627 results on '"Arun K. Ghosh"'
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2. A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication
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Shin-ichiro Hattori, Nobuyo Higashi-Kuwata, Hironori Hayashi, Srinivasa Rao Allu, Jakka Raghavaiah, Haydar Bulut, Debananda Das, Brandon J. Anson, Emma K. Lendy, Yuki Takamatsu, Nobutoki Takamune, Naoki Kishimoto, Kazutaka Murayama, Kazuya Hasegawa, Mi Li, David A. Davis, Eiichi N. Kodama, Robert Yarchoan, Alexander Wlodawer, Shogo Misumi, Andrew D. Mesecar, Arun K. Ghosh, and Hiroaki Mitsuya
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Science - Abstract
Here, using in vitro assays and structural analysis, the authors characterize the anti-SARS-CoV-2 properties of two small molcules, showing these to bind and target the virus main protease (Mpro), and to exhibit a synergistic antiviral effect when combined with remdesivir in vitro.
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- 2021
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3. Total Syntheses of the Proposed Structure of Iriomoteolide-1a, -1b and Synthesis of Three Derivatives for Structural Studies
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Arun K. Ghosh and Hao Yuan
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iriomoteolide-1a ,total synthesis ,macrolides ,cytotoxicity ,ene reaction ,diastereomers ,Biology (General) ,QH301-705.5 - Abstract
Iriomoteolide-1a and iriomoteolide-1b are very potent cytotoxic agents, isolated from marine dinoflagellates. We carried out the enantioselective syntheses of the proposed structures of these natural products. However, our analysis of the NMR spectra of the synthetic iriomoteolide-1a and the natural products revealed that the structures of iriomoteolide-1a and iriomoteolide-1b were assigned incorrectly. Based upon our detailed analysis of the spectral data of the synthetic iriomoteolide-1a and the natural products, we rationally designed three diastereomers of the proposed structure of 1 in an effort to assign the correct structures. The key steps of our syntheses of the proposed structures of iriomoteolides involved a highly diastereoselective ene reaction, a carbocupration that utilized a Gilman reagent, a Julia–Kocienski olefination to couple fragments, and Yamaguchi macrolactonization to form the target macrolactone. This synthetic route was then utilized to carry out syntheses of three diastereomers to the proposed structure of 1. These diastereomeric structures show close similarities to natural iriomoteolide-1a; however, there were differences in their spectral data. While natural iriomoteolides exhibited potent cytotoxicies, our preliminary biological evaluation of synthetic iriomoteolide-1a, iriomoteolide-1b, and all three synthetic derivatives did not show any appreciable cytotoxic properties.
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- 2022
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4. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap–Core Interface of HIV‑1 Protease
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Andres Wong-Sam, Yuan-Fang Wang, Ying Zhang, Arun K. Ghosh, Robert W. Harrison, and Irene T. Weber
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Chemistry ,QD1-999 - Published
- 2018
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5. GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection
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Shin-ichiro Hattori, Nobuyo Higshi-Kuwata, Jakka Raghavaiah, Debananda Das, Haydar Bulut, David A. Davis, Yuki Takamatsu, Kouki Matsuda, Nobutoki Takamune, Naoki Kishimoto, Tadashi Okamura, Shogo Misumi, Robert Yarchoan, Kenji Maeda, Arun K. Ghosh, and Hiroaki Mitsuya
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COVID-19 ,SARS-CoV-2 ,main protease ,antiviral agents ,Microbiology ,QR1-502 - Abstract
ABSTRACT We assessed various newly generated compounds that target the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. Here, we show that two indole-chloropyridinyl-ester derivatives, GRL-0820 and GRL-0920, exerted potent activity against SARS-CoV-2 in cell-based assays performed using VeroE6 cells and TMPRSS2-overexpressing VeroE6 cells. While GRL-0820 and the nucleotide analog remdesivir blocked SARS-CoV-2 infection, viral breakthrough occurred. No significant anti-SARS-CoV-2 activity was found for several compounds reportedly active against SARS-CoV-2 such as lopinavir, nelfinavir, nitazoxanide, favipiravir, and hydroxychroloquine. In contrast, GRL-0920 exerted potent activity against SARS-CoV-2 (50% effective concentration [EC50] = 2.8 μM) and dramatically reduced the infectivity, replication, and cytopathic effect of SARS-CoV-2 without significant toxicity as examined with immunocytochemistry. Structural modeling shows that indole and chloropyridinyl of the derivatives interact with two catalytic dyad residues of Mpro, Cys145 and His41, resulting in covalent bonding, which was verified using high-performance liquid chromatography–mass spectrometry (HPLC/MS), suggesting that the indole moiety is critical for the anti-SARS-CoV-2 activity of the derivatives. GRL-0920 might serve as a potential therapeutic for coronavirus disease 2019 (COVID-19) and might be optimized to generate more-potent anti-SARS-CoV-2 compounds. IMPORTANCE Targeting the main protease (Mpro) of SARS-CoV-2, we identified two indole-chloropyridinyl-ester derivatives, GRL-0820 and GRL-0920, active against SARS-CoV-2, employing RNA-qPCR and immunocytochemistry and show that the two compounds exerted potent activity against SARS-CoV-2. While GRL-0820 and remdesivir blocked SARS-CoV-2 infection, viral breakthrough occurred as examined with immunocytochemistry. In contrast, GRL-0920 completely blocked the infectivity and cytopathic effect of SARS-CoV-2 without significant toxicity. Structural modeling showed that indole and chloropyridinyl of the derivatives interacted with two catalytic dyad residues of Mpro, Cys145 and His41, resulting in covalent bonding, which was verified using HPLC/MS. The present data should shed light on the development of therapeutics for COVID-19, and optimization of GRL-0920 based on the present data is essential to develop more-potent anti-SARS-CoV-2 compounds for treating COVID-19.
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- 2020
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6. Chloropyridinyl Esters of Nonsteroidal Anti-Inflammatory Agents and Related Derivatives as Potent SARS-CoV-2 3CL Protease Inhibitors
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Arun K. Ghosh, Dana Shahabi, Monika Yadav, Satish Kovela, Brandon J. Anson, Emma K. Lendy, Connie Bonham, Devika Sirohi, Carlos A. Brito-Sierra, Shin-ichiro Hattori, Richard Kuhn, Hiroaki Mitsuya, and Andrew D. Mesecar
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indomethacin derivative ,antiviral activity ,COVID-19 ,3CLpro inhibitors ,covalent inhibitors ,ibuprofen derivative ,Organic chemistry ,QD241-441 - Abstract
We report the design and synthesis of a series of new 5-chloropyridinyl esters of salicylic acid, ibuprofen, indomethacin, and related aromatic carboxylic acids for evaluation against SARS-CoV-2 3CL protease enzyme. These ester derivatives were synthesized using EDC in the presence of DMAP to provide various esters in good to excellent yields. Compounds are stable and purified by silica gel chromatography and characterized using 1H-NMR, 13C-NMR, and mass spectral analysis. These synthetic derivatives were evaluated in our in vitro SARS-CoV-2 3CLpro inhibition assay using authentic SARS-CoV-2 3CLpro enzyme. Compounds were also evaluated in our in vitro antiviral assay using quantitative VeroE6 cell-based assay with RNAqPCR. A number of compounds exhibited potent SARS-CoV-2 3CLpro inhibitory activity and antiviral activity. Compound 9a was the most potent inhibitor, with an enzyme IC50 value of 160 nM. Compound 13b exhibited an enzyme IC50 value of 4.9 µM. However, it exhibited a potent antiviral EC50 value of 24 µM in VeroE6 cells. Remdesivir, an RdRp inhibitor, exhibited an antiviral EC50 value of 2.4 µM in the same assay. We assessed the mode of inhibition using mass spectral analysis which suggested the formation of a covalent bond with the enzyme. To obtain molecular insight, we have created a model of compound 9a bound to SARS-CoV-2 3CLpro in the active site.
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- 2021
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7. Mechanism of Darunavir (DRV)’s High Genetic Barrier to HIV-1 Resistance: A Key V32I Substitution in Protease Rarely Occurs, but Once It Occurs, It Predisposes HIV-1 To Develop DRV Resistance
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Manabu Aoki, Debananda Das, Hironori Hayashi, Hiromi Aoki-Ogata, Yuki Takamatsu, Arun K. Ghosh, and Hiroaki Mitsuya
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darunavir ,genetic barrier ,drug resistance ,dual mechanism ,HIV-1 ,V32I ,Microbiology ,QR1-502 - Abstract
ABSTRACT Darunavir (DRV) has bimodal activity against HIV-1 protease, enzymatic inhibition and protease dimerization inhibition, and has an extremely high genetic barrier against development of drug resistance. We previously generated a highly DRV-resistant HIV-1 variant (HIVDRVRP51). We also reported that four amino acid substitutions (V32I, L33F, I54M, and I84V) identified in the protease of HIVDRVRP51 are largely responsible for its high-level resistance to DRV. Here, we attempted to elucidate the role of each of the four amino acid substitutions in the development of DRV resistance. We found that V32I is a key substitution, which rarely occurs, but once it occurs, it predisposes HIV-1 to develop high-level DRV resistance. When two infectious recombinant HIV-1 clones carrying I54M and I84V (rHIVI54M and rHIVI84V, respectively) were selected in the presence of DRV, V32I emerged, and the virus rapidly developed high-level DRV resistance. rHIVV32I also developed high-level DRV resistance. However, wild-type HIVNL4-3 (rHIVWT) failed to acquire V32I and did not develop DRV resistance. Compared to rHIVWT, rHIVV32I was highly susceptible to DRV and had significantly reduced fitness, explaining why V32I did not emerge upon selection of rHIVWT with DRV. When the only substitution is at residue 32, structural analysis revealed much stronger van der Waals interactions between DRV and I-32 than between DRV and V-32. These results suggest that V32I is a critical amino acid substitution in multiple pathways toward HIV-1’s DRV resistance development and elucidate, at least in part, a mechanism of DRV’s high genetic barrier to development of drug resistance. The results also show that attention should be paid to the initiation or continuation of DRV-containing regimens in people with HIV-1 containing the V32I substitution. IMPORTANCE Darunavir (DRV) is the only protease inhibitor (PI) recommended as a first-line therapeutic and represents the most widely used PI for treating HIV-1-infected individuals. DRV possesses a high genetic barrier to development of HIV-1’s drug resistance. However, the mechanism(s) of the DRV’s high genetic barrier remains unclear. Here, we show that the preexistence of certain single amino acid substitutions such as V32I, I54M, A71V, and I84V in HIV-1 protease facilitates the development of high-level DRV resistance. Interestingly, all in vitro-selected highly DRV-resistant HIV-1 variants acquired V32I but never emerged in wild-type HIV (HIVWT), and V32I itself rendered HIV-1 more sensitive to DRV and reduced viral fitness compared to HIVWT, strongly suggesting that the emergence of V32I plays a critical role in the development of HIV-1’s resistance to DRV. Our results would be of benefit in the treatment of HIV-1-infected patients receiving DRV-containing regimens.
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- 2018
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8. Activation of RAF1 (c-RAF) by the Marine Alkaloid Lasonolide A Induces Rapid Premature Chromosome Condensation
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Rozenn Jossé, Yong-Wei Zhang, Valentin Giroux, Arun K. Ghosh, Ji Luo, and Yves Pommier
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chromosome condensation ,c-raf ,lasonolide A ,shRNA ,myosin phosphatase ,Biology (General) ,QH301-705.5 - Abstract
Lasonolide A (LSA), a potent antitumor polyketide from the marine sponge, Forcepia sp., induces rapid and reversible protein hyperphosphorylation and premature chromosome condensation (PCC) at nanomolar concentrations independent of cyclin-dependent kinases. To identify cellular targets of LSA, we screened 2951 shRNAs targeting a pool of human kinases and phosphatases (1140 RefSeqs) to identify genes that modulate PCC in response to LSA. This led to the identification of RAF1 (C-RAF) as a mediator of LSA-induced PCC, as shRNAs against RAF1 conferred resistance to LSA. We found that LSA induced RAF1 phosphorylation on Serine 338 within minutes in human colorectal carcinoma HCT-116, ovarian carcinoma OVCAR-8, and Burkitt’s lymphoma CA46 cell lines. RAF1 depletion by siRNAs attenuated LSA-induced PCC in HCT-116 and OVCAR-8 cells. Furthermore, mouse embryonic fibroblasts (MEF) with homozygous deletion in Raf1, but not deletion in the related kinase Braf, were resistant to LSA-induced PCC. Complementation of Raf1−/− MEFs with wild-type human RAF1, but not with kinase-dead RAF1 mutant, restored LSA-induced PCC. Finally, the Raf inhibitor sorafenib, but not the MEK inhibitor AZD6244, effectively suppressed LSA-induced PCC. Our findings implicate a previously unknown, MAPK-independent role of RAF1 in chromatin condensation and potent activation of this pathway by LSA.
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- 2015
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9. A Mouse Model for Betacoronavirus Subgroup 2c Using a Bat Coronavirus Strain HKU5 Variant
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Sudhakar Agnihothram, Boyd L. Yount, Eric F. Donaldson, Jeremy Huynh, Vineet D. Menachery, Lisa E. Gralinski, Rachel L. Graham, Michelle M. Becker, Sakshi Tomar, Trevor D. Scobey, Heather L. Osswald, Alan Whitmore, Robin Gopal, Arun K. Ghosh, Andrew Mesecar, Maria Zambon, Mark Heise, Mark R. Denison, and Ralph S. Baric
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Microbiology ,QR1-502 - Abstract
ABSTRACT Cross-species transmission of zoonotic coronaviruses (CoVs) can result in pandemic disease outbreaks. Middle East respiratory syndrome CoV (MERS-CoV), identified in 2012, has caused 182 cases to date, with ~43% mortality, and no small animal model has been reported. MERS-CoV and Pipistrellus bat coronavirus (BtCoV) strain HKU5 of Betacoronavirus (β-CoV) subgroup 2c share >65% identity at the amino acid level in several regions, including nonstructural protein 5 (nsp5) and the nucleocapsid (N) protein, which are significant drug and vaccine targets. BtCoV HKU5 has been described in silico but has not been shown to replicate in culture, thus hampering drug and vaccine studies against subgroup 2c β-CoVs. We report the synthetic reconstruction and testing of BtCoV HKU5 containing the severe acute respiratory syndrome (SARS)-CoV spike (S) glycoprotein ectodomain (BtCoV HKU5-SE). This virus replicates efficiently in cell culture and in young and aged mice, where the virus targets airway and alveolar epithelial cells. Unlike some subgroup 2b SARS-CoV vaccines that elicit a strong eosinophilia following challenge, we demonstrate that BtCoV HKU5 and MERS-CoV N-expressing Venezuelan equine encephalitis virus replicon particle (VRP) vaccines do not cause extensive eosinophilia following BtCoV HKU5-SE challenge. Passage of BtCoV HKU5-SE in young mice resulted in enhanced virulence, causing 20% weight loss, diffuse alveolar damage, and hyaline membrane formation in aged mice. Passaged virus was characterized by mutations in the nsp13, nsp14, open reading frame 5 (ORF5) and M genes. Finally, we identified an inhibitor active against the nsp5 proteases of subgroup 2c β-CoVs. Synthetic-genome platforms capable of reconstituting emerging zoonotic viral pathogens or their phylogenetic relatives provide new strategies for identifying broad-based therapeutics, evaluating vaccine outcomes, and studying viral pathogenesis. IMPORTANCE The 2012 outbreak of MERS-CoV raises the specter of another global epidemic, similar to the 2003 SARS-CoV epidemic. MERS-CoV is related to BtCoV HKU5 in target regions that are essential for drug and vaccine testing. Because no small animal model exists to evaluate MERS-CoV pathogenesis or to test vaccines, we constructed a recombinant BtCoV HKU5 that expressed a region of the SARS-CoV spike (S) glycoprotein, thereby allowing the recombinant virus to grow in cell culture and in mice. We show that this recombinant virus targets airway epithelial cells and causes disease in aged mice. We use this platform to (i) identify a broad-spectrum antiviral that can potentially inhibit viruses closely related to MERS-CoV, (ii) demonstrate the absence of increased eosinophilic immune pathology for MERS-CoV N protein-based vaccines, and (iii) mouse adapt this virus to identify viral genetic determinants of cross-species transmission and virulence. This study holds significance as a strategy to control newly emerging viruses.
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- 2014
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10. Delineation of the G Protein-Coupled Receptor Kinase Phosphorylation Sites Within the D1 Dopamine Receptor and Their Role in Regulating Receptor Function
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Nora S. Madaras, Michele L. Rankin, R. Benjamin Free, Raphael Haider, Julia Drube, Arun K. Ghosh, John JG. Tesmer, Carsten Hoffmann, David R. Sibley, and Amy E. Moritz
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- 2023
11. Four decades of continuing innovations in the development of antiretroviral therapy for HIV/AIDS: Progress to date and future challenges
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Arun K. Ghosh
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General Medicine - Published
- 2023
12. Beyond darunavir: recent development of next generation HIV-1 protease inhibitors to combat drug resistance
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Arun K. Ghosh, Irene T. Weber, and Hiroaki Mitsuya
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Drug Resistance ,Metals and Alloys ,HIV Protease Inhibitors ,General Chemistry ,Crystallography, X-Ray ,Ether ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,HIV Protease ,Drug Design ,Drug Resistance, Viral ,HIV-1 ,Materials Chemistry ,Ceramics and Composites ,Peptides ,Darunavir - Abstract
We report our recent development of a conceptually new generation of exceptionally potent non-peptidic HIV-1 protease inhibitors that displayed excellent pharmacological and drug-resistance profiles. Our X-ray structural studies of darunavir and other designed inhibitors from our laboratories led us to create a variety of inhibitors incorporating fused ring polycyclic ethers and aromatic heterocycles to promote hydrogen bonding interactions with the backbone atoms of HIV-1 protease as well as van der Waals interactions with residues in the S2 and S2' subsites. We have also incorporated specific functionalities to enhance van der Waals interactions in the S1 and S1' subsites. The combined effects of these structural templates are critical to the inhibitors' exceptional potency and drug-like properties. We highlight here our molecular design strategies to promote backbone hydrogen bonding interactions to combat drug-resistance and specific design of polycyclic ether templates to mimic peptide-like bonds in the HIV-1 protease active site. Our medicinal chemistry and drug development efforts led to the development of new generation inhibitors significantly improved over darunavir and displaying unprecedented antiviral activity against multidrug-resistant HIV-1 variants.
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- 2022
13. Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation
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Arun K. Ghosh, Jennifer L. Mishevich, Satish Kovela, Ryan Shaktah, Ajay K. Ghosh, Megan Johnson, Yuan-Fang Wang, Andres Wong-Sam, Johnson Agniswamy, Masayuki Amano, Yuki Takamatsu, Shin-ichiro Hattori, Irene T. Weber, and Hiroaki Mitsuya
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Pharmacology ,Organic Chemistry ,Drug Discovery ,General Medicine - Published
- 2023
14. Recent Drug Development and Medicinal Chemistry Approaches for the Treatment of SARS-CoV-2 Infection and COVID-19
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Arun K. Ghosh, Jennifer L. Mishevich, Andrew Mesecar, and Hiroaki Mitsuya
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Pharmacology ,Drug Development ,SARS-CoV-2 ,Chemistry, Pharmaceutical ,Organic Chemistry ,Drug Discovery ,Molecular Medicine ,Humans ,General Pharmacology, Toxicology and Pharmaceutics ,Biochemistry ,Antiviral Agents ,COVID-19 Drug Treatment - Abstract
COVID-19, caused by SARS-CoV-2 infection, continues to be a major public health crisis around the globe. Development of vaccines and the first cluster of antiviral drugs has brought promise and hope for prevention and treatment of severe coronavirus disease. However, continued development of newer, safer, and more effective antiviral drugs are critically important to combat COVID-19 and counter the looming pathogenic variants. Studies of the coronavirus life cycle revealed several important biochemical targets for drug development. In the present review, we focus on recent drug design and medicinal chemistry efforts in small molecule drug discovery, including the development of nirmatrelvir that targets viral protein synthesis and remdesivir and molnupiravir that target viral RdRp. These are recent FDA approved drugs for the treatment of COVID-19.
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- 2022
15. Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site mutations of highly drug resistant mutant PRS17
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Johnson Agniswamy, Irene T. Weber, Arun K. Ghosh, and Daniel W. Kneller
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Models, Molecular ,0301 basic medicine ,Proteases ,medicine.medical_treatment ,Biophysics ,HIV Infections ,medicine.disease_cause ,Biochemistry ,Article ,03 medical and health sciences ,Amprenavir ,0302 clinical medicine ,HIV Protease ,Catalytic Domain ,Drug Resistance, Viral ,medicine ,Humans ,Point Mutation ,Protease inhibitor (pharmacology) ,Molecular Biology ,Darunavir ,Mutation ,Protease ,biology ,Chemistry ,Active site ,HIV Protease Inhibitors ,Cell Biology ,Molecular biology ,Multiple drug resistance ,030104 developmental biology ,030220 oncology & carcinogenesis ,HIV-1 ,biology.protein ,medicine.drug - Abstract
The emergence of multidrug resistant (MDR) HIV strains severely reduces the effectiveness of antiretroviral therapy. Clinical inhibitor darunavir (1) has picomolar binding affinity for HIV-1 protease (PR), however, drug resistant variants like PR(S17) show poor inhibition by 1, despite the presence of only two mutated residues in the inhibitor-binding site. Antiviral inhibitors that target MDR proteases like PR(S17) would be valuable as therapeutic agents. Inhibitors 2 and 3 derived from 1 through substitutions at P1, P2 and P2ʹ positions exhibit 3.4- to 500-fold better inhibition than clinical inhibitors for PR(S17) with the exception of amprenavir. Crystal structures of PR(S17)/2 and PR(S17)/3 reveal how these inhibitors target the two active site mutations of PR(S17). The substituted methoxy P2 group of 2 forms new interactions with G48V mutation, while the modified bis-fluoro-benzyl P1 group of 3 forms a halogen interaction with V82S mutation, contributing to improved inhibition of PR(S17).
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- 2021
16. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics
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Andres Wong-Sam, Yuan-Fang Wang, Daniel W. Kneller, Andrey Y. Kovalevsky, Arun K. Ghosh, Robert W. Harrison, and Irene T. Weber
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HIV Protease ,Drug Resistance, Viral ,Mutation ,Materials Chemistry ,Humans ,HIV Protease Inhibitors ,Physical and Theoretical Chemistry ,Molecular Dynamics Simulation ,Crystallography, X-Ray ,Computer Graphics and Computer-Aided Design ,Spectroscopy ,Lopinavir ,Darunavir - Abstract
Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical isolate including 10 mutations associated with resistance to lopinavir and darunavir. Compared to the wild-type protease, PR10x exhibits ∼3-fold decrease in catalytic efficiency and K
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- 2022
17. Evaluation of darunavir-derived HIV-1 protease inhibitors incorporating P2′ amide-derivatives: Synthesis, biological evaluation and structural studies
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Arun K. Ghosh, Dana Shahabi, Maya Kipfmiller, Ajay K. Ghosh, Megan Johnson, Yuan-Fang Wang, Johnson Agniswamy, Masayuki Amano, Irene T. Weber, and Hiroaki Mitsuya
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Organic Chemistry ,Clinical Biochemistry ,Drug Discovery ,Pharmaceutical Science ,Molecular Medicine ,Molecular Biology ,Biochemistry - Published
- 2023
18. Asymmetric 1,2-Carbamoyl Rearrangement of Lithiated Chiral Oxazolidine Carbamates and Diastereoselective Synthesis of α-Hydroxy Amides
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Arun K. Ghosh, Amartyo J. Basu, Che‐Sheng Hsu, and Monika Yadav
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Molecular Structure ,Organic Chemistry ,Stereoisomerism ,General Chemistry ,Carbamates ,Acids ,Amides ,Oxazoles ,Catalysis - Abstract
Asymmetric 1,2-carbamoyl rearrangement of lithiated 2-alkenyl carbamates has been investigated. Deprotonation of chiral 2-alkenyl oxazolidine carbamates with sec-butyllithium in ether at -78 °C followed by warming of the resulting 1-lithio-2-alkenyl derivatives to room temperature resulted in 1,2-carbamoyl rearrangement to provide α-hydroxy amides. The rearrangement proceeded with excellent diastereoselectivity and in good to excellent isolated yield of the α-hydroxy amide derivatives. The substrate scope of the reaction was investigated with a variety of 2-alkenyl and benzyl oxazolidine carbamates. A stereochemical model is provided to explain the stereochemical outcome associated with the rearrangement. Acid-catalyzed removal of the chiral oxazolidine afforded α-hydroxy acid in high optical purity.
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- 2022
19. Design, Synthesis and X‐Ray Structural Studies of Potent HIV‐1 Protease Inhibitors Containing C‐4 Substituted Tricyclic Hexahydro‐Furofuran Derivatives as P2 Ligands
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Arun K. Ghosh, Satish Kovela, Ashish Sharma, Dana Shahabi, Ajay K. Ghosh, Denver R. Hopkins, Monika Yadav, Megan E. Johnson, Johnson Agniswamy, Yuan‐Fang Wang, Shin‐Ichiro Hattori, Nobuyo Higashi‐Kuwata, Manabu Aoki, Masayuki Amano, Irene T. Weber, and Hiroaki Mitsuya
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Pharmacology ,X-Rays ,Organic Chemistry ,HIV Protease Inhibitors ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Article ,Structure-Activity Relationship ,HIV Protease ,Drug Design ,Drug Discovery ,HIV-1 ,Molecular Medicine ,General Pharmacology, Toxicology and Pharmaceutics - Abstract
The design, synthesis, X-ray structural, and biological evaluation of a series of highly potent HIV-1 protease inhibitors are reported herein. These inhibitors incorporated novel cyclohexane-fused tricyclic bis-tetrahydrofuran as P2 ligands in combination with a variety of P1 and P2’-ligands. The inhibitor with a difluoromethylphenyl P1 ligand and a cyclopropylaminobenzothiazole P2’ ligand exhibited the most potent antiviral activity. Also, it maintained potent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The corresponding inhibitor with an enantiomeric ligand was significantly less potent in these antiviral assays. The new P2 ligands were synthesized in optically active form using enzymatic desymmetrization of meso-diols as the key step. To obtain molecular insight, two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined and structural analyses have been highlighted.
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- 2022
20. Herboxidiene Features That Mediate Conformation-Dependent SF3B1 Interactions to Inhibit Splicing
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Srinivasa Rao Allu, Adriana Gamboa Lopez, Hannah M. Maul-Newby, Guddeti Chandrashekar Reddy, Melissa S. Jurica, Patricia Mendez, and Arun K. Ghosh
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Models, Molecular ,0301 basic medicine ,Protein Conformation ,Messenger ,01 natural sciences ,Biochemistry ,Adenosine Triphosphate ,Models ,Chemistry ,Temperature ,General Medicine ,Biological Sciences ,Small molecule ,5.1 Pharmaceuticals ,RNA splicing ,Molecular Medicine ,RNA Splicing Factors ,Fatty Alcohols ,Development of treatments and therapeutic interventions ,Protein Binding ,Spliceosome ,Base pair ,RNA Splicing ,Context (language use) ,Article ,Structure-Activity Relationship ,03 medical and health sciences ,Humans ,snRNP ,RNA, Messenger ,Pyrans ,U2 Small Nuclear ,Binding Sites ,Base Sequence ,010405 organic chemistry ,Organic Chemistry ,Intron ,Molecular ,Ribonucleoprotein ,Ribonucleoprotein, U2 Small Nuclear ,Phosphoproteins ,0104 chemical sciences ,030104 developmental biology ,Hela Cells ,Chemical Sciences ,Spliceosomes ,Biophysics ,RNA ,Herboxidiene ,HeLa Cells - Abstract
Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Employing an inactive herboxidiene analog (iHB) as a competitor, we investigated factors that influence inhibitor interactions with SF3B to inhibit pre-mRNA splicing in vitro. Order-of addition experiments show that inhibitor interactions are long lasting and affected by both temperature and the presence of ATP. Our data are also consistent with the idea that not all SF3B conformations observed in structural studies are conducive to productive inhibitor interactions. Notably, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure activity relationship analysis of the splicing inhibitor herboxidiene. We identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. Analyzing our data in the context of recent structural models of SF3B interactions with inhibitors, our results lead us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 sidechains in the inhibitor binding channel are required to maintain inhibitor occupancy while counteracting the SF3B transition to a closed state that is required for stable U2 snRNP interactions with the intron.
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- 2021
21. A Structure-Based Discovery Platform for BACE2 and the Development of Selective BACE Inhibitors
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Andrew D. Mesecar, Yu-Chen Yen, Jagannadharao Tirlangi, Annalissa M Kammeyer, and Arun K. Ghosh
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Drug ,Physiology ,Cognitive Neuroscience ,media_common.quotation_subject ,Biochemistry ,Article ,law.invention ,Type ii diabetes ,03 medical and health sciences ,0302 clinical medicine ,Alzheimer Disease ,law ,Escherichia coli ,Aspartic Acid Endopeptidases ,Humans ,Crystallization ,030304 developmental biology ,media_common ,0303 health sciences ,Chemistry ,Cell Biology ,General Medicine ,Combinatorial chemistry ,Diabetes Mellitus, Type 2 ,Structure based ,Amyloid Precursor Protein Secretases ,Selectivity ,030217 neurology & neurosurgery - Abstract
The ability to perform routine structure-guided drug design for selective BACE inhibitors has been limited because of the lack of robust platform for BACE2 expression, purification, and crystallization. To overcome this limitation, we developed a platform that produces 2–3 mg of pure BACE2 protein per liter of E. coli culture, and we used this protein to design macrocyclic compounds that potently and selectively inhibit BACE1 over BACE2. Compound 2 was found to potently inhibit BACE 1 (K(i) = 5 nM) with a selectivity of 214-fold over BACE2. The X-ray crystal structures of unbound BACE2 (2.2 Å) and BACE2 bound to compound 3 (3.0 Å and K(i) = 7 nM) were determined and compared to the X-ray structures of BACE1 revealing the S1–S3 subsite as a selectivity determinant. This platform should enable a more rapid development of new and selective BACE inhibitors for the treatment of Alzheimer’s disease or type II diabetes.
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- 2021
22. Aspartic Acid Proteases as Therapeutic Targets
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Arun K. Ghosh, Arun K. Ghosh and Arun K. Ghosh, Arun K. Ghosh
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- 2011
23. The Chiron Approach to (3R,3aS,6aR)-Hexahydrofuro[2,3-b]furan-3-ol, a Key Subunit of HIV-1 Protease Inhibitor Drug, Darunavir
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Arun K. Ghosh, Shivaji B. Markad, and William L. Robinson
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Anomer ,biology ,010405 organic chemistry ,Chemistry ,Stereochemistry ,Ligand ,Organic Chemistry ,Enantioselective synthesis ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,HIV-1 protease ,medicine ,biology.protein ,Protease inhibitor (pharmacology) ,Stereoselectivity ,Lewis acids and bases ,Darunavir ,medicine.drug - Abstract
We describe an enantioselective synthesis of (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-ol which is a key subunit of darunavir, a widely used HIV-1 protease inhibitor drug for the treatment of HIV/AIDS patients. The synthesis was achieved in optically pure form utilizing commercially available sugar derivatives as the starting material. The key steps involve a highly stereoselective substrate-controlled hydrogenation, a Lewis acid catalyzed anomeric reduction of a 1,2-O-isopropylidene-protected glycofuranoside, and a Baeyer-Villiger oxidation of a tetrahydrofuranyl-2-aldehyde derivative. This optically active ligand alcohol was converted to darunavir efficiently.
- Published
- 2020
24. Structure-based Design of Drugs and Other Bioactive Molecules: Tools and Strategies
- Author
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Arun K. Ghosh, Sandra Gemma and Arun K. Ghosh, Sandra Gemma
- Published
- 2014
25. Fluorine Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System-Targeting HIV-1 Protease Inhibitors In Vitro
- Author
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Masayuki Amano, Ravikiran S. Yedidi, Pedro Miguel Salcedo-Gómez, Hironori Hayashi, Kazuya Hasegawa, Cuthbert D. Martyr, Arun K. Ghosh, and Hiroaki Mitsuya
- Subjects
Central Nervous System ,Pharmacology ,Infectious Diseases ,HIV Protease ,Blood-Brain Barrier ,HIV-1 ,Humans ,Pharmacology (medical) ,Fluorine ,HIV Protease Inhibitors ,Virus Replication ,Antiviral Agents - Abstract
To date, there are no specific treatment regimens for HIV-1-related central nervous system (CNS) complications, such as HIV-1-associated neurocognitive disorders (HAND). Here, we report that two newly generated CNS-targeting HIV-1 protease (PR) inhibitors (PIs), GRL-08513 and GRL-08613, which have a P1-3,5-bis-fluorophenyl or P1-para-monofluorophenyl ring and P2-tetrahydropyrano-tetrahydrofuran (Tp-THF) with a sulfonamide isostere, are potent against wild-type HIV-1 strains and multiple clinically isolated HIV-1 strains (50% effective concentration [EC(50)]: 0.0001 to ∼0.0032 μM). As assessed with HIV-1 variants that had been selected in vitro to propagate at a 5 μM concentration of each HIV-1 PI (atazanavir, lopinavir, or amprenavir), GRL-08513 and GRL-08613 efficiently inhibited the replication of these highly PI-resistant variants (EC(50): 0.003 to ∼0.006 μM). GRL-08513 and GRL-08613 also maintained their antiviral activities against HIV-2(ROD) as well as severely multidrug-resistant clinical HIV-1 variants. Additionally, when we assessed with the in vitro blood-brain barrier (BBB) reconstruction system, GRL-08513 and GRL-08613 showed the most promising properties of CNS penetration among the evaluated compounds, including the majority of FDA-approved combination antiretroviral therapy (cART) drugs. In the crystallographic analysis of compound-PR complexes, it was demonstrated that the Tp-THF rings at the P2 moiety of GRL-08513 and GRL-08613 form robust hydrogen bond interactions with the active site of HIV-1 PR. Furthermore, both the P1-3,5-bis-fluorophenyl- and P1-para-monofluorophenyl rings sustain greater contact surfaces and form stronger van der Waals interactions with PR than is the case with darunavir-PR complex. Taken together, these results strongly suggest that GRL-08513 and GRL-08613 have favorable features for patients infected with wild-type/multidrug-resistant HIV-1 strains and might serve as candidates for a preventive and/or therapeutic agent for HAND and other CNS complications.
- Published
- 2022
26. Benzimidazole-Based FabI Inhibitors: A Promising Novel Scaffold for Anti-staphylococcal Drug Development
- Author
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Tina Mistry, Lena Truong, Michael E. Johnson, Arun K. Ghosh, and Shahila Mehboob
- Subjects
0301 basic medicine ,Staphylococcus aureus ,Benzimidazole ,030106 microbiology ,medicine.disease_cause ,Gene Expression Regulation, Enzymologic ,Article ,Microbiology ,Inhibitory Concentration 50 ,Structure-Activity Relationship ,03 medical and health sciences ,chemistry.chemical_compound ,Drug Discovery ,medicine ,Cloning, Molecular ,Mode of action ,Francisella tularensis ,Uncategorized ,chemistry.chemical_classification ,Molecular Structure ,biology ,Drug discovery ,Active site ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) ,Anti-Bacterial Agents ,030104 developmental biology ,Infectious Diseases ,Enzyme ,chemistry ,Drug development ,Biochemistry ,Drug Design ,biology.protein ,Benzimidazoles - Abstract
The enoyl-ACP reductase (FabI) enzyme is a well validated target for anti-staphylococcal drug discovery and development. With the goal of finding alternate therapeutics for drug-resistant strains of Staphylococcus aureus, such as methicillin-resistant S. aureus (MRSA), our previously published series of benzimidazole-based inhibitors of the FabI enzyme from Francisella tularensis (FtFabI) have been evaluated against FabI from S. aureus (SaFabI). We report here the preliminary structure-activity relationship of this series and the prioritization of compounds toward lead optimization. Mutational studies have identified key residues that contribute toward stabilizing the inhibitors in the active site of FabI. Mutations that do not significantly impact enzyme function but destabilize inhibitor binding are more likely to occur in nature as organisms evolve to evade the action of antibiotics leading to resistance. Identifying these residues provides guidance for minimizing susceptibility to resistance. Additionally, we have identified compounds that elicit antibacterial activity through off-target effects and observe that close analogs can display differing modes of action (on-target vs off-target) and need to be individually evaluated early on to prioritize compounds for lead optimization. Overall, our data suggest that the benzimidazole scaffold is a promising scaffold for anti-staphylococcal drug development.
- Published
- 2022
- Full Text
- View/download PDF
27. The Assembly-Inducing Laulimalide/Peloruside A Binding Site on Tubulin: Molecular Modeling and Biochemical Studies with [3H]Peloruside A.
- Author
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Tam Luong Nguyen, Xiaoming Xu, Rick Gussio, Arun K. Ghosh, and Ernest Hamel
- Published
- 2010
- Full Text
- View/download PDF
28. Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model.
- Author
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Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh, and Hiroaki Mitsuya
- Published
- 2009
- Full Text
- View/download PDF
29. Lewis Acid-Catalyzed Vinyl Acetal Rearrangement of 4,5-Dihydro-1,3-dioxepines: Stereoselective Synthesis of cis- and trans-2,3-Disubstituted Tetrahydrofurans
- Author
-
Miranda R Belcher and Arun K. Ghosh
- Subjects
Olefin fiber ,010405 organic chemistry ,Organic Chemistry ,Acetal ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Catalysis ,chemistry.chemical_compound ,chemistry ,Stereoselectivity ,Lewis acids and bases ,Isomerization ,Tetrahydrofuran ,Cis–trans isomerism - Abstract
Lewis acid-catalyzed rearrangements of 4,5-dihydro-1,3-dioxepines have been investigated. Rearrangement of vinyl acetals under a variety of conditions resulted in cis- and trans-2,3-disubstituted tetrahydrofuran derivatives in a highly stereoselective manner. Rearrangements at lower temperatures typically provided the cis-2,3-disubstituted tetrahydrofuran carbaldehydes. At higher temperatures, the corresponding trans-2,3-disubstituted tetrahydrofuran carbaldehydes are formed. The requisite substrates for the vinyl acetal rearrangement were synthesized via ring-closing olefin metathesis of bis(allyoxy)methyl derivatives using Grubbs second-generation catalyst followed by olefin isomerization using a catalytic amount of RuCl2(PPh3)3. We examined the substrate scope using substituted aromatic and aliphatic derivatives. Additionally, the rearrangement was utilized in the synthesis of a stereochemically-defined bis-tetrahydrofuran (bis-THF) derivative, which is one of the key structural elements of darunavir, an FDA-approved drug for the treatment of HIV/AIDS.
- Published
- 2020
30. Potent antiviral HIV-1 protease inhibitor combats highly drug resistant mutant PR20
- Author
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Arun K. Ghosh, Johnson Agniswamy, Irene T. Weber, and Daniel W. Kneller
- Subjects
Models, Molecular ,0301 basic medicine ,medicine.medical_treatment ,Dimer ,Mutant ,Molecular Conformation ,Biophysics ,Drug resistance ,Pharmacology ,Crystallography, X-Ray ,Antiviral Agents ,Biochemistry ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,HIV Protease ,HIV-1 protease ,Drug Resistance, Viral ,medicine ,Humans ,Molecular Biology ,Darunavir ,chemistry.chemical_classification ,Protease ,biology ,Chemistry ,HIV Protease Inhibitors ,Cell Biology ,Ligand (biochemistry) ,Kinetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,Mutation ,HIV-1 ,biology.protein ,Tricyclic ,medicine.drug - Abstract
Drug-resistance threatens effective treatment of HIV/AIDS. Clinical inhibitors, including darunavir (1), are ineffective for highly resistant protease mutant PR20, however, antiviral compound 2 derived from 1 with fused tricyclic group at P2, extended amino-benzothiazole P2’ ligand and two fluorine atoms on P1 shows 16-fold better inhibition of PR20 enzyme activity. Crystal structures of PR20 and wild-type PR complexes reveal how the extra groups of 2 counteract the expanded ligand-binding pocket, dynamic flaps, and faster dimer dissociation of PR20.
- Published
- 2019
31. Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors
- Author
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Jagannadharao Tirlangi, Katherine C. Jensen, Andrew D. Mesecar, Annalissa M Kammeyer, Yu-Chen Yen, and Arun K. Ghosh
- Subjects
Macrocyclic Compounds ,Kinetics ,Crystallography, X-Ray ,Biochemistry ,Protein Refolding ,Article ,law.invention ,03 medical and health sciences ,law ,Catalytic Domain ,Cell Line, Tumor ,Drug Discovery ,mental disorders ,Amyloid precursor protein ,Aspartic Acid Endopeptidases ,Humans ,Protease Inhibitors ,Crystallization ,Enzyme Assays ,chemistry.chemical_classification ,0303 health sciences ,biology ,Chemistry ,Drug discovery ,030302 biochemistry & molecular biology ,Isothermal titration calorimetry ,Combinatorial chemistry ,Enzyme assay ,Dissociation constant ,Enzyme ,biology.protein ,Amyloid Precursor Protein Secretases ,Protein Binding - Abstract
BACE1 (Beta-site Amyloid Precursor Protein (APP) Cleaving Enzyme 1) is a promising therapeutic target for Alzheimer’s Disease (AD). However, efficient expression, purification, and crystallization systems are not well described or detailed in the literature nor are approaches for treatment of enzyme kinetic data for potent inhibitors well described. We therefore developed a platform for expression and purification of BACE1, including protein refolding from E.coli inclusion bodies, in addition to optimizing a reproducible crystallization procedure of BACE1 bound with inhibitors. We also report a detailed approach to the proper analysis of enzyme kinetic data for compounds that exhibit either rapid-equilibrium or tight-binding mechanisms. Our methods allow for the purification of ~15 mg of BACE1 enzyme from 1 L of culture which is higher than reported yields in the current literature. To evaluate the data analysis approach developed here, a well-known potent inhibitor and two of its derivatives were tested, analyzed, and compared. The inhibitory constants (K(i)) obtained from the kinetic studies are in agreement with dissociation constants (K(d)) that were also determined using isothermal titration calorimetry (ITC) experiments. The X-ray structures of these three compounds in complex with BACE1 were readily obtained and provide important insight into the structure and thermodynamics of the BACE1-inhibitor interactions.
- Published
- 2019
32. Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure-Activity Relationship, and X-ray Structural Studies
- Author
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Brandon J. Anson, Dana Shahabi, Emma K. Lendy, Andrew D. Mesecar, Monika Yadav, Hiroaki Mitsuya, Jakka Raghavaiah, Nobuyo Higashi-Kuwata, Arun K. Ghosh, and Shin-ichiro Hattori
- Subjects
Indoles ,Stereochemistry ,Pyridines ,medicine.medical_treatment ,Molecular Dynamics Simulation ,Crystallography, X-Ray ,Article ,chemistry.chemical_compound ,Structure-Activity Relationship ,Drug Discovery ,Chlorocebus aethiops ,medicine ,Structure–activity relationship ,Animals ,Humans ,Protease Inhibitors ,Carboxylate ,Binding site ,IC50 ,Vero Cells ,Coronavirus 3C Proteases ,Indole test ,Protease ,Alanine ,Binding Sites ,Chemistry ,SARS-CoV-2 ,COVID-19 ,Adenosine Monophosphate ,RNA Polymerase Inhibitor ,Vero cell ,Molecular Medicine - Abstract
Here, we report the synthesis, structure-activity relationship studies, enzyme inhibition, antiviral activity, and X-ray crystallographic studies of 5-chloropyridinyl indole carboxylate derivatives as a potent class of SARS-CoV-2 chymotrypsin-like protease inhibitors. Compound 1 exhibited a SARS-CoV-2 3CLpro inhibitory IC50 value of 250 nM and an antiviral EC50 value of 2.8 µM in VeroE6 cells. Remdesivir, an RNA-dependent RNA polymerase inhibitor, showed an antiviral EC50 value of 1.2 µM in the same assay. Compound 1 showed comparable antiviral activity with remdesivir in immunocytochemistry assays. Compound 7d with an N-allyl derivative showed the most potent enzyme inhibitory IC50 value of 73 nM. To obtain molecular insight into the binding properties of these molecules, X-ray crystal structures of compounds 2, 7b, and 9d-bound to SARS-CoV 3CLpro were determined, and their binding properties were compared.
- Published
- 2021
33. A convenient synthesis of (3S,3aR,5R,7aS,8S)-Hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-ol, a high-affinity nonpeptidyl ligand for highly potent HIV-1 protease inhibitors
- Author
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Arun K. Ghosh and Shivaji B. Markad
- Subjects
Organic Chemistry ,Drug Discovery ,Biochemistry - Published
- 2022
34. Chloropyridinyl Esters of Nonsteroidal Anti-Inflammatory Agents and Related Derivatives as Potent SARS-CoV-2 3CL Protease Inhibitors
- Author
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Carlos A Brito-Sierra, Andrew D. Mesecar, Devika Sirohi, Satish Kovela, Monika Yadav, Hiroaki Mitsuya, Dana Shahabi, Emma K. Lendy, Arun K. Ghosh, Brandon J. Anson, Shinichiro Hattori, Richard J. Kuhn, and Connie C. Bonham
- Subjects
Halogenation ,Pyridines ,medicine.medical_treatment ,Indomethacin ,Pharmaceutical Science ,Organic chemistry ,Ibuprofen ,indomethacin derivative ,Analytical Chemistry ,chemistry.chemical_compound ,QD241-441 ,Drug Discovery ,Chlorocebus aethiops ,Coronavirus 3C Proteases ,chemistry.chemical_classification ,biology ,Anti-Inflammatory Agents, Non-Steroidal ,Esters ,Molecular Docking Simulation ,Chemistry (miscellaneous) ,Covalent bond ,antiviral activity ,Molecular Medicine ,covalent inhibitors ,Salicylic Acid ,Stereochemistry ,medicine.drug_class ,Antiviral Agents ,Anti-inflammatory ,Article ,3CLpro inhibitors ,medicine ,Animals ,Humans ,Protease Inhibitors ,Physical and Theoretical Chemistry ,IC50 ,Vero Cells ,Protease ,SARS-CoV-2 ,ibuprofen derivative ,Active site ,COVID-19 ,In vitro ,COVID-19 Drug Treatment ,salicylic acid derivative ,Enzyme ,chemistry ,biology.protein ,Salicylic acid - Abstract
We report the design and synthesis of a series of new 5-chloropyridinyl esters of salicylic acid, ibuprofen, indomethacin, and related aromatic carboxylic acids for evaluation against SARS-CoV-2 3CL protease enzyme. These ester derivatives were synthesized using EDC in the presence of DMAP to provide various esters in good to excellent yields. Compounds are stable and purified by silica gel chromatography and characterized using 1H-NMR, 13C-NMR, and mass spectral analysis. These synthetic derivatives were evaluated in our in vitro SARS-CoV-2 3CLpro inhibition assay using authentic SARS-CoV-2 3CLpro enzyme. Compounds were also evaluated in our in vitro antiviral assay using quantitative VeroE6 cell-based assay with RNAqPCR. A number of compounds exhibited potent SARS-CoV-2 3CLpro inhibitory activity and antiviral activity. Compound 9a was the most potent inhibitor, with an enzyme IC50 value of 160 nM. Compound 13b exhibited an enzyme IC50 value of 4.9 µM. However, it exhibited a potent antiviral EC50 value of 24 µM in VeroE6 cells. Remdesivir, an RdRp inhibitor, exhibited an antiviral EC50 value of 2.4 µM in the same assay. We assessed the mode of inhibition using mass spectral analysis which suggested the formation of a covalent bond with the enzyme. To obtain molecular insight, we have created a model of compound 9a bound to SARS-CoV-2 3CLpro in the active site.
- Published
- 2021
35. U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors
- Author
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Arun K. Ghosh, Veronica K. Urabe, Meredith Stevers, Melissa S. Jurica, and Singh, Ravindra N
- Subjects
Secondary ,Molecular biology ,genetic processes ,Artificial Gene Amplification and Extension ,Biochemistry ,environment and public health ,Protein Structure, Secondary ,RNA, Small Nuclear ,RNA structure ,Protein secondary structure ,Multidisciplinary ,Small nuclear RNA ,Nucleotides ,Chemistry ,RNA Conformation ,Nucleotide Mapping ,Genomics ,Cell biology ,Nucleic acids ,RNA splicing ,Medicine ,Research Article ,Protein Structure ,Spliceosome ,General Science & Technology ,Science ,information science ,Nucleotide Sequencing ,Research and Analysis Methods ,Genome Complexity ,Small Nuclear ,Primer Extension ,Genetics ,Humans ,snRNP ,Non-coding RNA ,Molecular Biology Techniques ,Sequencing Techniques ,U2 Small Nuclear ,Biology and life sciences ,urogenital system ,Gene Mapping ,Intron ,Computational Biology ,RNA ,Ribonucleoprotein ,Ribonucleoprotein, U2 Small Nuclear ,Introns ,Protein Subunits ,Macromolecular structure analysis ,Spliceosomes ,health occupations ,Nucleic Acid Conformation ,Generic health relevance ,HeLa Cells - Abstract
U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. We previously found that the first SF3B inhibited-complex is less stable than A-complex and hypothesized that SF3B inhibitors interfere with U2 snRNA secondary structure changes required to form the branch helix. Using RNA chemical modifiers, we probed U2 snRNA structure in A-complex and SF3B inhibited splicing complexes. The reactivity pattern for U2 snRNA in the SF3B inhibited-complex is indistinguishable from that of A-complex, suggesting that they have the same secondary structure conformation, including the branch helix. This observation suggests SF3B inhibited-complex instability does not stem from an alternate RNA conformation and instead points to the inhibitors interfering with protein component interactions that normally stabilize U2 snRNP’s association with an intron. In addition, we probed U2 snRNA in the free U2 snRNP in the presence of SF3B inhibitor and again saw no differences. However, increased protection of nucleotides upstream of Stem I in the absence of SF3A and SF3B proteins suggests a change of secondary structure at the very 5′ end of U2 snRNA. Chemical probing of synthetic U2 snRNA in the absence of proteins results in similar protections and predicts a previously uncharacterized extension of Stem I. Because this stem must be disrupted for SF3A and SF3B proteins to stably join the snRNP, the structure has the potential to influence snRNP assembly and recycling after spliceosome disassembly.
- Published
- 2021
36. Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors
- Author
-
Nicholas A. Larsen, Xiang Liu, Patricia Gee, Andrew Cook, Constantin Cretu, Melissa S. Jurica, Vladimir Pena, Anant A. Agrawal, Tuong-Vi Nguyen, and Arun K. Ghosh
- Subjects
Models, Molecular ,RNA splicing ,Protein Conformation ,Protein subunit ,Science ,General Physics and Astronomy ,Crystallography, X-Ray ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Lactones ,0302 clinical medicine ,Models ,Genetics ,Humans ,snRNP ,Spiro Compounds ,Strand invasion ,030304 developmental biology ,X-ray crystallography ,Pyrans ,Zinc finger ,0303 health sciences ,Multidisciplinary ,U2 Small Nuclear ,Crystallography ,Chemistry ,Cryoelectron Microscopy ,Intron ,Molecular ,General Chemistry ,Ribonucleoprotein ,DNA ,Ribonucleoprotein, U2 Small Nuclear ,Introns ,Cell biology ,Prespliceosome ,Pyrones ,Spliceosomes ,X-Ray ,Nucleic Acid Conformation ,Generic health relevance ,030217 neurology & neurosurgery ,Small nuclear ribonucleoprotein ,Protein Binding - Abstract
Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept., Chemical modulation of intron selection has emerged as a route for cancer therapy. Here, structures of the U2 snRNP’s SF3B module and of prespliceosome- both in complexes with splicing modulators- provide insight into the mechanisms of intron recognition and branch site inactivation.
- Published
- 2021
37. Catalytic function and substrate specificity of alpha and beta coronavirus papain-like proteases: targeting human NL63, SARS-CoV and SARS-CoV-2 (Covid-19) with designed inhibitors
- Author
-
Mackenzie E. Chapman, Courtney M. Daczkowski, Arun K. Ghosh, and Andrew D. Mesecar
- Subjects
Biophysics - Published
- 2022
38. Highly Diastereoselective Intramolecular Asymmetric Oxidopyrylium-olefin [5 + 2] Cycloaddition and Synthesis of 8-Oxabicyclo[3.2.1]oct-3-enone Containing Ring Systems
- Author
-
Monika Yadav and Arun K. Ghosh
- Subjects
chemistry.chemical_classification ,Cycloaddition Reaction ,010405 organic chemistry ,Stereochemistry ,Chemistry ,Alkene ,Lactol ,Organic Chemistry ,Stereoisomerism ,Alkenes ,010402 general chemistry ,01 natural sciences ,Cycloaddition ,Article ,0104 chemical sciences ,Stereocenter ,chemistry.chemical_compound ,Ylide ,Achmatowicz reaction ,Alkoxy group ,Enone - Abstract
We have the investigated base mediated asymmetric intramolecular oxidopyrylium-alkene [5 + 2]-cycloaddition reaction which resulted in the synthesis of functionalized tricyclic ring systems containing an 8-oxabicyclo[3.2.1]octane core. Intramolecular cycloaddition constructed two new rings, three new stereogenic centers, and provided a tricyclic cycloadduct with high diastereoselectivity and isolated yield. We incorporated an α-chiral center and an alkoxy alkene tether on the substrates and examined the effect of the size of alkyl groups and alkene tether length on diastereoselectivity. The requisite substrates for the oxidopyrylium-alkene cycloaddition reaction were synthesized in a few steps involving alkylation of optically active α-hydroxy amide, furyllithium addition, reduction of resulting ketone, and Achmatowicz reaction followed by acylation of a lactol intermediate. We have proposed stereochemical models for the [5 + 2] cycloaddition reaction via the oxidopyrylium ylide. Interestingly, the alkoxy substituent on the stereocenter and the chain length are responsible for the degree of stereoselectivity of the cycloadduct.
- Published
- 2021
39. Spliceostatins and Derivatives: Chemical Syntheses and Biological Properties of Potent Splicing Inhibitors
- Author
-
Melissa S. Jurica, Jennifer L. Mishevich, and Arun K. Ghosh
- Subjects
Spliceosome ,Diene ,Medicinal & Biomolecular Chemistry ,RNA Splicing ,Pharmaceutical Science ,Antineoplastic Agents ,01 natural sciences ,Medical and Health Sciences ,Article ,Analytical Chemistry ,Stereocenter ,chemistry.chemical_compound ,Underpinning research ,Drug Discovery ,Moiety ,Peptide bond ,Humans ,Cancer ,Pyrans ,Pharmacology ,Biological Products ,Molecular Structure ,010405 organic chemistry ,Organic Chemistry ,Total synthesis ,Tetrahydropyran ,Biological Sciences ,Combinatorial chemistry ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,1.3 Chemical and physical sciences ,Complementary and alternative medicine ,chemistry ,5.1 Pharmaceuticals ,RNA splicing ,Chemical Sciences ,Spliceosomes ,Molecular Medicine ,Generic health relevance ,Development of treatments and therapeutic interventions - Abstract
Spliceostatins and thailanstatins are intriguing natural products due to their structural features as well as their biological significance. This family of natural products has been the subject of immense synthetic interest because they exhibit very potent cytotoxicity in representative human cancer cell lines. The cytotoxic properties of these natural products are related to their ability to inhibit spliceosomes. FR901564 and spliceostatins have been shown to inhibit spliceosomes by binding to their SF3B component. Structurally, these natural products contain two highly functionalized tetrahydropyran rings with multiple stereogenic centers joined by a diene moiety and an acyclic side chain linked with an amide bond. Total syntheses of this family of natural products led to the development of useful synthetic strategies, which enabled the synthesis of potent derivatives. The spliceosome modulating properties of spliceostatins and synthetic derivatives opened the door for understanding the underlying spliceosome mechanism as well as the development of new therapies based upon small-molecule splicing modulators. This review outlines the total synthesis of spliceostatins, synthetic studies of structural derivatives, and their bioactivity.
- Published
- 2021
40. Enantioselective Total Synthesis of (+)-EBC-23, a Potent Anticancer Agent from the Australian Rainforest
- Author
-
Che-Sheng Hsu and Arun K. Ghosh
- Subjects
Rainforest ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Diol ,Enantioselective synthesis ,Convergent synthesis ,Australia ,Total synthesis ,Noyori asymmetric hydrogenation ,Antineoplastic Agents ,Stereoisomerism ,010402 general chemistry ,01 natural sciences ,Cycloaddition ,Article ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Epimer ,Spiro Compounds ,Sharpless asymmetric dihydroxylation ,Pyrans - Abstract
We describe here an enantioselective synthesis of (+)-EBC-23, a potent anticancer agent from the Australian rainforest. Our convergent synthesis features a [3+2] dipolar cycloaddition of an olefin-bearing 1,3-syn diol unit and an oxime segment containing 1,2-syn diol functionality as the key step. The segments were synthesized in a highly enantioselective manner using Noyori asymmetric hydrogenation of a β-keto ester and Sharpless asymmetric dihydroxylation of an α,β-unsaturated ester. Cycloaddition provided isoxazoline derivative which upon hydrogenolysis furnished the β-hydroxy ketone expediently. A one-pot, acid-catalyzed reaction removed the isopropylidene group, promoted spirocyclization, constructed the complex spiroketal lactone core, and furnished EBC-23 and its C11 epimer. The C11 epimer was also converted to EBC-23 by chemoselective oxidation and reduction sequence. The present synthesis provides convenient access to this family of natural products in an efficient manner.
- Published
- 2021
41. Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure–Activity Studies and Biological and X-ray Structural Studies
- Author
-
Arun K. Ghosh, Jacqueline N. Williams, Rachel Y. Ho, Hannah M. Simpson, Shin-ichiro Hattori, Hironori Hayashi, Johnson Agniswamy, Yuan-Fang Wang, Irene T. Weber, and Hiroaki Mitsuya
- Subjects
Models, Molecular ,0301 basic medicine ,010405 organic chemistry ,030106 microbiology ,Stereoisomerism ,Chemistry Techniques, Synthetic ,HIV Protease Inhibitors ,Ligands ,01 natural sciences ,Article ,0104 chemical sciences ,Structure-Activity Relationship ,03 medical and health sciences ,HIV Protease ,Catalytic Domain ,Drug Design ,Drug Discovery ,HIV-1 ,Molecular Medicine ,Oxazolidinones - Abstract
We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a key o-iodoxybenzoic acid mediated cyclization. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Compound 4k has shown an enzyme K(i) of 40 pM and antiviral IC(50) of 31 nM. Inhibitors 4k and 4l were evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants, and their fold-changes in antiviral activity were similar to those observed with darunavir. Additionally, two X-ray crystal structures of the related inhibitors 4a and 4e bound to HIV-1 protease were determined at 1.22 and 1.30 Å resolution, respectively, and revealed important interactions in the active site that have not yet been explored.
- Published
- 2018
42. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap–Core Interface of HIV-1 Protease
- Author
-
Robert W. Harrison, Ying Zhang, Andres Wong-Sam, Yuan-Fang Wang, Arun K. Ghosh, and Irene T. Weber
- Subjects
0301 basic medicine ,General Chemical Engineering ,Dimer ,medicine.medical_treatment ,030106 microbiology ,Mutant ,Article ,Hydrophobic effect ,lcsh:Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,HIV-1 protease ,medicine ,chemistry.chemical_classification ,Protease ,biology ,Lopinavir ,General Chemistry ,3. Good health ,030104 developmental biology ,Enzyme ,chemistry ,lcsh:QD1-999 ,biology.protein ,Biophysics ,Tipranavir ,medicine.drug - Abstract
Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5, were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PRL76V). Compound 5 exhibited the best Ki value of 1.9 nM for PRL76V, whereas the other three inhibitors had Ki values of 4.5–7.6 nM, 2–3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PRL76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PRL76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.
- Published
- 2018
43. Synthesis of amide derivatives for electron deficient amines and functionalized carboxylic acids using EDC and DMAP and a catalytic amount of HOBt as the coupling reagents
- Author
-
Dana Shahabi and Arun K. Ghosh
- Subjects
Reaction conditions ,010405 organic chemistry ,Organic Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Combinatorial chemistry ,Article ,0104 chemical sciences ,Catalysis ,Coupling (electronics) ,chemistry.chemical_compound ,Aniline ,chemistry ,Reagent ,Amide ,Drug Discovery ,Peptide bond - Abstract
A convenient protocol for amide bond formation for electron deficient amines and carboxylic acids is described. Amide coupling of aniline derivatives has been investigated with a number of reagents under a variety of reaction conditions. The use of 1 equivalent of EDC and 1 equivalent of DMAP, catalytic amount of HOBt and DIPEA provided the best results. This method is amenable to the synthesis of a range of functionalized amide derivatives with electron deficient and unreactive amines.
- Published
- 2021
44. Identification of herboxidiene features that mediate conformation-dependent SF3B1 interactions to inhibit splicing
- Author
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Guddeti Chandrashekar Reddy, Allu, Maul-Newby Hm, Mendez P, Lopez Ag, Jurica Ms, and Arun K. Ghosh
- Subjects
Spliceosome ,Chemistry ,RNA splicing ,Biophysics ,Intron ,snRNP ,Herboxidiene ,Small molecule ,Small nuclear RNA ,Protein–protein interaction - Abstract
Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Recent cryo-EM models of U2 snRNP before and after intron recognition suggest several large-scale rearrangements of RNA and protein interactions involving SF3B. Employing an inactive herboxidiene analog as a competitor with SF3B inhibitors, we present evidence for multiple conformations of SF3B in the U2 snRNP, only some of which are available for productive inhibitor interactions. We propose that both thermodynamics and an ATP-binding event promote the conformation conducive to SF3B inhibitor interactions. However, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure activity relationship analysis of herboxidiene, which identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In combination with structural models of SF3B interactions with inhibitors, our data leads us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 sidechains in the inhibitor binding channel are required to maintain inhibitor occupancy and counteract the SF3B transition to a closed state that is promoted by stable U2 snRNA interactions with the intron.
- Published
- 2020
45. Exploring the structural determinants for inhibitor selectivity towards the BACE protein family using structure-based molecular design
- Author
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Emma K. Lendy, Yu-Chen Yen, Emilio L. Cardenas, Margherita Brindisi, Arun K. Ghosh, and Andrew D. Mesecar
- Subjects
Biophysics - Published
- 2022
46. Lewis Acid-Catalyzed Vinyl Acetal Rearrangement of 4,5-Dihydro-1,3-dioxepines: Stereoselective Synthesis of
- Author
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Arun K, Ghosh and Miranda R, Belcher
- Subjects
Acetals ,Stereoisomerism ,Furans ,Catalysis ,Article ,Lewis Acids - Abstract
Lewis acid-catalyzed rearrangements of 4,5-dihydro-1,3-dioxepines have been investigated. Rearrangement of vinyl acetals under a variety of conditions resulted in cis- and trans-2,3-disubstituted tetrahydrofuran derivatives in a highly stereoselective manner. Rearrangements at lower temperatures typically provided the cis-2,3-disubstituted tetrahydrofuran carbaldehydes. At higher temperatures, the corresponding trans-2,3-disubstituted tetrahydrofuran carbaldehydes are formed. The requisite substrates for the vinyl acetal rearrangement were synthesized via ring-closing olefin metathesis of bis(allyoxy)methyl derivatives using Grubbs second-generation catalyst followed by olefin isomerization using a catalytic amount of RuCl(2)(PPh(3))(3). We examined the substrate scope using substituted aromatic and aliphatic derivatives. Additionally, the rearrangement was utilized in the synthesis of a stereochemically-defined bis-tetrahydrofuran (bis-THF) derivative, which is one of the key structural elements of darunavir, an FDA-approved drug for the treatment of HIV/AIDS.
- Published
- 2020
47. Asymmetric Diels-Alder reaction of 3-(acyloxy) acryloyl oxazolidinones: optically active synthesis of a high-affinity ligand for potent HIV-1 protease inhibitors
- Author
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Margherita Brindisi, Alessandro Grillo, Arun K. Ghosh, Satish Kovela, Ghosh, A. K., Grillo, A., Kovela, S., and Brindisi, M.
- Subjects
Protease ,Cyclopentadiene ,biology ,Stereochemistry ,Chemistry ,Ligand ,General Chemical Engineering ,medicine.medical_treatment ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Protease inhibitor (biology) ,Cycloaddition ,Article ,0104 chemical sciences ,chemistry.chemical_compound ,HIV-1 protease ,biology.protein ,medicine ,Enantiomer ,0210 nano-technology ,medicine.drug ,Diels–Alder reaction - Abstract
We describe here our investigation of the asymmetric Diels-Alder reaction of chiral 3-(acyloxy)acryloyl oxazolidinones as dienophiles in various Lewis-acid promoted reactions with cyclopentadiene. The resulting highly functionalized cycloadducts are useful intermediates for the synthesis, particularly for the optically active synthesis of 6-5-5 tricyclic hexahydro-4H-3,5-methanofuro[2,3-b]pyranol (3) with five contiguous chiral centers. This stereochemically defined crown-like heterocyclic derivative is an important high affinity ligand for a variety of highly potent HIV-1 protease inhibitors. Among the various dienophiles and Lewis acid-mediated reactions surveyed, 3-(4-methoxybenzoyl)acryloyl oxazolidinone as the dienophile and diethylaluminum chloride as the Lewis-acid provided the desired endo product with excellent diastereoselectivity. The cycloaddition was carried out in multi-gram scale and the cycloadduct was efficiently converted to alcohol 3 with high enantiomeric purity. The optically active ligand was then transformed into potent HIV-1 protease inhibitor 2.
- Published
- 2020
48. Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity
- Author
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Kanury V. S. Rao, Prasanth R. Nyalapatla, Hiroaki Mitsuya, Hironori Hayashi, Arun K. Ghosh, Debananda Das, Hiromi Aoki-Ogata, David A. Davis, Shin-ichiro Hattori, Haydar Bulut, and Manabu Aoki
- Subjects
0301 basic medicine ,endocrine system ,Stereochemistry ,medicine.medical_treatment ,lcsh:Medicine ,HIV Infections ,Virus Replication ,010402 general chemistry ,01 natural sciences ,Article ,Cell Line ,03 medical and health sciences ,chemistry.chemical_compound ,HIV Protease ,Drug Resistance, Viral ,medicine ,Humans ,Single bond ,HIV Protease Inhibitor ,lcsh:Science ,Bond cleavage ,Darunavir ,Oxazole ,chemistry.chemical_classification ,Multidisciplinary ,Protease ,Drug discovery ,lcsh:R ,virus diseases ,HIV Protease Inhibitors ,biochemical phenomena, metabolism, and nutrition ,Chemical biology ,0104 chemical sciences ,Amino acid ,030104 developmental biology ,chemistry ,Structural biology ,HIV-1 ,lcsh:Q ,medicine.drug - Abstract
HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. However, HIV-1 often acquires resistance to PIs. Here, seven novel PIs were synthesized, by introducing single atom changes such as an exchange of a sulfur to an oxygen, scission of a single bond in P2′-cyclopropylaminobenzothiazole (or -oxazole), and/or P1-benzene ring with fluorine scan of mono- or bis-fluorine atoms around DRV’s scaffold. X-ray structural analyses of the PIs complexed with wild-type Protease (PRWT) and highly-multi-PI-resistance-associated PRDRVRP51 revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2′-subsite. Furthermore, these PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Our work provides the basis for developing novel PIs with high potency against PI-resistant HIV-1 variants with a high genetic barrier.
- Published
- 2020
49. Copper-Catalyzed Stille Cross-Coupling Reaction and Application in the Synthesis of the Spliceostatin Core Structure
- Author
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Arun K. Ghosh, Melissa S. Jurica, Joshua R. Born, and Anne M. Veitschegger
- Subjects
Allylic rearrangement ,Diene ,010405 organic chemistry ,Organic Chemistry ,Sulfolene ,Tetrahydropyran ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,Coupling reaction ,Article ,Catalysis ,0104 chemical sciences ,Stille reaction ,chemistry.chemical_compound ,chemistry ,Achmatowicz reaction ,Copper ,Palladium - Abstract
An efficient palladium-free Stille cross-coupling reaction of allylic bromides and functionalized organostannylfuran using catalytic copper halide has been developed. The coupling reaction was optimized using CuI and low catalyst loading (down to 5 mol %). The reaction was conveniently carried out at ambient temperature in the presence of inorganic base to afford the coupling product in good-to-excellent yields. The utility of this reaction was demonstrated in the synthesis of a furan with sensitive functionalities. A sulfolene moiety was utilized as a masking group for the sensitive diene. Noyori asymmetric reduction, Achmatowicz reaction, and Kishi reduction steps converted sulfolene to a highly substituted tetrahydropyran intermediate used in the synthesis of the highly potent antitumor agents, spliceostatins, and their derivatives.
- Published
- 2020
50. A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication
- Author
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Srinivasa Rao Allu, Emma K. Lendy, Jakka Raghavaiah, Alexander Wlodawer, Arun K. Ghosh, Debananda Das, David A. Davis, Kazutaka Murayama, Hiroaki Mitsuya, Shogo Misumi, Yuki Takamatsu, Nobuyo Higashi-Kuwata, Mi Li, Brandon J. Anson, Hironori Hayashi, Kazuya Hasegawa, Naoki Kishimoto, Nobutoki Takamune, Shin ichiro Hattori, Eiichi Kodama, Robert Yarchoan, Haydar Bulut, and Andrew D. Mesecar
- Subjects
0301 basic medicine ,Indoles ,Pyridines ,Science ,medicine.medical_treatment ,viruses ,General Physics and Astronomy ,Antiviral Agents ,General Biochemistry, Genetics and Molecular Biology ,Article ,Cell Line ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Chlorocebus aethiops ,medicine ,Moiety ,Animals ,Humans ,Vero Cells ,Indole test ,Multidisciplinary ,Protease ,Alanine ,biology ,Chemistry ,SARS-CoV-2 ,Viral Proteases ,Antimicrobials ,Active site ,virus diseases ,General Chemistry ,Small molecule ,In vitro ,Adenosine Monophosphate ,COVID-19 Drug Treatment ,030104 developmental biology ,Coronavirus Protease Inhibitors ,Viral replication ,Biochemistry ,030220 oncology & carcinogenesis ,Indoline ,biology.protein - Abstract
Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (Mpro). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC50 values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with Mpro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead Mpro inhibitor for the development of therapeutics for SARS-CoV-2 infection., Here, using in vitro assays and structural analysis, the authors characterize the anti-SARS-CoV-2 properties of two small molcules, showing these to bind and target the virus main protease (Mpro), and to exhibit a synergistic antiviral effect when combined with remdesivir in vitro.
- Published
- 2020
Catalog
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