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The First Snake Venom KTS/Disintegrins-Integrin Interactions Using Bioinformatics Approaches. Molecules 2022; 28:molecules28010325. [PMID: 36615520 PMCID: PMC9822126 DOI: 10.3390/molecules28010325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Snake venom contains a number of active molecules that have been shown to possess high anti-tumor activities; disintegrins are an excellent example among these. Their ability to interact and bind with integrins suggests that they could be very valuable molecules for the development of new cancer therapeutic approaches. However, in the absence of a clear Lysine-Threonine-Serine (KTS) Disintegrins Integrin interaction model, the exact compound features behind it are still unknown. In this study, we investigated the structural characteristics of three KTS-disintegrins and the interaction mechanisms with the α1β1 integrin receptor using in silico bioinformatics approaches. Normal mode analysis showed that the flexibility of the KTSR motif and the C-terminal region play a key role and influence the KTS-Disintegrin-integrin interaction. Protein-protein docking also suggested that the interaction involving the KTSR motif is highly dependent on the residue following K21, S23 and R24. These findings contribute to a better understanding of the KTS-Disintegrin-Integrin structural differences and their interactions with α1β1 receptors, which could improve the selection process of the best active molecules for antitumor therapies.
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Vasconcelos AA, Estrada JC, David V, Wermelinger LS, Almeida FCL, Zingali RB. Structure-Function Relationship of the Disintegrin Family: Sequence Signature and Integrin Interaction. Front Mol Biosci 2021; 8:783301. [PMID: 34926583 PMCID: PMC8678471 DOI: 10.3389/fmolb.2021.783301] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/11/2021] [Indexed: 01/09/2023] Open
Abstract
Disintegrins are small cysteine-rich proteins found in a variety of snake venom. These proteins selectively modulate integrin function, heterodimeric receptors involved in cell-cell and cell-matrix interaction that are widely studied as therapeutic targets. Snake venom disintegrins emerged from the snake venom metalloproteinase and are classified according to the sequence size and number of disulfide bonds. Evolutive structure and function diversification of disintegrin family involves a stepwise decrease in the polypeptide chain, loss of cysteine residues, and selectivity. Since the structure elucidation of echistatin, the description of the structural properties of disintegrins has allowed the investigation of the mechanisms involved in integrin-cell-extracellular matrix interaction. This review provides an analysis of the structures of all family groups enabling the description of an expanded classification of the disintegrin family in seven groups. Each group presents a particular disulfide pattern and sequence signatures, facilitating the identification of new disintegrins. The classification was based on the disintegrin-like domain of the human metalloproteinase (ADAM-10). We also present the sequence and structural signatures important for disintegrin-integrin interaction, unveiling the relationship between the structure and function of these proteins.
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Affiliation(s)
- Ariana A Vasconcelos
- Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, Centro Nacional de Ressonância Magnética Nuclear, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge C Estrada
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor David
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana S Wermelinger
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, Centro Nacional de Ressonância Magnética Nuclear, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B Zingali
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Lindemann WR, Mijalis AJ, Alonso JL, Borbat PP, Freed JH, Arnaout MA, Pentelute BL, Ortony JH. Conformational Dynamics in Extended RGD-Containing Peptides. Biomacromolecules 2020; 21:2786-2794. [PMID: 32469507 PMCID: PMC7388056 DOI: 10.1021/acs.biomac.0c00506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RGD is a prolific example of a tripeptide used in biomaterials for cell adhesion, but the potency of free or surface-bound RGD tripeptide is orders-of-magnitude less than the RGD domain within natural proteins. We designed a set of peptides with varying lengths, composed of fragments of fibronectin protein whose central three residues are RGD, in order to vary their conformational behavior without changing the binding site's chemical environment. With these peptides, we measure the conformational dynamics and transient structure of the active site. Our studies reveal how flanking residues affect conformational behavior and integrin binding. We find that disorder of the binding site is important to the potency of RGD peptides and that transient hydrogen bonding near the RGD site affects both the energy landscape roughness of the peptides and peptide binding. This phenomenon is independent of longer-range folding interactions and helps explain why short binding sequences, including RGD itself, do not fully replicate the integrin-targeting properties of extracellular matrix proteins. Our studies reinforce that peptide binding is a holistic event and fragments larger than those directly involved in binding should be considered in the design of peptide epitopes for functional biomaterials.
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Affiliation(s)
- William R Lindemann
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José L Alonso
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Strizzi L, Sandomenico A, Margaryan NV, Focà A, Sanguigno L, Bodenstine TM, Chandler GS, Reed DW, Gilgur A, Seftor EA, Seftor RE, Khalkhali-Ellis Z, Leonardi A, Ruvo M, Hendrix MJ. Effects of a novel Nodal-targeting monoclonal antibody in melanoma. Oncotarget 2015; 6:34071-86. [PMID: 26460952 PMCID: PMC4741437 DOI: 10.18632/oncotarget.6049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022] Open
Abstract
Nodal is highly expressed in various human malignancies, thus supporting the rationale for exploring Nodal as a therapeutic target. Here, we describe the effects of a novel monoclonal antibody (mAb), 3D1, raised against human Nodal. In vitro treatment of C8161 human melanoma cells with 3D1 mAb shows reductions in anchorage-independent growth and vasculogenic network formation. 3D1 treated cells also show decreases of Nodal and downstream signaling molecules, P-Smad2 and P-ERK and of P-H3 and CyclinB1, with an increase in p27. Similar effects were previously reported in human breast cancer cells where Nodal expression was generally down-regulated; following 3D1 mAb treatment, both Nodal and P-H3 levels are reduced. Noteworthy is the reduced growth of human melanoma xenografts in Nude mice treated with 3D1 mAb, where immunostaining of representative tumor sections show diminished P-Smad2 expression. Similar effects both in vitro and in vivo were observed in 3D1 treated A375SM melanoma cells harboring the active BRAF(V600E) mutation compared to treatments with IgG control or a BRAF inhibitor, dabrafenib. Finally, we describe a 3D1-based ELISA for the detection of Nodal in serum samples from cancer patients. These data suggest the potential of 3D1 mAb for selecting and targeting Nodal expressing cancers.
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Affiliation(s)
- Luigi Strizzi
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Università Federico II di Napoli, Naples, Italy
| | - Naira V. Margaryan
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Annalia Focà
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Università Federico II di Napoli, Naples, Italy
| | - Luca Sanguigno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II di Napoli, Naples, Italy
| | - Thomas M. Bodenstine
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Grace S. Chandler
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - David W. Reed
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Alina Gilgur
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Elisabeth A. Seftor
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Richard E.B. Seftor
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhila Khalkhali-Ellis
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Antonio Leonardi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II di Napoli, Naples, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini del CNR and CIRPeB, Università Federico II di Napoli, Naples, Italy
| | - Mary J.C. Hendrix
- Cancer Biology and Epigenomics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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