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- HIV Protease (26)
- HIV-1 (18)
- Models, Molecular (18)
- HIV Protease Inhibitors (17)
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- Binding Sites (15)
- Crystallography, X-Ray (15)
- Protein Conformation (13)
- Mutation (11)
- Substrate Specificity (10)
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- Amino Acid Sequence (7)
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- Molecular Structure (6)
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- Sulfonamides (5)
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- Animals (4)
- Aprotinin (4)
- Cell Line (4)
- Crystallography (4)
- Dimerization (4)
- Drug Resistance, Multiple, Viral (4)
- Hydrogen Bonding (4)
- Kinetics (4)
- Ligands (4)
Articles 1 - 30 of 62
Full-Text Articles in Life Sciences
Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer
Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer
Celia A. Schiffer
Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate …
Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer
Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer
Celia A. Schiffer
Asunaprevir (ASV), an isoquinoline-based competitive inhibitor targeting the hepatitis C virus (HCV) NS3/4A protease, is very potent in vivo. However, the potency is significantly compromised by the drug resistance mutations R155K and D168A. In this study three crystal structures of ASV and an analogue were determined to analyze the structural basis of drug resistance susceptibility. These structures revealed that ASV makes extensive contacts with Arg155 outside the substrate envelope. Arg155 in turn is stabilized by Asp168, and thus when either residue is mutated, the enzyme's interaction with ASV's P2* isoquinoline is disrupted. Adding a P1-P3 macrocycle to ASV enhances the …
A Sensitive Assay Using A Native Protein Substrate For Screening Hiv-1 Maturation Inhibitors Targeting The Protease Cleavage Site Between The Matrix And Capsid, Sook-Kyung Lee, Nancy Cheng, Emily Hull-Ryde, Marc Potempa, Celia Schiffer, William Janzen, Ronald Swanstrom
A Sensitive Assay Using A Native Protein Substrate For Screening Hiv-1 Maturation Inhibitors Targeting The Protease Cleavage Site Between The Matrix And Capsid, Sook-Kyung Lee, Nancy Cheng, Emily Hull-Ryde, Marc Potempa, Celia Schiffer, William Janzen, Ronald Swanstrom
Celia A. Schiffer
The matrix/capsid processing site in the HIV-1 Gag precursor is likely the most sensitive target to inhibit HIV-1 replication. We have previously shown that modest incomplete processing at the site leads to a complete loss of virion infectivity. In the study presented here, a sensitive assay based on fluorescence polarization that can monitor cleavage at the MA/CA site in the context of the folded protein substrate is described. The substrate, an MA/CA fusion protein, was labeled with the fluorescein-based FlAsH (fluorescein arsenical hairpin) reagent that binds to a tetracysteine motif (CCGPCC) that was introduced within the N-terminal domain of CA. …
Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer
Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer
Celia A. Schiffer
HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure …
Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor
Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor
Celia A. Schiffer
Acquired resistance to therapeutic agents is a significant barrier to the development of clinically effective treatments for diseases in which evolution occurs on clinical time scales, frequently arising from target mutations. We previously reported a general strategy to design effective inhibitors for rapidly mutating enzyme targets, which we demonstrated for HIV-1 protease inhibition [Altman et al. J. Am. Chem. Soc. 2008, 130, 6099-6113]. Specifically, we developed a computational inverse design procedure with the added constraint that designed inhibitors bind entirely inside the substrate envelope, a consensus volume occupied by natural substrates. The rationale for the substrate-envelope constraint is that it …
Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen
Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen
Celia A. Schiffer
Current antiretroviral treatments target multiple pathways important for human immunodeficiency virus (HIV) multiplication, including viral entry, synthesis and integration of the DNA provirus, and the processing of viral polyprotein precursors. However, HIV is becoming increasingly resistant to these "combination therapies." Recent findings show that inhibition of HIV Gag protein cleavage into its two structural proteins, matrix (MA) and capsid (CA), has a devastating effect on viral production, revealing a potential new target class for HIV treatment. Unlike the widely used HIV protease inhibitors, this new class of inhibitor would target the substrate, not the protease enzyme itself. This approach offers …
Hiv-1 Protease-Substrate Coevolution In Nelfinavir Resistance, Madhavi Kolli, Aysegul Ozen, Nese Yilmaz, Celia Schiffer
Hiv-1 Protease-Substrate Coevolution In Nelfinavir Resistance, Madhavi Kolli, Aysegul Ozen, Nese Yilmaz, Celia Schiffer
Celia A. Schiffer
Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue …
Substrate Envelope-Designed Potent Hiv-1 Protease Inhibitors To Avoid Drug Resistance, Madhavi Nalam, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima Anjum, Michael Altman, Nese Yilmaz, Bruce Tidor, Tariq Rana, Celia Schiffer
Substrate Envelope-Designed Potent Hiv-1 Protease Inhibitors To Avoid Drug Resistance, Madhavi Nalam, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima Anjum, Michael Altman, Nese Yilmaz, Bruce Tidor, Tariq Rana, Celia Schiffer
Celia A. Schiffer
The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against …
Quantitative Comparison Of Errors In 15n Transverse Relaxation Rates Measured Using Various Cpmg Phasing Schemes, Wazo Myint, Yufeng Cai, Celia Schiffer, Rieko Ishima
Quantitative Comparison Of Errors In 15n Transverse Relaxation Rates Measured Using Various Cpmg Phasing Schemes, Wazo Myint, Yufeng Cai, Celia Schiffer, Rieko Ishima
Celia A. Schiffer
Nitrogen-15 Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation experiment are widely used to characterize protein backbone dynamics and chemical exchange parameters. Although an accurate value of the transverse relaxation rate, R(2), is needed for accurate characterization of dynamics, the uncertainty in the R(2) value depends on the experimental settings and the details of the data analysis itself. Here, we present an analysis of the impact of CPMG pulse phase alternation on the accuracy of the (15)N CPMG R(2). Our simulations show that R(2) can be obtained accurately for a relatively wide spectral width, either using the conventional phase cycle or using phase alternation …
Extreme Entropy-Enthalpy Compensation In A Drug-Resistant Variant Of Hiv-1 Protease, Nancy King, Moses Prabu-Jeyabalan, Rajintha Bandaranayake, Madhavi Nalam, Ellen Nalivaika, Aysegul Ozen, Turkan Haliloglu, Nese Yilmaz, Celia Schiffer
Extreme Entropy-Enthalpy Compensation In A Drug-Resistant Variant Of Hiv-1 Protease, Nancy King, Moses Prabu-Jeyabalan, Rajintha Bandaranayake, Madhavi Nalam, Ellen Nalivaika, Aysegul Ozen, Turkan Haliloglu, Nese Yilmaz, Celia Schiffer
Celia A. Schiffer
The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug-resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, …
Decomposing The Energetic Impact Of Drug-Resistant Mutations: The Example Of Hiv-1 Protease-Drv Binding, Yufeng Cai, Celia Schiffer
Decomposing The Energetic Impact Of Drug-Resistant Mutations: The Example Of Hiv-1 Protease-Drv Binding, Yufeng Cai, Celia Schiffer
Celia A. Schiffer
HIV-1 protease is a major drug target for AIDS therapy. With the appearance of drug-resistant HIV-1 protease variants, understanding the mechanism of drug resistance becomes critical for rational drug design. Computational methods can provide more details about inhibitor-protease binding than crystallography and isothermal titration calorimetry. The latest FDA-approved HIV-1 protease inhibitor is Darunavir (DRV). Herein, each DRV atom is evaluated by free energy component analysis for its contribution to the binding affinity with wild-type protease and ACT, a drug-resistant variant. This information can contribute to the rational design of new HIV-1 protease inhibitors.
Mass Spectrometry Tools For Analysis Of Intermolecular Interactions, Jared Auclair, Mohan Somasundaran, Karin Green, James Evans, Celia Schiffer, Dagmar Ringe, Gregory Petsko, Jeffrey Agar
Mass Spectrometry Tools For Analysis Of Intermolecular Interactions, Jared Auclair, Mohan Somasundaran, Karin Green, James Evans, Celia Schiffer, Dagmar Ringe, Gregory Petsko, Jeffrey Agar
Celia A. Schiffer
The small quantities of protein required for mass spectrometry (MS) make it a powerful tool to detect binding (protein-protein, protein-small molecule, etc.) of proteins that are difficult to express in large quantities, as is the case for many intrinsically disordered proteins. Chemical cross-linking, proteolysis, and MS analysis, combined, are a powerful tool for the identification of binding domains. Here, we present a traditional approach to determine protein-protein interaction binding sites using heavy water ((18)O) as a label. This technique is relatively inexpensive and can be performed on any mass spectrometer without specialized software.
Context Surrounding Processing Sites Is Crucial In Determining Cleavage Rate Of A Subset Of Processing Sites In Hiv-1 Gag And Gag-Pro-Pol Polyprotein Precursors By Viral Protease, Sook-Kyung Lee, Marc Potempa, Madhavi Kolli, Aysegul Ozen, Celia Schiffer, Ronald Swanstrom
Context Surrounding Processing Sites Is Crucial In Determining Cleavage Rate Of A Subset Of Processing Sites In Hiv-1 Gag And Gag-Pro-Pol Polyprotein Precursors By Viral Protease, Sook-Kyung Lee, Marc Potempa, Madhavi Kolli, Aysegul Ozen, Celia Schiffer, Ronald Swanstrom
Celia A. Schiffer
Processing of the human immunodeficiency virus type 1 (HIV-1) Gag and Gag-Pro-Pol polyproteins by the HIV-1 protease (PR) is essential for the production of infectious particles. However, the determinants governing the rates of processing of these substrates are not clearly understood. We studied the effect of substrate context on processing by utilizing a novel protease assay in which a substrate containing HIV-1 matrix (MA) and the N-terminal domain of capsid (CA) is labeled with a FlAsH (fluorescein arsenical hairpin) reagent. When the seven cleavage sites within the Gag and Gag-Pro-Pol polyproteins were placed at the MA/CA site, the rates of …
Structural, Kinetic, And Thermodynamic Studies Of Specificity Designed Hiv-1 Protease, Oscar Alvizo, Seema Mittal, Stephen Mayo, Celia Schiffer
Structural, Kinetic, And Thermodynamic Studies Of Specificity Designed Hiv-1 Protease, Oscar Alvizo, Seema Mittal, Stephen Mayo, Celia Schiffer
Celia A. Schiffer
HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational …
Methyl- And Normal-Cytosine Deamination By The Foreign Dna Restriction Enzyme Apobec3a, Michael Carpenter, Ming Li, Anurag Rathore, Lela Lackey, Emily Law, Allison Land, Brandon Leonard, Shivender Shandilya, Markus-Frederik Bohn, Celia Schiffer, William Brown, Reuben Harris
Methyl- And Normal-Cytosine Deamination By The Foreign Dna Restriction Enzyme Apobec3a, Michael Carpenter, Ming Li, Anurag Rathore, Lela Lackey, Emily Law, Allison Land, Brandon Leonard, Shivender Shandilya, Markus-Frederik Bohn, Celia Schiffer, William Brown, Reuben Harris
Celia A. Schiffer
Multiple studies have indicated that the TET oxidases and, more controversially, the AID/APOBEC deaminases have the capacity to convert genomic DNA 5-methylcytosine (MeC) into altered nucleobases that provoke excision repair and culminate in the replacement of the original MeC with a normal cytosine (C). We show that human APOBEC3A (A3A) efficiently deaminates both MeC to thymine (T) and normal C to uracil (U) in single-stranded DNA substrates. In comparison, the related enzyme APOBEC3G (A3G) has undetectable MeC-to-T activity and 10-fold less C-to-U activity. Upon 100-fold induction of endogenous A3A by interferon, the MeC status of bulk chromosomal DNA is unaltered …
Design, Synthesis, And Biological And Structural Evaluations Of Novel Hiv-1 Protease Inhibitors To Combat Drug Resistance, Maloy Parai, David Huggins, Hong Cao, Madhavi Nalam, Akbar Ali, Celia Schiffer, Bruce Tidor, Tariq Rana
Design, Synthesis, And Biological And Structural Evaluations Of Novel Hiv-1 Protease Inhibitors To Combat Drug Resistance, Maloy Parai, David Huggins, Hong Cao, Madhavi Nalam, Akbar Ali, Celia Schiffer, Bruce Tidor, Tariq Rana
Celia A. Schiffer
A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C …
Hydrophobic Core Flexibility Modulates Enzyme Activity In Hiv-1 Protease, Seema Mittal, Yufeng Cai, Madhavi Nalam, Daniel Bolon, Celia Schiffer
Hydrophobic Core Flexibility Modulates Enzyme Activity In Hiv-1 Protease, Seema Mittal, Yufeng Cai, Madhavi Nalam, Daniel Bolon, Celia Schiffer
Celia A. Schiffer
Human immunodeficiency virus Type-1 (HIV-1) protease is crucial for viral maturation and infectivity. Studies of protease dynamics suggest that the rearrangement of the hydrophobic core is essential for enzyme activity. Many mutations in the hydrophobic core are also associated with drug resistance and may modulate the core flexibility. To test the role of flexibility in protease activity, pairs of cysteines were introduced at the interfaces of flexible regions remote from the active site. Disulfide bond formation was confirmed by crystal structures and by alkylation of free cysteines and mass spectrometry. Oxidized and reduced crystal structures of these variants show the …
Crystal Structure Of Human Thymidylate Synthase: A Structural Mechanism For Guiding Substrates Into The Active Site, Celia Schiffer, Ian Clifton, V. Jo Davisson, Daniel Santi, Robert Stroud
Crystal Structure Of Human Thymidylate Synthase: A Structural Mechanism For Guiding Substrates Into The Active Site, Celia Schiffer, Ian Clifton, V. Jo Davisson, Daniel Santi, Robert Stroud
Celia A. Schiffer
The crystal structure of human thymidylate synthase, a target for anti-cancer drugs, is determined to 3.0 A resolution and refined to a crystallographic residual of 17.8%. The structure implicates the enzyme in a mechanism for facilitating the docking of substrates into the active site. This mechanism involves a twist of approximately 180 degrees of the active site loop, pivoted around the neighboring residues 184 and 204, and implicates ordering of external, eukaryote specific loops along with the well-characterized closure of the active site upon substrate binding. The highly conserved, but eukaryote-specific insertion of twelve residues 90-101 (h117-128), and of eight …
Evaluation Of The Substrate Envelope Hypothesis For Inhibitors Of Hiv-1 Protease, Sripriya Chellappan, Visvaldas Kairys, Miguel Fernandes, Celia Schiffer, Michael Gilson
Evaluation Of The Substrate Envelope Hypothesis For Inhibitors Of Hiv-1 Protease, Sripriya Chellappan, Visvaldas Kairys, Miguel Fernandes, Celia Schiffer, Michael Gilson
Celia A. Schiffer
Crystallographic data show that various substrates of HIV protease occupy a remarkably uniform region within the binding site; this region has been termed the substrate envelope. It has been suggested that an inhibitor that fits within the substrate envelope should tend to evade viral resistance because a protease mutation that reduces the affinity of the inhibitor will also tend to reduce the affinity of substrate, and will hence decrease the activity of the enzyme. Accordingly, inhibitors that fit the substrate envelope better should be less susceptible to clinically observed resistant mutations, since these must also allow substrates to bind. The …
Expression, Purification, And Characterization Of Thymidylate Synthase From Lactococcus Lactis, Patricia Greene, Pak-Lam Yu, Jia Zhao, Celia Schiffer, Daniel Santi
Expression, Purification, And Characterization Of Thymidylate Synthase From Lactococcus Lactis, Patricia Greene, Pak-Lam Yu, Jia Zhao, Celia Schiffer, Daniel Santi
Celia A. Schiffer
The thymidylate synthase (TS) gene from Lactococcus lactis has been highly expressed in Escherichia coli. The TS protein was purified by sequential chromatography on Q-Sepharose and phenyl-Sepharose. Six grams of cell pellet yielded 140 mg of homogeneous TS. TS is a highly conserved enzyme, and several of the conserved amino acid residues that have been implicated in catalytic function are altered in L. lactis TS. By use of a 3-dimensional homology model, we have predicted covariant changes that might compensate for these differences. With the large amounts of L. lactis TS now available, studies can be pursued to understand the …
Investigations Of Peptide Hydration Using Nmr And Molecular Dynamics Simulations: A Study Of Effects Of Water On The Conformation And Dynamics Of Antamanide, Jeffrey Peng, Celia Schiffer, Ping Xu, Wilfred Van Gunsteren, Richard Ernst
Investigations Of Peptide Hydration Using Nmr And Molecular Dynamics Simulations: A Study Of Effects Of Water On The Conformation And Dynamics Of Antamanide, Jeffrey Peng, Celia Schiffer, Ping Xu, Wilfred Van Gunsteren, Richard Ernst
Celia A. Schiffer
The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 mgrs at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight …
Discovery Of Hiv-1 Protease Inhibitors With Picomolar Affinities Incorporating N-Aryl-Oxazolidinone-5-Carboxamides As Novel P2 Ligands, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima Anjum, Madhavi Nalam, Celia Schiffer, Tariq Rana
Discovery Of Hiv-1 Protease Inhibitors With Picomolar Affinities Incorporating N-Aryl-Oxazolidinone-5-Carboxamides As Novel P2 Ligands, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima Anjum, Madhavi Nalam, Celia Schiffer, Tariq Rana
Celia A. Schiffer
Here, we describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors incorporating N-phenyloxazolidinone-5-carboxamides into the (hydroxyethylamino)sulfonamide scaffold as P2 ligands. Series of inhibitors with variations at the P2 phenyloxazolidinone and the P2' phenylsulfonamide moieties were synthesized. Compounds with the (S)-enantiomer of substituted phenyloxazolidinones at P2 show highly potent inhibitory activities against HIV-1 protease. The inhibitors possessing 3-acetyl, 4-acetyl, and 3-trifluoromethyl groups at the phenyl ring of the oxazolidinone fragment are the most potent in each series, with K(i) values in the low picomolar (pM) range. The electron-donating groups 4-methoxy and 1,3-dioxolane are preferred at P2' phenyl ring, …
The Role Of Protein-Solvent Interactions In Protein Unfolding, Celia Schiffer, Volker Dötsch
The Role Of Protein-Solvent Interactions In Protein Unfolding, Celia Schiffer, Volker Dötsch
Celia A. Schiffer
Protein unfolding occurs when the balance of forces between the protein's interaction with itself and the protein's interaction with its environment is disrupted. The disruption of this balance of forces may be as simple as a perturbance of the normal water structure around the protein. A decrease in the normal water-water interaction will result in an increase in the relative interaction of water with the protein. An increase in the number of interactions between water and the protein may initiate a protein's unfolding. This model for protein unfolding is supported by a range of recent experimental and computational data.
Association Of A Novel Human Immunodeficiency Virus Type 1 Protease Substrate Cleft Mutation, L23i, With Protease Inhibitor Therapy And In Vitro Drug Resistance, Elizabeth Johnston, Mark Winters, Soo-Yon Rhee, Thomas Merigan, Celia Schiffer, Robert Shafer
Association Of A Novel Human Immunodeficiency Virus Type 1 Protease Substrate Cleft Mutation, L23i, With Protease Inhibitor Therapy And In Vitro Drug Resistance, Elizabeth Johnston, Mark Winters, Soo-Yon Rhee, Thomas Merigan, Celia Schiffer, Robert Shafer
Celia A. Schiffer
We observed a previously uncharacterized mutation in the protease substrate cleft, L23I, in 31 of 4,303 persons undergoing human immunodeficiency virus type 1 genotypic resistance testing. In combination with V82I, L23I was associated with a sevenfold reduction in nelfinavir susceptibility and a decrease in replication capacity. In combination with other drug resistance mutations, L23I was associated with multidrug resistance and a compensatory increase in replication capacity.
Reca Dimers Serve As A Functional Unit For Assembly Of Active Nucleoprotein Filaments, Anthony Forget, Michelle Kudron, Dharia Mcgrew, Melissa Calmann, Celia Schiffer, Kendall Knight
Reca Dimers Serve As A Functional Unit For Assembly Of Active Nucleoprotein Filaments, Anthony Forget, Michelle Kudron, Dharia Mcgrew, Melissa Calmann, Celia Schiffer, Kendall Knight
Celia A. Schiffer
All RecA-like recombinase enzymes catalyze DNA strand exchange as elongated filaments on DNA. Despite numerous biochemical and structural studies of RecA and the related Rad51 and RadA proteins, the unit oligomer(s) responsible for nucleoprotein filament assembly and coordinated filament activity remains undefined. We have created a RecA fused dimer protein and show that it maintains in vivo DNA repair and LexA co-protease activities, as well as in vitro ATPase and DNA strand exchange activities. Our results support the idea that dimeric RecA is an important functional unit both for assembly of nucleoprotein filaments and for their coordinated activity during the …
Substrate Shape Determines Specificity Of Recognition For Hiv-1 Protease: Analysis Of Crystal Structures Of Six Substrate Complexes, Moses Prabu-Jeyabalan, Ellen Nalivaika, Celia Schiffer
Substrate Shape Determines Specificity Of Recognition For Hiv-1 Protease: Analysis Of Crystal Structures Of Six Substrate Complexes, Moses Prabu-Jeyabalan, Ellen Nalivaika, Celia Schiffer
Celia A. Schiffer
The homodimeric HIV-1 protease is the target of some of the most effective antiviral AIDS therapy, as it facilitates viral maturation by cleaving ten asymmetric and nonhomologous sequences in the Gag and Pol polyproteins. Since the specificity of this enzyme is not easily determined from the sequences of these cleavage sites alone, we solved the crystal structures of complexes of an inactive variant (D25N) of HIV-1 protease with six peptides that correspond to the natural substrate cleavage sites. When the protease binds to its substrate and buries nearly 1000 A2 of surface area, the symmetry of the protease is broken, …
Accounting For Molecular Mobility In Structure Determination Based On Nuclear Magnetic Resonance Spectroscopic And X-Ray Diffraction Data, Wilfred Van Gunsteren, Roger Brunne, P. Gros, René Van Schaik, Celia Schiffer, Andrew Torda
Accounting For Molecular Mobility In Structure Determination Based On Nuclear Magnetic Resonance Spectroscopic And X-Ray Diffraction Data, Wilfred Van Gunsteren, Roger Brunne, P. Gros, René Van Schaik, Celia Schiffer, Andrew Torda
Celia A. Schiffer
No abstract provided.
Substrate Specificity In Hiv-1 Protease By A Biased Sequence Search Method, Nevra Ozer, Turkan Haliloglu, Celia Schiffer
Substrate Specificity In Hiv-1 Protease By A Biased Sequence Search Method, Nevra Ozer, Turkan Haliloglu, Celia Schiffer
Celia A. Schiffer
Drug resistance in HIV-1 protease can also occasionally confer a change in the substrate specificity. Through the use of computational techniques, a relationship can be determined between the substrate sequence and three-dimensional structure of HIV-1 protease, and be utilized to predict substrate specificity. In this study, we introduce a biased sequence search threading (BSST) methodology to analyze the preferences of substrate positions and correlations between them that might also identify which positions within known substrates can likely tolerate sequence variability and which cannot. The potential sequence space was efficiently explored using a low-resolution knowledge-based scoring function. The low-energy substrate sequences …
Additivity In The Analysis And Design Of Hiv Protease Inhibitors, Robert Jorissen, G. S. Kiran Kumar Reddy, Akbar Ali, Michael Altman, Sripriya Chellappan, Saima Anjum, Bruce Tidor, Celia Schiffer, Tariq Rana, Michael Gilson
Additivity In The Analysis And Design Of Hiv Protease Inhibitors, Robert Jorissen, G. S. Kiran Kumar Reddy, Akbar Ali, Michael Altman, Sripriya Chellappan, Saima Anjum, Bruce Tidor, Celia Schiffer, Tariq Rana, Michael Gilson
Celia A. Schiffer
We explore the applicability of an additive treatment of substituent effects to the analysis and design of HIV protease inhibitors. Affinity data for a set of inhibitors with a common chemical framework were analyzed to provide estimates of the free energy contribution of each chemical substituent. These estimates were then used to design new inhibitors whose high affinities were confirmed by synthesis and experimental testing. Derivations of additive models by least-squares and ridge-regression methods were found to yield statistically similar results. The additivity approach was also compared with standard molecular descriptor-based QSAR; the latter was not found to provide superior …
Insights Into Interferon Regulatory Factor Activation From The Crystal Structure Of Dimeric Irf5, Weijun Chen, Suvana Lam, Hema Srinath, Zhaozhao Jiang, John Correia, Celia Schiffer, Katherine Fitzgerald, Kai Lin, William Royer
Insights Into Interferon Regulatory Factor Activation From The Crystal Structure Of Dimeric Irf5, Weijun Chen, Suvana Lam, Hema Srinath, Zhaozhao Jiang, John Correia, Celia Schiffer, Katherine Fitzgerald, Kai Lin, William Royer
Celia A. Schiffer
Interferon regulatory factors (IRFs) are essential in the innate immune response and other physiological processes. Activation of these proteins in the cytoplasm is triggered by phosphorylation of serine and threonine residues in a C-terminal autoinhibitory region, which stimulates dimerization, transport into the nucleus, assembly with the coactivator CBP/p300 and initiation of transcription. The crystal structure of the transactivation domain of pseudophosphorylated human IRF5 strikingly reveals a dimer in which the bulk of intersubunit interactions involve a highly extended C-terminal region. The corresponding region has previously been shown to block CBP/p300 binding to unphosphorylated IRF3. Mutation of key interface residues supports …