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Fan Z, Pavlova A, Jenkins MC, Bassit L, Salman M, Lynch DL, Patel D, Korablyov M, Finn MG, Schinazi RF, Gumbart JC. Biophysics-Guided Lead Discovery of HBV Capsid Assembly Modifiers. ACS Infect Dis 2024; 10:1162-1173. [PMID: 38564659 PMCID: PMC11019538 DOI: 10.1021/acsinfecdis.3c00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Hepatitis B virus (HBV) is the leading cause of chronic liver pathologies worldwide. HBV nucleocapsid, a key structural component, is formed through the self-assembly of the capsid protein units. Therefore, interfering with the self-assembly process is a promising approach for the development of novel antiviral agents. Applied to HBV, this approach has led to several classes of capsid assembly modulators (CAMs). Here, we report structurally novel CAMs with moderate activity and low toxicity, discovered through a biophysics-guided approach combining docking, molecular dynamics simulations, and a series of assays with a particular emphasis on biophysical experiments. Several of the identified compounds induce the formation of aberrant capsids and inhibit HBV DNA replication in vitro, suggesting that they possess modest capsid assembly modulation effects. The synergistic computational and experimental approaches provided key insights that facilitated the identification of compounds with promising activities. The discovery of preclinical CAMs presents opportunities for subsequent optimization efforts, thereby opening new avenues for HBV inhibition.
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Affiliation(s)
- Zixing Fan
- Interdisciplinary
Bioengineering Graduate Program, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew C. Jenkins
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Mohammad Salman
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dharmeshkumar Patel
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT
Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - M. G. Finn
- School
of Chemistry & Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Raymond F. Schinazi
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
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Bader CS, Pavlova A, Lowsky R, Muffly LS, Shiraz P, Arai S, Johnston LJ, Rezvani AR, Weng WK, Miklos DB, Frank MJ, Tamaresis JS, Agrawal V, Bharadwaj S, Sidana S, Shizuru JA, Fernhoff NB, Putnam A, Killian S, Xie BJ, Negrin RS, Meyer EH. Single-center randomized trial of T-reg graft alone vs T-reg graft plus tacrolimus for the prevention of acute GVHD. Blood Adv 2024; 8:1105-1115. [PMID: 38091578 PMCID: PMC10907400 DOI: 10.1182/bloodadvances.2023011625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 02/29/2024] Open
Abstract
ABSTRACT Allogeneic hematopoietic cell transplantation (HCT) is a curative therapy for hematological malignancies for which graft-versus-host disease (GVHD) remains a major complication. The use of donor T-regulatory cells (Tregs) to prevent GVHD appears promising, including in our previous evaluation of an engineered graft product (T-reg graft) consisting of the timed, sequential infusion of CD34+ hematopoietic stem cells and high-purity Tregs followed by conventional T cells. However, whether immunosuppressive prophylaxis can be removed from this protocol remains unclear. We report the results of the first stage of an open-label single-center phase 2 study (NCT01660607) investigating T-reg graft in myeloablative HCT of HLA-matched and 9/10-matched recipients. Twenty-four patients were randomized to receive T-reg graft alone (n = 12) or T-reg graft plus single-agent GVHD prophylaxis (n = 12) to determine whether T-reg graft alone was noninferior in preventing acute GVHD. All patients developed full-donor myeloid chimerism. Patients with T-reg graft alone vs with prophylaxis had incidences of grade 3 to 4 acute GVHD of 58% vs 8% (P = .005) and grade 3 to 4 of 17% vs 0% (P = .149), respectively. The incidence of moderate-to-severe chronic GVHD was 28% in the T-reg graft alone arm vs 0% with prophylaxis (P = .056). Among patients with T-reg graft and prophylaxis, CD4+ T-cell-to-Treg ratios were reduced after transplantation, gene expression profiles showed reduced CD4+ proliferation, and the achievement of full-donor T-cell chimerism was delayed. This study indicates that T-reg graft with single-agent tacrolimus is preferred over T-reg graft alone for the prevention of acute GVHD. This trial was registered at www.clinicaltrials.gov as #NCT01660607.
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Affiliation(s)
- Cameron S. Bader
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Anna Pavlova
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Robert Lowsky
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
- Cellular Immune Tolerance Program, Stanford Department of Medicine, Stanford University, Stanford, CA
| | - Lori S. Muffly
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Parveen Shiraz
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Sally Arai
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
- Cellular Immune Tolerance Program, Stanford Department of Medicine, Stanford University, Stanford, CA
| | - Laura J. Johnston
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Andrew R. Rezvani
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Wen-Kai Weng
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
- Cellular Immune Tolerance Program, Stanford Department of Medicine, Stanford University, Stanford, CA
| | - David B. Miklos
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Matthew J. Frank
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | | | - Vaibhav Agrawal
- Department of Hematology and Hematopoietic Stem Cell Transplantation, City of Hope, Duarte, CA
| | - Sushma Bharadwaj
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Surbhi Sidana
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Judith A. Shizuru
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
| | | | | | | | | | - Robert S. Negrin
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
- Cellular Immune Tolerance Program, Stanford Department of Medicine, Stanford University, Stanford, CA
| | - Everett H. Meyer
- Stanford Blood and Marrow Transplantation and Cellular Therapy Division, Stanford School of Medicine, Stanford University, Stanford, CA
- Cellular Immune Tolerance Program, Stanford Department of Medicine, Stanford University, Stanford, CA
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Preisler B, Pezeshkpoor B, Merzenich A, Ohlenforst S, Rühl H, Ivaškevičius V, Scholz U, Bönigk H, Eberl W, Zieger B, Pavlova A, Oldenburg J. Genetic Landscape of Factor VII Deficiency: Insights from a Comprehensive Analysis of Pathogenic Variants and Their Impact on Coagulation Activity. Int J Mol Sci 2024; 25:2384. [PMID: 38397060 PMCID: PMC10889322 DOI: 10.3390/ijms25042384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Congenital factor VII (FVII) deficiency is a rare genetic bleeding disorder characterized by deficient or reduced activity of coagulation FVII. It is caused by genetic variants in the F7 gene. We aimed to evaluate the rate of detection of pathogenic variants in the F7 gene in a large group of patients with FVII deficiency and investigate the correlations between the F7 genotype and FVII activity (FVII:C). Moreover, the influence of the common genetic variant rs6046: c.1238G>A; p.(Arg413Gln), designated as the M2 allele, on FVII:C was investigated. Genetic analysis of the F7 gene was performed on 704 index patients (IPs) using either direct Sanger- or next-generation sequencing. Genetic variants were detected in 390 IPs, yielding a variant detection rate (VDR) of 55%. Notably, the VDR exhibited a linear decline with increasing FVII:C levels. We identified 124 genetic variants, of which 48 were not previously reported. Overall, the frequency of the M2 allele was considerably higher in patients with mild deficiency (FVII:C > 20 IU/dl). Furthermore, IPs lacking an identified pathogenic variant exhibited a significantly higher prevalence of the M2 allele (69%) compared to IPs with a disease-causing variant (47%). These results strongly support the association of the M2 allele with decreased FVII:C levels. This study shows the utility of FVII:C as a predictive marker for identifying pathogenic variants in patients with FVII deficiency. The M2 allele contributes to the reduction of FVII:C levels, particularly in cases of mild deficiency.
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Affiliation(s)
- Barbara Preisler
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Anja Merzenich
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Sandra Ohlenforst
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Vytautas Ivaškevičius
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Ute Scholz
- Center of Hemostasis, MVZ Labor Leipzig, 04289 Leipzig, Germany;
| | - Hagen Bönigk
- MVZ Limbach Magdeburg, Lab Dr. Franke, Bönigk and Colleagues, Center of Coagulation Disorders and Vascular Diseases, 39104 Magdeburg, Germany;
| | - Wolfgang Eberl
- Pediatric Hematology and Oncology, Klinikum Braunschweig, 38118 Braunschweig, Germany;
| | - Barbara Zieger
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center–University of Freiburg, Faculty of Medicine, 79110 Freiburg, Germany;
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Faculty of Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (S.O.); (H.R.); (V.I.); (A.P.)
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Borikun T, Mushii O, Pavlova A, Burda T, Zadvornyi T. TUMOR MICROENVIRONMENT-ASSOCIATED miR-7-5p, miR-19a-3p, AND miR-23b-3p EXPRESSION IN PROSTATE CANCER WITH DIFFERENT PROGRESSION RISK. Exp Oncol 2024; 45:432-442. [PMID: 38328847 DOI: 10.15407/exp-oncology.2023.04.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND The tumor microenvironment (TME) plays an important role in the occurrence and progression of prostate cancer (PCa). At the same time, the mechanisms and features of the interaction between tumor cells and individual components of the TME in PCa remain not fully elucidated. The aim was to study the expression levels of tumor-associated miR-7-5p, miR-19a-3p, and miR-23b-3p in the PCa tissue and to analyze their relationship with the features of TME. MATERIALS AND METHODS The work is based on the analysis of the results of the examination and treatment of 50 patients with PCa of stages II-IV. The expression of miRNA in the PCa tissue was analyzed by the real-time polymerase chain reaction. The expression of alpha-smooth muscle actin (α-SMA), vimentin (VIM), and CD68 in PCa tissue was determined by the immunohistochemical method. The identification of mast cells in the PCa tissue was assessed by the histochemical method. RESULTS The analysis of the expression levels of tumor-associated miRNAs demonstrated that the tumor tissue of patients with a high risk of PCa progression was characterized by 4.93 (p < 0.01) and 8.97 (p < 0.05) times higher levels of miR-19a-3p and miR-23b-3p, respectively, compared to similar indicators in the group of patients with a low risk of PCa progression. The levels of miR-7-5p and miR-19a-3p expression in the PCa tissue correlated with the expression level of α-SMA (r = 0.49 and r = 0.45, respectively; p < 0.05) and VIM (r = 0.45 and r = 0.46; respectively, p < 0.05). A direct relationship (r = 0.44; p < 0.05) was established between the level of miR-7-5p expression and the degree of infiltration of the prostate gland tissue by tumor-associated macrophages. CONCLUSIONS The features of the expression of tumor-associated miR-7-5p, miR-19a-3p, and miR-23b-3p indicated the prospect of their use as markers of the aggressiveness of the PCa course.
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Affiliation(s)
- T Borikun
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - O Mushii
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - A Pavlova
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - T Burda
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - T Zadvornyi
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine.
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Singh S, Pezeshkpoor B, Jamil MA, Dodt J, Sharma A, Ramar V, Ivaskevicius V, Hethershaw E, Philippou H, Pavlova A, Oldenburg J, Biswas A. Heterozygosity in factor XIII genes and the manifestation of mild inherited factor XIII deficiency. J Thromb Haemost 2024; 22:379-393. [PMID: 37832789 DOI: 10.1016/j.jtha.2023.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The characterization of inherited mild factor XIII deficiency is more imprecise than its rare, inherited severe forms. It is known that heterozygosity at FXIII genetic loci results in mild FXIII deficiency, characterized by circulating FXIII activity levels ranging from 20% to 60%. There exists a gap in information on 1) how genetic heterozygosity renders clinical bleeding manifestations among these individuals and 2) the reversal of unexplained bleeding upon FXIII administration in mild FXIII-deficient individuals. OBJECTIVES To assess the prevalence and burden of mild FXIII deficiency among the apparently healthy German-Caucasian population and correlate it with genetic heterozygosity at FXIII and fibrinogen gene loci. METHODS Peripheral blood was collected from 752 donors selected from the general population with essentially no bleeding complications to ensure asymptomatic predisposition. These were assessed for FXIII and fibrinogen activity, and FXIII and fibrinogen genes were resequenced using next-generation sequencing. For comparison, a retrospective analysis was performed on a cohort of mild inherited FXIII deficiency patients referred to us. RESULTS The prevalence of mild FXIII deficiency was high (∼0.8%) among the screened German-Caucasian population compared with its rare-severe forms. Although no new heterozygous missense variants were found, certain combinations were relatively dominant/prevalent among the mild FXIII-deficient individuals. CONCLUSION This extensive, population-based quasi-experimental approach revealed that the burden of heterozygosity in FXIII and fibrinogen gene loci causes the clinical manifestation of inherited mild FXIII deficiency, resulting in ''unexplained bleeding'' upon provocation.
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Affiliation(s)
- Sneha Singh
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Behnaz Pezeshkpoor
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Muhammad Ahmer Jamil
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | | | - Amit Sharma
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Vasanth Ramar
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Vytautas Ivaskevicius
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Emma Hethershaw
- Division of Cardiovascular and Diabetes Research, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Helen Philippou
- Division of Cardiovascular and Diabetes Research, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Anna Pavlova
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Johannes Oldenburg
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Arijit Biswas
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany.
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Zadvornyi T, Lukianova N, Mushii O, Pavlova A, Voronina O, Chekhun V. Benign and malignant prostate neoplasms show different spatial organization of collagen. Croat Med J 2023; 64:413-420. [PMID: 38168522 PMCID: PMC10797232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
AIM To compare the indicators of the spatial organization of collagen and its regulating factors between benign and malignant prostate neoplasms. METHODS The study involved tumor tissue samples from 40 patients with stage II-III prostate cancer (PCa) and 20 patients with benign prostatic hyperplasia (BPH). The localization of collagen was determined with a Masson trichrome stain. To establish quantitative indicators of the spatial organization of collagen, morphometric studies were carried out with the CurveAlign and ImageJ programs. RESULTS PCa tissue had two times lower collagen density (P<0.0001) and 1.3 times lower levels of collagen alignment (P=0.018) compared with BPH tissue. In PCa tissue, collagen fibers were shorter (by 24.2%; P<0.001) and thicker (by 15.5%; P<0.001). PCa tissue samples showed significantly higher levels of metalloproteinase (MMP)-2 (by 2.4 times; P=0.001), MMP-8 (by 2.3 times; P=0.007), and MMP-13 (by 1.9 times; P=0.004). CONCLUSIONS Collagen matrix spatial organization features, as well as its regulatory factors, could be potential biomarkers of malignant prostate neoplasms.
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Affiliation(s)
- Taras Zadvornyi
- Taras Zadvornyi, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, Vasylkivska str. 45, Kyiv-03022, Ukraine,
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Marakshina J, Pavlova A, Ismatullina V, Adamovich T, Mironets S, Sitnikova MA, Lobaskova M, Malykh S. The Russian version of the Abbreviated Math Anxiety Scale: psychometric properties in adolescents aged 13-16 years. Front Psychol 2023; 14:1275212. [PMID: 38162961 PMCID: PMC10757330 DOI: 10.3389/fpsyg.2023.1275212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
This study is the first to assess the internal consistency and factor validity of the Abbreviated Math Anxiety Scale (AMAS) in a sample of Russian adolescents as well as gender differences and gender invariance. The study included 4,218 adolescents in grades 7-9 (M = 14.23, SD = 0.92). Internal consistency, measured with Cronbach's alpha, was high. Analysis of the factor structure revealed the best correspondence of the second-order factor model, which included two scales (learning math anxiety and math evaluation anxiety) and the general scale of math anxiety. There were greater gender differences in the all three scales. Analysis of gender invariance demonstrated that the mathematics anxiety construct was uniform in boys and girls. These findings confirm the reliable psychometric properties and validity of the AMAS, enabling its use in adolescents.
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Affiliation(s)
- Julia Marakshina
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Anna Pavlova
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Victoria Ismatullina
- Developmental Behavioral Genetics Laboratory, Federal Research Centre of Psychological and Interdisciplinary Studies, Moscow, Russia
| | - Timofey Adamovich
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Sofia Mironets
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Maria A. Sitnikova
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Marina Lobaskova
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
| | - Sergey Malykh
- Center for Interdisciplinary Research in the Educational Sciences, Russian Academy of Education, Moscow, Russia
- Developmental Behavioral Genetics Laboratory, Federal Research Centre of Psychological and Interdisciplinary Studies, Moscow, Russia
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Ivaškevičius V, Biswas A, Singh S, Stulpinaitė U, Reda S, Rühl H, Pezeshkpoor B, Pavlova A, Oldenburg J. Fibrinogen Bonn (p. Arg510Cys) in the Aα-Chain Is Associated with High Risk of Venous Thrombosis. Hamostaseologie 2023; 43:440-446. [PMID: 37442158 DOI: 10.1055/a-2094-7191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023] Open
Abstract
INTRODUCTION Inherited dysfibrinogenemia is a qualitative defect of fibrinogen caused by various mutations among three fibrinogen genes. Dysfibrinogenemia can be associated with an increased risk of thrombosis, bleeding, or both. Here, we report a 36-year-old female with dysfibrinogenemia who experienced two successful pregnancies under thromboprophylaxis after cerebral venous sinus thrombosis (CVST). PATIENTS AND METHODS In addition to plasmatic coagulation tests, fibrinogen genes FGA, FGB, and FGG were screened using direct genomic DNA sequencing. The structural-functional implications of the detected mutation were analyzed in silico. RESULTS Inherited dysfibrinogenemia was diagnosed in an index patient after CVST in a risk situation. Anticoagulation with warfarin was stopped after 12 months when the first pregnancy was planned. Pregnancy and spontaneous delivery (2020) was uncomplicated. A second pregnancy was interrupted because of acute cytomegalovirus infection and the third pregnancy was successful in 2022. Pregnancies were accompanied by thromboprophylaxis with enoxaparin 40 mg once daily until 6 weeks postpartum. Substitution of fibrinogen has not become necessary in the index patient so far. Genetic analysis revealed a novel missense mutation (p. Arg510Cys) in the FGA gene ("fibrinogen Bonn") in the index patient, as well as an asymptomatic sister, and their father who experienced recurrent pulmonary embolism. Surface exposure of wild-type Arg510 suggested the mutated Cys510 to form nonnative disulfide bonds with surface-exposed reactive cysteines from other plasma proteins like albumin leading to formation of aggregates and impaired fibrinolysis. CONCLUSIONS Fibrinogen Bonn might be associated with an increased risk of thrombosis, possibly due to impaired polymerization.
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Affiliation(s)
- V Ivaškevičius
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - A Biswas
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - S Singh
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - U Stulpinaitė
- Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - S Reda
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - H Rühl
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - B Pezeshkpoor
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - A Pavlova
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - J Oldenburg
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
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Muñoz-Ruiz M, Llorian M, D'Antuono R, Pavlova A, Mavrigiannaki AM, McKenzie D, García-Cassani B, Iannitto ML, Wu Y, Dart R, Davies D, Jamal-Hanjani M, Jandke A, Ushakov DS, Hayday AC. IFN-γ-dependent interactions between tissue-intrinsic γδ T cells and tissue-infiltrating CD8 T cells limit allergic contact dermatitis. J Allergy Clin Immunol 2023; 152:1520-1540. [PMID: 37562754 DOI: 10.1016/j.jaci.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Elicitation of allergic contact dermatitis (ACD), an inflammatory type 4 hypersensitivity disease, induces skin infiltration by polyclonal effector CD8 αβ T cells and precursors of tissue-resident memory T (TRM) cells. Because TRM have long-term potential to contribute to body-surface immunoprotection and immunopathology, their local regulation needs a fuller understanding. OBJECTIVE We sought to investigate how TRM-cell maturation might be influenced by innate-like T cells pre-existing within many epithelia. METHODS This study examined CD8+ TRM-cell maturation following hapten-induced ACD in wild-type mice and in strains harboring altered compartments of dendritic intraepidermal γδ T cells (DETCs), a prototypic tissue-intrinsic, innate-like T-cell compartment that reportedly regulates ACD, but by no elucidated mechanism. RESULTS In addition to eliciting CD8 TRM, ACD induced DETC activation and an intimate coregulatory association of the 2 cell types. This depended on DETC sensing IFN-γ produced by CD8 cells and involved programmed death-ligand 1 (PD-L1). Thus, in mice lacking DETC or lacking IFN-γ receptor solely on γδ cells, ACD-elicited CD8 T cells showed enhanced proliferative and effector potentials and reduced motility, collectively associated with exaggerated ACD pathology. Comparable dysregulation was elicited by PD-L1 blockade in vitro, and IFN-γ-regulated PD-L1 expression was a trait of human skin-homing and intraepithelial γδ T cells. CONCLUSIONS The size and quality of the tissue-infiltrating CD8 T-cell response during ACD can be profoundly regulated by local innate-like T cells responding to IFN-γ and involving PD-L1. Thus, interindividual and tissue-specific variations in tissue-intrinsic lymphocytes may influence responses to allergens and other challenges and may underpin inflammatory pathologies such as those repeatedly observed in γδ T-cell-deficient settings.
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Affiliation(s)
- Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Department of Immunology, Ophthalmology and Ear, Nose and Throat, Complutense University School of Medicine and 12 de Octubre Health Research Institute, Madrid, Spain
| | - Miriam Llorian
- Bioinformatics and Biostatistics science technology platform (STP), The Francis Crick Institute, London, United Kingdom
| | - Rocco D'Antuono
- Light Microscopy STP, The Francis Crick Institute, London, United Kingdom
| | - Anna Pavlova
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Erlangen, Germany
| | | | - Duncan McKenzie
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Bethania García-Cassani
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria Luisa Iannitto
- Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Yin Wu
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Robin Dart
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Daniel Davies
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Anett Jandke
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Dmitry S Ushakov
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Adrian C Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom.
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10
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Weaver L, Pavlova A, Lunden M, Brunsvold ME, Kendrick D. Are COVID-Era General Surgery Interns Starting Residency Behind on Basic Surgical Skills? J Surg Educ 2023; 80:1567-1573. [PMID: 37563000 DOI: 10.1016/j.jsurg.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/30/2023] [Accepted: 07/08/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVE To compare incoming general surgery interns' performance on a basic skills assessment before and after the COVID pandemic. DESIGN A retrospective cohort study compared surgical skill performances of incoming general surgery interns. Each underwent an evidence-based standardized assessment (pretest) with 12-basic surgical knot tying and suturing tasks. A post-test was administered after a 3-month self-directed skills curriculum. Student's t-tests compared proficiency scores from pre-COVID vs. COVID-era general surgery interns before and after curriculum completion. p < 0.05 was significant. SETTING Data was collected from surgical residents in an academic general surgery program in the United States. PARTICIPANTS General surgery interns from 2017 to 2019 (pre-COVID) and 2021 to 2022 (COVID-era) were included. Interns with missing data or extreme outliers were excluded. A total of 100 interns in general surgery were included in the pretest cohort (59 pre-COVID, 41 COVID-era) and 101 interns were in the post-test cohort (66 pre-COVID, 35 COVID-era). RESULTS COVID-era interns scored significantly lower on the pretest compared to pre-COVID interns (COVID-era 721.9+/-268.8 vs. pre-COVID 935.9+/- 228.0, p < 0.001). After the skills curriculum both cohorts improved their proficiency scores. However COVID-era interns still scored significantly lower (COVID-era 1255.0+/-166.3 vs. pre-COVID 1369.8+/-165.6, p = 0.001). CONCLUSIONS This analysis objectively described deficits in fundamental surgical skills for incoming interns whose medical school education was disrupted by the COVID-19 pandemic. A targeted surgical skills curriculum partially remediated these deficiencies. However, many surgical interns may need additional intervention and potentially more time in order to fully develop their surgical skills and meet the competency requirements required for advancement.
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Affiliation(s)
- Lauren Weaver
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota.
| | - Anna Pavlova
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Michelle Lunden
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Melissa E Brunsvold
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota; Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Daniel Kendrick
- Department of Surgery, University of Minnesota Medical School, Minneapolis, Minnesota; Department of Surgery, University of Minnesota, Minneapolis, Minnesota
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11
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Kuo K, Liu J, Pavlova A, Gumbart JC. Drug Binding to BamA Targets Its Lateral Gate. J Phys Chem B 2023; 127:7509-7517. [PMID: 37587651 PMCID: PMC10476194 DOI: 10.1021/acs.jpcb.3c04501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/30/2023] [Indexed: 08/18/2023]
Abstract
BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer-membrane protein (OMP) in Gram-negative bacteria. Its function is to insert and fold substrate OMPs into the outer membrane (OM). Evidence suggests that BamA follows the asymmetric hybrid-barrel model where the first and last strands of BamA separate, a process known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially insert and fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA's function have been identified. We modeled and then docked one of these compounds into either the extracellular loops of BamA or the open lateral gate. With the compound docked in the loops, we found that the lateral gate remains closed during 5 μs molecular dynamics simulations. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds. In these simulations, we observed a differing degree and/or frequency of opening of BamA's lateral gate compared to BamA-apo, suggesting that the mutations grant resistance by altering the dynamics at the gate. We conclude that the compounds act by inhibiting BamA lateral gate opening and/or binding of substrate, thus preventing subsequent OMP folding and insertion.
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Affiliation(s)
- Katie
M. Kuo
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jinchan Liu
- Department
of Molecular Biophysics and Biochemistry (MB&B), Yale University, New Haven, Connecticut 06510, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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12
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Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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13
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Hahn AM, Vogg L, Brey S, Schneider A, Schäfer S, Palmisano R, Pavlova A, Sandrock I, Tan L, Fichtner AS, Prinz I, Ravens S, Winkler TH. A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages. Cell Rep 2023; 42:112558. [PMID: 37182210 DOI: 10.1016/j.celrep.2023.112558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
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14
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Hahn AM, Vogg L, Brey S, Schneider A, Schäfer S, Palmisano R, Pavlova A, Sandrock I, Tan L, Fichtner AS, Prinz I, Ravens S, Winkler TH. A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages. Cell Rep 2023; 42:112253. [PMID: 36920908 DOI: 10.1016/j.celrep.2023.112253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/14/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
The clonal selection theory describes key features of adaptive immune responses of B and T cells. For αβ T cells and B cells, antigen recognition and selection principles are known at a detailed molecular level. The precise role of the antigen receptor in γδ T cells remains less well understood. To better understand the role of the γδ T cell receptor (TCR), we generate an orthotopic TCRδ transgenic mouse model. We demonstrate a multi-layered functionality of γδ TCRs and diverse roles of CDR3δ-mediated selection during γδ T cell development. Whereas epithelial populations using Vγ5 or Vγ7 chains are almost unaffected in their biology in the presence of the transgenic TCRδ chain, pairing with Vγ1 positively selects γδ T cell subpopulations with distinct programs in several organs, thereby distorting the repertoire. In conclusion, our data support dictation of developmental tropism together with adaptive-like recognition principles in a single antigen receptor.
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Affiliation(s)
- Anne M Hahn
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Lisa Vogg
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Stefanie Brey
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Andrea Schneider
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Simon Schäfer
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Ralph Palmisano
- Optical Imaging Centre Erlangen (OICE), Competence Unit, FAU, 91058 Erlangen, Germany
| | - Anna Pavlova
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | | | - Likai Tan
- Medizinische Hochschule Hannover, Hannover, Germany
| | | | - Immo Prinz
- Medizinische Hochschule Hannover, Hannover, Germany; Institute for Systems Immunology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | | | - Thomas H Winkler
- Division of Genetics, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany.
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15
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Pavlova A, Tyulenev N, Tretyakova V, Skavronskaya V, Nikolaeva A, Prokofyev A, Stroganova T, Chernyshev B. Learning of new associations invokes a major change in modulations of cortical beta oscillations in human adults. Psychophysiology 2023:e14284. [PMID: 36906906 DOI: 10.1111/psyp.14284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 01/21/2023] [Accepted: 02/18/2023] [Indexed: 03/13/2023]
Abstract
Large-scale cortical beta (β) oscillations were implicated in the learning processes, but their exact role is debated. We used MEG to explore the dynamics of movement-related β-oscillations while 22 adults learned, through trial and error, novel associations between four auditory pseudowords and movements of four limbs. As learning proceeded, spatial-temporal characteristics of β-oscillations accompanying cue-triggered movements underwent a major transition. Early in learning, widespread suppression of β-power occurred long before movement initiation and sustained throughout the whole behavioral trial. When learning advanced and performance reached asymptote, β-suppression after the initiation of correct motor response was replaced by a rise in β-power mainly in the prefrontal and medial temporal regions of the left hemisphere. This post-decision β-power predicted trial-by-trial response times (RT) at both stages of learning (before and after the rules become familiar), but with different signs of interaction. When a subject just started to acquire associative rules and gradually improved task performance, a decrease in RT correlated with the increase in the post-decision β-band power. When the participants implemented the already acquired rules, faster (more confident) responses were associated with the weaker post-decision β-band synchronization. Our findings suggest that maximal beta activity is pertinent to a distinct stage of learning and may serve to strengthen the newly learned association in a distributed memory network.
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Affiliation(s)
- Anna Pavlova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation.,Department of Psychology, HSE University, Moscow, Russian Federation
| | - Nikita Tyulenev
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Vera Tretyakova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Valeriya Skavronskaya
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Anastasia Nikolaeva
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Andrey Prokofyev
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Tatiana Stroganova
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Boris Chernyshev
- Center for Neurocognitive Research (MEG Center), Moscow State University of Psychology and Education, Moscow, Russian Federation.,Department of Psychology, HSE University, Moscow, Russian Federation.,Department of Higher Nervous Activity, Lomonosov Moscow State University, Moscow, Russian Federation
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16
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Fan Z, Pavlova A, Jenkins M, Korablyov MD, Finn MG, Gumbart JC. Development of novel HBV capsid assembly modifiers through molecular dynamics, docking, and experiments. Biophys J 2023; 122:185a. [PMID: 36782881 DOI: 10.1016/j.bpj.2022.11.1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Zixing Fan
- Bioengineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew Jenkins
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - M G Finn
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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17
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Tik Pang Y, Acharya A, Lynch DL, Pavlova A, Gumbart JC. SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact. Biophys J 2023; 122:468a. [PMID: 36784403 DOI: 10.1016/j.bpj.2022.11.2511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA; BioInspired Syracuse, Syracuse University, Syracuse, NY, USA; Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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18
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Srour SA, Salhotra A, Lowsky R, Hoeg RT, Saad A, Pavlova A, Waller EK, Chao MM, McClellan JS, Fernhoff NB, Meyer EH, Abedi M. Orca-Q Demonstrates Favorable GvHD-and-Relapse-Free Survival with Haploidentical Donors without Post-Transplant Cyclophosphamide. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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Bobe A, Pavlova A, Polyakov V. In Situ Downhole Fluid Analysis Systems Using LED, Laser-Induced Fluorescence, and Uranine-Traced Drilling Water. Appl Spectrosc 2023; 77:116-122. [PMID: 36194524 DOI: 10.1177/00037028221128845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The paper discusses a novel three-channel method to distinguish the formation oils, water, and uranine-based drilling mud and to monitor the clean-up process in the downhole fluid analysis systems. The proposed method is based on the study of the fluorescence spectra of the formation fluid or drilling mud samples. The experiment for different excitation sources (365 nm, 395 nm LEDs, and 405 nm, 460 nm laser sources) was carried out; the spectra were recorded with a VISION2GO VIS spectrometer. The characteristic features in fluorescence spectra of the crude oil sample and various concentrations of the uranine solution in pH-neutral water (5 mg/l, 10 mg/l, 25 mg/l, 50 mg/l, 100 mg/l) were observed. The sufficient unambiguous criterion for differentiating the type of fluid and clean-up process analysis is presented.
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Affiliation(s)
- Alexandra Bobe
- Geophotonics LLC, Saint Petersburg, Russia
- 65071ITMO University, Saint Petersburg, Russia
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20
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Pezeshkpoor B, Oldenburg J, Pavlova A. Insights into the Molecular Genetic of Hemophilia A and Hemophilia B: The Relevance of Genetic Testing in Routine Clinical Practice. Hamostaseologie 2022; 42:390-399. [PMID: 36549291 PMCID: PMC9779947 DOI: 10.1055/a-1945-9429] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hemophilia A and hemophilia B are rare congenital, recessive X-linked disorders caused by lack or deficiency of clotting factor VIII (FVIII) or IX (FIX), respectively. The severity of the disease depends on the reduction of coagulation FVIII or FIX activity levels, which is determined by the type of the pathogenic variants in the genes encoding the two factors (F8 and F9, respectively). Molecular genetic analysis is widely applied in inherited bleeding disorders. The outcome of genetic analysis allows genetic counseling of affected families and helps find a link between the genotype and the phenotype. Genetic analysis in hemophilia has tremendously improved in the last decades. Many new techniques and modifications as well as analysis softwares became available, which made the genetic analysis and interpretation of the data faster and more accurate. Advances in genetic variant detection strategies facilitate identification of the causal variants in up to 97% of patients. In this review, we discuss the milestones in genetic analysis of hemophilia and highlight the importance of identification of the causative genetic variants for genetic counseling and particularly for the interpretation of the clinical presentation of hemophilia patients.
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Affiliation(s)
- Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany,Address for correspondence Anna Pavlova, MD, PhD Institute of Experimental Hematology and Transfusion Medicine, University of BonnVenusberg Campus 1, 53127, BonnGermany
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21
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Pang YT, Acharya A, Lynch DL, Pavlova A, Gumbart JC. SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact. Commun Biol 2022; 5:1170. [PMID: 36329138 PMCID: PMC9631587 DOI: 10.1038/s42003-022-04138-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,BioInspired Syracuse and Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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22
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Allsopp R, Pavlova A, Cline T, Salyapongse AM, Gillilan RE, Di YP, Deslouches B, Klauda JB, Gumbart JC, Tristram-Nagle S. Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation. J Phys Chem B 2022; 126:6922-6935. [PMID: 36067064 PMCID: PMC10392866 DOI: 10.1021/acs.jpcb.2c03193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an effort to combat rising antimicrobial resistance, our labs have rationally designed cationic, helical, amphipathic antimicrobial peptides (AMPs) as alternatives to traditional antibiotics since AMPs incur bacterial resistance in weeks, rather than days. One highly positively charged AMP, WLBU2 (+13e), (RRWV RRVR RWVR RVVR VVRR WVRR), has been shown to be effective in killing both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria by directly perturbing the bacterial membrane nonspecifically. Previously, we used two equilibrium experimental methods: synchrotron X-ray diffuse scattering (XDS) providing lipid membrane thickness and neutron reflectometry (NR) providing WLBU2 depth of penetration into three lipid model membranes (LMMs). The purpose of the present study is to use the results from the scattering experiments to guide molecular dynamics (MD) simulations to investigate the detailed biophysics of the interactions of WLBU2 with LMMs of Gram-negative outer and inner membranes, and Gram-positive cell membranes, to elucidate the mechanisms of bacterial killing. Instead of coarse-graining, backmapping, or simulating without bias for several microseconds, all-atom (AA) simulations were guided by the experimental results and then equilibrated for ∼0.5 μs. Multiple replicas of the inserted peptide were run to probe stability and reach a combined time of at least 1.2 μs for G(-) and also 2.0 μs for G(+). The simulations with experimental comparisons help rule out certain structures and orientations and propose the most likely set of structures, orientations, and effects on the membrane. The simulations revealed that water, phosphates, and ions enter the hydrocarbon core when WLBU2 is positioned there. For an inserted peptide, the three types of amino acids, arginine, tryptophan, and valine (R, W, V), are arranged with the 13 Rs extending from the hydrocarbon core to the phosphate group, Ws are located at the interface, and Vs are more centrally located. For a surface state, R, W, and V are positioned relative to the bilayer interface as expected from their hydrophobicities, with Rs closest to the phosphate group, Ws close to the interface, and Vs in between. G(-) and G(+) LMMs are thinned ∼1 Å by the addition of WLBU2. Our results suggest a dual anchoring mechanism for WLBU2 both in the headgroup and in the hydrocarbon region that promotes a defect region where water and ions can flow across the slightly thinned bacterial cell membrane.
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Affiliation(s)
- Robert Allsopp
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tyler Cline
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Aria M Salyapongse
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Richard E Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Berthony Deslouches
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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23
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Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, Ponikarovskaya N, Rebrikov D, Korostin D. Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing. BMC Genomics 2022; 23:582. [PMID: 35962321 PMCID: PMC9375261 DOI: 10.1186/s12864-022-08825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+ 3.06%) and indels (+ 8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.
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Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation.
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anastasia Tabanakova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Natalya Ponikarovskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
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24
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Yu B, Roy Choudhury M, Yang X, Benoit SL, Womack E, Van Mouwerik Lyles K, Acharya A, Kumar A, Yang C, Pavlova A, Zhu M, Yuan Z, Gumbart JC, Boykin DW, Maier RJ, Eichenbaum Z, Wang B. Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants. ACS Infect Dis 2022; 8:1491-1508. [PMID: 35801980 DOI: 10.1021/acsinfecdis.2c00121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rapid and persistent emergence of drug-resistant bacteria poses a looming public health crisis. The possible task of developing new sets of antibiotics to replenish the existing ones is daunting to say the least. Searching for adjuvants that restore or even enhance the potency of existing antibiotics against drug-resistant strains of bacteria represents a practical and cost-effective approach. Herein, we describe the discovery of potent adjuvants that extend the antimicrobial spectrum of existing antibiotics and restore their effectiveness toward drug-resistant strains including mcr-1-expressing strains. From a library of cationic compounds, MD-100, which has a diamidine core structure, was identified as a potent antibiotic adjuvant against Gram-negative bacteria. Further optimization efforts including the synthesis of ∼20 compounds through medicinal chemistry work led to the discovery of a much more potent compound MD-124. MD-124 was shown to sensitize various Gram-negative bacterial species and strains, including multidrug resistant pathogens, toward existing antibiotics with diverse mechanisms of action. We further demonstrated the efficacy of MD-124 in an ex vivo skin infection model and in an in vivo murine systemic infection model using both wild-type and drug-resistant Escherichia coli strains. MD-124 functions through selective permeabilization of the outer membrane of Gram-negative bacteria. Importantly, bacteria exhibited low-resistance frequency toward MD-124. In-depth computational investigations of MD-124 binding to the bacterial outer membrane using equilibrium and steered molecular dynamics simulations revealed key structural features for favorable interactions. The very potent nature of such adjuvants distinguishes them as very useful leads for future drug development in combating bacterial drug resistance.
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Affiliation(s)
- Bingchen Yu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Manjusha Roy Choudhury
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Edroyal Womack
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | | | - Atanu Acharya
- School of Physics and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ce Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Anna Pavlova
- School of Physics and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mengyuan Zhu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zhengnan Yuan
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - James C Gumbart
- School of Physics and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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25
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Escuriola Ettingshausen C, Vdovin V, Zozulya N, Svirin P, Andreeva T, Benedik-Dolničar M, Jiménez-Yuste V, Kitanovski L, Zupancic-Šalek S, Pavlova A, Bátorová A, Montaño Mejía C, Abdilova G, Knaub S, Jansen M, Lowndes S, Belyanskaya L, Walter O, Oldenburg J. Immune Tolerance Induction (ITI) with a pdFVIII/VWF Concentrate (octanate) in 100 Patients in the Observational ITI (ObsITI) Study. TH Open 2022; 6:e124-e134. [PMID: 35707623 PMCID: PMC9135478 DOI: 10.1055/s-0042-1748756] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/02/2022] [Indexed: 11/15/2022] Open
Abstract
Background
Immune tolerance induction (ITI) with repeated factor VIII (FVIII) administration is the only strategy proven to eradicate inhibitors. The observational ITI study is evaluating ITI with a range of FVIII products.
Methods
This subgroup analysis reports prospective interim data for patients treated with a plasma-derived, von Willebrand factor-stabilized FVIII concentrate (pdFVIII/VWF, octanate). Complete success (CS) of ITI required achievement of three criteria: inhibitor titer < 0.6 BU/mL; FVIII recovery ≥ 66%; FVIII half-life ≥6 hours. Partial success (PS) required achievement of two criteria and partial response (PR) one. ITI success was defined as CS or PS. Data were analyzed for patients who achieved CS, had 36 months' observation, or failed ITI.
Results
One-hundred prospectively enrolled patients were included in the analysis; 91 had poor prognosis factors for ITI success. The mean (standard deviation) daily ITI dose was 116.4 (61.1) IU FVIII/kg in 14 low responders (< 5 BU/mL) and 173.7 (112.0) IU FVIII/kg in 86 high responders (≥ 5 BU/mL). Inhibitor titers < 0.6 BU/mL were achieved in 71% of patients in a median of 4.01 months, accompanied by a 93% reduction in bleeding rate. ITI success was achieved by 70% of patients and 56 of 72 (78%) primary (first-line) ITI patients. PR was achieved by 5 patients; ITI failed in 25 patients. PS and CS were achieved in a median of 5.55 and 11.25 months, respectively.
Conclusions
ITI with pdFVIII/VWF led to rapid eradication of FVIII inhibitors, normalization of FVIII pharmacokinetics in the majority of patients, and a significant reduction in bleeding rates.
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Affiliation(s)
| | - Vladimír Vdovin
- Morozovskaya Children's Hospital, Moscow, Russian Federation
| | - Nadezhda Zozulya
- National Research Center for Hematology, Moscow, Russian Federation
| | - Pavel Svirin
- Morozovskaya Children's Hospital, Moscow, Russian Federation
| | - Tatiana Andreeva
- City Center for the Treatment of Hemophilia Patients, City Polyclinic N° 37, St. Petersburg, Russian Federation
| | - Majda Benedik-Dolničar
- Children's Hospital Oncology-Hematology Unit, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Victor Jiménez-Yuste
- Servicio de Hematología, Hospital Univeristario La Paz, Autónoma University, Madrid, Spain
| | - Lidija Kitanovski
- Children's Hospital Oncology-Hematology Unit, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Silva Zupancic-Šalek
- Division of Haematology, Haemophilia Centre, University Hospital REBRO, Zagreb, Croatia
| | - Anna Pavlova
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Angelika Bátorová
- Department of Hematology and Transfusion Medicine, National Hemophilia Center, Faculty of Medicine of the Comenius University and University Hospital, Bratislava, Slovak Republic
| | | | - Gulnara Abdilova
- Scientific Center of Pediatrics and Pediatric Surgery, Almaty, Kazakhstan
| | | | - Martina Jansen
- Octapharma Pharmazeutika Produktionsges.mbH, Vienna, Austria
| | | | | | | | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
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26
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Fedorova D, Ovsyannikova G, Kurnikova M, Pavlova A, Konyukhova T, Pshonkin A, Smetanina N. De novo TP53 germline activating mutations in two patients with the phenotype mimicking Diamond-Blackfan anemia. Pediatr Blood Cancer 2022; 69:e29558. [PMID: 35084091 DOI: 10.1002/pbc.29558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022]
Abstract
Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome, associated with mutations in ribosomal protein (RP) genes. Growing data on mutations in non-RP genes in patients with DBA-like phenotype became available over recent years. We describe two patients with the phenotype of DBA (onset of macrocytic anemia within the first year of life, paucity of erythroid precursors in bone marrow) and germline de novo variants in the TP53 gene. Both patients became transfusion independent, probably due to L-leucine therapy. The possible role of TP53 variants should be considered in patients with DBA-like phenotype and no mutations in RP genes.
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Affiliation(s)
- Daria Fedorova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Galina Ovsyannikova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Maria Kurnikova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Anna Pavlova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Tatiana Konyukhova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexey Pshonkin
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Nataliya Smetanina
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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27
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Pavlova A, Bassit L, Cox BD, Korablyov M, Chipot C, Patel D, Lynch DL, Amblard F, Schinazi RF, Gumbart JC. The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates. J Med Chem 2022; 65:4854-4864. [PMID: 35290049 PMCID: PMC9026740 DOI: 10.1021/acs.jmedchem.1c02040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into noncapsid-like particles, thereby inhibiting the HBV replication cycle. Here, we have assessed the structures of early nucleocapsid assembly intermediates, bound with and without CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly. Specifically, the assembly intermediates with bound misdirecting CAMs appear to be flattened relative to those with bound accelerators. Finally, the potency of CAMs within the same class was studied. We find that an increased number of contacts with the capsid protein and favorable binding energies inferred from free energy perturbation calculations are indicative of increased potency.
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Affiliation(s)
- Anna Pavlova
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Bryan D Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Laboratoire international associé CNRS-UIUC, UMR 7019, Université de Lorraine, B.P. 70239, 54506 Vandæuvre-lès-Nancy, France
| | - Dharmeshkumar Patel
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L Lynch
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C Gumbart
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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28
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Fu H, Chen H, Blazhynska M, Goulard Coderc de Lacam E, Szczepaniak F, Pavlova A, Shao X, Gumbart JC, Dehez F, Roux B, Cai W, Chipot C. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nat Protoc 2022; 17:1114-1141. [PMID: 35277695 PMCID: PMC10082674 DOI: 10.1038/s41596-021-00676-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/07/2021] [Indexed: 11/09/2022]
Abstract
Designing a reliable computational methodology to calculate protein:ligand standard binding free energies is extremely challenging. The large change in configurational enthalpy and entropy that accompanies the association of ligand and protein is notoriously difficult to capture in naive brute-force simulations. Addressing this issue, the present protocol rests upon a rigorous statistical mechanical framework for the determination of protein:ligand binding affinities together with the comprehensive Binding Free-Energy Estimator 2 (BFEE2) application software. With the knowledge of the bound state, available from experiments or docking, application of the BFEE2 protocol with a reliable force field supplies in a matter of days standard binding free energies within chemical accuracy, for a broad range of protein:ligand complexes. Limiting undesirable human intervention, BFEE2 assists the end user in preparing all the necessary input files and performing the post-treatment of the simulations towards the final estimate of the binding affinity.
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Affiliation(s)
- Haohao Fu
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - Haochuan Chen
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - Marharyta Blazhynska
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Emma Goulard Coderc de Lacam
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Florence Szczepaniak
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Department of Chemistry, University of Chicago, Chicago, IL, USA.,Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL, USA
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China.
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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29
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Pezeshkpoor B, Oldenburg J, Pavlova A. Experiences in Routine Genetic Analysis of Hereditary Hemorrhagic, Thrombotic, and Platelet Disorders. Hamostaseologie 2022; 42:S5-S12. [PMID: 35226963 DOI: 10.1055/a-1726-4793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Hemostasis is a complex and tightly regulated system that attempts to maintain a homeostatic balance to permit normal blood flow, without bleeding or thrombosis. Hemostasis reflects the subtle balance between procoagulant and anticoagulant factors in the pathways of primary hemostasis, secondary hemostasis, and fibrinolysis. The major components in this interplay include the vascular endothelium, platelets, coagulation factors, and fibrinolytic factors. After vessel wall injury, the subendothelium is exposed to the blood stream, followed by rapid activation of platelets via collagen binding and von Willebrand factor-mediated platelet adhesion to the damaged vessel wall through platelet glycoprotein receptor Ib/IX/V. Activated platelets change their shape, release bioactive molecules from their granules, and expose negatively charged phospholipids on their surface. For a proper function of this process, an adequate number of functional platelets are required. Subsequently, a rapid generation of sufficient amounts of thrombin begins; followed by activation of the coagulation system and its coagulation factors (secondary hemostasis), generating fibrin that consolidates the platelet plug. To maintain equilibrium between coagulation and anticoagulation, the naturally occurring anticoagulants such as protein C, protein S, and antithrombin keep this process in balance. Deficiencies (inherited or acquired) at any level of this fine-tuned system result in pathologic bleedings or increased hypercoagulability states leading to thrombosis. This review will focus on genetic diagnosis of inherited bleeding, thrombotic, and platelet disorders, discussing strengths and limitations of existing diagnostic settings and genetic tools and highlight some important considerations necessary for clinical application.
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Affiliation(s)
- B Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Medical Faculty, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - J Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Medical Faculty, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - A Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Medical Faculty, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
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30
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Kneller DW, Gerlits O, Daemen LL, Pavlova A, Gumbart JC, Cheng Y, Kovalevsky A. Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor. Phys Chem Chem Phys 2022; 24:3586-3597. [PMID: 35089990 PMCID: PMC8940534 DOI: 10.1039/d1cp05487b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 cm-1. This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effects of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal mol-1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, U.S.A
| | - Luke L. Daemen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Yongqiang Cheng
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Acharya A, Yi D, Pavlova A, Agarwal V, Gumbart JC. Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole. Biochemistry 2022; 61:206-215. [DOI: 10.1021/acs.biochem.1c00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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32
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Belova V, Pavlova A, Afasizhev R, Moskalenko V, Korzhanova M, Krivoy A, Cheranev V, Nikashin B, Bulusheva I, Rebrikov D, Korostin D. System analysis of the sequencing quality of human whole exome samples on BGI NGS platform. Sci Rep 2022; 12:609. [PMID: 35022470 PMCID: PMC8755732 DOI: 10.1038/s41598-021-04526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022] Open
Abstract
Human exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia. The reliability and quality of the obtained data are already beyond any doubt. However, only a few kits compatible with these sequencers can be used for such specific tasks as exome sequencing. We developed our own solution for library pre-capture pooling and exome enrichment with Agilent probes. In this work, using a set of the standard benchmark samples from the Platinum Genome collection, we demonstrate that the qualitative and quantitative parameters of our protocol which we called "RSMU_exome" exceed those of the MGI Tech kit. Our protocol allows for identifying more SNV and indels, generates fewer PCR duplicates, enables pooling of more samples in a single enrichment procedure, and requires less raw data to obtain results comparable with the MGI Tech's protocol. The cost of our protocol is also lower than that of MGI Tech's solution.
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Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997.
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Viktoriya Moskalenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Andrey Krivoy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Boris Nikashin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Irina Bulusheva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
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van Nisselrooij AEL, Moon-Grady AJ, Wacker-Gussmann A, Tomek V, Malčić I, Grzyb A, Pavlova A, Kazamia K, Thakur V, Sinkovskaya E, Harkel ADJT, Haak MC. The aorto-left ventricular tunnel from a fetal perspective: original case series and literature review. Prenat Diagn 2022; 42:267-277. [PMID: 35018638 PMCID: PMC9303731 DOI: 10.1002/pd.6090] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022]
Abstract
Introduction Aorto‐left ventricular tunnel (ALVT) accounts for <0.1% of congenital heart defects. Evidence on the prognosis from a fetal perspective is limited. With this retrospective international case series, we provide information on the outcome of fetuses with ALVT. Methods All members of the Association for European Pediatric and Congenital Cardiology's (AEPC) fetal working group and fetal medicine units worldwide were invited for participation. We observed antenatal parameters, neonatal outcome and postnatal follow‐up. Additionally, a systematic search of the literature was performed. Results Twenty fetuses with ALVT were identified in 10 participating centers (2001–2019). Fetal echocardiographic characteristics of ALVT included an increased cardiac–thorax ratio (95%), left ventricular end‐diastolic diameter (90%) and a dysplastic aortic valve (90%). Extracardiac malformations were rare (5%). Eight fetuses died at a median gestational age (GA) of 21 + 6 weeks (range, 19–24): all showed signs of hydrops prior to 24 weeks or at autopsy. All others (60%, 12/2) were live–born (median GA 38 + 4, range 37–40), underwent surgery and were alive at last follow up (median 3.2 years, range 0.1–17). The literature reported 22 ALVT fetuses with similar outcome. Conclusions In the absence of fetal hydrops, ALVT carries a good prognosis. Fetuses who survive to 24 weeks without hydrops are likely to have a good outcome. What's already known about this topic?Aorto‐left ventricular tunnel (ALVT) is an extremely rare diagnosis that may cause congenital heart failure and fetal hydrops, leading to fetal or neonatal death. A few case reports show that after corrective surgery in the neonatal period, cases with ALVT tend to have a good prognosis.
What does this study add?This is the first study that evaluates prenatal characteristics, prognostic parameters and outcome following a prenatal diagnosis of ALVT in a cohort of cases worldwide, including a systematic review of the literature as well. In the absence of fetal hydrops, ALVT carries a good prognosis. Fetuses who survive to 24 weeks without hydrops are likely to have a good outcome.
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Affiliation(s)
- A E L van Nisselrooij
- Department of Fetal Medicine and Obstetrics, Leiden University Medical Centre, Leiden, the Netherlands
| | - A J Moon-Grady
- Division of Pediatric Cardiology, Department of Pediatrics, University of California, San Francisco, California
| | - A Wacker-Gussmann
- Department of Pediatric Cardiology and Congenital Heart Disease, German Heart Centre Munich, Munich, Germany
| | - V Tomek
- Children's Heart Centre Prague, University Hospital Motol, Prague, Czech Republic
| | - I Malčić
- Department of Child's Cardiology, Zagreb University Hospital, Zagreb, Croatia
| | - A Grzyb
- Department of Perinatal Cardiology and Congenital Anomalies, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Pavlova
- Department of Cardiology, Ukrainian Children's Cardiac Centre, Kyiv, Ukraine
| | - K Kazamia
- Children's Heart Centre Stockholm-Uppsala, Karolinska University Hospital, Stockholm, Sweden
| | - V Thakur
- Division of Cardiology, Labatt Family Heart Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E Sinkovskaya
- Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, Virginia
| | - A D J Ten Harkel
- Department of Fetal Medicine and Obstetrics, Leiden University Medical Centre, Leiden, the Netherlands
| | - M C Haak
- Department of Fetal Medicine and Obstetrics, Leiden University Medical Centre, Leiden, the Netherlands
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Ovsyannikova G, Pavlova A, Deordieva E, Raykina E, Pshonkin A, Maschan A, Maschan M. Single Center Experience With Pediatric Patients With GATA2 Deficiency. Front Pediatr 2022; 10:801810. [PMID: 35273927 PMCID: PMC8901576 DOI: 10.3389/fped.2022.801810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
GATA2 deficiency is one of the most common predisposing conditions for MDS in young individuals. It is characterized by autosomal dominant inheritance and a high rate of de novo mutations. Here we describe the clinical phenotype and hematological presentation of 10 pediatric patients with GATA2 deficiency presented to the Dmitry Rogachev Center between 2013 and 2020. All patients had been referred for neutropenia or suspected aplastic anemia. While some patients presented with an immunological phenotype, others displayed monosomy 7 and MDS. The clinical presentation with MDS in infancy and the constitutional phenotypes in our patients underline the great variability in clinical manifestation. Careful description of cohorts with GATA2 deficiency from different countries and genetic backgrounds will help to unravel the enormous heterogeneity of this recently discovered genetic disorder.
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Affiliation(s)
- Galina Ovsyannikova
- Department of Pediatric Hematology and Oncology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Pavlova
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Deordieva
- Department of Pediatric Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Elena Raykina
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexey Pshonkin
- Department of Pediatric Hematology and Oncology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexey Maschan
- Department of Pediatric Hematology and Oncology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Michael Maschan
- Department of Hematopoietic Stem Cell Transplantation, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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35
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Kranzhöfer D, Pavlova A, Schneider H, Franck P, Glonnegger H, Büchsel M, Yoshimi-Nöllke A, Oldenburg J, Zieger B. Type 2B von Willebrand Disease: Early Manifestation as Neonatal Thrombocytopenia. Hamostaseologie 2021; 41:469-474. [PMID: 34942660 DOI: 10.1055/a-1665-6185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Here, we report about a preterm female newborn with a prolonged course of severe thrombocytopenia and hematomas. The family history was positive for von Willebrand disease type 2B (VWD 2B). Diagnosis of VWD 2B was identified analyzing von Willebrand factor (VWF) parameters (VWF:antigen, VWF:activity, VWF multimer analyses) and performing light transmission aggregometry (with half concentration of ristocetin). In addition, the diagnosis was confirmed by molecular genetic analysis: identification of a disease-causing missense mutation (Val1316Met) in the VWF gene associated with a severe course of VWD 2B, which had been previously reported. Treatment with a VWF-containing plasma concentrate was initiated. Because the combination of prematurity and very low platelet count is often associated with intracranial bleeding, at the beginning platelet concentrates were transfused. Fortunately, the patient did not develop serious bleeding episodes. Interestingly, the patient had a mutation in the VWF gene, which had been described to be associated with aggravation of thrombocytopenia especially in stressful situations. Therefore, we replaced venous blood withdrawals by capillary blood samplings when possible and, consequently, we observed an increase of the platelet count after this change in management. At the age of 2 months, the patient was discharged after stabilization of the platelet count without any bleeding signs and without a need of long-term medication.
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Affiliation(s)
- David Kranzhöfer
- Department for General Pediatrics, Adolescent Medicine and Neonatology, University Medical Center Freiburg, Freiburg, Germany
| | - Anna Pavlova
- Institute of Experimental Haematology and Transfusion Medicine (IHT), University Hospital Bonn, Bonn, Germany
| | - Hendryk Schneider
- Department for General Pediatrics, Adolescent Medicine and Neonatology, University Medical Center Freiburg, Freiburg, Germany
| | - Peter Franck
- Department for General Pediatrics, Adolescent Medicine and Neonatology, University Medical Center Freiburg, Freiburg, Germany
| | - Hannah Glonnegger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Martin Büchsel
- Clinical Chemistry, University Medical Center Freiburg, Freiburg, Germany
| | - Ayami Yoshimi-Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine (IHT), University Hospital Bonn, Bonn, Germany
| | - Barbara Zieger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany
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36
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Reda S, Rühl H, Witkowski J, Müller J, Pavlova A, Oldenburg J, Pötzsch B. PC Deficiency Testing: Thrombin-Thrombomodulin as PC Activator and Aptamer-Based Enzyme Capturing Increase Diagnostic Accuracy. Front Cardiovasc Med 2021; 8:755281. [PMID: 34708097 PMCID: PMC8542722 DOI: 10.3389/fcvm.2021.755281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/12/2021] [Indexed: 11/30/2022] Open
Abstract
Protein C (PC) activity tests are routinely performed in a thrombophilia workup to screen for PC deficiency. Currently used tests combine conversion of PC to activated PC (APC) by the snake venom Protac with subsequent APC detection through hydrolysis of a chromogenic peptide substrate or prolongation of a clotting time. In this prospective cohort study, we analyzed how different modes of PC activation and subsequent APC determination influence the diagnostic accuracy of PC activity testing in a cohort of 31 patients with genetically confirmed PC deficiency. In addition to chromogenic and clot-based measurement, an oligonucleotide-based enzyme capture assay utilizing a basic exosite-targeting aptamer was used for APC detection. To study the influence of the PC activation step on diagnostic sensitivity, PC activation through Protac and through the thrombin-thrombomodulin (TM) complex were compared. Twenty-six (84%) and 24 (77%) PC deficient patients were identified as true-positive using the chromogenic and the clot-based PC activity assay, respectively. True-positive results increased to 27 (87%) when the basic exosite-targeting aptamer approach was used for APC measurement. Additional replacement of the PC activator Protac by thrombin-TM gave true-positive results in all patients. These data indicate that the mode of PC activation is crucial in determining the accuracy of PC activity testing and that diagnostic sensitivity can be significantly improved by replacing the PC activator Protac with thrombin-TM. APC detection using a basic exosite-targeting aptamer achieves high sensitivity toward mutations outside the active center while being less subject to interfering factors than clot-based PC activity assays.
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Affiliation(s)
- Sara Reda
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Jana Witkowski
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Jens Müller
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
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Pavlova A, Tyulenev N, Tretyakova V, Skavronskaya V, Nikolaeva A, Prokofyev A, Chernyshev B, Stroganova T. Learning of Pseudoword-Movement Association is Accompanied by Enhanced Beta Synchronization. Int J Psychophysiol 2021. [DOI: 10.1016/j.ijpsycho.2021.07.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
We report a distinct difference in the interactions of the glycans of the host-cell receptor, ACE2, with SARS-CoV-2 and SARS-CoV S-protein receptor-binding domains (RBDs). Our analysis demonstrates that the ACE2 glycan at N322 enhances interactions with the SARS-CoV-2 RBD while the ACE2 glycan at N90 may offer protection against infections of both coronaviruses depending on its composition. The interactions of the ACE2 glycan at N322 with SARS-CoV RBD are blocked by the presence of the RBD glycan at N357 of the SARS-CoV RBD. The absence of this glycosylation site on SARS-CoV-2 RBD may enhance its binding with ACE2.
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Affiliation(s)
- Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. J Phys Chem Lett 2021; 12:5494-5502. [PMID: 34086459 PMCID: PMC8204752 DOI: 10.1021/acs.jpclett.1c01494] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 05/06/2023]
Abstract
SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.
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Affiliation(s)
- Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zijian Zhang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Atanu Acharya
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yui Tik Pang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhongyu Mou
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jerry M. Parks
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Chris Chipot
- Université
de Lorraine, UMR 7019, Laboratoire International Associé
CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-lès-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana 61801-3003, Illinois, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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40
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Khatwani SL, Pavlova A, Pirot Z. Anion-exchange HPLC assay for separation and quantification of empty and full capsids in multiple adeno-associated virus serotypes. Mol Ther Methods Clin Dev 2021; 21:548-558. [PMID: 33997103 PMCID: PMC8099603 DOI: 10.1016/j.omtm.2021.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022]
Abstract
Gene therapy has entered a new era where numerous therapies for severe and rare diseases are generating robust and compelling clinical results. The rapid improvements in gene therapies over the past few years can be attributed to better scientific understanding of the critical quality attributes that contribute to a safe and efficacious product, as well as a better understanding of the manufacturing processes that are required to yield consistent products, which routinely meet the quality standards required for clinical studies. Of particular concern is the need for an effective, quality control (QC)-compatible, and versatile test method for the quantification of empty and full capsids in recombinant adeno-associated virus (rAAV) samples from multiple serotypes. In that regard, we describe the development of a QC-compatible anion-exchange chromatography method consisting of a modular discontinuous gradient to achieve full baseline peak separation and quantification of empty and full AAV capsids. Using an rAAV6 vector, our assay was shown to be precise, linear, robust, and accurate-correlating well with orthogonal methods such as analytical ultracentrifugation (AUC) and cryogenic transmission electron microscopy (Cryo-TEM). Additionally, we demonstrate the versatility of our approach by adapting the method to separate and quantify empty/full capsids in samples from several rAAV serotypes.
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Affiliation(s)
| | - Anna Pavlova
- Sangamo Therapeutics, Inc., 7000 Marina Blvd., Brisbane, CA 94005, USA
| | - Zhu Pirot
- Sangamo Therapeutics, Inc., 7000 Marina Blvd., Brisbane, CA 94005, USA
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41
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Pang YT, Pavlova A, Tajkhorshid E, Gumbart JC. Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison. J Chem Phys 2021; 153:164104. [PMID: 33138412 DOI: 10.1063/5.0022802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Halogen atoms are widely used in drug molecules to improve their binding affinity for the receptor proteins. Many of the examples involve "halogen bonding" between the molecule and the binding site, which is a directional interaction between a halogen atom and a nucleophilic atom. Such an interaction is induced by an electron cloud shift of the halogen atom toward its covalently bonded neighbor to form the σ-bond, leaving a small electrostatic positive region opposite to the bond called the "σ-hole." To mimic the effect of the σ-hole in the CHARMM non-polarizable force field, recently CGenFF added a positively charged massless particle to halogen atoms, positioned at the opposite side of the carbon-halogen bond. This particle is referred to as a lone pair (LP) particle because it uses the lone pair implementation in the CHARMM force field. Here, we have added support for LP particles to ffTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software VMD. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus. Our results indicate that parameterization with the LP particle significantly improves the accuracy of the electrostatic response of the molecule, especially around the halogen atom. Although the inclusion of the LP particle does not produce a prominent effect on the interactions between the molecule and its target protein, the protein-ligand binding performance is greatly improved by optimization of the parameters.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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42
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design. J Phys Chem Lett 2021; 12:4195-4202. [PMID: 33900080 PMCID: PMC8097931 DOI: 10.1021/acs.jpclett.1c00425] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 05/03/2023]
Abstract
The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b. We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| | - Chris Chipot
- UMR 7019, Université de Lorraine, Laboratoire
International Associé CNRS, 54506 Vandœuvre-lès-Nancy, France
- University
of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Jeremy C. Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via
Vetoio, I-67010 L’Aquila, Italy
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43
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Levina A, Repkova M, Shikina N, Ismagilov Z, Kupryushkin M, Pavlova A, Mazurkova N, Pyshnyi D, Zarytova V. Pronounced therapeutic potential of oligonucleotides fixed on inorganic nanoparticles against highly pathogenic H5N1 influenza A virus in vivo. Eur J Pharm Biopharm 2021; 162:92-98. [PMID: 33753212 DOI: 10.1016/j.ejpb.2021.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/20/2020] [Accepted: 03/14/2021] [Indexed: 11/26/2022]
Abstract
This study describes the effective attack of oligonucleotides on the viral genome of highly pathogenic H5N1 influenza A virus (IAV) in vivo using for the first time the new delivery system consisting of biocompatible low-toxic titanium dioxide nanoparticles and immobilized polylysine-containing oligonucleotides with the native (ODN) and partially modified (ODNm) internucleotide bonds. Intraperitoneal injection of the TiO2•PL-ODN nanocomposite provided 65-70% survival of mice, while intraperitoneal or oral administration of TiO2•PL-ODNm was somewhat more efficient (~80% survival). The virus titer in the lung was reduced by two-three orders of magnitude. The nanocomposites are nontoxic to mice under the used conditions. TiO2 nanoparticles, unbound ODN, and the nanocomposite bearing the random oligonucleotide showed an insignificant protective effect, which indicates the ability of targeted oligonucleotides delivered in mice in the nanocomposites to site-specifically interact with complementary RNAs. The protection of oligonucleotides in nanocomposites by TiO2 nanoparticles and partial modification of the internucleotide bonds provides a continued presence of oligonucleotides in the body for the effective and specific action on the viral RNA. The proposed oligonucleotide delivery system can claim not only to effectively inhibit IAV genes but also to turn off other genes responsible for diseases caused by nucleic acids.
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Affiliation(s)
- Asya Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Marina Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Nadezhda Shikina
- Boreskov Institute of Catalysis, Siberian Branch of RAS, pr. Lavrent'eva 5, 630090 Novosibirsk, Russia
| | - Zinfer Ismagilov
- Boreskov Institute of Catalysis, Siberian Branch of RAS, pr. Lavrent'eva 5, 630090 Novosibirsk, Russia
| | - Maxim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Anna Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Natalia Mazurkova
- FBRI State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - Dmitrii Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Valentina Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia.
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Liesner RJ, Abraham A, Altisent C, Belletrutti MJ, Carcao M, Carvalho M, Chambost H, Chan AKC, Dubey L, Ducore J, Gattens M, Gresele P, Gruel Y, Guillet B, Jimenez-Yuste V, Kitanovski L, Klukowska A, Lohade S, Mancuso ME, Oldenburg J, Pavlova A, Pollio B, Sigaud M, Vdovin V, Vilchevska K, Wu JKM, Jansen M, Belyanskaya L, Walter O, Knaub S, Neufeld EJ. Simoctocog Alfa (Nuwiq) in Previously Untreated Patients with Severe Haemophilia A: Final Results of the NuProtect Study. Thromb Haemost 2021; 121:1400-1408. [PMID: 33581698 PMCID: PMC8570909 DOI: 10.1055/s-0040-1722623] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Introduction
FVIII inhibitor development is the most serious contemporary treatment complication in haemophilia A, particularly in previously untreated patients (PUPs). No inhibitors developed in clinical trials in previously treated patients treated with simoctocog alfa (Nuwiq), a fourth-generation recombinant FVIII produced in a human cell line.
Methods
The NuProtect study investigated the immunogenicity of simoctocog alfa in PUPs. NuProtect was a prospective, multinational, open-label, non-controlled, phase III study. PUPs with severe haemophilia A (FVIII:C <1%) of any age and ethnicity were treated with simoctocog alfa for 100 exposure days or a maximum of 5 years. Patients were true PUPs without prior exposure to FVIII concentrates or blood components. Inhibitor titres were measured with the Nijmegen-modified Bethesda assay; cut-off for positivity was 0.6 BU mL
−1
(≥0.6 to <5 low-titre, ≥5 high titre).
Results
A total of 108 PUPs with a median age at first treatment of 12.0 months (interquartile range: 8.0–23.5) were treated with simoctocog alfa.
F8
mutation type was known for 102 patients (94.4%) of whom 90 (88.2%) had null
F8
mutations and 12 (11.8%) had non-null mutations. Of 105 PUPs evaluable for inhibitor development, 28 (26.7%) developed inhibitors; 17 high titre (16.2%) and 11 low titre (10.5%). No PUPs with non-null
F8
mutations developed inhibitors.
Conclusion
In the NuProtect study, the rate of inhibitor development in PUPs with severe haemophilia A treated with simoctocog alfa was lower than the rate reported for hamster-cell-derived recombinant factor VIII products in other recent clinical trials. No inhibitors were reported in PUPs with non-null
F8
mutations.
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Affiliation(s)
- Ri J Liesner
- Great Ormond Street Hospital for Children NHS Trust Haemophilia Centre, NIHR GOSH BRC, London, United Kingdom
| | - Aby Abraham
- Department of Hematology, Christian Medical College, Vellore, India
| | - Carmen Altisent
- Unitat d'Hemofilia, Hospital Vall D'Hebron, Barcelona, Spain
| | - Mark J Belletrutti
- Pediatric Hematology, Department of Pediatrics, University of Alberta, Edmonton, Canada
| | - Manuel Carcao
- Division of Haematology/Oncology and Child Health Evaluative Sciences, Department of Paediatrics, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Manuela Carvalho
- Congenital Coagulopathies Reference Centre, São João University Hospital Centre, Porto, Portugal
| | - Hervé Chambost
- AP-HM, Department of Pediatric Hematology Oncology, Children Hospital La Timone, Aix Marseille Univ, INSERM, INRA, C2VN, Marseille, France
| | - Anthony K C Chan
- Division of Pediatric Hematology/Oncology, McMaster University, Hamilton, Canada
| | - Leonid Dubey
- Department of Pediatrics, Western Ukrainian Specialized Children's Medical Centre, Lviv, Ukraine
| | - Jonathan Ducore
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, United States
| | - Michael Gattens
- Department of Paediatric Haematology and Oncology, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Paolo Gresele
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Yves Gruel
- Centre Régional de Traitement de l'Hémophilie, Hôpital Trousseau, Tours, France
| | - Benoit Guillet
- Haemophilia Treatment Centre, Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Victor Jimenez-Yuste
- Servicio de Hematología, Hospital Univeristario La Paz, Autónoma University, Madrid, Spain
| | - Lidija Kitanovski
- Department of Haemato-Oncology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Anna Klukowska
- Department of Pediatrics, Haematology and Oncology, Warsaw Medical University, Warsaw, Poland
| | - Sunil Lohade
- Department of Hematology, Sahyadri Speciality Hospital, Pune, India
| | - Maria Elisa Mancuso
- Center for Thrombosis and Hemorrhagic Diseases, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Anna Pavlova
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany
| | - Berardino Pollio
- Department of Transfusion Medicine, Regina Margherita Children Hospital of Turin, Turin, Italy
| | - Marianne Sigaud
- Centre Régional de Traitement de I'Hémophilie, University Hospital of Nantes, Nantes, France
| | - Vladimir Vdovin
- Department of Hematology, Morozovskaya Children's Hospital, Moscow, Russian Federation
| | - Kateryna Vilchevska
- Department of Hematology, State Institution "Institute of Urgent and Reconstructive Surgery named after V.K. Gusak of National Academy of Medical Sciences of Ukraine," Donetsk, Ukraine
| | - John K M Wu
- British Columbia Children's Hospital, Vancouver, Canada
| | - Martina Jansen
- Octapharma Pharmazeutika Produktionsges.mbH, Vienna, Austria
| | | | | | | | - Ellis J Neufeld
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States
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45
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Pavlova A, Lynch DL, Dean Smith M, Smith JD, Gumbart JC. Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease. Biophys J 2021. [PMCID: PMC7879742 DOI: 10.1016/j.bpj.2020.11.1395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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46
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Preisler B, Pezeshkpoor B, Banchev A, Fischer R, Zieger B, Scholz U, Rühl H, Kemkes-Matthes B, Schmitt U, Redlich A, Unal S, Laws HJ, Olivieri M, Oldenburg J, Pavlova A. Familial Multiple Coagulation Factor Deficiencies (FMCFDs) in a Large Cohort of Patients-A Single-Center Experience in Genetic Diagnosis. J Clin Med 2021; 10:jcm10020347. [PMID: 33477601 PMCID: PMC7831305 DOI: 10.3390/jcm10020347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Familial multiple coagulation factor deficiencies (FMCFDs) are a group of inherited hemostatic disorders with the simultaneous reduction of plasma activity of at least two coagulation factors. As consequence, the type and severity of symptoms and the management of bleeding/thrombotic episodes vary among patients. The aim of this study was to identify the underlying genetic defect in patients with FMCFDs. Methods: Activity levels were collected from the largest cohort of laboratory-diagnosed FMCFD patients described so far. Genetic analysis was performed using next-generation sequencing. Results: In total, 52 FMCFDs resulted from coincidental co-inheritance of single-factor deficiencies. All coagulation factors (except factor XII (FXII)) were involved in different combinations. Factor VII (FVII) deficiency showed the highest prevalence. The second group summarized 21 patients with FMCFDs due to a single-gene defect resulting in combined FV/FVIII deficiency or vitamin K–dependent coagulation factor deficiency. In the third group, nine patients with a combined deficiency of FVII and FX caused by the partial deletion of chromosome 13 were identified. The majority of patients exhibited bleeding symptoms while thrombotic events were uncommon. Conclusions: FMCFDs are heritable abnormalities of hemostasis with a very low population frequency rendering them orphan diseases. A combination of comprehensive screening of residual activities and molecular genetic analysis could avoid under- and misdiagnosis.
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Affiliation(s)
- Barbara Preisler
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (H.R.); (J.O.)
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (H.R.); (J.O.)
| | - Atanas Banchev
- Department of Paediatric Haematology and Oncology, University Hospital “Tzaritza Giovanna—ISUL”, 1527 Sofia, Bulgaria;
| | - Ronald Fischer
- Hemophilia Care Center, SRH Kurpfalzkrankenhaus Heidelberg, 69123 Heidelberg, Germany;
| | - Barbara Zieger
- Department of Pediatrics and Adolescent Medicine, University Medical Center–University of Freiburg, 79106 Freiburg, Germany;
| | - Ute Scholz
- Center of Hemostasis, MVZ Labor Leipzig, 04289 Leipzig, Germany;
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (H.R.); (J.O.)
| | | | - Ursula Schmitt
- Center of Hemostasis Berlin, 10789 Berlin-Schöneberg, Germany;
| | - Antje Redlich
- Pediatric Oncology Department, Otto von Guericke University Children’s Hospital Magdeburg, 39120 Magdeburg, Germany;
| | - Sule Unal
- Division of Pediatric Hematology Ankara, Hacettepe University, 06100 Ankara, Turkey;
| | - Hans-Jürgen Laws
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Duesseldorf, 40225 Duesseldorf, Germany;
| | - Martin Olivieri
- Pediatric Hemostasis and Thrombosis Unit, Department of Pediatrics, Pediatric Hemophilia Centre, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, 80337 Munich, Germany;
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (H.R.); (J.O.)
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; (B.P.); (B.P.); (H.R.); (J.O.)
- Correspondence: ; Tel.: +49-228-287-19711
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47
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chem Sci 2021; 12:1513-1527. [PMID: 35356437 PMCID: PMC8899719 DOI: 10.1039/d0sc04942e] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored Nδ (HD) and Nϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.![]()
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48
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen S, Coates L, Cooper C, Demerdash O, Daidone I, Eblen J, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller D, Kovalevsky A, Larkin J, Lawrence T, LeGrand S, Liu SH, Mitchell J, Park G, Parks J, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith J, Smith M, Soto C, Tsaris A, Thavappiragasam M, Tillack A, Vermaas J, Vuong V, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model 2020; 60:5832-5852. [PMID: 33326239 PMCID: PMC7754786 DOI: 10.1021/acs.jcim.0c01010] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
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Affiliation(s)
- A. Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - R. Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M. Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - J. Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - D. Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - S. Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - K. G. Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - S.Y. Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - L. Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C.J. Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - O. Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - I. Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, I-67010 L’Aquila, Italy
| | - J.D. Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - S. Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536, USA
| | - S. Forli
- Scripps Research, La Jolla, CA, 92037, USA
| | - J. Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - J. C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - J. Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121, USA
| | - O. Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - D.W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - A. Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Larkin
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - T.J. Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - S.-H. Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - J.C. Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - G. Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J.M. Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - A. Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - L. Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - D. Poole
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - L. Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439, USA
| | - D. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - A. Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - Y. Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - J.C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - M.D. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - C. Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - J.V. Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - V.Q. Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - J. Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - S. Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - M. Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201, USA
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. ChemRxiv 2020:13200227. [PMID: 33200115 PMCID: PMC7668740 DOI: 10.26434/chemrxiv.13200227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
In this comutational work a hybrid quantum mechanics/molecular mechanics approach, the MD-PMM approach, is used to investigate the proton transfer reaction the activates the catalytic activity of SARS-CoV-2 main protease. The proton transfer thermodynamics is investigated for the apo ensyme (i.e., without any bound substrate or inhibitor) and in the presence of a inhibitor, N3, which was previously shown to covalently bind SARS-CoV-2 main protease.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Chris Chipot
- UMR 7019, Universite de Lorraine, Laboratoire International Associe CNRS
- University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, TN 37831, United States
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. bioRxiv 2020. [PMID: 32935106 DOI: 10.1101/2020.09.07.286344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M pro , a cysteine protease, have been determined, facilitating structure-based drug design. M pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, M pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV M pro , but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N δ (HD) and N ϵ (HE) protonation of His41 and His164, respectively, the α -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.
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