Biology subjects

Rizvi, Z.

Publications and source records attributed to Rizvi, Z..

5 recordsLinked to original sources

bioRxiv2026

Allosteric covalent inhibition of cereblon through cryptic cysteine targeting

Thalidomide-derived cereblon (CRBN) modulators are among the most clinically impactful targeted protein degradation therapeutics, redirecting the CRL4-CRBN E3 ubiquitin ligase to degrade disease-driving neosubstrates. All current CRBN-targeting IMiDs and CELMoDs engage a single orthosteric pocket, leaving CRBN's conformational landscape largely unexploited pharmacologically. Using cysteine-directed chemoproteomic screening, we identified covalent ligands that engage Cys287, a cryptic allosteric pocket distal to the orthosteric site. Our lead compound, VVD-105917, acts as a pan-inhibitor of IMiD/CELMoD-driven neosubstrate degradation. Cryo-EM structures reveal that covalent Cys287 engagement traps CRBN in its open, inactive conformation, resolving a previously unobserved N-terminal segment and sensor loop. Sequential incubation experiments show the conformational outcome depends on ligand addition order, demonstrating that even potent CELMoD-driven closure can be overridden by allosteric engagement. A recently reported ligand at this same pocket produces the opposite effect, promoting rather than blocking closure, indicating the Cys287 site is mechanistically sign-switchable. These findings establish covalent chemoproteomics as a strategy for discovering and controlling E3 ligase conformational switches.

biochemistry↗

bioRxiv2025

Oral Microbiota Interactions with Titanium Implants: A pilot in-vivo and in-vitro study on the impact of Peri-implantitis

IntroductionDental implant therapy is widely recognized as the best solution for replacing missing teeth. However, it still has a 1.9-11% failure rate. Oral microbiota is suspected to play a significant role in implant failure and peri-implant infections. Hence the impact of oral microbiota on titanium dental implants, particularly in the context of dysbiosis and peri-implant diseases, was investigated by in-vivo and in-vitro methods in this study. Materials and MethodsThis pilot study aimed to investigate the role of oral microbiota in peri-implant diseases associated with titanium implants. For the in-vivo study, oral microbiota was collected from titanium and hydroxyapatite (tooth-mimicking) discs placed in a custom-made intra-oral device worn by four healthy subjects. Biofilm formation, pathobionts, and bacterial diversity were assessed using DAPI staining, qPCR, and next generation sequencing (NGS)-16S rRNA sequencing. For the in-vitro study scanning electron microscopy was employed to examine the effect of oral pathogens on titanium implants. ResultsThe study found enhanced biofilm formation on titanium implants compared to controls (p < 0.0002). Systematic colonization by Streptococcus oralis, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans was observed. An abundance of Firmicutes and Bacteroidetes, with a decrease in Proteobacteria on titanium implants was observed by NGS. SEM showed corrosion and damage to titanium implants caused by oral pathogens. ConclusionThe results demonstrate that the use of titanium-based dental implants promotes oral microbiota dysbiosis, tipping the scale towards oral pathogens, which in turn contributes to the damage of the titanium implant surface. Increased biofilm formation of periodontal pathogens and microbial dysbiosis may play a role in implant failure and peri-implant diseases.

cell biology↗

bioRxiv2023

Plasmodium falciparum contains functional SCF and CRL4 ubiquitin E3 ligases, and CRL4 is critical for cell division and membrane integrity

Protein ubiquitination is essential for cellular homeostasis and regulation of several processes, including cell division and genome integrity. Ubiquitin E3 ligases determine substrate specificity for ubiquitination, and Cullin-RING ubiquitin E3 Ligases (CRLs) make the largest group among the ubiquitin E3 ligases. Although conserved and most studied in model eukaryotes, CRLs remain underappreciated in Plasmodium and related parasites. To investigate the CRLs of human malaria parasite Plasmodium falciparum, we generated parasites expressing tagged P. falciparum cullin-1 (PfCullin-1), cullin-2 (PfCullin-2), Rbx1 (PfRbx1) and Skp1 (PfSkp1). PfCullin-1 and PfCullin-2 were predominantly expressed in erythrocytic trophozoite and schizont stages, with nucleocytoplasmic localization and chromatin association, suggesting their roles in different cellular compartments and DNA-associated processes. Immunoprecipitation, in vitro protein-protein interaction and ubiquitination assay confirmed the presence of a functional SCF (PfSCF), comprising of PfCullin-1, PfRbx1, PfSkp1, PfFBXO1 and calcyclin binding protein. Immunoprecipitation, sequence analysis and ubiquitination assay indicated that PfCullin-2 forms a functional human CRL4-like complex (PfCRL4), consisting of PfRbx1, cleavage and polyadenylation specific factor subunit_A and WD40 repeat proteins. PfCullin-2 knock-down at the protein level, which would hinder PfCRL4 assembly, significantly decreased asexual and sexual erythrocytic stage development. Several pathways, including protein translation and folding, lipid biosynthesis and transport, DNA replication, and protein degradation were dysregulated upon PfCullin-2-depletion, which likely reflects association of PfCRL4 with multiple pathways. Consistent with dysregulation of multiple pathways, PfCullin-2-depleted schizonts had poorly delimited merozoites and internal membraned structures, suggesting a role of PfCRL4 in maintaining membrane integrity. PfCullin-2-depleted parasites had significantly lower number of nuclei/parasite than the normal parasites, indicating a crucial role of PfCRL4 in cell division. Taken together, we for the first time demonstrate the presence of functional CRLs in P. falciparum, with crucial roles for PfCRL4 in cell division and maintaining membrane integrity. This study will benefit investigation of similar ligases in related parasites.

microbiology↗

bioRxiv2021

Plasmodium DDI1 is an essential chromatin-associated protein with a role in DNA-protein crosslink repair

DDI1 proteins are involved in a variety of cellular processes, including proteasomal degradation of specific proteins. All DDI1 proteins contain a ubiquitin-like (UBL) domain and a retroviral aspartyl protease (RVP) domain. Some DDI1 proteins also contain a ubiquitin-associated (UBA) domain. The three domains confer distinct activities to DDI1 proteins. The presence of RVP domain makes DDI1 a potential target of HIV protease inhibitors, which also block the development of malaria parasites. Hence, we investigated the DDI1 of malaria parasites to identify its roles during parasite development and potential as a therapeutic target. DDI1 proteins of Plasmodium and other Apicomplexan parasites share the UBL-RVP domain architecture, and some also contain the UBA domain. Plasmodium DDI1 is expressed across all the major life cycle stages and is important for parasite survival, as conditional depletion of DDI1 protein in the mouse malaria parasite Plasmodium berghei and the human malaria parasite Plasmodium falciparum compromised parasite development. Infection of mice with DDI1 knock-down P. berghei was self-limiting and protected the recovered mice from subsequent infection with homologous as well as heterologous parasites, indicating potential of DDI1 knock-down parasites as a whole organism vaccine. P. falciparum DDI1 (PfDDI1) is associated with chromatin and DNA-protein crosslinks. PfDDI1-depleted parasites accumulated DNA-protein crosslinks and showed enhanced susceptibility to DNA damaging chemicals, indicating a role of PfDDI1 in removal of DNA-protein crosslinks. Knock-down of PfDDI1 increased susceptibility to the retroviral protease inhibitor lopinavir and antimalarial artemisinin, which suggests that simultaneous inhibition of DDI1 could potentiate antimalarial activity of these drugs. As DDI1 knock-down parasites confer protective immunity and it could be a target of HIV protease inhibitors, Plasmodium DDI1 is a potential therapeutic target for malaria control.

cell biology↗

bioRxiv2020

Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates

A variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles. The neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulate diverse cellular processes, including the cell-cycle. Although neddylation pathway is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. Towards studying the neddylation pathway in malaria parasites, we characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Gly76 mutated to Ala75Ala76) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 to proteins through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified several proteins, including two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 ({Delta}rub1) or NEDD8 conjugating E2 enzyme ({Delta}Ubc12). The western blot of complemented strains and mass spectrometry of PfNEDD8 immunoprecipitate showed conjugation of PfNEDD8 to S. cerevisiae cullin cdc53, demonstrating functional conservation and cullins as the physiological substrates of PfNEDD8. The characterization of PfNEDD8 and identification of cullins as its substrates make ground for investigation of specific roles and drug target potential of neddylation pathway in malaria parasites.

biochemistry↗