1
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Gau D, Daoud A, Allen A, Joy M, Sagan A, Lee S, Lucas PC, Duensing S, Boone D, Osmanbeyoglu HU, Roy P. Vascular endothelial profilin-1 drives a protumorigenic tumor microenvironment and tumor progression in renal cancer. J Biol Chem 2023; 299:105044. [PMID: 37451478 PMCID: PMC10432806 DOI: 10.1016/j.jbc.2023.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/06/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Overexpression of actin-binding protein profilin-1 (Pfn1) correlates with advanced disease features and adverse clinical outcome of patients with clear cell renal carcinoma, the most prevalent form of renal cancer. We previously reported that Pfn1 is predominantly overexpressed in tumor-associated vascular endothelial cells in human clear cell renal carcinoma. In this study, we combined in vivo strategies involving endothelial cell-specific depletion and overexpression of Pfn1 to demonstrate a role of vascular endothelial Pfn1 in promoting tumorigenicity and enabling progressive growth and metastasis of renal carcinoma cells in a syngeneic orthotopic mouse model of kidney cancer. We established an important role of endothelial Pfn1 in tumor angiogenesis and further identified endothelial Pfn1-dependent regulation of several pro- (VEGF, SERPINE1, CCL2) and anti-angiogenic factors (platelet factor 4) in vivo. Endothelial Pfn1 overexpression increases tumor infiltration by macrophages and concomitantly diminishes tumor infiltration by T cells including CD8+ T cells in vivo, correlating with the pattern of endothelial Pfn1-dependent changes in tumor abundance of several prominent immunomodulatory cytokines. These data were also corroborated by multiplexed quantitative immunohistochemistry and immune deconvolution analyses of RNA-seq data of clinical samples. Guided by Upstream Regulator Analysis of tumor transcriptome data, we further established endothelial Pfn1-induced Hif1α elevation and suppression of STAT1 activation. In conclusion, this study demonstrates for the first time a direct causal relationship between vascular endothelial Pfn1 dysregulation, immunosuppressive tumor microenvironment, and disease progression with mechanistic insights in kidney cancer. Our study also provides a conceptual basis for targeting Pfn1 for therapeutic benefit in kidney cancer.
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Affiliation(s)
- David Gau
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Andrew Daoud
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Abigail Allen
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Marion Joy
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - April Sagan
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Peter C Lucas
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stefan Duensing
- Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - David Boone
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hatice U Osmanbeyoglu
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Partha Roy
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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2
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Dans MG, Piirainen H, Nguyen W, Khurana S, Mehra S, Razook Z, Geoghegan ND, Dawson AT, Das S, Parkyn Schneider M, Jonsdottir TK, Gabriela M, Gancheva MR, Tonkin CJ, Mollard V, Goodman CD, McFadden GI, Wilson DW, Rogers KL, Barry AE, Crabb BS, de Koning-Ward TF, Sleebs BE, Kursula I, Gilson PR. Sulfonylpiperazine compounds prevent Plasmodium falciparum invasion of red blood cells through interference with actin-1/profilin dynamics. PLoS Biol 2023; 21:e3002066. [PMID: 37053271 PMCID: PMC10128974 DOI: 10.1371/journal.pbio.3002066] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/25/2023] [Accepted: 03/06/2023] [Indexed: 04/15/2023] Open
Abstract
With emerging resistance to frontline treatments, it is vital that new antimalarial drugs are identified to target Plasmodium falciparum. We have recently described a compound, MMV020291, as a specific inhibitor of red blood cell (RBC) invasion, and have generated analogues with improved potency. Here, we generated resistance to MMV020291 and performed whole genome sequencing of 3 MMV020291-resistant populations. This revealed 3 nonsynonymous single nucleotide polymorphisms in 2 genes; 2 in profilin (N154Y, K124N) and a third one in actin-1 (M356L). Using CRISPR-Cas9, we engineered these mutations into wild-type parasites, which rendered them resistant to MMV020291. We demonstrate that MMV020291 reduces actin polymerisation that is required by the merozoite stage parasites to invade RBCs. Additionally, the series inhibits the actin-1-dependent process of apicoplast segregation, leading to a delayed death phenotype. In vitro cosedimentation experiments using recombinant P. falciparum proteins indicate that potent MMV020291 analogues disrupt the formation of filamentous actin in the presence of profilin. Altogether, this study identifies the first compound series interfering with the actin-1/profilin interaction in P. falciparum and paves the way for future antimalarial development against the highly dynamic process of actin polymerisation.
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Affiliation(s)
- Madeline G. Dans
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Henni Piirainen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - William Nguyen
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Sachin Khurana
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Somya Mehra
- Burnet Institute, Melbourne, Victoria, Australia
| | - Zahra Razook
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | | | | | - Sujaan Das
- Ludwig Maximilian University, Faculty of Veterinary Medicine, Munich, Germany
| | | | - Thorey K. Jonsdottir
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mikha Gabriela
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Maria R. Gancheva
- Research Centre for Infectious Diseases, The University of Adelaide, Adelaide, Australia
| | | | - Vanessa Mollard
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Geoffrey I. McFadden
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Danny W. Wilson
- Research Centre for Infectious Diseases, The University of Adelaide, Adelaide, Australia
| | - Kelly L. Rogers
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Alyssa E. Barry
- Burnet Institute, Melbourne, Victoria, Australia
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Brendan S. Crabb
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tania F. de Koning-Ward
- School of Medicine and Institute for Mental and Physical Health and Clinical Translation, Deakin University, Waurn Ponds, Victoria, Australia
| | - Brad E. Sleebs
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Paul R. Gilson
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
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3
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Li Y, Wang D, Ge H, Güngör C, Gong X, Chen Y. Cytoskeletal and Cytoskeleton-Associated Proteins: Key Regulators of Cancer Stem Cell Properties. Pharmaceuticals (Basel) 2022; 15:1369. [PMID: 36355541 PMCID: PMC9698833 DOI: 10.3390/ph15111369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 08/08/2023] Open
Abstract
Cancer stem cells (CSCs) are a subpopulation of cancer cells possessing stemness characteristics that are closely associated with tumor proliferation, recurrence and resistance to therapy. Recent studies have shown that different cytoskeletal components and remodeling processes have a profound impact on the behavior of CSCs. In this review, we outline the different cytoskeletal components regulating the properties of CSCs and discuss current and ongoing therapeutic strategies targeting the cytoskeleton. Given the many challenges currently faced in targeted cancer therapy, a deeper comprehension of the molecular events involved in the interaction of the cytoskeleton and CSCs will help us identify more effective therapeutic strategies to eliminate CSCs and ultimately improve patient survival.
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Affiliation(s)
- Yuqiang Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Dan Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Heming Ge
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cenap Güngör
- Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Xuejun Gong
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yongheng Chen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, China
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4
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Uddin A, Gupta S, Mohammad T, Shahi D, Hussain A, Alajmi MF, El-Seedi HR, Hassan I, Singh S, Abid M. Target-Based Virtual Screening of Natural Compounds Identifies a Potent Antimalarial With Selective Falcipain-2 Inhibitory Activity. Front Pharmacol 2022; 13:850176. [PMID: 35462917 PMCID: PMC9020225 DOI: 10.3389/fphar.2022.850176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
We employed a comprehensive approach of target-based virtual high-throughput screening to find potential hits from the ZINC database of natural compounds against cysteine proteases falcipain-2 and falcipain-3 (FP2 and FP3). Molecular docking studies showed the initial hits showing high binding affinity and specificity toward FP2 were selected. Furthermore, the enzyme inhibition and surface plasmon resonance assays were performed which resulted in a compound ZINC12900664 (ST72) with potent inhibitory effects on purified FP2. ST72 exhibited strong growth inhibition of chloroquine-sensitive (3D7; EC50 = 2.8 µM) and chloroquine-resistant (RKL-9; EC50 = 6.7 µM) strains of Plasmodium falciparum. Stage-specific inhibition assays revealed a delayed and growth defect during parasite growth and development in parasites treated with ST72. Furthermore, ST72 significantly reduced parasite load and increased host survival in a murine model infected with Plasmodium berghei ANKA. No Evans blue staining in ST72 treatment indicated that ST72 mediated protection of blood–brain barrier integrity in mice infected with P. berghei. ST72 did not show any significant hemolysis or cytotoxicity against human HepG2 cells suggesting a good safety profile. Importantly, ST72 with CQ resulted in improved growth inhibitory activity than individual drugs in both in vitro and in vivo studies.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonal Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Diksha Shahi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hesham R. El-Seedi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
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5
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Abstract
Dynamic remodeling of the actin cytoskeleton is an essential feature for virtually all actin-dependent cellular processes, including cell migration, cell cycle progression, chromatin remodeling and gene expression, and even the DNA damage response. An altered actin cytoskeleton is a structural hallmark associated with numerous pathologies ranging from cardiovascular diseases to immune disorders, neurological diseases and cancer. The actin cytoskeleton in cells is regulated through the orchestrated actions of a myriad of actin-binding proteins. In this Review, we provide a brief overview of the structure and functions of the actin-monomer-binding protein profilin-1 (Pfn1) and then discuss how dysregulated expression of Pfn1 contributes to diseases associated with the cardiovascular system.
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Affiliation(s)
| | - David Gau
- Bioengineering, University of Pittsburgh
| | - Partha Roy
- Bioengineering, University of Pittsburgh.,Pathology, University of Pittsburgh, 306 Center for Bioengineering, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, USA
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6
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Yuan G, Cui S, Chen X, Song H, Huang C, Tong J, Yuan Z, Yu L, Xiong X, Zhao J, Huang B, Wu Q, Zhou Y, Chen G, Zhou H, Xia XG. Detergent-insoluble inclusion constitutes the first pathology in PFN1 transgenic rats. J Neurochem 2021; 157:1244-1252. [PMID: 32754913 PMCID: PMC8994973 DOI: 10.1111/jnc.15139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022]
Abstract
Mutation of profilin 1 (PFN1) can cause amyotrophic lateral sclerosis (ALS). To assess how PFN1 mutation causes the disease, we created transgenic rats with human genomic DNA that harbors both the coding and the regulatory sequences of the human PFN1 gene. Selected transgenic lines expressed human PFN1 with or without the pathogenic mutation C71G at a moderate and a comparable level and in the similar pattern of spatial and temporal expression to rat endogenous PFN1. The artificial effects of arbitrary transgene expression commonly observed in cDNA transgenic animals were minimized in PFN1 transgenic rats. Expression of the mutant, but not the wild type, human PFN1 in rats recapitulated the cardinal features of ALS including the progressive loss of motor neurons and the subsequent denervation atrophy of skeletal muscles. Detergent-insoluble PFN1 inclusions were detected as the first pathology in otherwise asymptomatic transgenic rats expressing mutant human PFN1. The findings suggest that protein aggregation is involved in the neurodegeneration of ALS associated with PFN1 mutation. The resulting rat model is useful to mechanistic study on the ALS.
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Affiliation(s)
- Guixiu Yuan
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Shiquan Cui
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Xuan Chen
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Haochang Song
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Cao Huang
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jianbin Tong
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Zhentin Yuan
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Lin Yu
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Xinrui Xiong
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Jihe Zhao
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Bo Huang
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Qinxue Wu
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yibo Zhou
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Gong Chen
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Hongxia Zhou
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Xu-Gang Xia
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, USA
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7
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Dhankhar P, Dalal V, Singh V, Tomar S, Kumar P. Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. J Biomol Struct Dyn 2020; 40:4084-4099. [PMID: 33251943 PMCID: PMC7754992 DOI: 10.1080/07391102.2020.1852968] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with elevated mortality and morbidity. There are currently no efficacious drugs targeting coronavirus disease 2019, therefore, it is an urgent requirement for the development of drugs to control this emerging disease. Owing to the importance of nucleocapsid protein, the present study focuses on targeting the N-terminal domain of nucleocapsid protein from severe acute respiratory syndrome coronavirus 2 to identify the potential compounds by computational approaches such as pharmacophore modeling, virtual screening, docking and molecular dynamics. We found three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056), which adopted a similar conformation as guanosine monophosphate (GMP) within the N-terminal domain active site and exhibiting high binding affinity (>−8.0 kcalmol−1). All the identified compounds were stabilized by hydrogen bonding with Arg107, Tyr111 and Arg149 of N-terminal domain. Additionally, the aromatic ring of lead molecules formed π interactions with Tyr109 of N-terminal domain. Molecular dynamics and Molecular mechanic/Poisson–Boltzmann surface area results revealed that N-terminal domain – ligand(s) complexes are less dynamic and more stable than N-terminal domain – GMP complex. As the identified compounds share the same corresponding pharmacophore properties, therefore, the present results may serve as a potential lead for the development of inhibitors against severe acute respiratory syndrome coronavirus 2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Poonam Dhankhar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vishakha Singh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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8
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Allen A, Gau D, Francoeur P, Sturm J, Wang Y, Martin R, Maranchie J, Duensing A, Kaczorowski A, Duensing S, Wu L, Lotze MT, Koes D, Storkus WJ, Roy P. Actin-binding protein profilin1 promotes aggressiveness of clear-cell renal cell carcinoma cells. J Biol Chem 2020; 295:15636-15649. [PMID: 32883810 PMCID: PMC7667959 DOI: 10.1074/jbc.ra120.013963] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/01/2020] [Indexed: 12/14/2022] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC), the most common subtype of renal cancer, has a poor clinical outcome. A hallmark of ccRCC is genetic loss-of-function of VHL (von Hippel-Lindau) that leads to a highly vascularized tumor microenvironment. Although many ccRCC patients initially respond to antiangiogenic therapies, virtually all develop progressive, drug-refractory disease. Given the role of dysregulated expressions of cytoskeletal and cytoskeleton-regulatory proteins in tumor progression, we performed analyses of The Cancer Genome Atlas (TCGA) transcriptome data for different classes of actin-binding proteins to demonstrate that increased mRNA expression of profilin1 (Pfn1), Arp3, cofilin1, Ena/VASP, and CapZ, is an indicator of poor prognosis in ccRCC. Focusing further on Pfn1, we performed immunohistochemistry-based classification of Pfn1 staining in tissue microarrays, which indicated Pfn1 positivity in both tumor and stromal cells; however, the vast majority of ccRCC tumors tend to be Pfn1-positive selectively in stromal cells only. This finding is further supported by evidence for dramatic transcriptional up-regulation of Pfn1 in tumor-associated vascular endothelial cells in the clinical specimens of ccRCC. In vitro studies support the importance of Pfn1 in proliferation and migration of RCC cells and in soluble Pfn1's involvement in vascular endothelial cell tumor cell cross-talk. Furthermore, proof-of-concept studies demonstrate that treatment with a novel computationally designed Pfn1-actin interaction inhibitor identified herein reduces proliferation and migration of RCC cells in vitro and RCC tumor growth in vivo Based on these findings, we propose a potentiating role for Pfn1 in promoting tumor cell aggressiveness in the setting of ccRCC.
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Affiliation(s)
- Abigail Allen
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David Gau
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paul Francoeur
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jordan Sturm
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yue Wang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ryan Martin
- Department of Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jodi Maranchie
- Department of Urology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anette Duensing
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam Kaczorowski
- Department of Urology, Heidelberg School of Medicine, Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, Heidelberg School of Medicine, Heidelberg, Germany
| | - Lily Wu
- Department of Urology, University of California, Los Angeles, Los Angeles, California, USA
| | - Michael T. Lotze
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania USA
| | - David Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Walter J. Storkus
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Urology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania USA,Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania USA
| | - Partha Roy
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Urology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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9
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Francoeur PG, Masuda T, Sunseri J, Jia A, Iovanisci RB, Snyder I, Koes DR. Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. J Chem Inf Model 2020; 60:4200-4215. [PMID: 32865404 PMCID: PMC8902699 DOI: 10.1021/acs.jcim.0c00411] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One of the main challenges in drug discovery is predicting protein-ligand binding affinity. Recently, machine learning approaches have made substantial progress on this task. However, current methods of model evaluation are overly optimistic in measuring generalization to new targets, and there does not exist a standard data set of sufficient size to compare performance between models. We present a new data set for structure-based machine learning, the CrossDocked2020 set, with 22.5 million poses of ligands docked into multiple similar binding pockets across the Protein Data Bank, and perform a comprehensive evaluation of grid-based convolutional neural network (CNN) models on this data set. We also demonstrate how the partitioning of the training data and test data can impact the results of models trained with the PDBbind data set, how performance improves by adding more lower-quality training data, and how training with docked poses imparts pose sensitivity to the predicted affinity of a complex. Our best performing model, an ensemble of five densely connected CNNs, achieves a root mean squared error of 1.42 and Pearson R of 0.612 on the affinity prediction task, an AUC of 0.956 at binding pose classification, and a 68.4% accuracy at pose selection on the CrossDocked2020 set. By providing data splits for clustered cross-validation and the raw data for the CrossDocked2020 set, we establish the first standardized data set for training machine learning models to recognize ligands in noncognate target structures while also greatly expanding the number of poses available for training. In order to facilitate community adoption of this data set for benchmarking protein-ligand binding affinity prediction, we provide our models, weights, and the CrossDocked2020 set at https://github.com/gnina/models.
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Affiliation(s)
- Paul G Francoeur
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tomohide Masuda
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jocelyn Sunseri
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Andrew Jia
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Richard B Iovanisci
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ian Snyder
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David R Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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10
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Pimm ML, Hotaling J, Henty-Ridilla JL. Profilin choreographs actin and microtubules in cells and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 355:155-204. [PMID: 32859370 PMCID: PMC7461721 DOI: 10.1016/bs.ircmb.2020.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Actin and microtubules play essential roles in aberrant cell processes that define and converge in cancer including: signaling, morphology, motility, and division. Actin and microtubules do not directly interact, however shared regulators coordinate these polymers. While many of the individual proteins important for regulating and choreographing actin and microtubule behaviors have been identified, the way these molecules collaborate or fail in normal or disease contexts is not fully understood. Decades of research focus on Profilin as a signaling molecule, lipid-binding protein, and canonical regulator of actin assembly. Recent reports demonstrate that Profilin also regulates microtubule dynamics and polymerization. Thus, Profilin can coordinate both actin and microtubule polymer systems. Here we reconsider the biochemical and cellular roles for Profilin with a focus on the essential cytoskeletal-based cell processes that go awry in cancer. We also explore how the use of model organisms has helped to elucidate mechanisms that underlie the regulatory essence of Profilin in vivo and in the context of disease.
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Affiliation(s)
- Morgan L Pimm
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Jessica Hotaling
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Jessica L Henty-Ridilla
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States; Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States.
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11
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Gau D, Vignaud L, Allen A, Guo Z, Sahel J, Boone D, Koes D, Guillonneau X, Roy P. Disruption of profilin1 function suppresses developmental and pathological retinal neovascularization. J Biol Chem 2020; 295:9618-9629. [PMID: 32444495 PMCID: PMC7363146 DOI: 10.1074/jbc.ra120.012613] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Angiogenesis-mediated neovascularization in the eye is usually associated with visual complications. Pathological angiogenesis is particularly prominent in the retina in the settings of proliferative diabetic retinopathy, in which it can lead to permanent loss of vision. In this study, by bioinformatics analyses, we provide evidence for elevated expression of actin-binding protein PFN1 (profilin1) in the retinal vascular endothelial cells (VECs) of individuals with proliferative diabetic retinopathy, findings further supported by gene expression analyses for PFN1 in experimentally induced abnormal retinal neovascularization in an oxygen-induced retinopathy murine model. We observed that in a conditional knockout mouse model, postnatal deletion of the Pfn1 gene in VECs leads to defects in tip cell activity (marked by impaired filopodial protrusions) and reduced vascular sprouting, resulting in hypovascularization during developmental angiogenesis in the retina. Consistent with these findings, an investigative small molecule compound targeting the PFN1-actin interaction reduced random motility, proliferation, and cord morphogenesis of retinal VECs in vitro and experimentally induced abnormal retinal neovascularization in vivo In summary, these findings provide the first direct in vivo evidence that PFN1 is required for formation of actin-based protrusive structures and developmental angiogenesis in the retina. The proof of concept of susceptibility of abnormal angiogenesis to small molecule intervention of PFN1-actin interaction reported here lays a conceptual foundation for targeting PFN1 as a possible strategy in angiogenesis-dependent retinal diseases.
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Affiliation(s)
- David Gau
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lucile Vignaud
- Institut de la Vision, Sorbonne Université, INSERM, Paris, France
| | - Abigail Allen
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Zhijian Guo
- Department of Nephrology, Southern Medical University, Guangzhou, China
| | - Jose Sahel
- Institut de la Vision, Sorbonne Université, INSERM, Paris, France,Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - David Boone
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David Koes
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Partha Roy
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA .,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Pereira GRC, Tellini GHAS, De Mesquita JF. In silico analysis of PFN1 related to amyotrophic lateral sclerosis. PLoS One 2019; 14:e0215723. [PMID: 31216283 PMCID: PMC6583998 DOI: 10.1371/journal.pone.0215723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Profilin 1 (PFN1) protein plays key roles in neuronal growth and differentiation, membrane trafficking, and regulation of the actin cytoskeleton. Four natural variants of PFN1 were described as related to ALS, the most common adult-onset motor neuron disorder. However, the pathological mechanism of PFN1 in ALS is not yet completely understood. The goal of this work is to thoroughly analyze the effects of the ALS-related mutations on PFN1 structure and function using computational simulations. Here, PhD-SNP, PMUT, PolyPhen-2, SIFT, SNAP, SNPS&GO, SAAP, nsSNPAnalyzer, SNPeffect4.0 and I-Mutant2.0 were used to predict the functional and stability effects of PFN1 mutations. ConSurf was used for the evolutionary conservation analysis, and GROMACS was used to perform the MD simulations. The mutations C71G, M114T, and G118V, but not E117G, were predicted as deleterious by most of the functional prediction algorithms that were used. The stability prediction indicated that the ALS-related mutations could destabilize PFN1. The ConSurf analysis indicated that the mutation C71G, M114T, E117G, and G118V occur in highly conserved positions. The MD results indicated that the studied mutations could affect the PFN1 flexibility at the actin and PLP-binding domains, and consequently, their intermolecular interactions. It may be therefore related to the functional impairment of PFN1 upon C71G, M114T, E117G and G118V mutations, and their involvement in ALS development. We also developed a database, SNPMOL (http://www.snpmol.org/), containing the results presented on this paper for biologists and clinicians to exploit PFN1 and its natural variants.
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Affiliation(s)
- Gabriel Rodrigues Coutinho Pereira
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giovanni Henrique Almeida Silva Tellini
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joelma Freire De Mesquita
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Imrie F, Bradley AR, van der Schaar M, Deane CM. Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data. J Chem Inf Model 2018; 58:2319-2330. [DOI: 10.1021/acs.jcim.8b00350] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fergus Imrie
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, U.K
| | - Anthony R. Bradley
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- Diamond Light Source Ltd., Didcot OX11 0DE, U.K
| | - Mihaela van der Schaar
- Department of Engineering, University of Oxford, Oxford OX1 3PJ, U.K
- Alan Turing Institute, London NW1 2DB, U.K
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, U.K
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