In Silico Analysis of a Highly Mutated Gene in Cancer Provides Insight into Abnormal mRNA Splicing: Splicing Factor 3B Subunit 1K700E Mutant

Structural screening and molecular simulation identify potential ligands against the K700E hot spot variant and functional pockets of SF3B1 to modulate splicing in myelodysplastic syndrome

Myelodysplastic syndrome (MDS), a blood disorder with ineffective hematopoiesis and risk of transformation to acute myeloid leukemia, is characterized by recurring cytogenetic and molecular alterations. By chromosome analysis, approximately 60% of patients, carry chromosome 5 and 7 alterations, trisomy of chromosome 8 and may also present with increasingly complex karyotypes, especially in higher grade MDS (MDS with refractory anemia and increased blasts type 1 and 2). Moreover, somatic pathogenic variants in genes associated with aberrant mRNA splicing are frequently mutated with SF3B1 the most frequently mutated. In the setting of SF3B1, the K700E hot-spot mutation is present in approximately 50% of cases. Since recent studies have highlighted modulation of functional dynamics in SF3B1 by mutant splicing factors, the objective of the study was to identify potential small molecule modulators against the frequently mutated RNA splicing factor SF3B1(K700E) and functional allosteric sites by using a molecular structure-based approach and a molecular dynamic simulation. To identify potential SF3B1 modulators, we collected a series of chemical compounds from the Zinc and Enamine database. An initial screen followed by further molecular analysis and simulation using the Schrödinger suite was performed. Parameters used to monitor the stability and binding of the protein-ligand complex included: RMSF, protein-ligand contacts, electrostatic, Van Der Waals forces and binding energies (MMGBSA). A 100-nanosecond simulation showed strong binding between selected compounds and key amino acid residues, including the mutation hot-spot K700E and functional allosteric amino acid residue R630. Ligand binding energies between compounds and key amino acid residues ranged from -50.67 to -58.04 kcal/mol. In brief, small molecule modulators show strong binding to SF3B1 suggesting these compounds may be used against cells harboring the K700E variant or to modulate splicing by targeting functional allosteric sites.

Role of computational and structural biology in the development of small-molecule modulators of the spliceosome

INTRODUCTION

RNA splicing is a pivotal step of eukaryotic gene expression during which the introns are excised from the precursor (pre-)RNA and the exons are joined together to form mature RNA products (i.e a protein-coding mRNA or long non-coding (lnc)RNAs). The spliceosome, a complex ribonucleoprotein machine, performs pre-RNA splicing with extreme precision. Deregulated splicing is linked to cancer, genetic, and neurodegenerative diseases. Hence, the discovery of small-molecules targeting core spliceosome components represents an appealing therapeutic opportunity.

AREA COVERED

Several atomic-level structures of the spliceosome and distinct splicing-modulators bound to its protein/RNA components have been solved. Here, we review recent advances in the discovery of small-molecule splicing-modulators, discuss opportunities and challenges for their therapeutic applicability, and showcase how structural data and/or all-atom simulations can illuminate key facets of their mechanism, thus contributing to future drug-discovery campaigns.

EXPERT OPINION

This review highlights the potential of modulating pre-RNA splicing with small-molecules, and anticipates how the synergy of computer and wet-lab experiments will enrich our understanding of splicing regulation/deregulation mechanisms. This information will aid future structure-based drug-discovery efforts aimed to expand the currently limited portfolio of selective splicing-modulators.

Atomic-Level Mechanism of Pre-mRNA Splicing in Health and Disease

Intron removal from premature-mRNA (pre-mRNA splicing) is an essential part of gene expression and regulation that is required for the production of mature, protein-coding mRNA. The spliceosome (SPL), a majestic machine composed of five small nuclear RNAs and hundreds of proteins, behaves as an eminent transcriptome tailor, efficiently performing splicing as a protein-directed metallo-ribozyme. To select and excise long and diverse intronic sequences with single-nucleotide precision, the SPL undergoes a continuous compositional and conformational remodeling, forming eight distinct complexes throughout each splicing cycle. Splicing fidelity is of paramount importance to preserve the integrity of the proteome. Mutations in splicing factors can severely compromise the accuracy of this machinery, leading to aberrant splicing and altered gene expression. Decades of biochemical and genetic studies have provided insights into the SPL's composition and function, but its complexity and plasticity have prevented an in-depth mechanistic understanding. Single-particle cryogenic electron microscopy techniques have ushered in a new era for comprehending eukaryotic gene regulation, providing several near-atomic resolution structures of the SPL from yeast and humans. Nevertheless, these structures represent isolated snapshots of the splicing process and are insufficient to exhaustively assess the function of each SPL component and to unravel particular facets of the splicing mechanism in a dynamic environment.In this Account, building upon our contributions in this field, we discuss the role of biomolecular simulations in uncovering the mechanistic intricacies of eukaryotic splicing in health and disease. Specifically, we showcase previous applications to illustrate the role of atomic-level simulations in elucidating the function of specific proteins involved in the architectural reorganization of the SPL along the splicing cycle. Moreover, molecular dynamics applications have uniquely contributed to decrypting the channels of communication required for critical functional transitions of the SPL assemblies. They have also shed light on the role of carcinogenic mutations in the faithful selection of key intronic regions and the molecular mechanism of splicing modulators. Additionally, we emphasize the role of quantum-classical molecular dynamics in unraveling the chemical details of pre-mRNA cleavage in the SPL and in its evolutionary ancestors, group II intron ribozymes. We discuss methodological pitfalls of multiscale calculations currently used to dissect the splicing mechanism, presenting future challenges in this field. The results highlight how atomic-level simulations can enrich the interpretation of experimental results. We envision that the synergy between computational and experimental approaches will aid in developing innovative therapeutic strategies and revolutionary gene modulation tools to fight the over 200 human diseases associated with splicing misregulation, including cancer and neurodegeneration.

The biological function and clinical significance of SF3B1 mutations in cancer

Spliceosome mutations have become the most interesting mutations detected in human cancer in recent years. The spliceosome, a large, dynamic multimegadalton small nuclear ribonucleoprotein composed of small nuclear RNAs associated with proteins, is responsible for removing introns from precursor mRNA (premRNA) and generating mature, spliced mRNAs. SF3B1 is the largest subunit of the spliceosome factor 3b (SF3B) complex, which is a core component of spliceosomes. Recurrent somatic mutations in SF3B1 have been detected in human cancers, including hematological malignancies and solid tumors, and indicated to be related to patient prognosis. This review summarizes the research progress of SF3B1 mutations in cancer, including SF3B1 mutations in the HEAT domain, the multiple roles and aberrant splicing events of SF3B1 mutations in the pathogenesis of tumors, and changes in mutated cancer cells regarding sensitivity to SF3B small-molecule inhibitors. In addition, the potential of SF3B1 or its mutations to serve as biomarkers or therapeutic targets in cancer is discussed. The accumulated knowledge about SF3B1 mutations in cancer provides critical insight into the integral role the SF3B1 protein plays in mRNA splicing and suggests new targets for anticancer therapy.