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Galamba N. Sickle Cell Hemoglobin "Drugged" with Cyclic Peptides Is Aggregation Incompetent. J Phys Chem B 2024; 128:8662-8671. [PMID: 39205400 PMCID: PMC11403655 DOI: 10.1021/acs.jpcb.4c03805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sickle cell disease (SCD) is a monogenic blood disorder associated with a mutation in the hemoglobin subunit β gene encoding for the β-globin of normal adult hemoglobin (HbA). This mutation transcribes into a Glu-β6 → Val-β6 substitution in the β-globins, inducing the polymerization of this hemoglobin form (HbS) when in the T-state. Despite advances in stem cell and gene therapy, and the recent approval of a new antisickling drug, therapeutic limitations persist. Herein, we demonstrate through molecular dynamics and umbrella sampling, that (unrestrained) blockage of the hydrophobic pocket involved in the lateral contact of the HbS fibers by 5-mer cyclic peptides, recently proposed as SCD aggregation inhibitors (Neto, V.; J. Med. Chem. 2023, 66, 16062-16074), is enough to turn the dimerization of HbS thermodynamically unfavorable. Among these potential drugs, some exhibit an estimated pocket abandonment probability of around 15-20% within the simulations' time frame, and an impressive specificity toward the mutated Val-β6. Additionally, we show that the dimerization can be thermodynamically unfavored by blocking a nearby region while the pocket remains vacant. These results are compared with curcumin, an antisickling molecule and a pan-assay interference compound, with a good binding affinity for different proteins and protein domains. Our results confirm the potential of some of these cyclic peptides as antisickling drug candidates to reduce the concentration of aggregation-competent HbS.
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Affiliation(s)
- N Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande, 1749-016 Lisboa, Portugal
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Kerwash E, Sajic M, Rantell KR, McBlane JW, Johnston JD, Niewiarowska A, Butler AS, Cole S. Regulatory Assessment of Casgevy for the Treatment of Transfusion-Dependent β-Thalassemia and Sickle Cell Disease with Recurrent Vaso-Occlusive Crises. Curr Issues Mol Biol 2024; 46:8209-8225. [PMID: 39194702 DOI: 10.3390/cimb46080485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/23/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024] Open
Abstract
Sickle cell disease (SCD) and transfusion-dependent β-thalassemia (TDT) are hereditary haemoglobinopathies characterized by a reduction in functional β-globin chains. Both conditions cause tiredness and increase susceptibility to infection, which can lead organ failure, significantly reducing life expectancy and typically requiring those affected to undergo regular erythrocyte transfusion. Recently, a novel therapeutic treatment for SCD and TDT was approved by the UK regulatory body (Medicines and Healthcare products Regulatory Agency; MHRA). Exagamglogene autotemcel (Casgevy) is the first licensed therapy globally to utilize CRIPSR/Cas9 technology and induces an increase in expression of γ-globin chains to compensate for the reduction in functional β-globin. Casgevy represents a first-in-class therapeutic, and numerous considerations were made by the MHRA throughout its assessment of the medicine. These include, but are not limited to, the risk of tumorigenicity and off-target editing, a limited cohort size, the validity of proposed dosing and the conduction of only single-arm studies. The MHRA's analyses of the data to support the proposed indications are presented and discussed throughout this manuscript. Overall, the sponsors claims were considered well supported by their data, and Casgevy was licensed for the treatment of TDT or SCD in patients 12 years of age and older for whom hematopoietic stem cell (HSC) transplantation is appropriate, but a human leukocyte antigen-matched related HSC donor is not available.
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Affiliation(s)
- Essam Kerwash
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - Marija Sajic
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - Khadija Rerhou Rantell
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - James W McBlane
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - John D Johnston
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - Alison Niewiarowska
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - Andrew S Butler
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
| | - Susan Cole
- Medicines and Healthcare Products Regulatory Agency (MHRA), 10 South Colonnade, London E14 4PU, UK
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Kuczynski CE, Porada CD, Atala A, Cho SS, Almeida-Porada G. Evaluating sheep hemoglobins with MD simulations as an animal model for sickle cell disease. Sci Rep 2024; 14:276. [PMID: 38168584 PMCID: PMC10761887 DOI: 10.1038/s41598-023-50707-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/23/2023] [Indexed: 01/05/2024] Open
Abstract
Sickle cell disease (SCD) affects millions worldwide, yet there are few therapeutic options. To develop effective treatments, preclinical models that recapitulate human physiology and SCD pathophysiology are needed. SCD arises from a single Glu-to-Val substitution at position 6 in the β subunit of hemoglobin (Hb), promoting Hb polymerization and subsequent disease. Sheep share important physiological and developmental characteristics with humans, including the same developmental pattern of fetal to adult Hb switching. Herein, we investigated whether introducing the SCD mutation into the sheep β-globin locus would recapitulate SCD's complex pathophysiology by generating high quality SWISS-MODEL sheep Hb structures and performing MD simulations of normal/sickle human (huHbA/huHbS) and sheep (shHbB/shHbS) Hb, establishing how accurately shHbS mimics huHbS behavior. shHbS, like huHbS, remained stable with low RMSD, while huHbA and shHbB had higher and fluctuating RMSD. shHbB and shHbS also behaved identically to huHbA and huHbS with respect to β2-Glu6 and β1-Asp73 (β1-Asn72 in sheep) solvent interactions. These data demonstrate that introducing the single SCD-causing Glu-to-Val substitution into sheep β-globin causes alterations consistent with the Hb polymerization that drives RBC sickling, supporting the development of a SCD sheep model to pave the way for alternative cures for this debilitating, globally impactful disease.
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Affiliation(s)
| | | | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Winston-Salem, NC, 27101, USA
| | - Samuel S Cho
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27109, USA.
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, 27109, USA.
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Neto V, Victor BL, Galamba N. Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease. J Med Chem 2023; 66:16062-16074. [PMID: 37988411 DOI: 10.1021/acs.jmedchem.3c01484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Sickle cell disease is a missense genetic disorder characterized by the aggregation of deoxy-HbS into helical fibers that distort erythrocytes into a sickle-like shape. Herein, we investigate, through molecular dynamics, the effect of nine 5-mer cyclic peptides (CPs), tailor-designed to block key lateral contacts of the fibers. Our results show that the CPs bind orthogonally to the main HbS pocket involved in the latter contacts, with some revealing exceedingly long residence times. These CPs display moderate to high specificity, exhibiting molecular recognition events even at a HbS/CP (1:1) ratio. A much lower HbS-CP binding free energy, longer residence times, and higher specificity are also found relative to a previously reported CP with modest in vitro antisickling activity. These results indicate that some of these CPs have the potential to reduce the concentration of aggregation-competent deoxy-HbS, precluding or delaying the formation of lateral contact at the homogeneous nucleation stage.
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Affiliation(s)
- Vasco Neto
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Bruno Lourenço Victor
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Nuno Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
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Olagunju MO, Loschwitz J, Olubiyi OO, Strodel B. Multiscale
MD
simulations of wild‐type and sickle hemoglobin aggregation. Proteins 2022; 90:1811-1824. [DOI: 10.1002/prot.26352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/02/2022] [Accepted: 04/20/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Maryam O. Olagunju
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf Düsseldorf Germany
| | - Olujide O. Olubiyi
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy Afe Babalola University Ado‐Ekiti Nigeria
- Institute of Drug Research and Development, Bogoro Centre Afe Babalola University Ado‐Ekiti Nigeria
| | - Birgit Strodel
- Institute of Biological Information Processing Structural Biochemistry, Forschungszentrum Jülich Jülich Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf Düsseldorf Germany
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Maity D, Pal D. Molecular Dynamics of Hemoglobin Reveals Structural Alterations and Explains the Interactions Driving Sickle Cell Fibrillation. J Phys Chem B 2021; 125:9921-9933. [PMID: 34459602 DOI: 10.1021/acs.jpcb.1c01684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In sickle cell anemia, deoxyhemoglobin deforms RBCs by forming fibrils inside that disintegrate on oxygenation. We studied 100 ns long all-atom molecular dynamics (MD) for sickle and normal hemoglobin fibril models to understand this process, complemented by multiple 1 μs MD for a single tetramer of sickle and normal hemoglobin in deoxy and oxy states. We find that the presence of hydrophobic residues without a bulky side chain at β-6 in hemoglobin is the reason for the stability of the fibrils. Moreover, the free energy landscapes from MD of hemoglobin starting in the tensed (T) state capture the putative transition from T to relaxed (R) state, associated with oxygen binding. The three conformational wells in the landscapes are characterized by the quaternary changes where one αβ dimer rotates with respect to the other. The conformational changes from the oxygenation of sickle hemoglobin hinder the intermolecular contacts necessary for fibril formation.
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Affiliation(s)
- Dibyajyoti Maity
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India
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