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View article: CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 Open
A critical assessment of computational hit-finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comp…
View article: Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities
Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities Open
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, …
View article: CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 Open
A critical assessment of computational hit finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comp…
View article: CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 Open
A critical assessment of computational hit finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comp…
View article: CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 Open
A critical assessment of computational hit finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comp…
View article: A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity
A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity Open
Chikungunya is a mosquito-borne viral disease that causes fever and severe joint pain for which there is no direct acting drug treatments. Vinyl sulfone SGC-NSP2PRO-1 (3) was identified as a potent inhibitor of the nsP2 cysteine protease (…
View article: A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity
A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity Open
View article: Functionally active modulators targeting the LRRK2 WD40 repeat domain identified by FRASE-bot in CACHE Challenge #1
Functionally active modulators targeting the LRRK2 WD40 repeat domain identified by FRASE-bot in CACHE Challenge #1 Open
FRASE-bot, a virtual screening platform, won CACHE Challenge #1, which aimed to identify ligands to WDR LRRK2, a Parkinson's disease target. The hit compounds exibit low micromolar affinity for the target and modulate LRRK2 function in cel…
View article: A Covalent Chemical Probe for Chikungunya nsP2 Cysteine Protease with Antialphaviral Activity and Proteome-wide Selectivity
A Covalent Chemical Probe for Chikungunya nsP2 Cysteine Protease with Antialphaviral Activity and Proteome-wide Selectivity Open
View article: CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein Open
The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE challenge in which 23 computational teams each select…
View article: A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins
A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins Open
Target class-focused drug discovery has a strong track record in pharmaceutical research, yet public domain data indicate that many members of protein families remain unliganded. Here we present a systematic approach to scale up the discov…
View article: Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach
Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach Open
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV nonstruct…
View article: Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of <i>Chikungunya</i> nsP2 Cysteine Protease with Antialphavirus Activity
Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of <i>Chikungunya</i> nsP2 Cysteine Protease with Antialphavirus Activity Open
Despite their widespread impact on human health, there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 (1a) is a potent irreversible covalent inhibitor of the alphav…
View article: CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson’s Disease associated protein
CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson’s Disease associated protein Open
The CACHE challenges are a series of prospective benchmarking exercises meant to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE #1 challenge in which 23 computational teams ea…
View article: Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2
Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2 Open
We herewith applied a priori a generic hit identification method (POEM) for difficult targets of known three-dimensional structure, relying on the simple knowledge of physicochemical and topological properties of a user-selected cav…
View article: Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of<i>Chikungunya</i>nsP2 Cysteine Protease with Anti-alphavirus Activity
Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of<i>Chikungunya</i>nsP2 Cysteine Protease with Anti-alphavirus Activity Open
Despite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 ( 1a ) is a potent irreversible covalent inhibitor of the alphavirus n…
View article: Development of Peptide Displacement Assays to Screen for Antagonists of DDB1 Interactions
Development of Peptide Displacement Assays to Screen for Antagonists of DDB1 Interactions Open
The DNA damage binding protein 1 (DDB1) is an essential component of protein complexes involved in DNA damage repair and the ubiquitin-proteasome system (UPS) for protein degradation. As an adaptor protein specific to Cullin-RING E3 ligase…
View article: Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach
Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach Open
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-struc…
View article: A resource to enable chemical biology and drug discovery of WDR Proteins
A resource to enable chemical biology and drug discovery of WDR Proteins Open
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 t…
View article: Kinetic characterization of human mRNA guanine-N7 methyltransferase
Kinetic characterization of human mRNA guanine-N7 methyltransferase Open
View article: Development of Complementary Photo‐arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes
Development of Complementary Photo‐arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes Open
Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context‐specific and transient effectors of these marks…
View article: Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes
Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes Open
Workflow used for identifying inhibitors of the SARS-CoV-2 non-structural protein 14 (nsp14), a key player in viral RNA methylation.
View article: Chemical tools for the Gid4 subunit of the human E3 ligase C-terminal to LisH (CTLH) degradation complex
Chemical tools for the Gid4 subunit of the human E3 ligase C-terminal to LisH (CTLH) degradation complex Open
A chemical probe (PFI-7) for the Gid4 subunit of the human E3 ligase CTLH degradation complex.
View article: The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition
The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition Open
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…
View article: Chemical Tools for the Gid4 Subunit of the Human E3 Ligase C-terminal to LisH (CTLH) Degradation Complex
Chemical Tools for the Gid4 Subunit of the Human E3 Ligase C-terminal to LisH (CTLH) Degradation Complex Open
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 (S…
View article: Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors
Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors Open
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 …
View article: Probing the mechanism of Cbl-b inhibition by a small-molecule inhibitor
Probing the mechanism of Cbl-b inhibition by a small-molecule inhibitor Open
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…
View article: SS148 and WZ16 inhibit the activities of nsp10-nsp16 complexes from all seven human pathogenic coronaviruses
SS148 and WZ16 inhibit the activities of nsp10-nsp16 complexes from all seven human pathogenic coronaviruses Open
Seven coronaviruses have infected humans (HCoVs) to-date. SARS-CoV-2 caused the current COVID-19 pandemic with the well-known high mortality and severe socioeconomic consequences. MERS-CoV and SARS-CoV caused epidemic of MERS and SARS, res…
View article: Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)
Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4) Open
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…
View article: Probing the SAM Binding Site of SARS-CoV-2 Nsp14 In Vitro Using SAM Competitive Inhibitors Guides Developing Selective Bisubstrate Inhibitors
Probing the SAM Binding Site of SARS-CoV-2 Nsp14 In Vitro Using SAM Competitive Inhibitors Guides Developing Selective Bisubstrate Inhibitors Open