Publications by authors named "Nesr G"

Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce targeted recognition of antigen-MHC complex reporter for MHC I (TRACeR-I), a generalizable platform for targeting peptides on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming the cross-reactivity challenges of TCRs. Our TRACeR-MHC I co-crystal structure reveals a unique antigen recognition mechanism, with TRACeR forming extensive contacts across the entire peptide length to confer single-residue specificity at the accessible positions.

View Article and Find Full Text PDF

High-dose melphalan followed by stem cell rescue is the standard consolidative therapy for transplant-eligible patients with multiple myeloma (MM) in the United Kingdom. A melphalan dose of 200 mg/m (Mel200) is considered the "gold standard" for autologous stem cell transplant (ASCT) conditioning for fit patients ≤70 years old; however, with a peak diagnosis incidence at 80-89 years old in the UK dose adjustments will be inevitable to limit toxicities. In this single-centre UK-based retrospective analysis, data was collected from patients with plasma cell dyscrasias who underwent a first reduced-intensity, Mel140, ASCT from 2006 to 2019, a total of 81 patients.

View Article and Find Full Text PDF
Article Synopsis
  • Proteins perform their functions through chemical interactions, making it essential to model these interactions for protein design, especially focusing on sidechains.
  • The authors introduce Protpardelle, an all-atom diffusion model that represents all sidechain states as a "superposition" state, allowing for efficient sample generation of protein structures.
  • This model effectively combines structure and sequence design, producing high-quality proteins that mimic the properties of natural proteins, and has potential applications in designing proteins without relying on traditional backbone and rotamer frameworks.
View Article and Find Full Text PDF

The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite.

View Article and Find Full Text PDF

Advancements in the management of patients with chronic myeloid leukemia (CML) allowed them to achieve survival comparable with their healthy counterparts. Consequently, their care has widened with growing focus on quality of life, including parenting children. Although tyrosine kinase inhibitors (TKI) are contraindicated in pregnancy given their teratogenic effect, their effect on male fertility is less clear with contradictory results from animal studies and case reports/series.

View Article and Find Full Text PDF

Proteins mediate their functions through chemical interactions; modeling these interactions, which are typically through sidechains, is an important need in protein design. However, constructing an all-atom generative model requires an appropriate scheme for managing the jointly continuous and discrete nature of proteins encoded in the structure and sequence. We describe an all-atom diffusion model of protein structure, Protpardelle, which instantiates a "superposition" over the possible sidechain states, and collapses it to conduct reverse diffusion for sample generation.

View Article and Find Full Text PDF

High dose melphalan (HDM) followed by autologous stem cell transplantation (ASCT) remains the standard consolidation in transplant eligible multiple myeloma (MM) patients. The timing between HDM administration and hematopoietic stem cell return (HSCR) varies among institutions, with a 'rest period' of 48 hours (h) employed by some for patients with renal impairment (RI). We investigated the differences in hematopoietic recovery and HDM toxicity between MM patients with RI who had HSCR after 24 vs 48 h from HDM.

View Article and Find Full Text PDF
Article Synopsis
  • SVD is a powerful method for analyzing multiple sequence alignments (MSAs) that helps identify sequence subgroups and extract important features related to structure and function.
  • SVD can be made more accessible by explaining its mathematics intuitively, as demonstrated through a simplified model that shows how sequence conservation and covariance affect alignment features.
  • The study applies SVD to two protein families, revealing sequence clustering and providing Python scripts for users to conduct their own SVD analyses on MSAs, which are available for free on GitHub.
View Article and Find Full Text PDF

Targeted therapy for chronic myeloid leukaemia (CML) has allowed for a near-normal patient life-expectancy; however, quality of life and aggravation of existing co-morbidities have posed new treatment challenges. In clinical practice, TKI dose reduction occurs frequently, often on multiple occasions, because of intolerance. We conducted a retrospective 'real-world practice' review of 246 patients receiving lower than standard dose (LD) TKI after the achievement of major molecular response (MR3), because of intolerable adverse events.

View Article and Find Full Text PDF

The majority of patients with newly diagnosed chronic myeloid leukemia (CML) will enjoy a life expectancy equivalent to that of unaffected individuals, but will remain on life-long treatment with a concomitant requirement for on-going hospital interactions for molecular monitoring and drug dispensing. In order to determine more accurately the frequency of monitoring required, we performed a 'real-life' retrospective single-center cohort study of 450 patients with CML in at least major molecular remission (MR3) to analyze the risk of loss of MR3 [defined as at least 2 consecutive real-time quantitative polymerase chain reaction (RT-qPCR) results >0.1% International Scale (IS)].

View Article and Find Full Text PDF