Biology subjects

Perveen, S.

Publications and source records attributed to Perveen, S..

13 recordsLinked to original sources

bioRxiv2024

Heli-SMACC: Helicase-targeting SMAll Molecule Compound Collection

Helicases have emerged as promising targets for the development of antiviral drugs; however, the family remains largely undrugged. To support the focused development of viral helicase inhibitors we identified, collected, and integrated all chemogenomics data for all available helicases from the ChEMBL database. After thoroughly curating and enriching the data with relevant annotations we have created a derivative database of helicase inhibitors which we dubbed Heli-SMACC (Helicase-targeting SMAll Molecule Compound Collection). The current version of Heli-SMACC contains 20,432 bioactivity entries for viral, human, and bacterial helicases. We have selected 30 compounds with promising viral helicase activity and tested them in a SARS-CoV-2 NSP13 ATPase assay. Twelve compounds demonstrated ATPase inhibition and a consistent dose-response curve. The Heli-SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel helicase inhibitors. Heli-SMACC is publicly available at https://smacc.mml.unc.edu. HighlightsO_LIWe created a curated Helicase-Targeting SMAll Molecule Compound Collection (Heli-SMACC). C_LIO_LIHeli-SMACC covers 29 human, viral, and bacterial helicases. C_LIO_LITwelve of thirty selected compounds demonstrated inhibitory activity in a SARS-CoV-2 NSP13 ATPase Assay. C_LIO_LIHeli-SMACC is freely available online at https://smacc.mml.unc.edu. C_LI TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/602122v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@8e098forg.highwire.dtl.DTLVardef@115cb2borg.highwire.dtl.DTLVardef@1cd9da3org.highwire.dtl.DTLVardef@2870a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of Chikungunya nsP2 Cysteine Protease with Anti-alphavirus Activity

Despite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic {beta}-aminomethyl vinyl sulfone RA-0002034 (1a) is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad spectrum antiviral activity. Analogs of 1a that varied each of three regions of the molecule were synthesized to establish structure-activity relationships for inhibition of Chikungunya (CHIKV) nsP2 protease and viral replication. The covalent warhead was highly sensitive to modifications of the sulfone or vinyl substituents. However, numerous alterations to the core 5-membered heterocycle and its aryl substituent were well tolerated and several analogs were identified that enhanced CHIKV nsP2 binding. For example, the 4-cyanopyrazole analog 8d exhibited a kinact/Ki ratio >10,000 M-1s-1. 3-Arylisoxazole was identified an isosteric replacement for the 5-membered heterocycle, which circumvented the intramolecular cyclization that complicated the synthesis of pyrazole-based inhibitors like 1a. The accumulated structure-activity data was used to build a ligand-based model of the enzyme active site, which can be used to guide the design of covalent nsP2 protease inhibitors as potential therapeutics against alphaviruses.

cell biology↗

bioRxiv2024

A resource to enable chemical biology and drug discovery of WDR Proteins

Protein class-focused drug discovery has a long and successful history in pharmaceutical research, yet most members of druggable protein families remain unliganded, often for practical reasons. Here we combined experiment and computation to enable discovery of ligands for WD40 repeat (WDR) proteins, one of the largest human protein families. This resource includes expression clones, purification protocols, and a comprehensive assessment of the druggability for hundreds of WDR proteins. We solved 21 high resolution crystal structures, and have made available a suite of biophysical, biochemical, and cellular assays to facilitate the discovery and characterization of small molecule ligands. To this end, we use the resource in a hit-finding pilot involving DNA-encoded library (DEL) selection followed by machine learning (ML). This led to the discovery of first-in-class, drug-like ligands for 9 of 20 targets. This result demonstrates the broad ligandability of WDRs. This extensive resource of reagents and knowledge will enable further discovery of chemical tools and potential therapeutics for this important class of proteins.

biochemistry↗

bioRxiv2023

Chemical Tools for the Gid4 Subunit of the Human E3 Ligase C-terminal to LisH (CTLH) Degradation Complex

We have developed a novel chemical handle (PFI-E3H1) and a chemical probe (PFI-7) as ligands for the Gid4 subunit of the human E3 ligase CTLH degradation complex. Through an efficient initial hit-ID campaign, structure-based drug design (SBDD) and leveraging the sizeable Pfizer compound library, we identified a 500 nM ligand for this E3 ligase through file screening alone. Further exploration identified a vector that is tolerant to addition of a linker for future chimeric molecule design. The chemotype was subsequently optimized to sub-100 nM Gid4 binding affinity for a chemical probe. These novel tools, alongside the suitable negative control also identified, should enable the interrogation of this complex human E3 ligase macromolecular assembly.

biophysics↗

bioRxiv2023

Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 {+/-} 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148 (PDB:8BWU), a potent inhibitor of methyltransferase activity at the nanomolar level (IC50 value of 70 {+/-} 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.

biochemistry↗

bioRxiv2023

Probing the mechanism of Cbl-b inhibition by a small-molecule inhibitor

Cbl-b is a RING-type E3 ubiquitin ligase that is expressed in several immune cell lineages, where it negatively regulates the activity of immune cells. Cbl-b has specifically been identified as an attractive target for cancer immunotherapy due to its role in promoting an immunosuppressive tumor environment, and Nx-1607, is in phase I clinical trials for advanced solid tumor malignancies. Using a suite of biophysical and cellular assays, we confirmed potent binding of C7683 (an analogue of Nx-1607) to the full-length Cbl-b and its N-terminal fragment containing the TKBD-LHR-RING domains. To further elucidate its mechanism of inhibition, we determined the co-crystal structure of Cbl-b with C7683, revealing compound interaction with both the TKBD and LHR, but not the ring domain. Here, we provide structural insights into a novel mechanism of Cbl-b inhibition by a small-molecule inhibitor that locks the protein in an inactive conformation by acting as an intramolecular glue.

immunology↗

bioRxiv2022

Design And Optimization Studies Of Tablet In Tablet Formulation Of Diclofenac And Misoprostol: Application Of Response Surface Methodolgy And Compressional Behaviour Strategy

The present study was aimed to develop compression coated tablets of diclofenac sodium (75mg) in the inner core and misoprostol (200 mg) as the outer shell for the effective treatment of rheumatoid arthritis as this dosing frequency is not available in the market yet. Diclofenac sodium inner tablet was manufactured by wet granulation and its enteric coating was applied by Eudragit L 100-55, Isopropyl Alcohol and Opadry II Blue 85 F205034. While immediate-release misoprostol outer shell was also manufactured by wet granulation and coated by Opadry white and Polyethylene glycol 6000. Design of experiment(R) software was used for formulation design and optimization. Quality attributes such as tablet weight, hardness, disintegration time, percent drug dissolution and assay were performed as per official methods and satisfactory results were reported. Physical and chemical stability of selected formulations was evaluated following the ICH guidelines for accelerated stability testing. The compressional analysis of optimized formulation was performed to check the optimum compression pressure to obtain a stable formulation. Based on satisfactory quality attributes; formulation DF9MF7 was successfully developed as compression coated tablet with calculated shelf life of 4.8years. Compression coated tablets comprising of enteric coated diclofenac sodium as inner core and misoprostol as outer shell were successfully developed by wet granulation.

pharmacology and toxicology↗

bioRxiv2022

Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)

RBBP4 is a nuclear WD40 motif-containing protein widely implicated in various cancers and a putative drug target. It interacts with multiple proteins within diverse complexes such as nucleosome remodeling and deacetylase (NuRD) complex and polycomb repressive complex 2 (PRC2), as well as histone H3 and H4 through two distinct binding sites. B-cell lymphoma/leukemia 11A (BCL11A), friend of GATA-1 (FOG-1), plant homeodomain finger protein 6 (PHF6) and histone H3 bind to the top of the donut-shaped seven-bladed {beta}-propeller fold of RBBP4, while suppressor of zeste 12 (SUZ12), metastasis associated protein 1 (MTA1) and histone H4 bind to a pocket on the side of the WD40 repeats of this protein. Here, we report the discovery of the first small molecule antagonists of the RBBP4 top pocket, competing with interacting peptides from proteins such as BCL11A and histone H3. We also determined the first crystal structure of RBBP4 in complex with a small molecule (OICR17251), paving the path for structure-guided design and optimization towards more potent antagonists.

biochemistry↗

bioRxiv2021

Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

The COVID-19 pandemic has clearly brought the healthcare systems world-wide to a breaking point along with devastating socioeconomic consequences. The SARS-CoV-2 virus which causes the disease uses RNA capping to evade the human immune system. Non-structural protein (nsp) 14 is one of the 16 nsps in SARS-CoV-2 and catalyzes the methylation of the viral RNA at N7-guanosine in the cap formation process. To discover small molecule inhibitors of nsp14 methyltransferase (MT) activity, we developed and employed a radiometric MT assay to screen a library of 161 in house synthesized S-adenosylmethionine (SAM) competitive methyltransferase inhibitors and SAM analogs. Among seven identified screening hits, SS148 inhibited nsp14 MT activity with an IC50 value of 70 {+/-} 6 nM and was selective against 20 human protein lysine methyltransferases indicating significant differences in SAM binding sites. Interestingly, DS0464 with IC50 value of 1.1 {+/-} 0.2 M showed a bi-substrate competitive inhibitor mechanism of action. Modeling the binding of this compound to nsp14 suggests that the terminal phenyl group extends into the RNA binding site. DS0464 was also selective against 28 out of 33 RNA, DNA, and protein methyltransferases. The structure-activity relationship provided by these compounds should guide the optimization of selective bi-substrate nsp14 inhibitors and may provide a path towards a novel class of antivirals against COVID-19, and possibly other coronaviruses.

biochemistry↗

bioRxiv2021

A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex

Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA-capping through its 2-O-methylation activity. Like other methyltransferases, SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for methyltransferase activity of nsp10-nsp16 complex in a 384-well format, and kinetic characterization, and optimization of the assay for HTS (Z'-factor: 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.

biochemistry↗

bioRxiv2020

A high throughput RNA displacement assay for screening SARS-CoV-2 nsp10-nsp16 complex towards developing therapeutics for COVID-19

SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process including the nonstructural protein 16 (nsp16) which is an S-adenosyl-L-methionine (SAM)-dependent 2-O-methyltransferase. Nsp16 is significantly active when in complex with another nonstructural protein, nsp10, which plays a key role in its stability and activity. Here we report the development of a fluorescence polarization (FP)-based RNA displacement assay for nsp10-nsp16 complex in 384-well format with a Z'-Factor of 0.6, suitable for high throughput screening. In this process, we purified the nsp10-nsp16 complex to higher than 95% purity and confirmed its binding to the methyl donor SAM, product of the reaction, SAH, and a common methyltransferase inhibitor, sinefungin using Isothermal Titration Calorimetry (ITC). The assay was further validated by screening a library of 1124 drug-like compounds. This assay provides a cost-effective high throughput method for screening nsp10-nsp16 complex for RNA-competitive inhibitors towards developing COVID-19 therapeutics.

biochemistry↗

bioRxiv2020

Intense expression of Neurokinin-1 Receptor is associated with Urothelial carcinoma

I+ntroductionSubstance P (SP)/ Neurokinin-1 Receptor (NK-1R), induces inflammatory reactions in peripheral tissues but its regulatory effects in target tissues are dependent on receptor signaling. SP has a high affinity for the NK-1 receptor, to which it binds preferentially. SP/NK-1R complex plays a key role in the interaction in the onset of pain and inflammation. ObjectiveThe aim of this study was to investigate the expression of NK-1R in Urotheilial carcinoma and its association with cancer progression. MethodThe study included ten biopsy samples of Urinary bladder, obtained retrospectively from a tertiary care hospital of Lahore. An Immunohistochemical study was performed using monoclonal antibodies against NK-1R. The presence or absence of staining and the intensity of the immunoreactivity were noted, as well as the number and type of cells. Evaluation of the Immunohistochemical expression was determined by the semi-quantitative method and scored. ResultNK-1 receptor was intensely expressed in patients with higher grade Urotheilial carcinoma. The cases clinically diagnosed as High Grade Urotheilial Carcinoma showed intense expression of NK-1R. However, the cases clinically diagnosed as low grade Urotheilial carcinoma showed very weak staining with NK-1R. However, the normal margins of the same tissue showed negative expression. ConclusionsElevated expression of NK-1R was associated with advanced stage of urothelial carcinoma. It is the first study to our knowledge to report this association. It may serve as a good diagnostic as well as prognostic marker and therapeutic strategy.

pathology↗

bioRxiv2018

Performance evaluation of biosurfactant stabilized microbubbles in enhanced oil recovery

Microbubble technology is increasingly finding applications in biomedical engineering, soil remediation and wastewater treatment. Recently, the use of surfactant microbubbles has been studied as an alternate to aqueous solution in pollutant remediation since they have the advantage of improving the contact with the contaminant due to their surface properties. In this research endeavor, the application potential of microbubble suspension generated using a lipopeptide biosurfactant produced by a marine strain of Bacillus megaterium in tertiary oil recovery was investigated. The microbubbles were generated using a high speed homogenizer and their properties such as stability and size distribution were studied. The microbubble suspension was used as flooding agent to recover gear oil from an artificially saturated sand packed column. The performance of microbubbles in tertiary oil recovery was compared with that of aqueous biosurfactant solution. It was found that microbubble suspension generated using biosurfactant had higher oil recovery efficiency (46%) than aqueous solution (36%).\n\nMoreover, the pressure buildup across the sand packed column was fairly low while using microbubble suspension. The increased oil recovery using microbubbles can be attributed to their effective permeation through the pores of sand packed column and closer contact between biosurfactant molecules and oil. Thus, the results obtained in this study convincingly indicate that biosurfactant stabilized microbubble suspension, due to its higher performance and lower injection pressure requirement, can serve as a potentially efficient flooding agent for tertiary oil recovery.

bioengineering↗