstract
We report the impact of gut protease inhibition on the development of Helicoverpa armigera by trypsin inhibitor and the use of molecular modeling to understand the mechanism of trypsin inhibition. Larvae of H. armigera fed on an artificial diet containing 150 and 300 μg/ml SSTI showed a negative impact on the insects' development in terms of mean larval weight, larval fatality, survival rate, and nutritional indices. Prominent physical abnormalities like curled wings, malformed appendages, and small body size were observed during the development. Gene expression studies revealed down regulation in trypsin (HaTry 1, 2, 3, 4, 6, 8) and chymotrypsin (HaChy 1, 2, 3, 4) genes of the larval gut upon treatment of SSTI. Homology modeling has been used to build the three-dimensional structure of SSTI, which showed β-sheets having a stable canonical inhibitory loop (CIL) with conserved lysine residue. Molecular docking studies showed the strong binding of SSTI at the active site of trypsin. Molecular dynamic (MD) simulation revealed the stable interactions of the rigid CIL of SSTI at the active site of trypsin, leading to its destabilization. Conserved lysine63 of the P1 site in SSTI forms a strong hydrogen bonding network with residues Asp189 and Ser190 of trypsin.
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Affiliation(s)
- Abhijeet P Herwade
- Department of Biotechnology, Shivaji University, Kolhapur 416004, MS, India
| | - Sagar S Barale
- Department of Microbiology, Shivaji University, Kolhapur 416004, MS, India
| | - Kailas D Sonawane
- Department of Microbiology, Shivaji University, Kolhapur 416004, MS, India; Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, MS, India; Department of Biochemistry, Shivaji University, Kolhapur 416004, MS, India; Department of Chemistry, Shivaji University, Kolhapur 416004, MS, India
| | - Pankaj K Pawar
- Department of Biochemistry, Shivaji University, Kolhapur 416004, MS, India.
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Shanmuga Priya VG, Bhandare V, Muddapur UM, Swaminathan P, Fandilolu PM, Sonawane KD. Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:3242-3257. [DOI: 10.1080/07391102.2020.1846620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- V. G. Shanmuga Priya
- Department of Biotechnology, KLE Dr.M.S.Sheshgiri College of Engineering and Technology, Belagavi, India
| | - Vishwambhar Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, India
| | - Uday M. Muddapur
- Department of Biotechnology, B.V.B College of Engineering and Technology, KLE Technological University, Hubballi, India
| | - Priya Swaminathan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, India
| | - Prayagraj M. Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
| | - Kailas D. Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, India
- Department of Microbiology, Shivaji University, Kolhapur, India
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Sonawane KD, Barale SS, Dhanavade MJ, Waghmare SR, Nadaf NH, Kamble SA, Mohammed AA, Makandar AM, Fandilolu PM, Dound AS, Naik NM, More VB. Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: A molecular modeling approach. INFORMATICS IN MEDICINE UNLOCKED 2021; 24:100597. [PMID: 34075338 PMCID: PMC8152215 DOI: 10.1016/j.imu.2021.100597] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been responsible for the cause of global pandemic Covid-19 and to date, there is no effective treatment available. The spike ‘S’ protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design new drugs to control Covid-19. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell plays a significant role in the proteolytic cleavage of viral ‘S’ protein helpful for the priming of ACE2 receptors and viral entry into human cells. However, three-dimensional structural information and the inhibition mechanism of TMPRSS2 is yet to be explored experimentally. Hence, we have used a molecular dynamics (MD) simulated homology model of TMPRSS2 to study the inhibition mechanism of experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride (BHH) using molecular modeling techniques. Prior to docking, all three inhibitors were geometry optimized by semi-empirical quantum chemical RM1 method. Molecular docking analysis revealed that Camostat mesylate and its structural analogue Nafamostat interact strongly with residues His296 and Ser441 present in the catalytic triad of TMPRSS2, whereas BHH binds with Ala386 along with other residues. Comparative molecular dynamics simulations revealed the stable behavior of all the docked complexes. MM-PBSA calculations also revealed the stronger binding of Camostat mesylate to TMPRSS2 active site residues as compared to Nafamostat and BHH. Thus, this structural information could be useful to understand the mechanistic approach of TMPRSS2 inhibition, which may be helpful to design new lead compounds to prevent the entry of SARS-Coronavirus 2 in human cells.
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Affiliation(s)
- Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India.,Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Sagar S Barale
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Maruti J Dhanavade
- Department of Microbiology, Bharati Vidyapeeth's, Dr. Patangrao Kadam Mahavidyalaya, Sangali, Maharashtra, India
| | - Shailesh R Waghmare
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Naiem H Nadaf
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Subodh A Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Ali Abdulmawjood Mohammed
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Asiya M Makandar
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Prayagraj M Fandilolu
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Ambika S Dound
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Nitin M Naik
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | - Vikramsinh B More
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
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Ahmed S, Moni DA, Sonawane KD, Paek KY, Shohael AM. A comprehensive in silico exploration of pharmacological properties, bioactivities and COX-2 inhibitory potential of eleutheroside B from Eleutherococcus senticosus (Rupr. & Maxim.) Maxim. J Biomol Struct Dyn 2020; 39:6553-6566. [DOI: 10.1080/07391102.2020.1803135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sium Ahmed
- Cell Genetics and Plant Biotechnology Laboratory, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Bangladesh
| | - Dil Afroj Moni
- Cell Genetics and Plant Biotechnology Laboratory, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Bangladesh
| | - Kailas Dashrath Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra, India
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra, India
| | - Kee Yoeup Paek
- Research Center for the Development of Advanced Horticultural Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Abdullah Mohammad Shohael
- Cell Genetics and Plant Biotechnology Laboratory, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Bangladesh
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Sonawane KD, Dhanavade MJ. Molecular Docking Technique to Understand Enzyme-Ligand Interactions. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Molecular docking has advanced to such an extent that one can rapidly and accurately identify pharmaceutically useful lead compounds. It is being used routinely to understand molecular interactions between enzyme and ligand molecules. Several computational approaches are combined with experimental work to investigate molecular mechanisms in detail at the atomic level. Molecular docking method is also useful to investigate proper orientation and interactions between receptor and ligand. In this chapter we have discussed protein-protein approach to understand interactions between enzyme and amyloid beta (Aß) peptide. The Aß peptide is a causative agent of Alzheimer's disease. The Aß peptides can be cleaved specifically by several enzymes. Their interactions with Aß peptide and specific enzyme can be investigated using molecular docking. Thus, the molecular information obtained from docking studies might be useful to design new therapeutic approaches in treatment of Alzheimer's as well as several other diseases.
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Dhanavade MJ, Parulekar RS, Kamble SA, Sonawane KD. Molecular modeling approach to explore the role of cathepsin B from Hordeum vulgare in the degradation of Aβ peptides. MOLECULAR BIOSYSTEMS 2016; 12:162-8. [PMID: 26568474 DOI: 10.1039/c5mb00718f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pathological hallmark of Alzheimer's disease is the accumulation of Aβ peptides in human brains. These Aβ peptides can be degraded by several enzymes such as hACE, hECE, hIDE and cathepsin B. Out of which cathepsin B also belongs to the papain super family and has been found in human brains, it has a role in Aβ peptide degradation through limited proteolysis. The Aβ concentrations are maintained properly by its production and clearance via receptor-mediated cellular uptake and direct enzymatic degradation. However, the reduced production of Aβ degrading enzymes as well as their Aβ degrading activity in human brains initiate the process of accumulation of Aβ peptides. So it becomes essential to investigate the molecular interactions involved in the process of Aβ degradation in detail at the atomic level. Hence, homology modeling, molecular docking and molecular dynamics simulation techniques have been used to explore the possible role of cathepsin B from Hordeum vulgare in the degradation of amyloid beta (Aβ) peptides. The homology model of cathepsin B from Hordeum vulgare shows good similarity with human cathepsin B. Molecular docking and MD simulation results revealed that the active site residues Cys32, HIS112, HIS113 are involved in the catalytic activity of cathepsin B. The sulfhydryl group of the Cys32 residue of cathepsin B from Hordeum vulgare cleaves the Aβ peptide from the carboxylic end of Glu11. Hence, this structural study might be helpful in designing alternative strategies for the treatment of AD.
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Affiliation(s)
- Maruti J Dhanavade
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India
| | - Rishikesh S Parulekar
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India
| | - Subodh A Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India.
| | - Kailas D Sonawane
- Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India and Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India.
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Barage SH, Sonawane KD. Amyloid cascade hypothesis: Pathogenesis and therapeutic strategies in Alzheimer's disease. Neuropeptides 2015; 52:1-18. [PMID: 26149638 DOI: 10.1016/j.npep.2015.06.008] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease is an irreversible, progressive neurodegenerative disorder. Various therapeutic approaches are being used to improve the cholinergic neurotransmission, but their role in AD pathogenesis is still unknown. Although, an increase in tau protein concentration in CSF has been described in AD, but several issues remains unclear. Extensive and accurate analysis of CSF could be helpful to define presence of tau proteins in physiological conditions, or released during the progression of neurodegenerative disease. The amyloid cascade hypothesis postulates that the neurodegeneration in AD caused by abnormal accumulation of amyloid beta (Aβ) plaques in various areas of the brain. The amyloid hypothesis has continued to gain support over the last two decades, particularly from genetic studies. Therefore, current research progress in several areas of therapies shall provide an effective treatment to cure this devastating disease. This review critically evaluates general biochemical and physiological functions of Aβ directed therapeutics and their relevance.
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Affiliation(s)
- Sagar H Barage
- Department of Biotechnology, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India
| | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India; Department of Microbiology, Shivaji University, Kolhapur 416004, Maharashtra (M.S.), India.
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Jalkute CB, Sonawane KD. Evaluation of a possible role of Stigmatella aurantiaca ACE in Aβ peptide degradation: a molecular modeling approach. J Mol Microbiol Biotechnol 2015; 25:26-36. [PMID: 25677850 DOI: 10.1159/000370114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Amyloid-β (Aβ)-degrading enzymes are known to degrade Aβ peptides, a causative agent of Alzheimer's disease. These enzymes are responsible for maintaining Aβ concentration. However, loss of such enzymes or their Aβ-degrading activity because of certain genetic as well as nongenetic reasons initiates the accumulation of Aβ peptides in the human brain. Considering the limitations of the human enzymes in clearing Aβ peptide, the search for microbial enzymes that could cleave Aβ is necessary. Hence, we built a three-dimensional model of angiotensin-converting enzyme (ACE) from Stigmatella aurantiaca using homology modeling technique. Molecular docking and molecular dynamics simulation techniques were used to outline the possible cleavage mechanism of Aβ peptide. These findings suggest that catalytic residue Glu 434 of the model could play a crucial role to degrade Aβ peptide between Asp 7 and Ser 8. Thus, ACE from S. aurantiaca might cleave Aβ peptides similar to human ACE and could be used to design new therapeutic strategies against Alzheimer's disease.
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Jalkute CB, Barage SH, Sonawane KD. Insight into molecular interactions of Aβ peptide and gelatinase from Enterococcus faecalis: a molecular modeling approach. RSC Adv 2015. [DOI: 10.1039/c4ra09354b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease is characterized by the presence of extracellular deposition of amyloid beta (Aβ) peptides.
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Affiliation(s)
| | - Sagar H. Barage
- Department of Biotechnology
- Shivaji University
- Kolhapur 416004
- India
| | - Kailas D. Sonawane
- Department of Microbiology
- Shivaji University
- Kolhapur 416004
- India
- Structural Bioinformatics Unit
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Sonawane KD, Barage SH. Structural analysis of membrane-bound hECE-1 dimer using molecular modeling techniques: insights into conformational changes and Aβ1–42 peptide binding. Amino Acids 2014; 47:543-59. [DOI: 10.1007/s00726-014-1887-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
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