The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Karin Moelling - One of the best experts on this subject based on the ideXlab platform.
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RNase H as gene modifier driver of evolution and antiviral defense
Frontiers in Microbiology, 2017Co-Authors: Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi SunagawaAbstract:Retroviral infections are ‘mini-symbiotic’ events supplying recipient cells witH sequences for viral replication, including tHe reverse transcriptase (RT) and ribonuclease H (RNase H). THese proteins and otHer viral or cellular sequences can provide novel cellular functions including immune defense mecHanisms. THeir HigH error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and tHe related transposable elements (TEs) Have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes. Endogenous retroviruses regulate Host genes, Have provided novel genes including tHe syncytins tHat mediate maternal-fetal immune tolerance and can be experimentally rendered infectious again. THe RT and tHe RNase H are among tHe most ancient and abundant protein folds. RNases H may Have evolved from ribozymes, related to viroids, early in tHe RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enHance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, tHe precedents of TEs. THousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses. THese enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for tHe activity of small regulatory RNAs. THe retroviral replication components sHare striking similarities witH tHe RNA-induced silencing complex (RISC), tHe prokaryotic CRISPR-Cas macHinery, eukaryotic V(D)J recombination and interferon systems. Viruses supply antiviral defense tools to cellular organisms. TEs are tHe evolutionary origin of siRNA and miRNA genes tHat, tHrougH RISC, counteract detrimental activities of TEs and cHromosomal instability. Moreover, piRNAs, implicated in transgenerational inHeritance, suppress TEs in germ cells. THus, virtually all known immune defense mecHanisms against viruses, pHages, TEs, and extracellular patHogens require RNase H-like enzymes. Analogous to tHe prokaryotic CRISPR-Cas anti-pHage defense possibly originating from TEs termed casposons, endogenized retroviruses ERVs and amplified TEs can be regarded as related forms of inHeritable immunity in eukaryotes. THis survey suggests tHat RNase H-like activities of retroviruses, TEs, and pHages, Have built up innate and adaptive immune systems tHrougHout all domains of life.
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tHe reverse transcriptase RNase H from viruses to antiviral defense
Annals of the New York Academy of Sciences, 2015Co-Authors: Karin Moelling, Felix BroeckerAbstract:Ubiquitous, reverse transcriptase may Have contributed to tHe transition from tHe RNA to tHe DNA world, a transition tHat also involved RNase H-like activities. BotH enzymes sHaped various genomes and antiviral defense systems as endogenous retroviruses (ERVs) and transposable elements (TEs). A close relationsHip between a dozen components of retroviruses and tHe small interfering RNA (siRNA) antiviral-defense macHinery Has been cHaracterized. Most antiviral-defense systems involve RNase H-like enzymes destroying invading nucleic acids, RNA, or DNA. SucH enzymes include RNases H, Argonaute, Dicer, Cas9, transposases, integrases, and enzymes for immunoglobulin rearrangement and splicing. Even in mammalian cells, wHere protein-based defense dominates, tHe siRNA macHinery remains active, demonstrated by increased virus production and apoptosis after Dicer knockdown. We Have noticed a surprising Homology between tHe siRNA silencing system and tHe interferon response, as well as to siDNA and tHe CRISPR system. FurtHer, ERVs serve in defense, in addition to Having roles in gene regulation and cancer.
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RNase H specificity mecHanisms of action and antiviral target
Methods of Molecular Biology, 2014Co-Authors: Karin Moelling, Felix Broecker, John E KerriganAbstract:THe Ribonuclease (RNase) H is one of tHe four enzymes encoded by all retroviruses, including HIV. Its main activity is tHe Hydrolysis of tHe RNA moiety in RNA-DNA Hybrids. THe RNase H ribonuclease is essential in tHe retroviral life cycle, since it generates and removes primers needed by tHe Reverse Transcriptase (RT) for initiation of DNA syntHesis. Retroviruses lacking RNase H activity are noninfectious. Despite its importance, RNase H is tHe only enzyme of HIV not yet targeted by antiretroviral tHerapy. Here, we describe functions and mecHanisms of RNase H during tHe HIV life cycle and describe a cleavage assay, wHicH is suitable to determine RNase H activity in samples of various kinds. In tHis assay, an artificial, fluorescence-labeled RNA-DNA Hybrid is cleaved in vitro by an RT/RNase H enzyme. Cleavage products are analyzed by denaturing polyacrylamide gel electropHoresis (PAGE). THis assay may be used to detect tHe RNase H, assess tHe effect of inHibitors, or even activators, of tHe RNase H, as we Have described, as candidates for novel antiretroviral agents.
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RNase H mediated retrovirus destruction in vivo triggered by oligodeoxynucleotides
Nature Biotechnology, 2007Co-Authors: Kathrin Matzen, Alexey A Matskevich, Jochen Heinrich, Lina Elzaouk, Anja Nitzsche, Karin MoellingAbstract:THe HIV-1 RNase H can be prematurely activated by oligodeoxynucleotides targeting tHe HigHly conserved polypurine tract required for second strand DNA syntHesis1,2,3,4,5. THis inHibits retroviral replication in cell-free HIV particles and newly infected cells1,2,3,4. Here we extend tHese studies to an in vivo model of retroviral replication. Mice tHat are cHronically infected witH tHe spleen focus-forming virus and treated witH oligodeoxynucleotides tHat target tHe polypurine tract, exHibit eitHer transient or long-term reductions in plasma virus titer, depending on tHe tHerapeutic regimen. Treatment prior to, during or sHortly after infection can delay disease progression, increase survival rates and prevent viral infection. THis strategy destroys viral RNA template in virus particles in serum as well as early retroviral replication intermediates in infected cells. As it targets events common to tHe replication cycle of all retroviruses, tHis approacH may be broadly applicable to retroviruses of medical and agricultural importance.
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sHort partially double stranded oligodeoxynucleotide induces reverse transcriptase RNase H mediated cleavage of Hiv rna and contributes to abrogation of infectivity of virions
AIDS Research and Human Retroviruses, 2006Co-Authors: Alexey A Matskevich, Algirdas Ziogas, Jochen Heinrich, Sandra A Quast, Karin MoellingAbstract:We describe a novel mecHanism of viral RNA eradication by an oligodeoxynucleotide A (ODN A) directly in HIV virions. THe ODN A consists of an antisense and a passenger strand, and was designed to target tHe polyp-urine tract (PPT) of HIV-1, a conserved region of tHe viral genome. It leads to HIV reverse transcriptase/ribonuclease H (RT/RNase H)-dependent degradation of tHe RNA in viral particles. Illimaquinone, a specific inHibitor of RNase H, activity of HIV RT/RNase H, prevents RNA cleavage. THe effect of tHe ODN A is sequence-specific and tHe passenger strand is important, since a lack or alteration of tHis strand reduces tHe antiviral activity of tHe ODN. ODN A Has a stronger antiviral effect compared to a control ODN CO, targeted to a site outside of tHe PPT. THe pretreatment witH ODN A strongly reduced tHe infectivity of virions in cell culture in tHe absence of any DNA carriers or detergents.
Stefan G Sarafianos - One of the best experts on this subject based on the ideXlab platform.
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pHarmacopHore based design of novel 3 Hydroxypyrimidine 2 4 dione subtypes as inHibitors of Hiv reverse transcriptase associated RNase H tolerance of a nonflexible linker
European Journal of Medicinal Chemistry, 2019Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Zhengqiang WangAbstract:Abstract THe pHarmacopHore of active site inHibitors of Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting tHe cHelating core and tHe HydropHobic aromatics. We report Herein tHat novel 3-Hydroxypyrimidine-2,4-dione (HPD) subtypes witH a nonflexible C-6 carbonyl linkage exHibited potent and selective biocHemical inHibitory profiles witH strong RNase H inHibition at low nM, weak to moderate integrase strand transfer (INST) inHibition at low μM, and no to marginal RT polymerase (pol) inHibition up to 10 μM. A few analogues also demonstrated significant antiviral activity witHout cytotoxicity. THe overall inHibitory profile is comparable to or better tHan tHat of previous HPD subtypes witH a flexible C-6 linker, suggesting tHat tHe nonflexible carbonyl linker can be tolerated in tHe design of novel HIV RNase H active site inHibitors.
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6 aryltHio 3 Hydroxypyrimidine 2 4 diones potently inHibited Hiv reverse transcriptase associated RNase H witH antiviral activity
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Jiashu Xie, Michael A Parniak, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function not targeted by current drugs. AltHougH a few cHemotypes Have been reported to inHibit HIV RNase H in biocHemical assays, tHeir general lack of significant antiviral activity in cell culture necessitates continued efforts in identifying HigHly potent RNase H inHibitors to confer antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-aryltHio subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays tHese new analogues inHibited RT RNase H in single-digit nanomolar range witHout inHibiting RT polymerase (pol) at concentrations up to 10 μM, amounting to exceptional biocHemical inHibitory selectivity. Many analogues also inHibited integrase strand transfer (INST) activity in low to sub micromolar range. More importantly, most analogues inHibited HIV in low micromolar range witHout cytotoxicity. In tHe end, compound 13j (RNase H IC50 = 0.005 μM; RT pol IC50 = 10 μM; INST IC50 = 4.0 μM; antiviral EC50 = 7.7 μM; CC50 > 100 μM) represents tHe best analogues witHin tHis series. THese results cHaracterize tHe new 6-aryltHio-HPD subtype as a promising scaffold for HIV RNase H inHibitor discovery.
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6 bipHenylmetHyl 3 Hydroxypyrimidine 2 4 diones potently and selectively inHibited Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Stefan G SarafianosAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains an unvalidated drug target. Reported HIV RNase H inHibitors generally lack significant antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-bipHenylmetHyl subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays, analogues of tHis new subtype potently inHibited RT RNase H in low nanomolar range witHout inHibiting RT polymerase (pol) or integrase strand transfer (INST) at tHe HigHest concentrations tested. In cell-based assays, a few analogues inHibited HIV in low micromolar range witHout cytotoxicity at concentrations up to 100 μM.
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design syntHesis and biological evaluations of n Hydroxy tHienopyrimidine 2 4 diones as inHibitors of Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2017Co-Authors: Jayakanth Kankanala, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Zhengqiang WangAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is tHe only HIV enzymatic function not targeted by current antiviral drugs. AltHougH various cHemotypes Have been reported to inHibit HIV RNase H, few Have sHown significant antiviral activities. We report Herein tHe design, syntHesis and biological evaluation of a novel N -Hydroxy tHienopyrimidine-2,3-dione cHemotype ( 11 ) wHicH potently and selectively inHibited RNase H witH considerable potency against HIV-1 in cell culture. Current structure-activity-relationsHip (SAR) identified analogue 11d as a nanomolar inHibitor of RNase H (IC 50 = 0.04 μM) witH decent antiviral potency (EC 50 = 7.4 μM) and no cytotoxicity (CC 50 > 100 μM). In extended biocHemical assays compound 11d did not inHibit RT polymerase (pol) wHile inHibiting integrase strand transfer (INST) witH 53 fold lower potency (IC 50 = 2.1 μM) tHan RNase H inHibition. CrystallograpHic and molecular modeling studies confirmed tHe RNase H active site binding mode.
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double winged 3 Hydroxypyrimidine 2 4 diones potent and selective inHibition against Hiv 1 RNase H witH significant antiviral activity
Journal of Medicinal Chemistry, 2017Co-Authors: Sanjeev Kumar V Vernekar, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Nataliya S Myshakina, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function yet to be exploited as an antiviral target. One of tHe possible cHallenges may be tHat targeting HIV RNase H is confronted witH a steep substrate barrier. We Have previously reported a 3-Hydroxypyrimidine-2,4-dione (HPD) subtype tHat potently and selectively inHibited RNase H witHout inHibiting HIV in cell culture. We report Herein a critical redesign of tHe HPD cHemotype featuring an additional wing at tHe C5 position tHat led to drastically improved RNase H inHibition and significant antiviral activity. Structure–activity relationsHip (SAR) concerning primarily tHe lengtH and flexibility of tHe two wings revealed important structural features tHat dictate tHe potency and selectivity of RNase H inHibition as well as tHe observed antiviral activity. Our current medicinal cHemistry data also revealed tHat tHe RNase H biocHemical inHibition largely correlated ...
Karen A Kirby - One of the best experts on this subject based on the ideXlab platform.
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pHarmacopHore based design of novel 3 Hydroxypyrimidine 2 4 dione subtypes as inHibitors of Hiv reverse transcriptase associated RNase H tolerance of a nonflexible linker
European Journal of Medicinal Chemistry, 2019Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Zhengqiang WangAbstract:Abstract THe pHarmacopHore of active site inHibitors of Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting tHe cHelating core and tHe HydropHobic aromatics. We report Herein tHat novel 3-Hydroxypyrimidine-2,4-dione (HPD) subtypes witH a nonflexible C-6 carbonyl linkage exHibited potent and selective biocHemical inHibitory profiles witH strong RNase H inHibition at low nM, weak to moderate integrase strand transfer (INST) inHibition at low μM, and no to marginal RT polymerase (pol) inHibition up to 10 μM. A few analogues also demonstrated significant antiviral activity witHout cytotoxicity. THe overall inHibitory profile is comparable to or better tHan tHat of previous HPD subtypes witH a flexible C-6 linker, suggesting tHat tHe nonflexible carbonyl linker can be tolerated in tHe design of novel HIV RNase H active site inHibitors.
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6 aryltHio 3 Hydroxypyrimidine 2 4 diones potently inHibited Hiv reverse transcriptase associated RNase H witH antiviral activity
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Jiashu Xie, Michael A Parniak, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function not targeted by current drugs. AltHougH a few cHemotypes Have been reported to inHibit HIV RNase H in biocHemical assays, tHeir general lack of significant antiviral activity in cell culture necessitates continued efforts in identifying HigHly potent RNase H inHibitors to confer antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-aryltHio subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays tHese new analogues inHibited RT RNase H in single-digit nanomolar range witHout inHibiting RT polymerase (pol) at concentrations up to 10 μM, amounting to exceptional biocHemical inHibitory selectivity. Many analogues also inHibited integrase strand transfer (INST) activity in low to sub micromolar range. More importantly, most analogues inHibited HIV in low micromolar range witHout cytotoxicity. In tHe end, compound 13j (RNase H IC50 = 0.005 μM; RT pol IC50 = 10 μM; INST IC50 = 4.0 μM; antiviral EC50 = 7.7 μM; CC50 > 100 μM) represents tHe best analogues witHin tHis series. THese results cHaracterize tHe new 6-aryltHio-HPD subtype as a promising scaffold for HIV RNase H inHibitor discovery.
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6 bipHenylmetHyl 3 Hydroxypyrimidine 2 4 diones potently and selectively inHibited Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Stefan G SarafianosAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains an unvalidated drug target. Reported HIV RNase H inHibitors generally lack significant antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-bipHenylmetHyl subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays, analogues of tHis new subtype potently inHibited RT RNase H in low nanomolar range witHout inHibiting RT polymerase (pol) or integrase strand transfer (INST) at tHe HigHest concentrations tested. In cell-based assays, a few analogues inHibited HIV in low micromolar range witHout cytotoxicity at concentrations up to 100 μM.
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design syntHesis and biological evaluations of n Hydroxy tHienopyrimidine 2 4 diones as inHibitors of Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2017Co-Authors: Jayakanth Kankanala, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Zhengqiang WangAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is tHe only HIV enzymatic function not targeted by current antiviral drugs. AltHougH various cHemotypes Have been reported to inHibit HIV RNase H, few Have sHown significant antiviral activities. We report Herein tHe design, syntHesis and biological evaluation of a novel N -Hydroxy tHienopyrimidine-2,3-dione cHemotype ( 11 ) wHicH potently and selectively inHibited RNase H witH considerable potency against HIV-1 in cell culture. Current structure-activity-relationsHip (SAR) identified analogue 11d as a nanomolar inHibitor of RNase H (IC 50 = 0.04 μM) witH decent antiviral potency (EC 50 = 7.4 μM) and no cytotoxicity (CC 50 > 100 μM). In extended biocHemical assays compound 11d did not inHibit RT polymerase (pol) wHile inHibiting integrase strand transfer (INST) witH 53 fold lower potency (IC 50 = 2.1 μM) tHan RNase H inHibition. CrystallograpHic and molecular modeling studies confirmed tHe RNase H active site binding mode.
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double winged 3 Hydroxypyrimidine 2 4 diones potent and selective inHibition against Hiv 1 RNase H witH significant antiviral activity
Journal of Medicinal Chemistry, 2017Co-Authors: Sanjeev Kumar V Vernekar, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Nataliya S Myshakina, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function yet to be exploited as an antiviral target. One of tHe possible cHallenges may be tHat targeting HIV RNase H is confronted witH a steep substrate barrier. We Have previously reported a 3-Hydroxypyrimidine-2,4-dione (HPD) subtype tHat potently and selectively inHibited RNase H witHout inHibiting HIV in cell culture. We report Herein a critical redesign of tHe HPD cHemotype featuring an additional wing at tHe C5 position tHat led to drastically improved RNase H inHibition and significant antiviral activity. Structure–activity relationsHip (SAR) concerning primarily tHe lengtH and flexibility of tHe two wings revealed important structural features tHat dictate tHe potency and selectivity of RNase H inHibition as well as tHe observed antiviral activity. Our current medicinal cHemistry data also revealed tHat tHe RNase H biocHemical inHibition largely correlated ...
Zhengqiang Wang - One of the best experts on this subject based on the ideXlab platform.
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pHarmacopHore based design of novel 3 Hydroxypyrimidine 2 4 dione subtypes as inHibitors of Hiv reverse transcriptase associated RNase H tolerance of a nonflexible linker
European Journal of Medicinal Chemistry, 2019Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Zhengqiang WangAbstract:Abstract THe pHarmacopHore of active site inHibitors of Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting tHe cHelating core and tHe HydropHobic aromatics. We report Herein tHat novel 3-Hydroxypyrimidine-2,4-dione (HPD) subtypes witH a nonflexible C-6 carbonyl linkage exHibited potent and selective biocHemical inHibitory profiles witH strong RNase H inHibition at low nM, weak to moderate integrase strand transfer (INST) inHibition at low μM, and no to marginal RT polymerase (pol) inHibition up to 10 μM. A few analogues also demonstrated significant antiviral activity witHout cytotoxicity. THe overall inHibitory profile is comparable to or better tHan tHat of previous HPD subtypes witH a flexible C-6 linker, suggesting tHat tHe nonflexible carbonyl linker can be tolerated in tHe design of novel HIV RNase H active site inHibitors.
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design syntHesis and biological evaluations of n Hydroxy tHienopyrimidine 2 4 diones as inHibitors of Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2017Co-Authors: Jayakanth Kankanala, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Zhengqiang WangAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is tHe only HIV enzymatic function not targeted by current antiviral drugs. AltHougH various cHemotypes Have been reported to inHibit HIV RNase H, few Have sHown significant antiviral activities. We report Herein tHe design, syntHesis and biological evaluation of a novel N -Hydroxy tHienopyrimidine-2,3-dione cHemotype ( 11 ) wHicH potently and selectively inHibited RNase H witH considerable potency against HIV-1 in cell culture. Current structure-activity-relationsHip (SAR) identified analogue 11d as a nanomolar inHibitor of RNase H (IC 50 = 0.04 μM) witH decent antiviral potency (EC 50 = 7.4 μM) and no cytotoxicity (CC 50 > 100 μM). In extended biocHemical assays compound 11d did not inHibit RT polymerase (pol) wHile inHibiting integrase strand transfer (INST) witH 53 fold lower potency (IC 50 = 2.1 μM) tHan RNase H inHibition. CrystallograpHic and molecular modeling studies confirmed tHe RNase H active site binding mode.
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6 cycloHexylmetHyl 3 Hydroxypyrimidine 2 4 dione as an inHibitor scaffold of Hiv reverase transcriptase impacts of tHe 3 oH on inHibiting RNase H and polymerase
European Journal of Medicinal Chemistry, 2017Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Zhengqiang WangAbstract:3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile cHemical core in tHe design of inHibitors of Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report Herein tHe design, syntHesis and biological evaluation of an HPD subtype (4) featuring a cycloHexylmetHyl group at tHe C-6 position. Antiviral testing sHowed tHat most analogues of 4 inHibited HIV-1 in tHe low nanomolar to submicromolar range, witHout cytotoxicity at concentrations up to 100 μM. BiocHemically, tHese analogues dually inHibited botH tHe polymerase (pol) and tHe RNase H functions of RT, but not INST. Co-crystal structure of 4a witH RT revealed a nonnucleoside RT inHibitor (NNRTI) binding mode. Interestingly, cHemotype 11, tHe syntHetic precursor of 4 lacking tHe 3-OH group, did not inHibit RNase H wHile potently inHibiting pol. By virtue of tHe potent antiviral activity and biocHemical RNase H inHibition, HPD subtype 4 could provide a viable platform for eventually acHieving potent and selective RNase H inHibition tHrougH furtHer medicinal cHemistry.
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design syntHesis and biological evaluations of Hydroxypyridonecarboxylic acids as inHibitors of Hiv reverse transcriptase associated RNase H
Journal of Medicinal Chemistry, 2016Co-Authors: Jayakanth Kankanala, Stefan G Sarafianos, Karen A Kirby, Daniel J Wilson, Michael A Parniak, Feng Liu, Lena Miller, Eva Nagy, Zhengqiang WangAbstract:Targeting tHe clinically unvalidated reverse transcriptase (RT) associated ribonuclease H (RNase H) for Human immunodeficiency virus (HIV) drug discovery generally entails cHemotypes capable of cHelating two divalent metal ions in tHe RNase H active site. THe Hydroxypyridonecarboxylic acid scaffold Has been implicated in inHibiting Homologous HIV integrase (IN) and influenza endonuclease via metal cHelation. We report Herein tHe design, syntHesis, and biological evaluations of a novel variant of tHe Hydroxypyridonecarboxylic acid scaffold featuring a crucial N-1 benzyl or biarylmetHyl moiety. BiocHemical studies sHow tHat most analogues consistently inHibited HIV RT-associated RNase H in tHe low micromolar range in tHe absence of significant inHibition of RT polymerase or IN. One compound sHowed reasonable cell-based antiviral activity (EC50 = 10 μM). Docking and crystallograpHic studies corroborate favorable binding to tHe active site of HIV RNase H, providing a basis for tHe design of more potent analogues.
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3 Hydroxypyrimidine 2 4 diones as selective active site inHibitors of Hiv reverse transcriptase associated RNase H design syntHesis and biocHemical evaluations
Journal of Medicinal Chemistry, 2016Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Daniel J Wilson, Michael A Parniak, Feng Liu, Lena Miller, Eva Nagy, Zhengqiang WangAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains an unvalidated antiviral target. A major cHallenge of specifically targeting HIV RNase H arises from tHe general lack of selectivity over RT polymerase (pol) and integrase (IN) strand transfer (ST) inHibitions. We report Herein tHe syntHesis and biocHemical evaluations of tHree novel 3-Hydroxypyrimidine-2,4-dione (HPD) subtypes carefully designed to acHieve selective RNase H inHibition. BiocHemical studies sHowed tHe two subtypes witH an N-1 metHyl group (9 and 10) inHibited RNase H in low micromolar range witHout siginificantly inHibiting RT polymerase, wHereas tHe N-1 unsubstituted subtype 11 inHibited RNase H in submicromolar range and RT polymerase in low micromolar range. Subtype 11 also exHibited substantially reduced inHibition in tHe HIV-1 INST assay and no significant cytotoxicity in tHe cell viability assay, suggesting tHat it may be amenable to furtHer structure–activity relationsHip (SAR) ...
Michael A Parniak - One of the best experts on this subject based on the ideXlab platform.
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pHarmacopHore based design of novel 3 Hydroxypyrimidine 2 4 dione subtypes as inHibitors of Hiv reverse transcriptase associated RNase H tolerance of a nonflexible linker
European Journal of Medicinal Chemistry, 2019Co-Authors: Jing Tang, Stefan G Sarafianos, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Zhengqiang WangAbstract:Abstract THe pHarmacopHore of active site inHibitors of Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting tHe cHelating core and tHe HydropHobic aromatics. We report Herein tHat novel 3-Hydroxypyrimidine-2,4-dione (HPD) subtypes witH a nonflexible C-6 carbonyl linkage exHibited potent and selective biocHemical inHibitory profiles witH strong RNase H inHibition at low nM, weak to moderate integrase strand transfer (INST) inHibition at low μM, and no to marginal RT polymerase (pol) inHibition up to 10 μM. A few analogues also demonstrated significant antiviral activity witHout cytotoxicity. THe overall inHibitory profile is comparable to or better tHan tHat of previous HPD subtypes witH a flexible C-6 linker, suggesting tHat tHe nonflexible carbonyl linker can be tolerated in tHe design of novel HIV RNase H active site inHibitors.
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6 aryltHio 3 Hydroxypyrimidine 2 4 diones potently inHibited Hiv reverse transcriptase associated RNase H witH antiviral activity
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Jiashu Xie, Michael A Parniak, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function not targeted by current drugs. AltHougH a few cHemotypes Have been reported to inHibit HIV RNase H in biocHemical assays, tHeir general lack of significant antiviral activity in cell culture necessitates continued efforts in identifying HigHly potent RNase H inHibitors to confer antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-aryltHio subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays tHese new analogues inHibited RT RNase H in single-digit nanomolar range witHout inHibiting RT polymerase (pol) at concentrations up to 10 μM, amounting to exceptional biocHemical inHibitory selectivity. Many analogues also inHibited integrase strand transfer (INST) activity in low to sub micromolar range. More importantly, most analogues inHibited HIV in low micromolar range witHout cytotoxicity. In tHe end, compound 13j (RNase H IC50 = 0.005 μM; RT pol IC50 = 10 μM; INST IC50 = 4.0 μM; antiviral EC50 = 7.7 μM; CC50 > 100 μM) represents tHe best analogues witHin tHis series. THese results cHaracterize tHe new 6-aryltHio-HPD subtype as a promising scaffold for HIV RNase H inHibitor discovery.
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6 bipHenylmetHyl 3 Hydroxypyrimidine 2 4 diones potently and selectively inHibited Hiv reverse transcriptase associated RNase H
European Journal of Medicinal Chemistry, 2018Co-Authors: Lei Wang, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Stefan G SarafianosAbstract:Abstract Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains an unvalidated drug target. Reported HIV RNase H inHibitors generally lack significant antiviral activity. We report Herein tHe design, syntHesis, biocHemical and antiviral evaluations of a new 6-bipHenylmetHyl subtype of tHe 3-Hydroxypyrimidine-2,4-dione (HPD) cHemotype. In biocHemical assays, analogues of tHis new subtype potently inHibited RT RNase H in low nanomolar range witHout inHibiting RT polymerase (pol) or integrase strand transfer (INST) at tHe HigHest concentrations tested. In cell-based assays, a few analogues inHibited HIV in low micromolar range witHout cytotoxicity at concentrations up to 100 μM.
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double winged 3 Hydroxypyrimidine 2 4 diones potent and selective inHibition against Hiv 1 RNase H witH significant antiviral activity
Journal of Medicinal Chemistry, 2017Co-Authors: Sanjeev Kumar V Vernekar, Karen A Kirby, Jing Tang, Andrew D Huber, Mary C Casey, Daniel J Wilson, Jayakanth Kankanala, Michael A Parniak, Nataliya S Myshakina, Stefan G SarafianosAbstract:Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains tHe only virally encoded enzymatic function yet to be exploited as an antiviral target. One of tHe possible cHallenges may be tHat targeting HIV RNase H is confronted witH a steep substrate barrier. We Have previously reported a 3-Hydroxypyrimidine-2,4-dione (HPD) subtype tHat potently and selectively inHibited RNase H witHout inHibiting HIV in cell culture. We report Herein a critical redesign of tHe HPD cHemotype featuring an additional wing at tHe C5 position tHat led to drastically improved RNase H inHibition and significant antiviral activity. Structure–activity relationsHip (SAR) concerning primarily tHe lengtH and flexibility of tHe two wings revealed important structural features tHat dictate tHe potency and selectivity of RNase H inHibition as well as tHe observed antiviral activity. Our current medicinal cHemistry data also revealed tHat tHe RNase H biocHemical inHibition largely correlated ...
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design syntHesis and biological evaluations of Hydroxypyridonecarboxylic acids as inHibitors of Hiv reverse transcriptase associated RNase H
Journal of Medicinal Chemistry, 2016Co-Authors: Jayakanth Kankanala, Stefan G Sarafianos, Karen A Kirby, Daniel J Wilson, Michael A Parniak, Feng Liu, Lena Miller, Eva Nagy, Zhengqiang WangAbstract:Targeting tHe clinically unvalidated reverse transcriptase (RT) associated ribonuclease H (RNase H) for Human immunodeficiency virus (HIV) drug discovery generally entails cHemotypes capable of cHelating two divalent metal ions in tHe RNase H active site. THe Hydroxypyridonecarboxylic acid scaffold Has been implicated in inHibiting Homologous HIV integrase (IN) and influenza endonuclease via metal cHelation. We report Herein tHe design, syntHesis, and biological evaluations of a novel variant of tHe Hydroxypyridonecarboxylic acid scaffold featuring a crucial N-1 benzyl or biarylmetHyl moiety. BiocHemical studies sHow tHat most analogues consistently inHibited HIV RT-associated RNase H in tHe low micromolar range in tHe absence of significant inHibition of RT polymerase or IN. One compound sHowed reasonable cell-based antiviral activity (EC50 = 10 μM). Docking and crystallograpHic studies corroborate favorable binding to tHe active site of HIV RNase H, providing a basis for tHe design of more potent analogues.