Sequence-structure functional implications and molecular simulation of high deleterious nonsynonymous substitutions in IDH1 revealed the mechanism of drug resistance in glioma

Understanding the IDH1 missense SNPs on expression of genes involved in Glioblastoma multiforme

The IDH1 gene encodes isocitrate dehydrogenase 1 enzyme (IDH1), crucial in the citric acid cycle that converts isocitrate to alpha-ketoglutarate. Mutations in IDH1 at R132 lead to the production of the oncometabolite 2-hydroxyglutarate, which impacts cellular metabolism, differentiation, and epigenetic regulation, and is associated with GBM. This study utilized in silico methods (SIFT, PROVEAN, PolyPhen2, Predict SNP, MutPred2, InterPro, MusiteDeep, I-Mutant 3.0, MUpro, and INSP-MD) to identify high-risk missense SNPs in IDH1, located in highly conserved regions and overlapping with protein-ligand and PTM sites and assessed their impact on the structure and function of IDH1 protein. A total of 12 high-risk missense SNPs were found at T77, N96, S94, and K260 leading to the gain or loss of catalytic and allosteric sites, alteration in the metal binding site, as well as the gain or loss of PTMs such as acetylation, methylation, N-linked glycosylation, and ubiquitylation at different residues within the active sites of mutated IDH1 enzymes. These changes may significantly impact the structure and function of the IDH1 protein. Furthermore, GEPIA and survival analysis were performed to evaluate IDH1 expression in GBM and LGG and survival outcomes. GEPIA analysis showed significant (p < 0.05) upregulation of IDH1 expression in GBM and LGG. Survival analysis indicated that GBM patients with low IDH1 expression group had better survival outcomes, while LGG patients with low IDH1 expression group showed poorer survival rates. Overall, this study highlights the diagnostic and prognostic potential biomarker of IDH1 in glioblastoma. However, additional in vitro and in vivo studies will be valuable in confirming the role of IDH1 proteins in GBM.

Screening of medicinal phytocompounds with structure-based approaches to target key hotspot residues in tyrosyl-DNA phosphodiesterase 1: augmenting sensitivity of cancer cells to topoisomerase I inhibitors

One of cancer's well-known hallmarks is DNA damage, yet it's intriguing that DNA damage has been explored as a therapeutic strategy against cancer. Tyrosyl-DNA phosphodiesterase 1, involved in DNA repair from topoisomerase I inhibitors, a chemotherapy class for cancer treatment. Inhibiting TDP1 can increase unresolved Top1 cleavage complexes in cancer cells, inducing DNA damage and cell death. TDP1's catalytic activity depends on His263 and His493 residues. Using molecular simulation, structure-based drug design, and free energy calculation, we identified potential drugs against TDP1. A multi-step screening of medicinal plant compound databases (North Africa, East Africa, Northeast Africa, and South Africa) identified the top four candidates. Docking scores for top hits 1-4 were -7.76, -7.37, -7.35, and -7.24 kcal/mol. Top hit 3 exhibited the highest potency, forming a strong bonding network with both His263 and His493 residues. All-atoms simulations showed consistent dynamics for top hits 1-4, indicating stability and potential for efficient interaction with interface residues. Minimal fluctuations in residue flexibility suggest these compounds can stabilize internal flexibility upon binding. The binding free energies of -35.11, -36.70, -31.38, and -23.85 kcal/mol were calculated for the top hit 1-4 complexes. Furthermore, the chosen compounds demonstrate outstanding ADMET characteristics, such as excellent water solubility, effective gastrointestinal absorption, and the absence of hepatotoxicity. Cytotoxicity analysis revealed top hit 2 higher probability of activity against 24 cancer cell lines. Our findings suggest that these compounds (top hits 1-4) hold promise for innovative drug therapies, suitable for both in vivo and in vitro experiments.

Analysis of E2F1 single-nucleotide polymorphisms reveals deleterious non-synonymous substitutions that disrupt E2F1-RB protein interaction in cancer

Cancer is a medical condition that is caused by the abnormal growth and division of cells, leading to the formation of tumors. The E2F1 and RB pathways are critical in regulating cell cycle, and their dysregulation can contribute to the development of cancer. In this study, we analyzed experimentally reported SNPs in E2F1 and assessed their effects on the binding affinity with RB. Out of 46, nine mutations were predicted as deleterious, and further analysis revealed four highly destabilizing mutations (L206W, R232C, I254T, A267T) that significantly altered the protein structure. Molecular docking of wild-type and mutant E2F1 with RB revealed a docking score of -242 kcal/mol for wild-type, while the mutant complexes had scores ranging from -217 to -220 kcal/mol. Molecular simulation analysis revealed variations in the dynamics features of both mutant and wild-type complexes due to the acquired mutations. Furthermore, the total binding free energy for the wild-type E2F1-RB complex was -64.89 kcal/mol, while those of the L206W, R232C, I254T, and A267T E2F1-RB mutants were -45.90 kcal/mol, -53.52 kcal/mol, -55.67 kcal/mol, and -61.22 kcal/mol, respectively. Our study is the first to extensively analyze E2F1 gene mutations and identifies candidate mutations for further validation and potential targeting for cancer therapeutics.

Elucidating the binding mechanism of SARS-CoV-2 NSP6-TBK1 and structure-based designing of phytocompounds inhibitors for instigating the host immune response

SARS-CoV-2, also referred to as severe acute respiratory syndrome coronavirus 2, is the virus responsible for causing COVID-19, an infectious disease that emerged in Wuhan, China, in December 2019. Among its crucial functions, NSP6 plays a vital role in evading the human immune system by directly interacting with a receptor called TANK-binding kinase (TBK1), leading to the suppression of IFNβ production. Consequently, in the present study we used the structural and biophysical approaches to analyze the effect of newly emerged mutations on the binding of NSP6 and TBK1. Among the identified mutations, four (F35G, L37F, L125F, and I162T) were found to significantly destabilize the structure of NSP6. Furthermore, the molecular docking analysis highlighted that the mutant NSP6 displayed its highest binding affinity with TBK1, exhibiting docking scores of -1436.2 for the wildtype and -1723.2, -1788.6, -1510.2, and -1551.7 for the F35G, L37F, L125F, and I162T mutants, respectively. This suggests the potential for an enhanced immune system evasion capability of NSP6. Particularly, the F35G mutation exhibited the strongest binding affinity, supported by a calculated binding free energy of -172.19 kcal/mol. To disrupt the binding between NSP6 and TBK1, we conducted virtual drug screening to develop a novel inhibitor derived from natural products. From this screening, we identified the top 5 hit compounds as the most promising candidates with a docking score of -6.59 kcal/mol, -6.52 kcal/mol, -6.32 kcal/mol, -6.22 kcal/mol, and -6.21 kcal/mol. The molecular dynamic simulation of top 3 hits further verified the dynamic stability of drugs-NSP6 complexes. In conclusion, this study provides valuable insight into the higher infectivity of the SARS-CoV-2 new variants and a strong rationale for the development of novel drugs against NSP6.

Mutational analysis of SARS-CoV-2 ORF6-KPNA2 binding interface and identification of potent small molecule inhibitors to recuse the host immune system

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surfaced on 31 December, 2019, and was identified as the causative agent of the global COVID-19 pandemic, leading to a pneumonia-like disease. One of its accessory proteins, ORF6, has been found to play a critical role in immune evasion by interacting with KPNA2 to antagonize IFN signaling and production pathways, resulting in the inhibition of IRF3 and STAT1 nuclear translocation. Since various mutations have been observed in ORF6, therefore, a comparative binding, biophysical, and structural analysis was used to reveal how these mutations affect the virus's ability to evade the human immune system. Among the identified mutations, the V9F, V24A, W27L, and I33T, were found to have a highly destabilizing effect on the protein structure of ORF6. Additionally, the molecular docking analysis of wildtype and mutant ORF6 and KPNA2 revealed the docking score of - 53.72 kcal/mol for wildtype while, -267.90 kcal/mol, -258.41kcal/mol, -254.51 kcal/mol and -268.79 kcal/mol for V9F, V24A, W27L, and I33T respectively. As compared to the wildtype the V9F showed a stronger binding affinity with KPNA2 which is further verified by the binding free energy (-42.28 kcal/mol) calculation. Furthermore, to halt the binding interface of the ORF6-KPNA2 complex, we used a computational molecular search of potential natural products. A multi-step virtual screening of the African natural database identified the top 5 compounds with best docking scores of -6.40 kcal/mol, -6.10 kcal/mol, -6.09 kcal/mol, -6.06 kcal/mol, and -6.03 kcal/mol for tophit1-5 respectively. Subsequent all-atoms simulations of these top hits revealed consistent dynamics, indicating their stability and their potential to interact effectively with the interface residues. In conclusion, our study represents the first attempt to establish a foundation for understanding the heightened infectivity of new SARS-CoV-2 variants and provides a strong impetus for the development of novel drugs against them.

Challenges for the development of mutant isocitrate dehydrogenases 1 inhibitors to treat glioma

Glioma is one of the most common types of brain tumors, and its high recurrence and mortality rates threaten human health. In 2008, the frequent isocitrate dehydrogenase 1 (IDH1) mutations in glioma were reported, which brought a new strategy in the treatment of this challenging disease. In this perspective, we first discuss the possible gliomagenesis after IDH1 mutations (mIDH1). Subsequently, we systematically investigate the reported mIDH1 inhibitors and present a comparative analysis of the ligand-binding pocket in mIDH1. Additionally, we also discuss the binding features and physicochemical properties of different mIDH1 inhibitors to facilitate the future development of mIDH1 inhibitors. Finally, we discuss the possible selectivity features of mIDH1 inhibitors against WT-IDH1 and IDH2 by combining protein-based and ligand-based information. We hope that this perspective can inspire the development of mIDH1 inhibitors and bring potent mIDH1 inhibitors for the treatment of glioma.

Comparative mutational analysis of the Zika virus genome from different geographical locations and its effect on the efficacy of Zika virus-specific neutralizing antibodies

The Zika virus (ZIKV), which originated in Africa, has become a significant global health threat. It is an RNA virus that continues to mutate and accumulate multiple mutations in its genome. These genetic changes can impact the virus's ability to infect, cause disease, spread, evade the immune system, and drug resistance. In this study genome-wide analysis of 175 ZIKV isolates deposited at the National Center for Biotechnology Information (NCBI), was carried out. The comprehensive mutational analysis of these isolates was carried out by DNASTAR and Clustal W software, which revealed 257 different substitutions at the proteome level in different proteins when compared to the reference sequence (KX369547.1). The substitutions were capsid (17/257), preM (17/257), envelope (44/257), NS1 (34/257), NS2A (30/257), NS2B (11/257), NS3 (37/257), NS4A (6/257), 2K (1/257), NS4B (15/257), and NS5 (56/257). Based on the coexisting mutational analysis, the MN025403.1 isolate from Guinea was identified as having 111 substitutions in proteins and 6 deletions. The effect of coexisting/reoccurring mutations on the structural stability of each protein was also determined by I-mutant and MUpro online servers. Furthermore, molecular docking and simulation results showed that the coexisting mutations (I317V and E393D) in Domain III (DIII) of the envelope protein enhanced the bonding network with ZIKV-specific neutralizing antibodies. This study, therefore, highlighted the rapid accumulation of different substitutions in various ZIKV proteins circulating in different geographical regions of the world. Surveillance of such mutations in the respective proteins will be helpful in the development of effective ZIKV vaccines and neutralizing antibody engineering.