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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024. [PMID: 38577994 DOI: 10.1021/acsinfecdis.3c00592] [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] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V Krieger
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Ethan Clary
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Natalie Thornton
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Paolo A Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron Therapeutics, 55 Chapel Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen Therapeutics, 12 Gill Street, Woburn, Massachusetts 01801, United States
| | - Christopher D Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO Therapeutics, 150 Cambridgepark Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T S Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix Pharmaceuticals, 222 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Anthony D Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Suksard K, Luangtrakool K, Rungroung T, Chamsai S, Saetam P, Kittisares K, Permpikul P, Kittivorapart J. Two Cases of Anti-D Alloimmunization in D-Negative Thai Patients as a Result of the Asian-Type DEL on Transfused Red Cells. Transfus Med Hemother 2024; 51:122-125. [PMID: 38584693 PMCID: PMC10996056 DOI: 10.1159/000533625] [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] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/13/2023] [Indexed: 04/09/2024] Open
Abstract
Introduction DEL is known to be one of the weakest D variants, which can be detected by the adsorption-elution technique or by molecular study. Currently, in Thailand, we do not routinely test for DEL variants serologically or genetically among serologic RhD-negative blood donors. Case Presentation We reported 2 cases of alloimmunization after transfused with Rh DEL, RHD*DEL1 allele, in the Thai population. The first case was a 73-year-old male with anemia who presented with post-cardiac arrest and septic shock. The patient was group B, RhD-negative, and was transfused with RhD-negative red blood cells (RBCs). Antibody screening and identification found that the patient developed anti-D and anti-Mia during the admission course. The second case was a 38-year-old woman with pseudomyxoma peritonei who developed anti-D after receiving four units of RhD-negative RBCs during cytoreductive surgery with hyperthermic intraperitoneal chemotherapy. Both patients did not receive anti-D immunoglobulin and had no previous history of anti-D detection. We retrospectively investigated and found two units of RHD*DEL1 among the RBCs transfused to these patients. Discussion Previous reports of several cases of anti-D alloimmunization in RhD-negative recipients transfused by RHD*DEL1, an Asian-type DEL, are limited only to East Asia. We first identified 2 patients with anti-D alloimmunization after receiving the RHD*DEL1 RBCs in the Thai population. This raises concern about Rh DEL screening among D-negative Thai blood donors and whether to remove DEL units from the D-negative inventory to improve patient safety.
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Affiliation(s)
- Kanyapon Suksard
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komon Luangtrakool
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thongbai Rungroung
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sutthisak Chamsai
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pradermchai Saetam
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kulvara Kittisares
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parichart Permpikul
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Janejira Kittivorapart
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS Discov 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [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: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
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Rophina M, Sinha A, Biswas D, Basu D, Datta SS, Scaria V. Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases. Transfus Apher Sci 2024; 63:103872. [PMID: 38272782 DOI: 10.1016/j.transci.2024.103872] [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: 10/23/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
The DEL phenotype represents an intriguing and challenging aspect of blood group serology. This condition is characterized by an extremely weak expression of the D antigen on red blood cells, to the extent that it often eludes detection through routine serological methods. Identifying the DEL phenotype necessitates more specialized techniques, such as adsorption and elution tests, to reveal the presence of the D antigen. This distinctive phenotype underscores the complexity and subtlety of blood group genetics and highlights the importance of using advanced methods to accurately classify individuals with this condition, as their ability to form anti-D antibodies can have clinical implications during transfusion and pregnancy scenarios. There is a paucity of data for the DEL phenotype in the Indian population, and the molecular basis has not been elucidated yet. Our investigation delves into the genetic underpinnings of two distinct DEL phenotype cases that pose challenges for resolution through conventional serological techniques. We employ next-generation amplicon sequencing to unravel the intricate genetic landscape underlying these cases. In the D-negative donor, the DEL phenotype was first identified serologically, which was subsequently confirmed by molecular analysis. In the second case, it was associated with an anti-D antibody in a D-positive patient. Initial data analysis unveiled a substantial reduction in coverage across the exonic segments of the RHD gene in both samples, suggesting the potential presence of RHD exon deletions. On both occasions, we identified a homozygous intronic RHD polymorphism that is well established to be linked to the RHD* 01EL.32/RHD*DEL32 variant.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Ayesha Sinha
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Durba Biswas
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Debapriya Basu
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Suvro Sankha Datta
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India; Vishwanath Cancer Care Foundation, B 702, Neelkanth Business Park Kirol Village, Mumbai, 400 086, India
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5
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Benedetti E, Micouin L. Have spirocyclic scaffolds been properly utilized in recent drug discovery efforts? Expert Opin Drug Discov 2024; 19:263-266. [PMID: 38225892 DOI: 10.1080/17460441.2024.2305735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Affiliation(s)
| | - Laurent Micouin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, Paris, France
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6
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LegaardAndersson J, Christensen J, Kleine-Kohlbrecher D, Vacher Comet I, Fullerton Støier J, Antoku Y, Poljak V, Moretti L, Dolberg J, Jacso T, Jensby Nielsen S, Nørregaard-Madsen M, Franch T, Helin K, Cloos PAC. Discovery of NSD2-Degraders from Novel and Selective DEL Hits. Chembiochem 2023; 24:e202300515. [PMID: 37807669 DOI: 10.1002/cbic.202300515] [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: 07/17/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
NSD2 is a histone methyltransferase predominantly catalyzing di-methylation of histone H3 on lysine K36. Increased NSD2 activity due to mutations or fusion-events affecting the gene encoding NSD2 is considered an oncogenic event and a driver in various cancers, including multiple myelomas carrying t(4;14) chromosomal translocations and acute lymphoblastic leukemia's expressing the hyperactive NSD2 mutant E1099 K. Using DNA-encoded libraries, we have identified small molecule ligands that selectively and potently bind to the PWWP1 domain of NSD2, inhibit NSD2 binding to H3K36me2-bearing nucleosomes, but do not inhibit the methyltransferase activity. The ligands were subsequently converted to selective VHL1-recruiting NSD2 degraders and by using one of the most efficacious degraders in cell lines, we show that it leads to NSD2 degradation, decrease in K3 K36me2 levels and inhibition of cell proliferation.
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Affiliation(s)
- Jan LegaardAndersson
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Jesper Christensen
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Daniela Kleine-Kohlbrecher
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Itys Vacher Comet
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
- Bioorigin Aps, Ole Maaløes Vej 3, 2200, Copenhagen, Denmark
| | - Jonatan Fullerton Støier
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
- Bioorigin Aps, Ole Maaløes Vej 3, 2200, Copenhagen, Denmark
| | - Yasuko Antoku
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Visnja Poljak
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Loris Moretti
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Johannes Dolberg
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Tomas Jacso
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Søren Jensby Nielsen
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | | | - Thomas Franch
- Nuevolution A/S / Amgen Research Copenhagen, Rønnegade 8, 2100, Copenhagen, Denmark
| | - Kristian Helin
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
- The Institute of Cancer Research (ICR), 237 Fulham Road, London, SW3 6JB, UK
| | - Paul A C Cloos
- University of Copenhagen, Biotech Research & Innovation Centre (BRIC), Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
- Bioorigin Aps, Ole Maaløes Vej 3, 2200, Copenhagen, Denmark
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7
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Hou J, Li J, Xia Y, Zhang X, Yang J, Li M, Zhou Y. Frequency of the 'Asia type' DEL with weak D phenotype in chinese. Transfus Clin Biol 2023; 30:387-392. [PMID: 37380099 DOI: 10.1016/j.tracli.2023.06.003] [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: 03/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND DEL individuals account for 9-30% of serological RhD negative population in east Asia and majority of them carrying the RHD*DEL1 allele are referred to as 'Asia type' DEL individuals. There is a lack of data on the molecular basis for 'Asia type' DELs with weak RhD phenotype. Therefore, the aim of this study is to unveil 'Asia type' DELs by elucidating the genetic background and analyzing the serological results. METHODS With a microplate typing protocol, RhD characterization was performed in samples from one million blood donors collected at Chengdu blood center during the period from 2019 to 2022. RhD confirmatory test was performed by direct antiglobulin test and indirect antiglobulin test with five anti-D reagents to detect RhD variants. Molecular characterization of samples categorized as RhD variants was studied by using direct genomic DNA sequencing and RHD zygosity analysis, followed by adsorption and elution tests conduced for samples carrying RHD*DEL1 allele to confirm the presence of RhD antigens on the red cells. RESULTS We reported here 21 RhD variant samples were detected by micro-column gel agglutination assay with IgG anti-D antibodies. Moreover, the agglutination reaction was stronger with IgG anti-D reagents in micro-column gel card than with IgM/IgG blended anti-D antibodies. Each of the 21 samples carried the RHD*DEL1 allele, which indicated that they were 'Asia type' DEL. Of the 21 'Asia type' DEL samples, 9 samples were detected to be RHD+/ RHD + homozygotes, whereas the other 12 samples were RHD+/RHD- hemizygotes. Among the samples phenotyped for RhCE, seven were CCee and four were Ccee. CONCLUSIONS In this study, DEL samples carrying RHD*DEL1 showed weak RhD phenotype with some anti-D reagents in RhD confirmatory test, which suggest that a serology strategy using several anti-D reagents may be helpful to detect this 'Asia type' DEL. Further studies are needed to elucidate whether the 'Asia type' DELs with weak RhD phenotype have stronger antigenicity and could cause serious transfusion reaction.
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Affiliation(s)
- Jue Hou
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Jian Li
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Yu Xia
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Xuemei Zhang
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Jianying Yang
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Meng Li
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
| | - Ying Zhou
- Blood Grouping Reference Laboratory, Chengdu Blood Center, Chengdu, China
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Yin Q. DEL variants: review of molecular mechanisms, clinical consequences and molecular testing strategy. Funct Integr Genomics 2023; 23:318. [PMID: 37840046 DOI: 10.1007/s10142-023-01249-z] [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: 10/02/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
Patients with DEL phenotype, a D variant with a low number of D antigens per red blood cell, are routinely typed as RhD-negative in serology testing and are detectable only by adsorption and elution techniques or molecular methods. DEL is of clinical importance worldwide, as indicated by its genotype-phenotype discrepancies among different populations and its potential to cause anti-D alloimmunization when DEL phenotype individuals are inadvertently managed as RhD-negative. This narrative review summarized the DEL alleles causing DEL phenotype and the underlying mechanisms. The clinical consequences and current molecular testing approach were discussed to manage the transfusion needs of patients and donors with DEL phenotype.
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Affiliation(s)
- Qinan Yin
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China.
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
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Teske KA, Su W, Corona CR, Wen J, Deng J, Ping Y, Zhang Z, Zhang Q, Wilkinson J, Beck MT, Nealey KR, Vasta JD, Cong M, Meisenheimer PL, Kuai L, Robers MB. DELs enable the development of BRET probes for target engagement studies in cells. Cell Chem Biol 2023; 30:987-998.e24. [PMID: 37490918 DOI: 10.1016/j.chembiol.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 01/23/2023] [Revised: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023]
Abstract
DNA-encoded libraries (DELs) provide unmatched chemical diversity and starting points for novel drug modalities. Here, we describe a workflow that exploits the bifunctional attributes of DEL ligands as a platform to generate BRET probes for live cell target engagement studies. To establish proof of concept, we performed a DEL screen using aurora kinase A and successfully converted aurora DEL ligands as cell-active BRET probes. Aurora BRET probes enabled the validation and stratification of the chemical series identified from primary selection data. Furthermore, we have evaluated the effective repurposing of pre-existing DEL screen data to find suitable leads for BRET probe development. Our findings support the use of DEL workflows as an engine to create cell-active BRET probes independent of structure or compound SAR. The combination of DEL and BRET technology accelerates hit-to-lead studies in a live cell setting.
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Affiliation(s)
- Kelly A Teske
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Wenji Su
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Cesear R Corona
- Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, CA 93401, USA
| | - Jing Wen
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Jason Deng
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Yan Ping
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Zaihong Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | | | - Michael T Beck
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Kendra R Nealey
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - James D Vasta
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Mei Cong
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Letian Kuai
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China.
| | - Matthew B Robers
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA.
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10
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Ohto H, Ito S, Srivastava K, Ogiyama Y, Uchikawa M, Nollet KE, Flegel WA. Asian-type DEL (RHD*DEL1) with an allo-anti-D: A paradoxical observation in a healthy multiparous woman. Transfusion 2023; 63:1601-1611. [PMID: 37465939 PMCID: PMC10528739 DOI: 10.1111/trf.17465] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND The DEL phenotype is the D variant expressing the least amounts of D antigen per red cell. Asian-type DEL (RHD:c:1227G > A) is the most prevalent DEL in East Asia without any anti-D alloimmunization reported before. We investigated the first observation of an anti-D in any DEL phenotype, reported in the Japanese language at a 1987 conference, only 3 years after the discovery of DEL. METHODS We contacted the proband 35 years after the initial report. Standard hemagglutination, adsorption/elution, and flow cytometry tests were performed, as was nucleotide sequencing for the RHD, RHCE, and HLA class I and class II genes. RESULTS The healthy multiparous Japanese woman, a regular blood donor, still had the anti-D of titer 8 representing an alloantibody by standard serologic methods. Unexpectedly, she carried an Asian-type DEL without any additional RHD gene variation. All 12 HLA alleles identified were known in the Japanese population. Interestingly, one of her HLA-DRB1 and a variant of her HLA-DQB1 alleles had previously been associated with anti-D immunization. CONCLUSION We described an allo-anti-D, maintained for more than three decades, in an Asian-type DEL. The combination of two implicated HLA alleles were rare and could have contributed to the anti-D immunization. Continued monitoring of anti-D immunization events in patients with DEL is warranted, and we discuss possible mechanisms for further study. As only this single observation has been recognized in the last 35 years, the current recommendation is affirmed: Individuals with Asian-type DEL should be treated as Rh D-positive for transfusion and Rh immune prophylaxis purposes.
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Affiliation(s)
- Hitoshi Ohto
- Department of Mesenchymal Stem Cell Research, Fukushima Medical University, Fukushima, Japan
| | - Shoichi Ito
- Tohoku Block Blood Center, Japanese Red Cross Society, Sendai, Japan
| | - Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yoshiko Ogiyama
- Tohoku Block Blood Center, Japanese Red Cross Society, Sendai, Japan
| | - Makoto Uchikawa
- Kanto-Koshinetsu Block Blood Center, Japanese Red Cross Society, Tokyo, Japan
| | - Kenneth Eric Nollet
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Willy Albert Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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11
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Quancard J, Vulpetti A, Bach A, Cox B, Guéret SM, Hartung IV, Koolman HF, Laufer S, Messinger J, Sbardella G, Craft R. The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Hit Generation. ChemMedChem 2023; 18:e202300002. [PMID: 36892096 DOI: 10.1002/cmdc.202300002] [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: 01/03/2023] [Revised: 02/14/2023] [Indexed: 03/10/2023]
Abstract
Hit generation is a crucial step in drug discovery that will determine the speed and chance of success of identifying drug candidates. Many strategies are now available to identify chemical starting points, or hits, and each biological target warrants a tailored approach. In this set of best practices, we detail the essential approaches for target centric hit generation and the opportunities and challenges they come with. We then provide guidance on how to validate hits to ensure medicinal chemistry is only performed on compounds and scaffolds that engage the target of interest and have the desired mode of action. Finally, we discuss the design of integrated hit generation strategies that combine several approaches to maximize the chance of identifying high quality starting points to ensure a successful drug discovery campaign.
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Affiliation(s)
- Jean Quancard
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Brian Cox
- School of Life Sciences, University of Sussex, Brighton, BN1 9RH, UK
| | - Stéphanie M Guéret
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43183, Gothenburg, Sweden
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Hannes F Koolman
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
| | - Stefan Laufer
- Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy & Biochemistry, Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72070, Tübingen, Germany
| | - Josef Messinger
- Medicine Design, Orionpharma, Orionintie 1, 02101, Espoo, Finland
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Russell Craft
- Medicinal chemistry, Symeres, Kadijk 3, 9747 AT, Groningen, The Netherlands
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12
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Desai SH, Mwangi R, Smith AN, Maurer MJ, Farooq U, King RL, Cerhan JR, Feldman AL, Habermann TM, Thompson CA, Wang Y, Ansell SM, Witzig TE, Nowakowski GS. Cell of origin is not associated with outcomes of relapsed or refractory diffuse large B cell lymphoma. Hematol Oncol 2023; 41:39-49. [PMID: 36305717 PMCID: PMC10037910 DOI: 10.1002/hon.3098] [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: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 02/03/2023]
Abstract
Activated B cell (ABC) type diffuse large B cell lymphoma (DLBCL), double hit lymphoma (DHL) and double expressor lymphoma (DEL) have poor outcomes to frontline R-CHOP but impact of these molecular features on outcomes of relapsed/refractory (R/R) disease is not well-characterized. We evaluated the association of diagnostic cell of origin (COO), double hit and double expressor status with overall survival after first relapse in DLBCL patients who were enrolled into the Molecular Epidemiology Resource (MER) cohort. COO was available from immunohistochemistry (IHC) using Hans criteria or gene expression profiling (GEP) (Nanostring) on the diagnostic FFPE biopsy. Of 373 pts with R/R DLBCL, 278 had COO by IHC: 152 were GCB, 107 were non-GCB. One hundred and fourty had COO by GEP: 44 were ABC, 65 were GCB and 13 were unclassifiable. Nineteen out of 163 (12%) were DHL; 30 out of 135 (22%) had DEL. COO, either by IHC (2 years OS GCB: 45% [CI95 : 38-54] vs. non-GCB: 44% [CI95 :36-55], p > 0.05) or GEP (2 years OS ABC: 42% [CI95 : 29-59] vs. GCB: 40% [CI95 : 30-54], p > 0.05), was not associated with difference in OS. DHL (2 years OS 16 [CI95 :6-45] vs. 45% [CI95 : 34-59], p < 0.01) and DEL (2 years OS 33% [CI95 : 20-56], vs. 50% [CI95 : 41-60], p < 0.05) had lower OS than non-DHL and non-DEL/non-DHL counterparts, respectively. COO by IHC or GEP was not associated with OS in R/R DLBCL while DHL and DEL were adverse prognostic markers in DLBCL at first relapse.
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Affiliation(s)
- Sanjal H. Desai
- Department of HematologyMayo ClinicRochesterMinnesotaUSA
- Division of Hematology, Oncology and TransplantationUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Raphael Mwangi
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Alexandra N. Smith
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Matthew J. Maurer
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Umar Farooq
- Department of Hematology, Oncology and Bone Marrow TransplantUniversity of Iowa Hospitals and ClinicsIowa CityIowaUSA
| | - Rebecca L. King
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James R. Cerhan
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Andrew L. Feldman
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | | | | | - Yucai Wang
- Department of HematologyMayo ClinicRochesterMinnesotaUSA
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13
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Yin Q, Ouchari M. Transfusion management of Africans with RHD variants in China. Transfus Clin Biol 2023; 30:287-293. [PMID: 36702201 DOI: 10.1016/j.tracli.2023.01.003] [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: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The presence of D variant among minorities could produce a higher rate of alloimmunization observed in patients from this group. This is partly due to the ethnic and racial specificity of RHD variants and the limited availability of Rh-matched blood donors. Approximately half a million African migrants in China carrying distinct Rh blood type composition have presented to the health care system with an imperative safety requirement of blood transfusion among 1.3 billion Chinese individuals. We depict the clinically significant RHD alleles among African migrants living in China and identify the genetic similarities and disparities to Chinese. We discussed practical strategies to manage the unique transfusion needs of African migrants in China.
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Affiliation(s)
- Qinan Yin
- School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, Henan, China
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14
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Ohto H, Albert Flegel W, Safic Stanic H. When should RhD-negative recipients be spared the transfusion of DEL red cells to avoid anti-D alloimmunization? Transfusion 2022; 62:2405-2408. [PMID: 36156264 PMCID: PMC9643616 DOI: 10.1111/trf.17122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Hitoshi Ohto
- Department of Mesenchymal Stem Cell Research, and Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Willy Albert Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Hana Safic Stanic
- Department of Immunohematology, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
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15
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Safic Stanic H, Dogic V, Bingulac-Popovic J, Kruhonja Galic Z, Stojic Vidovic M, Puljic K, Jukic I. RhD alloimmunization by DEL variant missed in donor testing. Transfusion 2022; 62:1084-1088. [PMID: 35318689 DOI: 10.1111/trf.16862] [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] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/13/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Exposure to normal or variably expressed RhD antigens in an antigen-negative individual can elicit an immune response and lead to the formation of clinically significant anti-D alloantibodies. We present the case of anti-D alloimmunization by DEL variant missed in routine blood donor screening. MATERIAL AND METHODS Blood donors were typed for D antigen using the direct serologic micromethod. Nonreactive samples were confirmed in the indirect antiglobulin method with an IgM/IgG anti-D monoclonal reagent. Genomic DNA was extracted using a commercial QIAamp DNA Blood Mini kit on the QIAcube device (Qiaqen, Germany). RHD genotyping was performed using the PCR-SSP genotyping kits- Ready Gene D weak, Ready Gene D weak screen, Ready Gene CDE, and Ready Gene D AddOn (Inno-Train, Germany). Unidentified alleles were sent for DNA genome sequencing. RESULTS After identifying DEL positive blood units in RhD negative blood donor pool, a look-back study was performed to determine if their previous donations caused alloimmunization in recipients. Out of 40 D negative recipients, one developed anti-D alloantibody after 45 days. The patient did not receive other RhD positive blood products. Blood donor typed D negative in direct and indirect agglutination method. RHD screening was positive, but RHD genotyping and DNA sequencing showed no mutation indicating the normal genotype. CONCLUSION Currently used methods in RHD genotyping are insufficient to identify many variant alleles, especially intronic variations. We suggest additional gene investigation including yet unexplored regions of regulation and intron regions to justify our serological finding.
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Affiliation(s)
- Hana Safic Stanic
- Department of Immunohematology, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Vesna Dogic
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Jasna Bingulac-Popovic
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Zrinka Kruhonja Galic
- Department of Immunohematology, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Miljana Stojic Vidovic
- Department for Blood donor testing, Croatian Institute of Transfusion Medicine, Zagreb, Croatia
| | - Kresimir Puljic
- Department for woman's psychotic disorders, University Psychiatric Hospital "Vrapče", Zagreb, Croatia
| | - Irena Jukic
- Medical Department, Croatian Institute of Transfusion Medicine, Zagreb, Croatia.,Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
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16
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Chen Q, Zhu J. DEL Selections Against a Soluble Protein Target. Methods Mol Biol 2022; 2541:155-164. [PMID: 36083554 DOI: 10.1007/978-1-0716-2545-3_19] [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] [Indexed: 06/15/2023]
Abstract
Affinity-based DNA-encoded library (DEL) selection is considered a powerful tool for small molecule drug discovery. Such selections are a multi-round process that involves incubation of a target protein with the DEL, capture of the protein and associated DEL compounds on a solid support, separation of bound molecules from the bulk DEL that is unbound, and recovery of bound DEL molecules. Each step is of great importance in order to achieve successful selections. Here we describe the selection process against a soluble target protein in both the immobilized and in-solution modes.
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17
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Ito S, Ohto H, Ogiyama Y, Irino M, Omokawa S, Shibasaki I, Ogasawara K, Uchikawa M, Nollet KE, Flegel WA. A practical and effective strategy in East Asia to prevent anti-D alloimmunization in patients by C/c phenotyping of serologic RhD-negative blood donors. EJHaem 2021; 2:750-756. [PMID: 35757680 PMCID: PMC9175983 DOI: 10.1002/jha2.292] [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] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Serologic RhD‐negative red cells can cause anti‐D alloimmunization if they carry the Asian‐type DEL or other DEL variants. RHD genotyping is a viable countermeasure if available, but inexpensive alternatives are worthy of consideration. RhD‐negative blood donors in Japan were studied by anti‐D adsorption‐elution and RHD genotyping. We collated published case reports of RhD‐negative red cell transfusions associated with inexplicable anti‐D immunization. Of 2754 serologic RhD‐negative donors, 378 were genotyped D/d. Anti‐D adsorption‐elution revealed 63.5% (240 of 378) to be DEL, of whom 96.7% (232 of 240) had the 1227G > A variant, diagnostic for the Asian‐type DEL. All 240 donors also carried at least one C antigen; none had a cc phenotype. The chance of transfusing DEL red cells to genuinely RhD‐negative Asian patients (based on a three‐unit transfusion) ranges from 16.7% in Korea to 69.4% in Taiwan, versus 0.6% in Germany. Among 22 RhD‐negative recipients of serologic RhD‐negative red cells, who produced new or increased anti‐D antibody titers, all 17 from East Asia were transfused with red cells with a C‐positive phenotype or known to be Asian‐type DEL or both. Serologic RhD‐negative East Asians with a cc phenotype can be red cell donors for RhD‐negative recipients, especially those of childbearing potential.
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Affiliation(s)
- Shoichi Ito
- Japanese Red Cross Tohoku Block Blood Center, Sendai, Japan
| | | | | | - Michiyo Irino
- Japanese Red Cross Tohoku Block Blood Center, Sendai, Japan
| | - Susumu Omokawa
- Japanese Red Cross Tohoku Block Blood Center, Sendai, Japan
| | | | | | - Makoto Uchikawa
- Japanese Red Cross Kanto-Koshinetsu Block Blood Center, Tokyo, Japan
| | - Kenneth E Nollet
- Department of Blood Transfusion and Transplantation Immunology Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Willy A Flegel
- National Institutes of Health NIH Clinical Center Department of Transfusion Medicine, Bethesda, Maryland, USA
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18
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Liu C, Xue Y, Ouchari M, Yin Q. Transfusion management of a Chinese pregnant woman with RHD* DEL1 allele. Transfus Clin Biol 2021; 28:293-295. [PMID: 33991666 DOI: 10.1016/j.tracli.2021.05.001] [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: 12/16/2020] [Revised: 04/25/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
We report the case of a 33-year-old pregnant Chinese woman who typed as Rh-negative in routine serology. Two injections of RhIG were given and two Rh-negative red cell units were sourced and put aside then returned with a reduced shelf life. RHD*DEL1 allele was determined in this woman by RHD genotyping two month later after delivery occasionally. In this representative case, a pregnant woman with RHD*DEL1 allele can safely be managed as Rh-positive, avoiding the unnecessary procurement of Rh-negative red cells and payment for RhIG injections. We analyzed the cost benefit of using RHD genotyping to guide transfusion management on the Chinese pregnant woman in Beijing where the average salary level is top-ranked in China. Considering the healthcare condition in China, we recommend molecular analysis of serologic Rh-negative early in pregnancy before the Rh-negative transfusion and administration of RhIG become unnecessarily required.
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Affiliation(s)
- Chunyan Liu
- Department of Obstetrics & Gynecology, China-Japan Friendship Hospital, 100029 Beijing, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, 471023 Luoyang, Henan, China
| | - Mouna Ouchari
- Department of Immunology, Columbia University, 10027 New York, USA
| | - Qinan Yin
- College of Medical Technology and Engineering, Henan University of Science and Technology, 471023 Luoyang, Henan, China.
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19
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Ede S, Schenk M, Bierer D, Weinmann H, Graham K. Improved Diazo-Transfer Reaction for DNA-Encoded Chemistry and Its Potential Application for Macrocyclic DEL-Libraries. Molecules 2021; 26:1790. [PMID: 33810133 DOI: 10.3390/molecules26061790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
DNA-encoded libraries (DEL) are increasingly being used to identify new starting points for medicinal chemistry in drug discovery. Herein, we discuss the development of methods that allow the conversion of both primary amines and anilines, attached to DNA, to their corresponding azides in excellent yields. The scope of these diazo-transfer reactions was investigated, and a proof-of-concept has been devised to allow for the synthesis of macrocycles on DNA.
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20
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Wang N, Fan Y, Zhou S, Shao L, Xia Y, Liu M. Genotyping of RHD c.1227G>A allele by melting curve analysis. Transfus Apher Sci 2021; 60:103078. [PMID: 33642156 DOI: 10.1016/j.transci.2021.103078] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND DEL is the weakest known D-positive phenotype and is detectable only by adsorption and elution tests. RHD c.1227G>A is an important marker for DEL phenotype in East Asians. The aim of this study was to develop a method for RHD c.1227G>A genotyping by single-tube PCR with melting curve analysis. METHODS Two GC-rich tails of different lengths were attached to the 5'-end of allele-specific primers for RHD 1227G and 1227A alleles, such that RHD c.1227G>A could be distinguished by the melting temperature. A total of 145 D-negative Chinese Han blood donors were genotyped for RHD c.1227G>A by melting curve analysis, conventional polymerase chain reaction with sequence-specific primers (PCR-SSP), and sequencing. RESULTS In 143 subjects (143/145, 98.6%), PCR-SSP and melting curve analysis produced consistent results with RHD exon 9 sequencings. Two samples were genotyped as RHD 1227G/A by PCR-SSP, but as RHD 1227A/A or A/- by melting curve analysis. These two samples were confirmed to be RHD 1227A/A or A/-. Based on RHD exon 9 sequencing, the accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the melting curve analysis for detecting both RHD 1227A and 1227G were all 100%. In contrast, the accuracy, specificity and positive predictive value of PCR-SSP for RHD 1227G detection were 98.62%, 98.21% and 94.29%, respectively, which were lower than those observed with the melting curve analysis. CONCLUSION Melting curve analysis for RHD c.1227G>A genotyping is a simple, rapid, and reliable method, superior to conventional PCR-SSP.
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Affiliation(s)
- Ni Wang
- Blood Group Research Laboratory, Dalian Blood Center, Dalian 116001, China
| | - Yaxin Fan
- Blood Group Research Laboratory, Dalian Blood Center, Dalian 116001, China.
| | - Shihang Zhou
- Blood Group Research Laboratory, Dalian Blood Center, Dalian 116001, China
| | - Linnan Shao
- Blood Group Research Laboratory, Dalian Blood Center, Dalian 116001, China
| | - Yuexin Xia
- Blood Group Research Laboratory, Dalian Blood Center, Dalian 116001, China
| | - Ming Liu
- Department of Cell Biology, Dalian Medical University, Dalian 116044, China.
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21
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Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H, Peakman MC. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS Discov 2021; 26:263-280. [PMID: 33412987 DOI: 10.1177/2472555220979589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Layered on top of this are the constraints of the drug-hunters themselves, including budgets, timelines, and available platform capacity; each of these can play a part in dictating the hit identification strategy for a discovery program. In this article, we discuss some of the factors that we use to govern our building of a hit identification roadmap for a program and describe the increasing role that DELs are playing in our discovery strategy. Furthermore, we share our learning during our initial exploration of DEL and highlight the approaches we have evolved to maximize the value returned from DEL selections. Topics addressed include the optimization of library design and production, reagent validation, data analysis, and hit confirmation. We describe how our thinking in these areas has led us to build a DEL platform that has begun to deliver tractable matter to our global discovery portfolio.
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Affiliation(s)
| | | | - Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Hongyao Zhu
- Simulation and Modelling Sciences, Pfizer Inc., Groton, CT, USA
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22
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Flajolet M, Nguyen TL, Siripuram VK, Sunkari YK. Paul Greengard: A persistent desire to comprehend the brain, and also to fix it. Adv Pharmacol 2021; 90:1-18. [PMID: 33706929 DOI: 10.1016/bs.apha.2020.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Paul Greengard's name is and will remain profoundly associated with Neuroscience, with brain signaling and chemical transmission, with Parkinson's and Alzheimer's diseases, with fundamental discoveries and solving paradoxes, but much less perhaps with drug discovery. This should not be mistaken as disdain. Paul in fact did contemplate developing therapeutic avenues to actually treat brain diseases much more than it is known, perhaps during his entire career, and certainly over the last two decades. As a matter of fact, he did more than contemplate it, he directly and indirectly contributed in the development of treatments for neurological diseases and disorders. Paul's impact on fundamental aspects of the brain has been so gargantuan that any other aspect of Paul's life will have difficulty to shine. It is precisely this less known aspect of Paul's career that will be covered in this review. We will discover how Paul very early on moved away from biophysics to avoid working on nuclear weapons and instead started his career in the pharmacological spheres of a large pharmaceutical company.
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23
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Zhang X, Li G, Zhou Z, Shao C, Huang X, Li L, Li X, Liu Y, Fan H, Li J. Molecular and computational analysis of 45 samples with a serologic weak D phenotype detected among 132,479 blood donors in northeast China. J Transl Med 2019; 17:393. [PMID: 31775789 PMCID: PMC6880393 DOI: 10.1186/s12967-019-02134-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/08/2019] [Accepted: 11/09/2019] [Indexed: 02/07/2023] Open
Abstract
Background RH1 is one of the most clinically important blood group antigens in the field of transfusion and in the prevention of fetal incompatibility. The molecular analysis and characterization of serologic weak D phenotypes is essential to ensuring transfusion safety. Methods Blood samples from a northeastern Chinese population were randomly screened for a serologic weak D phenotype. The nucleotide sequences of all 10 exons, adjacent flanking intronic regions, and partial 5′ and 3′ untranslated regions (UTRs) were detected for RHD genes. Predicted deleterious structural changes in missense mutations of serologicl weak D phenotypes were analyzed using SIFT, PROVEAN and PolyPhen2 software. The protein structure of serologic weak D phenotypes was predicted using Swiss-PdbViewer 4.0.1. Results A serologic weak D phenotype was found in 45 individuals (0.03%) among 132,479 blood donors. Seventeen distinct RHD mutation alleles were detected, with 11 weak D, four partial D and two DEL alleles. Further analyses resulted in the identification of two novel alleles (RHD weak D 1102A and 399C). The prediction of a three-dimensional structure showed that the protein conformation was disrupted in 16 serologic weak D phenotypes. Conclusions Two novel and 15 rare RHD alleles were identified. Weak D type 15, DVI Type 3, and RHD1227A were the most prevalent D variant alleles in a northeastern Chinese population. Although the frequencies of the D variant alleles presented herein were low, their phenotypic and genotypic descriptions add to the repertoire of reported RHD alleles. Bioinformatics analysis on RhD protein can give us more interpretation of missense variants of RHD gene.
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Affiliation(s)
- Xu Zhang
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Guiji Li
- Department of Hematology, The Forth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhuren Zhou
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Chaopeng Shao
- Department of Transfusion, the Second People's Hospital of Shenzhen, Shenzhen, China
| | - Xuying Huang
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Lichun Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Xiaofeng Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Ying Liu
- Institute of Transfusion Medicine, Harbin Blood Center, Harbin, Heilongjiang, China
| | - Hua Fan
- Department of Hematology, The Forth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Jianping Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China. .,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China. .,Institute of Transfusion Medicine, Harbin Blood Center, Harbin, Heilongjiang, China. .,Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.
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24
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Kim TY, Hong YJ, Kim MJ, Kim H, Kim TS, Park JS, Park KU, Han KS. Recommendations Regarding Practical DEL Typing Strategies for Serologically D-Negative Asian Donors. Transfus Med Hemother 2019; 47:88-93. [PMID: 32110199 DOI: 10.1159/000500098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/06/2018] [Accepted: 03/31/2019] [Indexed: 12/25/2022] Open
Abstract
Background DEL, the weakest D variant, is mistyped as D-negative by routine serological assays. Transfusion of red blood cells expressing the DEL phenotype has the potential to elicit anti-D alloimmunization in D-negative recipients. The goal of this study was to recommend DEL typing strategies for serologically D-negative Asian donors. Methods RhCE phenotyping and the adsorption-elution test were performed on 674 serologically D-negative samples. RHD genotyping using real-time polymerase chain reaction and melting curve analysis were also undertaken to identify DEL alleles. Costs and turnaround time of RhCE phenotyping, the adsorption-elution test, and RHD genotyping were estimated. Results Sensitivity and specificity of the adsorption-elution test for serologically D-negative samples were 94.9% (93/98) and 91.5% (527/576), respectively. C+ phenotypes were detected in all 98 samples with DEL alleles. Despite comparable costs, RHD genotyping was more accurate and rapid than the adsorption-elution test. Conclusions Two practical DEL typing strategies using RhCE phenotyping as an initial screening method were recommended for serologically D-negative Asian donors. Compared with DEL typing using RHD genotyping, serological DEL typing using adsorption-elution test is predicted to increase the incidence of anti-D alloimmunization and decrease the D-negative donor pool without having any cost-competitiveness but can be used in laboratories where molecular methods are not applicable.
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Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Mi Jung Kim
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyungsuk Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jeong Su Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Kyou-Sup Han
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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25
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Zhu Z, Grady LC, Ding Y, Lind KE, Davie CP, Phelps CB, Evindar G. Development of a Selection Method for Discovering Irreversible (Covalent) Binders from a DNA-Encoded Library. SLAS Discov 2019; 24:169-174. [PMID: 30383465 PMCID: PMC7221453 DOI: 10.1177/2472555218808454] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/12/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
Abstract
DNA-encoded libraries (DELs) have been broadly applied to identify chemical probes for target validation and lead discovery. To date, the main application of the DEL platform has been the identification of reversible ligands using multiple rounds of affinity selection. Irreversible (covalent) inhibition offers a unique mechanism of action for drug discovery research. In this study, we report a developing method of identifying irreversible (covalent) ligands from DELs. The new method was validated by using 3C protease (3CP) and on-DNA irreversible tool compounds (rupintrivir derivatives) spiked into a library at the same concentration as individual members of that library. After affinity selections against 3CP, the irreversible tool compounds were specifically enriched compared with the library members. In addition, we compared two immobilization methods and concluded that microscale columns packed with the appropriate affinity resin gave higher tool compound recovery than magnetic beads.
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Affiliation(s)
| | | | - Yun Ding
- GlaxoSmithKline, Cambridge,
Massachusetts, USA
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26
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Abstract
Diffuse large B-cell lymphoma (DLBCL) is one of the most common causes of non-Hodgkin’s lymphoma (NHL). Some of these DLBCLs can have genetic mutations as well as protein overexpression. The genes involved are MYC, BCL-2 and BCL-6. These are very aggressive and do not respond well to standard chemotherapy regiment. Lymphomas usually show classic signs and symptoms but rarely can present with little or no symptoms or even mimic other disease processes. Here we will present a case where a spinal lymphoma mimicked a hematoma and the patient developed signs and symptoms only after mechanical fall and hitting his back.
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Affiliation(s)
- Muhammad Mufti
- Department of Medicine, St. Mary Medical Center, Long Beach, CA, USA
| | - Khalid Nawab
- Department of Medicine, Geisinger Holy Spirit Hospital, Camp Hill, PA, USA
| | - Rabia Mohammad
- Department of Medicine, Coney Island Hospital, Brooklyn, NY, USA
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27
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Satz AL. Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fi delity on Interpretation of Structure-Activity Relationships. ACS Comb Sci 2016; 18:415-24. [PMID: 27116029 DOI: 10.1021/acscombsci.6b00001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure-activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.
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Affiliation(s)
- Alexander L. Satz
- Roche Innovation Center Basel, Grenzacherstrasse
124, 4070 Basel, Switzerland
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28
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Abstract
Serological assays for the RhD blood group are based on detection of the RhD antigen on human red blood cells using a specific anti-D antibody. The weak expression of the RhD antigen in the DEL variant hinders the sensitivity of conventional serological assays. Evidence of anti-D immunization in patients with D-negativity who have received DEL-variant blood units has been reported in various populations. This observation has prompted the need for genetic epidemiological and clinical data on the DEL variant in the development of DEL molecular diagnostic testing. This review highlights the molecular features of the DEL variant, the clinical consequences of DEL-blood transfusion, and current approaches for detection of the DEL-variant for donor screening and transfusion.
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Affiliation(s)
- Pornlada Nuchnoi
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand Center for Innovation Development and Technology Transfer, Mahidol University, Bangkok, Thailand
| | - Jairak Thongbus
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand National Blood Center, Thai Red Cross Society, Bangkok, Thailand
| | - Apapan Srisarin
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
| | - Usanee Kerdpin
- Department of Chemistry, Naresuan University, Phitsanulok, Thailand
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29
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Abstract
SUMMARY RHD PCR of blood donors may be used to reveal weak D, partial D, DEL and chimeric D+/D- donors among presumed D-negative blood donors. Units donated by such donors pose a definite yet low risk for anti-D immunization of transfusion recipients. The frequency of DEL donors among D-negative donors is 1:350 to 1:2,000 in Europe and up to 1:5 in Asian countries. Different strategies for RHD PCR of blood donors have been used. Probably, the most cost-efficient implementation is replacement of sensitive D antigen testing with the indirect antiglobulin test by RHD PCR in pools which might even reduce total testing cost.
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