1
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Abdellateif MS, Bayoumi AK, Mohammed MA. c-Kit Receptors as a Therapeutic Target in Cancer: Current Insights. Onco Targets Ther 2023; 16:785-799. [PMID: 37790582 PMCID: PMC10544070 DOI: 10.2147/ott.s404648] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
c-Kit is a type III receptor tyrosine kinase (RTK) that has an essential role in various biological functions including gametogenesis, melanogenesis, hematopoiesis, cell survival, and apoptosis. c-KIT aberrations, either overexpression or loss-of-function mutations, have been implicated in the pathogenesis and development of many cancers, including gastrointestinal stromal tumors, mastocytosis, acute myeloid leukemia, breast, thyroid, and colorectal cancer, making c-KIT an attractive molecular target for the treatment of cancers. Therefore, a lot of effort has been put into investigating the utility of tyrosine kinase inhibitors for the management of c-KIT mutated tumors. This review of the literature illustrates the role of c-KIT mutations in many cancers, aiming to provide insights into the role of TKIs as a therapeutic option for cancer patients with c-KIT aberrations. In conclusion, c-KIT is implicated in different types of cancer, and it could be a successful molecular target; however, proper detection of the underlying mutation type is required before starting the appropriate personalized therapy.
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Affiliation(s)
- Mona S Abdellateif
- Medical Biochemistry and Molecular Biology, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Ahmed K Bayoumi
- Paediatric Oncology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
- Children’s Cancer Hospital 57357, Cairo, 11617, Egypt
| | - Mohammed Aly Mohammed
- Medical Biochemistry and Molecular Biology, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
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2
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Nadezhda N, Tyumentseva A, Ruksha T. Novel somatic Missense Mutations in Exon 11 of the KIT Gene are Detected in Melanoma. Asian Pac J Cancer Prev 2023; 24:3015-3020. [PMID: 37774052 PMCID: PMC10762753 DOI: 10.31557/apjcp.2023.24.9.3015] [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: 02/08/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023] Open
Abstract
OBJECTIVE The aim of the present study was to analyze mutations of the mast/stem cell growth factor receptor Kit (KIT) gene in patients with melanoma from Eastern Siberia regions of the Russian Federation. METHODS KIT gene mutations in exons 11 and 13 were analyzed by Sanger sequencing in 57 tumor samples obtained from patients with KIT-positive melanomas localized in preferable locations. RESULT Mutations were identified in 21% of patients. Among them, multiple mutations were identified in five patients. A total of 18 mutations were observed in the KIT gene, of which three were deletions and fourteen substitution mutations. Age, gender and clinicopathological characteristics of patients with cutaneous KIT-positive melanoma in Eastern Siberia corresponded to the European population. According to computational prediction tools, all mutations were evaluated as potentially harmful. CONCLUSION The six novel mutations reported in the present study expand our knowledge on the molecular pathogenesis of melanoma, which can be used to further explore methods to improve disease therapeutic strategies.
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Affiliation(s)
- Nadezhda Nadezhda
- Department of Pathophysiology, Krasnoyarsk State Medical University, P. Zeleznyaka str. 1, 660022, Krasnoyarsk, Russian Federation.
| | - Anna Tyumentseva
- Krasnoyarsk Scientific Center of the Siberian Branch the Russian Academy of Sciences, 50, Акаdemgorodok Str., Krasnoyarsk, 660036, Russian Federation.
| | - Tatiana Ruksha
- Department of Pathophysiology, Krasnoyarsk State Medical University, P. Zeleznyaka str. 1, 660022, Krasnoyarsk, Russian Federation.
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3
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Majumdar S, Di Palma F, Spyrakis F, Decherchi S, Cavalli A. Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. J Chem Inf Model 2023; 63:4814-4826. [PMID: 37462363 PMCID: PMC10428216 DOI: 10.1021/acs.jcim.3c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 08/15/2023]
Abstract
Tyrosine kinases are a subfamily of kinases with critical roles in cellular machinery. Dysregulation of their active or inactive forms is associated with diseases like cancer. This study aimed to holistically understand their flexibility-activity relationships, focusing on pockets and fluctuations. We studied 43 different tyrosine kinases by collecting 120 μs of molecular dynamics simulations, pocket and residue fluctuation analysis, and a complementary machine learning approach. We found that the inactive forms often have increased flexibility, particularly at the DFG motif level. Noteworthy, thanks to these long simulations combined with a decision tree, we identified a semiquantitative fluctuation threshold of the DGF+3 residue over which the kinase has a higher probability to be in the inactive form.
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Affiliation(s)
- Sarmistha Majumdar
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Francesco Di Palma
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University
of Turin, via Giuria
9, I-10125 Turin, Italy
| | - Sergio Decherchi
- Data
Science and Computation, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Andrea Cavalli
- Computational
& Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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4
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Sheikh E, Tran T, Vranic S, Levy A, Bonfil RD. Role and significance of c-KIT receptor tyrosine kinase in cancer: A review. Bosn J Basic Med Sci 2022; 22:683-698. [PMID: 35490363 PMCID: PMC9519160 DOI: 10.17305/bjbms.2021.7399] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
c-kit is a classical proto-oncogene that encodes a receptor tyrosine kinase (RTK) that responds to stem cell factor (SCF). C-KIT signaling is a critical regulator of cell proliferation, survival, and migration and is implicated in several physiological processes, including pigmentation, hematopoiesis and gut movement. Accumulating evidence suggests that dysregulated c-KIT function, caused by either overexpression or mutations in c-kit, promotes tumor development and progression in various human cancers. In this review, we discuss the most important structural and biological features of c-KIT, as well as insights into the activation of intracellular signaling pathways following SCF binding to this RTK. We then illustrate how different c-kit alterations are associated with specific human cancers and describe recent studies that highlight the contribution of c-KIT to cancer stemness, epithelial-mesenchymal transition and progression to metastatic disease in different experimental models. The impact of tyrosine kinase inhibitors in treating c-KIT-positive tumors and limitations due to their propensity to develop drug resistance are summarized. Finally, we appraise the potential of novel therapeutic approaches targeting c-KIT more selectively while minimizing toxicity to normal tissue.
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Affiliation(s)
- Emana Sheikh
- OMS-III, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States
| | - Tony Tran
- OMS-III, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States
| | - Semir Vranic
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Arkene Levy
- Department of Medical Education, Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States
| | - R. Daniel Bonfil
- Department of Medical Education, Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States
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5
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Ledoux J, Trouvé A, Tchertanov L. The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT. Int J Mol Sci 2022; 23:ijms23031589. [PMID: 35163518 PMCID: PMC8835827 DOI: 10.3390/ijms23031589] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events.
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6
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Recognition of distinct chemical molecules as inhibitors for KIT receptor mutants D816H/Y/V: A simulation approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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7
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Nedoszytko B, Arock M, Lyons JJ, Bachelot G, Schwartz LB, Reiter A, Jawhar M, Schwaab J, Lange M, Greiner G, Hoermann G, Niedoszytko M, Metcalfe DD, Valent P. Clinical Impact of Inherited and Acquired Genetic Variants in Mastocytosis. Int J Mol Sci 2021; 22:ijms22010411. [PMID: 33401724 PMCID: PMC7795405 DOI: 10.3390/ijms22010411] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023] Open
Abstract
Mastocytosis is a rare and complex disease characterized by expansion of clonal mast cells (MC) in skin and/or various internal organ systems. Involvement of internal organs leads to the diagnosis of systemic mastocytosis (SM). The WHO classification divides SM into indolent SM, smoldering SM and advanced SM variants, including SM with an associated hematologic neoplasm, aggressive SM, and MC leukemia. Historically, genetic analysis of individuals with pure cutaneous mastocytosis (CM) and SM have focused primarily on cohort studies of inherited single nucleotide variants and acquired pathogenic variants. The most prevalent pathogenic variant (mutation) in patients with SM is KIT p.D816V, which is detectable in most adult patients. Other somatic mutations have also been identified-especially in advanced SM-in TET2, SRSF2, ASXL1, RUNX1, CBL and JAK2, and shown to impact clinical and cellular phenotypes. Although only small patient cohorts have been analyzed, disease associations have also been identified in several germline variants within genes encoding certain cytokines or their receptors (IL13, IL6, IL6R, IL31, IL4R) and toll-like receptors. More recently, an increased prevalence of hereditary alpha-tryptasemia (HαT) caused by increased TPSAB1 copy number encoding alpha-tryptase has been described in patients with SM. Whereas HαT is found in 3-6% of general Western populations, it is identified in up to 17% of patients with SM. In the current manuscript we review the prevalence, functional role and clinical impact of various germline and somatic genetic variants in patients with mastocytosis.
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Affiliation(s)
- Boguslaw Nedoszytko
- Department of Dermatology, Allergology and Venereology, Medical University of Gdansk, 80-211 Gdansk, Poland;
- Correspondence:
| | - Michel Arock
- Department of Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, 75013 Paris, France; (M.A.); (G.B.)
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Cell Death and Drug Resistance in Hematological Disorders Team, 75006 Paris, France
| | - Jonathan J. Lyons
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-188, USA; (J.J.L.); (D.D.M.)
| | - Guillaume Bachelot
- Department of Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, 75013 Paris, France; (M.A.); (G.B.)
| | - Lawrence B. Schwartz
- Department of Internal Medicine, Division of Rheumatology, Allergy & Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany; (A.R.); (M.J.); (J.S.)
| | - Mohamad Jawhar
- University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany; (A.R.); (M.J.); (J.S.)
| | - Juliana Schwaab
- University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany; (A.R.); (M.J.); (J.S.)
| | - Magdalena Lange
- Department of Dermatology, Allergology and Venereology, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria; (G.H.); (P.V.)
- Ihr Labor, Medical Diagnostic Laboratories, 1220 Vienna, Austria
| | - Gregor Hoermann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria; (G.H.); (P.V.)
- MLL Munich Leukemia Laboratory, 81377 Munich, Germany
| | - Marek Niedoszytko
- Department of Allergology, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Dean D. Metcalfe
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-188, USA; (J.J.L.); (D.D.M.)
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria; (G.H.); (P.V.)
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria
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8
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Liang J, Bonvino NP, Hung A, Karagiannis TC. In silico characterisation of olive phenolic compounds as potential cyclooxygenase modulators. Part 2. J Mol Graph Model 2020; 101:107743. [PMID: 32920237 DOI: 10.1016/j.jmgm.2020.107743] [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: 05/01/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to reduce pain, and function by targeting cyclooxygenase (COX) enzymes to inhibit the production of prostaglandins that facilitate inflammation. Since oleocanthal derived from Olea europaea is known to inhibit COX, we sought to characterise novel olive compounds with COX inhibitory activity using in silico techniques. Following on from part 1 of this study which identified 1-oleyltyrosol (1OL) and ligstroside derivative 2 (LG2) with COX inhibitory potential, the mechanisms of COX interactions by these selected compounds were further examined using molecular dynamics (MD) simulations. Classical MD simulations were carried out on COX-1 and COX-2 complexed with 1OL and LG2 to determine the stability and protein backbone fluctuation. Protein dynamics were examined using essential dynamics methods and network analysis, which identified that the N-terminal epidermal growth factor-like domain and membrane bound domains of COX-1 and -2 exhibited altered motions when ligands were bound. Distinct dynamical modules were identified, and that COX-2 inter-residue communications were more sensitive to ligand binding compared to COX-1. The use of various network metrics presents a novel approach in the characterisation of network behaviour of different ligands. It is proposed that inter-residue network metrics provide additional measures of the potential bioactivity of ligands, which may form a useful adjunct to conventional direct predictions of binding affinity, in determining the efficacy of potential small-molecule inhibitors. Overall, this two-part study characterises anti-inflammatory effects of low dosage dietary COX inhibitors, and provides a possible avenue for the development of therapeutics in inflammatory diseases.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, RMIT University, VIC, 3001, Australia
| | - Natalie P Bonvino
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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9
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Martorana A, Lauria A. Design of antitumor drugs targeting c-kit receptor by a new mixed ligand-structure based method. J Mol Graph Model 2020; 100:107666. [PMID: 32659630 DOI: 10.1016/j.jmgm.2020.107666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 10/23/2022]
Abstract
An important challenge, in the medicinal chemistry field, is the research of novel forceful drugs to overcome tumor-acquired resistance. The c-Kit tyrosine kinase receptor (TKR) represents a suitable target for the carcinogenesis control of gastro-intestinal stromal (GIST), leukemia, and mastocytosis tumors; nevertheless, several hotspot mutations of the protein limit the efficacy of a few clinical administered TKRs inhibitors. In this study, a new in silico protocol based on ligand and structure-based combined method is proposed, with the aim to identify a set of new c-Kit inhibitors able to complex c-Kit mutated proteins. A recent and freely available web-server DRUDIT is used for the ligand-based method. The protocol application allows for identifying a new generation of potential TKR inhibitors, which, in silico, complex the V654A and T670I mutated proteins and potentially overcome resistant mutations (D816H). The structure-based analysis is performed by Induced Fit Docking (IFD) studies. The comparison between the explored ligands and well-known drugs highlights the possibility to overcome tumor-acquired resistance. The best-selected structures (630705 and SML1348) provide valuable binding affinities with the mutated c-Kit forms (respectively T670I and V654A).
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Affiliation(s)
- Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF" - University of Palermo, Viale delle Scienze - Ed. 17, 90128, Palermo, Italy
| | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF" - University of Palermo, Viale delle Scienze - Ed. 17, 90128, Palermo, Italy.
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10
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Srikakulam SK, Bastys T, Kalinina OV. A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance. Proteins 2020; 88:1434-1446. [PMID: 32530065 DOI: 10.1002/prot.25963] [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: 11/19/2019] [Revised: 04/11/2020] [Accepted: 06/06/2020] [Indexed: 11/11/2022]
Abstract
Tyrosine phosphorylation, a highly regulated post-translational modification, is carried out by the enzyme tyrosine kinase (TK). TKs are important mediators in signaling cascades, facilitating diverse biological processes in response to stimuli. TKs may acquire mutations leading to malignancy and are viable targets for anti-cancer drugs. Mast/stem cell growth factor receptor KIT is a TK involved in cell differentiation, whose dysregulation leads to various types of cancer, including gastrointestinal stromal tumors, leukemia, and melanoma. KIT can be targeted by a range of inhibitors that predominantly bind to the inactive state of the enzyme. A mutation Y823D in the activation loop of KIT is known to be responsible for the loss of sensitivity to some drugs in metastatic tumors. We used all-atom molecular dynamics simulations to study the impact of Y823D on the KIT conformation and dynamics and compared it to the effect of phosphorylation of Y823. We simulated in total 6.4 μs of wild-type, mutant and phosphorylated KIT in the active- and inactive-state conformations. We found that Y823D affects the protein dynamics differently: in the active state, the mutation increases the protein stability, whereas in the inactive state it induces local destabilization, thus shifting the dynamic equilibrium towards the active state, altering the communication between distant regulatory regions. The observed dynamics of the Y823D mutant is similar to the dynamics of KIT phosphorylated at position Y823, thus we hypothesize that this mutation mimics a constitutively active kinase, which is not responsive to inhibitors that bind its inactive conformation.
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Affiliation(s)
- Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,Graduate School of Computer Science, Saarland University, Saarbrücken, Germany.,Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken, Germany
| | - Tomas Bastys
- Graduate School of Computer Science, Saarland University, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,Medical Faculty, Saarland University, Homburg, Germany
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11
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The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor. Sci Rep 2020; 10:5401. [PMID: 32214210 PMCID: PMC7096506 DOI: 10.1038/s41598-020-62460-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are key regulators of normal cellular processes and have a critical role in the development and progression of many diseases. RTK ligand-induced stimulation leads to activation of the cytoplasmic kinase domain that controls the intracellular signalling. Although the kinase domain of RTKs has been extensively studied using X-ray analysis, the kinase insert domain (KID) and the C-terminal are partially or fully missing in all reported structures. We communicate the first structural model of the full-length RTK KIT cytoplasmic domain, a crucial target for cancer therapy. This model was achieved by integration of ab initio KID and C-terminal probe models into an X-ray structure, and by their further exploration through molecular dynamics (MD) simulation. An extended (2-µs) MD simulation of the proper model provided insight into the structure and conformational dynamics of the full-length cytoplasmic domain of KIT, which can be exploited in the description of the KIT transduction processes.
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12
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Kim C, Kim E. Rational Drug Design Approach of Receptor Tyrosine Kinase Type III Inhibitors. Curr Med Chem 2020; 26:7623-7640. [PMID: 29932031 DOI: 10.2174/0929867325666180622143548] [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: 02/02/2018] [Revised: 04/27/2018] [Accepted: 05/30/2018] [Indexed: 01/16/2023]
Abstract
Rational drug design is accomplished through the complementary use of structural biology and computational biology of biological macromolecules involved in disease pathology. Most of the known theoretical approaches for drug design are based on knowledge of the biological targets to which the drug binds. This approach can be used to design drug molecules that restore the balance of the signaling pathway by inhibiting or stimulating biological targets by molecular modeling procedures as well as by molecular dynamics simulations. Type III receptor tyrosine kinase affects most of the fundamental cellular processes including cell cycle, cell migration, cell metabolism, and survival, as well as cell proliferation and differentiation. Many inhibitors of successful rational drug design show that some computational techniques can be combined to achieve synergistic effects.
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Affiliation(s)
- Cheolhee Kim
- College of Pharmacy, Chosun University, Gwangju 61452, Korea
| | - Eunae Kim
- College of Pharmacy, Chosun University, Gwangju 61452, Korea
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13
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Liang Z, Verkhivker GM, Hu G. Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Brief Bioinform 2019; 21:815-835. [DOI: 10.1093/bib/bbz029] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 12/24/2022] Open
Abstract
Abstract
Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein–DNA/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.
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Affiliation(s)
- Zhongjie Liang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Gennady M Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Guang Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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14
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Karami Y, Bitard-Feildel T, Laine E, Carbone A. "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations. Sci Rep 2018; 8:16126. [PMID: 30382169 PMCID: PMC6208415 DOI: 10.1038/s41598-018-34508-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/17/2018] [Indexed: 11/09/2022] Open
Abstract
Characterizing a protein mutational landscape is a very challenging problem in Biology. Many disease-associated mutations do not seem to produce any effect on the global shape nor motions of the protein. Here, we use relatively short all-atom biomolecular simulations to predict mutational outcomes and we quantitatively assess the predictions on several hundreds of mutants. We perform simulations of the wild type and 175 mutants of PSD95’s third PDZ domain in complex with its cognate ligand. By recording residue displacements correlations and interactions, we identify “communication pathways” and quantify them to predict the severity of the mutations. Moreover, we show that by exploiting simulations of the wild type, one can detect 80% of the positions highly sensitive to mutations with a precision of 89%. Importantly, our analysis describes the role of these positions in the inter-residue communication and dynamical architecture of the complex. We assess our approach on three different systems using data from deep mutational scanning experiments and high-throughput exome sequencing. We refer to our analysis as “infostery”, from “info” - information - and “steric” - arrangement of residues in space. We provide a fully automated tool, COMMA2 (www.lcqb.upmc.fr/COMMA2), that can be used to guide medicinal research by selecting important positions/mutations.
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Affiliation(s)
- Yasaman Karami
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France.,Sorbonne Université, Institut des Sciences du Calcul et de des Données (ISCD), Paris, France
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France.
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France. .,Institut Universitaire de France (IUF), Paris, France.
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15
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Kim HR, Kang HN, Shim HS, Kim EY, Kim J, Kim DJ, Lee JG, Lee CY, Hong MH, Kim SM, Kim H, Pyo KH, Yun MR, Park HJ, Han JY, Youn HA, Ahn MJ, Paik S, Kim TM, Cho BC. Co-clinical trials demonstrate predictive biomarkers for dovitinib, an FGFR inhibitor, in lung squamous cell carcinoma. Ann Oncol 2018; 28:1250-1259. [PMID: 28460066 DOI: 10.1093/annonc/mdx098] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background We conducted co-clinical trials in patient-derived xenograft (PDX) models to identify predictive biomarkers for the multikinase inhibitor dovitinib in lung squamous cell carcinoma (LSCC). Methods The PDX01-02 were established from LSCC patients enrolled in the phase II trial of dovitinib (NCT01861197) and PDX03-05 were established from LSCC patients receiving surgery. These five PDX tumors were subjected to in vivo test of dovitinib efficacy, whole exome sequencing and gene expression profiling. Results The PDX tumors recapitulate histopathological properties and maintain genomic characteristics of originating tumors. Concordant with clinical outcomes of the trial enrolled-LSCC patients, dovitinib produced substantial tumor regression in PDX-01 and PDX-05, whereas it resulted in tumor progression in PDX-02. PDX-03 and -04 also displayed poor antitumor efficacy to dovitinib. Mutational and genome-wide copy number profiles revealed no correlation between genomic alterations of FGFR1-3 and sensitivity to dovitinib. Of note, gene expression profiles revealed differentially expressed genes including FGF3 and FGF19 between PDX-01 and 05 and PDX-02-04. Pathway analysis identified two FGFR signaling-related gene sets, FGFR ligand binding/activation and SHC-mediated cascade pathway were substantially up-regulated in PDX-01 and 05, compared with PDX-02-04. The comparison of gene expression profiles between dovitinib-sensitive versus -resistant lung cancer cell lines in the Cancer Cell Line Encyclopedia database also found that transcriptional activation of 18 key signaling components in FGFR pathways can predict the sensitivity to dovitinib both in cell lines and PDX tumors. These results highlight FGFR pathway activation as a key molecular determinant for sensitivity to dovitinib. Conclusions FGFR gene expression signatures are predictors for the response to dovitinib in LSCC.
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Affiliation(s)
- H R Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul
| | - H N Kang
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | | | - E Y Kim
- Pulmonology, Yonsei University College of Medicine, Seoul
| | - J Kim
- Department of Radiology, Severance Hospital, Yonsei University College of Medicine, Seoul
| | - D J Kim
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul
| | - J G Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul
| | - C Y Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul
| | - M H Hong
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul
| | - S-M Kim
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - H Kim
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - K-H Pyo
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - M R Yun
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - H J Park
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - J Y Han
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - H A Youn
- JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
| | - M-J Ahn
- Division of Hematology & Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - S Paik
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul
| | - T-M Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - B C Cho
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul.,JE-UK Institute for Cancer Research, JEUK Co, Ltd, Gumi-City, Kyungbuk
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16
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Nguyen TD, Takasuka H, Kaku Y, Inoue S, Nagamune T, Kawahara M. Engineering a growth sensor to select intracellular antibodies in the cytosol of mammalian cells. J Biosci Bioeng 2017; 124:125-132. [PMID: 28319021 DOI: 10.1016/j.jbiosc.2017.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/24/2017] [Indexed: 02/02/2023]
Abstract
Intracellular antibodies (intrabodies) are expected to function as therapeutics as well as tools for elucidating in vivo function of proteins. In this study, we propose a novel intrabody selection method in the cytosol of mammalian cells by utilizing a growth signal, induced by the interaction of the target antigen and an scFv-c-kit growth sensor. Here, we challenge this method to select specific intrabodies against rabies virus nucleoprotein (RV-N) for the first time. As a result, we successfully select antigen-specific intrabodies from a naïve synthetic library using phage panning followed by our growth sensor-based intracellular selection method, demonstrating the feasibility of the method. Additionally, we succeed in improving the response of the growth sensor by re-engineering the linker region of its construction. Collectively, the described selection method utilizing a growth sensor may become a highly efficient platform for selection of functional intrabodies in the future.
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Affiliation(s)
- Thuy Duong Nguyen
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hitoshi Takasuka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Teruyuki Nagamune
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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17
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Fang L, Hou Y, An J, Li B, Song M, Wang X, Sørensen P, Dong Y, Liu C, Wang Y, Zhu H, Zhang S, Yu Y. Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus. Front Cell Infect Microbiol 2016; 6:193. [PMID: 28083515 PMCID: PMC5183581 DOI: 10.3389/fcimb.2016.00193] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is problematic for lactating mammals and public health. Understanding of mechanisms by which the hosts respond to severe invasion of S. aureus remains elusive. In this study, the genome-wide expression of mRNAs and miRNAs in bovine mammary gland cells were interrogated at 24 h after intra-mammary infection (IMI) with high or low concentrations of S. aureus. Compared to the negative control quarters, 194 highly-confident responsive genes were identified in the quarters with high concentration (109 cfu/mL) of S. aureus, which were predominantly implicated in pathways and biological processes pertaining to innate immune system, such as cytokine-cytokine receptor interaction and inflammatory response. In contrast, only 21 highly-confident genes were significantly differentially expressed in face of low concentration (106 cfu/mL) of S. aureus, which slightly perturbed the cell signaling and invoked corresponding responses like vasoconstriction, indicating limited perturbations and immunological evading. Additionally, the significant up-regulations of bta-mir-223 and bta-mir-21-3p were observed in the quarters infected by high concentration of S. aureus. Network analysis suggested that the two miRNAs' pivotal roles in defending hosts against bacterial infection probably through inhibiting CXCL14 and KIT. The significant down-regulation of CXCL14 was also observed in bovine mammary epithelial cells at 24 h post-infection of S. aureus (108 cfu/mL) in vitro. Integrated analysis with QTL database further suggested 28 genes (e.g., CXCL14, KIT, and SLC4A11) as candidates of bovine mastitis. This study first systematically revealed transcriptional and post-transcriptional responses of bovine mammary gland cells to invading S. aureus in a dosage-dependent pattern, and highlighted a complicated responsive mechanism in a network of miRNA-gene-pathway interplay.
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Affiliation(s)
- Lingzhao Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityBeijing, China; Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus UniversityTjele, Denmark
| | - Yali Hou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jing An
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Bingjie Li
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
| | - Minyan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Xiao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityBeijing, China; Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus UniversityTjele, Denmark
| | - Peter Sørensen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
| | - Yichun Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Chao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Huabin Zhu
- Department of Animal Biotechnology and Reproduction, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University Beijing, China
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18
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Insight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KIT. PLoS One 2016; 11:e0160165. [PMID: 27467080 PMCID: PMC4965071 DOI: 10.1371/journal.pone.0160165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/14/2016] [Indexed: 01/22/2023] Open
Abstract
The receptors tyrosine kinases (RTKs) for the colony stimulating factor-1, CSF-1R, and for the stem cell factor, SCFR or KIT, are important mediators of signal transduction. The abnormal function of these receptors, promoted by gain-of-function mutations, leads to their constitutive activation, associated with cancer or other proliferative diseases. A secondary effect of the mutations is the alteration of receptors' sensitivity to tyrosine kinase inhibitors, compromising effectiveness of these molecules in clinical treatment. In particular, the mutation V560G in KIT increases its sensitivity to Imatinib, while the D816V in KIT, and D802V in CSF-1R, triggers resistance to the drug. We analyzed the Imatinib binding affinity to the native and mutated KIT (mutations V560G, S628N and D816V) and CSF-1R (mutation D802V) by using molecular dynamics simulations and energy calculations of Imatinib•target complexes. Further, we evaluated the sensitivity of the studied KIT receptors to Imatinib by measuring the inhibition of KIT phosphorylation. Our study showed that (i) the binding free energy of Imatinib to the targets is highly correlated with their experimentally measured sensitivity; (ii) the electrostatic interactions are a decisive factor affecting the binding energy; (iii) the most deleterious impact to the Imatinib sensitivity is promoted by D802V (CSF-1R) and D816V (KIT) mutations; (iv) the role of the juxtamembrane region, JMR, in the imatinib binding is accessory. These findings contribute to a better description of the mutation-induced effects alternating the targets sensitivity to Imatinib.
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19
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Dissecting protein architecture with communication blocks and communicating segment pairs. BMC Bioinformatics 2016; 17 Suppl 2:13. [PMID: 26823083 PMCID: PMC4959365 DOI: 10.1186/s12859-015-0855-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins adapt to environmental conditions by changing their shape and motions. Characterising protein conformational dynamics is increasingly recognised as necessary to understand how proteins function. Given a conformational ensemble, computational tools are needed to extract in a systematic way pertinent and comprehensive biological information. RESULTS Here, we present a method, Communication Mapping (COMMA), to decipher the dynamical architecture of a protein. The method first extracts residue-based dynamic properties from all-atom molecular dynamics simulations. Then, it integrates them in a graph theoretic framework, where it identifies groups of residues or protein regions that mediate short- and long-range communication. COMMA introduces original concepts to contrast the different roles played by these regions, namely communication blocks and communicating segment pairs, and evaluates the connections and communication strengths between them. We show the utility and capabilities of COMMA by applying it to three archetypal proteins, namely protein A, the tyrosine kinase KIT and the tumour suppressor p53. CONCLUSION Our method permits to compare in a direct way the dynamical behaviour either of proteins with different characteristics or of the same protein in different conditions. It is useful to identify residues playing a key role in protein allosteric regulation and to explain the effects of deleterious mutations in a mechanistic way. COMMA is a fully automated tool with broad applicability. It is freely available to the community at www.lcqb.upmc.fr/COMMA .
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20
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Langenfeld F, Guarracino Y, Arock M, Trouvé A, Tchertanov L. How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5. PLoS One 2015; 10:e0145142. [PMID: 26717567 PMCID: PMC4696835 DOI: 10.1371/journal.pone.0145142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/01/2015] [Indexed: 01/12/2023] Open
Abstract
Signal Transducer and Activator of Transcription STAT5 is a key mediator of cell proliferation, differentiation and survival. While STAT5 activity is tightly regulated in normal cells, its constitutive activation directly contributes to oncogenesis and is associated with a broad range of hematological and solid tumor cancers. Therefore the development of compounds able to modulate pathogenic activation of this protein is a very challenging endeavor. A crucial step of drug design is the understanding of the protein conformational features and the definition of putative binding site(s) for such modulators. Currently, there is no structural data available for human STAT5 and our study is the first footprint towards the description of structure and dynamics of this protein. We investigated structural and dynamical features of the two STAT5 isoforms, STAT5a and STAT5b, taken into account their phosphorylation status. The study was based on the exploration of molecular dynamics simulations by different analytical methods. Despite the overall folding similarity of STAT5 proteins, the MD conformations display specific structural and dynamical features for each protein, indicating first, sequence-encoded structural properties and second, phosphorylation-induced effects which contribute to local and long-distance structural rearrangements interpreted as allosteric event. Further examination of the dynamical coupling between distant sites provides evidence for alternative profiles of the communication pathways inside and between the STAT5 domains. These results add a new insight to the understanding of the crucial role of intrinsic molecular dynamics in mediating intramolecular signaling in STAT5. Two pockets, localized in close proximity to the phosphotyrosine-binding site and adjacent to the channel for communication pathways across STAT5, may constitute valid targets to develop inhibitors able to modulate the function-related communication properties of this signaling protein.
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Affiliation(s)
- Florent Langenfeld
- Laboratoire de Biologie et Pharmacologie Appliquée Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
- Centre de Mathématiques et de Leurs applications, Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
| | - Yann Guarracino
- Laboratoire de Biologie et Pharmacologie Appliquée Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
| | - Michel Arock
- Laboratoire de Biologie et Pharmacologie Appliquée Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
| | - Alain Trouvé
- Centre de Mathématiques et de Leurs applications, Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
| | - Luba Tchertanov
- Centre de Mathématiques et de Leurs applications, Ecole Normale Supérieure de Cachan, CNRS, Université Paris-Saclay, Cachan, France
- * E-mail:
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21
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Jatana N, Thukral L, Latha N. Structural signatures of DRD4 mutants revealed using molecular dynamics simulations: Implications for drug targeting. J Mol Model 2015; 22:14. [PMID: 26680992 DOI: 10.1007/s00894-015-2868-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/17/2015] [Indexed: 01/08/2023]
Abstract
Human Dopamine Receptor D4 (DRD4) orchestrates several neurological functions and represents a target for many psychological disorders. Here, we examined two rare variants in DRD4; V194G and R237L, which elicit functional alterations leading to disruption of ligand binding and G protein coupling, respectively. Using atomistic molecular dynamics (MD) simulations, we provide in-depth analysis to reveal structural signatures of wild and mutant complexes with their bound agonist and antagonist ligands. We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. The data suggest that the mutation in transmembrane V (V194G) drastically disrupts the organization of ligand binding site and causes disorder in the native helical arrangement. Interestingly, the R237L mutation leads to significant rewiring of side-chain contacts in the intracellular loop 3 (site of mutation) and also affects the distant transmembrane topology. Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. Our findings thus reveal unreported structural determinants of the mutated DRD4 receptor and provide a robust framework for design of effective novel drugs.
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Affiliation(s)
- Nidhi Jatana
- Bioinformatics Infrastructure Facility, Sri Venkateswara College (University of Delhi), Benito Juarez Road, Dhaula Kuan, New Delhi, 110 021, India.,CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110020, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110020, India.
| | - N Latha
- Bioinformatics Infrastructure Facility, Sri Venkateswara College (University of Delhi), Benito Juarez Road, Dhaula Kuan, New Delhi, 110 021, India.
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22
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Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding. PLoS Comput Biol 2015; 11:e1004496. [PMID: 26394388 PMCID: PMC4578939 DOI: 10.1371/journal.pcbi.1004496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 08/03/2015] [Indexed: 11/23/2022] Open
Abstract
Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. Several non-native proteins require molecular chaperones for proper folding. Many unfolded proteins if not folded accurately, become causal factors in various types of misfolding or aggregation induced diseases such as Alzheimer′s, Huntington′s and several other neurodegenerative disorders. However, structural information of non-folded proteins especially chaperone-dependent proteins is difficult to probe experimentally due to their inherent aggregation propensities. In this work, we study DapA protein, which exhibits obligate requirement on GroEL chaperonin machinery for its folding. We use molecular dynamics simulations to reveal populated intermediate structures of DapA in atomic details. The most plausible intermediate was found to be in agreement with recently reported hydrogen-exchange experimental data. Significant increase in surface exposed hydrophobicity was observed in intermediates compared to native, which was further validated using ANS binding experiments. We also constructed network model of these intermediates that provides remarkable insights into stable hubs (or important residues) underlying diverse states of unfolded proteins. In summary, our work provides a molecular picture of an unfolded protein that is en route to chaperone binding, and these underlying structural properties might act as a molecular signal for their productive folding.
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23
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Lasho T, Finke C, Zblewski D, Hanson CA, Ketterling RP, Butterfield JH, Tefferi A, Pardanani A. Concurrent activatingKITmutations in systemic mastocytosis. Br J Haematol 2015; 173:153-6. [DOI: 10.1111/bjh.13560] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Terra Lasho
- Divisions of Hematology; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
| | - Christy Finke
- Divisions of Hematology; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
| | - Darci Zblewski
- Divisions of Hematology; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
| | - Curtis A. Hanson
- Division of Hematopathology; Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN USA
| | - Rhett P. Ketterling
- Division of Cytogenetics; Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN USA
| | - Joseph H. Butterfield
- Divisions of Allergy; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
| | - Ayalew Tefferi
- Divisions of Hematology; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
| | - Animesh Pardanani
- Divisions of Hematology; Department of Internal Medicine; Mayo Clinic; Rochester MN USA
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