1
|
Shahbazi B, Mafakher L, Arab SS, Teimoori-Toolabi L. Kallistatin as an inhibitory protein against colorectal cancer cells through binding to LRP6. J Biomol Struct Dyn 2024; 42:918-934. [PMID: 37114408 DOI: 10.1080/07391102.2023.2196704] [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: 09/28/2022] [Accepted: 03/22/2023] [Indexed: 04/29/2023]
Abstract
Kallistatin (KL) is a member of the serine proteinase inhibitor (serpin) family regulating oxidative stress, vascular relaxation, inflammation, angiogenesis, cell proliferation, and invasion. The heparin-binding site of Kallistatin has an important role in the interaction with LRP6 leading to the blockade of the Wnt signaling pathway. In this study, we aimed to explore the structural basis of the Kallistatin-LRP6E1E4 complex using in silico approaches and evaluating the anti-proliferative, apoptotic, and cell cycle arrest activities of Kallistatin in colon cancer lines. The molecular docking showed Kallistatin could bind to the LRP6E3E4 much stronger than LRP6E1E2. The Kallistatin-LRP6E1E2 and Kallistatin-LRP6E3E4 complexes were stable during Molecular Dynamics (MD) simulation. The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) showed that the Kallistatin-LRP6E3E4 has a higher binding affinity compared to Kallistatin-LRP6E1E2. Kallistatin induced higher cytotoxicity and apoptosis in HCT116 compared to the SW480 cell line. This protein-induced cell-cycle arrest in both cell lines at the G1 phase. The B-catenin, cyclin D1, and c-Myc expression levels were decreased in response to treatment with Kallistatin in both cell lines while the LRP6 expression level was decreased in the HCT116 cell line. Kallistatin has a greater effect on the HCT116 cell line compared to the SW480 cell line. Kallistatin can be used as a cytotoxic and apoptotic-inducing agent in colorectal cancer cell lines.
Collapse
Affiliation(s)
- Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Mafakher
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
2
|
Kalyan G, Junghare V, Bhattacharya S, Hazra S. Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources. J Biomol Struct Dyn 2020; 39:635-649. [PMID: 32048568 DOI: 10.1080/07391102.2020.1715836] [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] [Indexed: 01/20/2023]
Abstract
Functional foods are emerging as essential healthy nutritional component due to their abundant wellbeing benefits. Especially the food-derived peptides are considered as key components for playing their biologically active roles. One such robust therapeutics that already exploited with food peptides that help treating high blood pressure via targeting Angiotensin-Converting Enzyme (ACE). This in silico study demonstrated the inhibitory potential of antihypertensive peptides derived from food sources. This study involves an intensive structure-based analysis of enzyme-peptide interactions using Molecular Dynamics (MD) simulations. Interestingly, this study will help us to get deeper understanding on how food peptides achieve successful inhibition of ACE. In this study, the peptide-enzyme complexes revealed two binding pockets, A and B, on either side of the active site Zn atom. Pocket B has a smaller binding site volume than pocket A, comprised of β-sheets and the active site opening cleft. The interface of the binding sites showed that the enzyme structure was negative to neutral charge, and the peptide structure was positive to neutral charge. The dynamics of complex structures of seven highly potential peptides were performed for 20 ns each at 300 K. Comparative analysis of RMSD, RMSF and binding energies show the enzyme-peptide complexes and the overall stability of apo-enzyme. Importantly, two peptides AFKAWAVAR and IWHHTF showed the highest variation in their RMSD as compared to the apo-enzyme. This study will further be useful for the assessment of the characteristics to predict novel inhibitory peptides that can be generated from food proteins.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gazal Kalyan
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vivek Junghare
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sourya Bhattacharya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Centre of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| |
Collapse
|
3
|
DeLeon-Pennell KY, Iyer RP, Ero OK, Cates CA, Flynn ER, Cannon PL, Jung M, Shannon D, Garrett MR, Buchanan W, Hall ME, Ma Y, Lindsey ML. Periodontal-induced chronic inflammation triggers macrophage secretion of Ccl12 to inhibit fibroblast-mediated cardiac wound healing. JCI Insight 2017; 2:94207. [PMID: 28931761 DOI: 10.1172/jci.insight.94207] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 12/20/2022] Open
Abstract
Chronic inflammatory diseases, such as periodontal disease, associate with adverse wound healing in response to myocardial infarction (MI). The goal of this study was to elucidate the molecular basis for impaired cardiac wound healing in the setting of periodontal-induced chronic inflammation. Causal network analysis of 168 inflammatory and extracellular matrix genes revealed that chronic inflammation induced by a subseptic dose of Porphyromonas gingivalis lipopolysaccharide (LPS) exacerbated infarct expression of the proinflammatory cytokine Ccl12. Ccl12 prevented initiation of the reparative response by prolonging inflammation and inhibiting fibroblast conversion to myofibroblasts, resulting in diminished scar formation. Macrophage secretion of Ccl12 directly impaired fibronectin and collagen deposition and indirectly stimulated collagen degradation through upregulation of matrix metalloproteinase-2. In post-MI patients, circulating LPS levels strongly associated with the Ccl12 homologue monocyte chemotactic protein 1 (MCP-1). Patients with LPS levels ≥ 1 endotoxin units (EU)/ml (subseptic endotoxemia) at the time of hospitalization had increased end diastolic and systolic dimensions compared with post-MI patients with < 1 EU/ml, indicating that low yet pathological concentrations of circulating LPS adversely impact post-MI left ventricle (LV) remodeling by increasing MCP-1. Our study provides the first evidence to our knowledge that chronic inflammation inhibits reparative fibroblast activation and generates an unfavorable cardiac-healing environment through Ccl12-dependent mechanisms.
Collapse
Affiliation(s)
- Kristine Y DeLeon-Pennell
- Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi, USA.,Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | | | - Osasere K Ero
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - Courtney A Cates
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - Elizabeth R Flynn
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - Presley L Cannon
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - Mira Jung
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - De'Aries Shannon
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | | | | | - Michael E Hall
- Mississippi Center for Heart Research, Department of Physiology and Biophysics.,Division of Cardiology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yonggang Ma
- Mississippi Center for Heart Research, Department of Physiology and Biophysics
| | - Merry L Lindsey
- Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi, USA.,Mississippi Center for Heart Research, Department of Physiology and Biophysics
| |
Collapse
|
4
|
El-Baba TJ, Kim D, Rogers DB, Khan FA, Hales DA, Russell DH, Clemmer DE. Long-Lived Intermediates in a Cooperative Two-State Folding Transition. J Phys Chem B 2016; 120:12040-12046. [PMID: 27933943 DOI: 10.1021/acs.jpcb.6b08932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biomolecular folding often occurs through a cooperative two-state reactant ↔ product transition; the term cooperative does not convey that intermediate structures are nonexistent but rather that these states are not observable by existing experimental techniques. Because of this, few intermediates have been studied and characterized. Recently, ion mobility spectrometry (IMS) measurements revealed that the oligomer polyproline-13 (Pro13, which in propanol (PrOH) favors the right-handed helical PPI structure having adjacent pyrrolidine rings in a cis configuration) folds through six sequential long-lived intermediates as it converts to the all-trans-configured PPII structure that is favored in aqueous solutions. Here, we examine the PPIPrOH → PPIIaq folding transition for a HisPro13 sequence, i.e., Pro13 having a single histidine residue added to the N-terminus. Remarkably, the IMS measurements show that, upon addition of histidine, all of the IMS peaks associated with intermediate structures disappear. Instead, HisPro13 folds via a cooperative two-state transition, delayed by a significant induction period. The induction period is temperature dependent-shifting the transition to longer times at lower temperatures. Equilibrium studies show that the HisPro13 PPIPrOH → PPIIaq transition is endothermic but favored entropically. From these clues, we propose a sequential folding mechanism and develop a model that suggests that ∼13-17 long-lived intermediates are likely responsible for the induction period. In this model, intermediates are separated by average individual activation barriers of ∼90 kJ·mol-1, and are entropically favorable.
Collapse
Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Doyong Kim
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Dylan B Rogers
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - Faizan A Khan
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - David A Hales
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| |
Collapse
|
5
|
Jas GS, Middaugh CR, Kuczera K. Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution. J Phys Chem B 2016; 120:6939-50. [DOI: 10.1021/acs.jpcb.6b04528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gouri S. Jas
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - C. Russell Middaugh
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Krzysztof Kuczera
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Department
of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045, United States
| |
Collapse
|
6
|
Abstract
This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.
Collapse
Affiliation(s)
- Krzysztof Kuczera
- Departments of Chemistry and Molecular Biosciences, University of Kansas, 1251 Wescoe Hall Drive, Room 5090, Lawrence, KS, 66045, USA,
| |
Collapse
|
7
|
Nonose S, Yamashita K, Sudo A, Kawashima M. Proton transfer and complex formation of angiotensin I ions with gaseous molecules at various temperature. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Brás NF, Fernandes PA, Ramos MJ. Molecular dynamics studies on both bound and unbound renin protease. J Biomol Struct Dyn 2013; 32:351-63. [PMID: 23527826 DOI: 10.1080/07391102.2013.768553] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The aspartic protease renin (REN) catalyses the rate-limiting step in the Renin-Angiotensin-Aldosterone System (RAAS), which regulates cardiovascular and renal homoeostasis in living organisms. Renin blockage is therefore an attractive therapeutic strategy for the treatment of hypertension. Herein, computational approaches were used to provide a structural characterization of the binding site, flap opening and dynamic rearrangements of REN in the key conserved residues and water molecules, with the binding of a dodecapeptide substrate or different inhibitors. All these structural insights during catalysis may assist future studies in developing novel strategies for REN inactivation. Our molecular dynamics simulations of several unbound-REN and bound-REN systems indicate similar flexible-segments plasticity with larger fluctuations in those belonging to the C-domain (exposed to the solvent). These segments are thought to assist the flap opening and closure to allow the binding of the substrate and catalytic water molecules. The unbound-REN simulation suggests that the flap can acquire three different conformations: closed, semi-open and open. Our results indicate that the semi-open conformation is already sufficient and appropriate for the binding of the angiotensinogen (Ang) tail, thus contributing to the high specificity of REN, and that both semi-open and open flap conformations are present in free and complexed enzymes. We additionally observed that the Tyr75-Trp39 H-bond has an important role in assisting flap movement, and we highlight several conserved water molecules and amino acids that are essential for the proper catalytic activity of REN.
Collapse
Affiliation(s)
- Natércia F Brás
- a REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre s/n, 4169-007 , Porto , Portugal
| | | | | |
Collapse
|