WO2003017934A2 - Folded monomers of the hiv-1 protease and methods of their use - Google Patents
Folded monomers of the hiv-1 protease and methods of their use Download PDFInfo
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- WO2003017934A2 WO2003017934A2 PCT/US2002/026757 US0226757W WO03017934A2 WO 2003017934 A2 WO2003017934 A2 WO 2003017934A2 US 0226757 W US0226757 W US 0226757W WO 03017934 A2 WO03017934 A2 WO 03017934A2
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- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
- C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
- C12N9/503—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from viruses
- C12N9/506—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from viruses derived from RNA viruses
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2740/00—Reverse transcribing RNA viruses
- C12N2740/00011—Details
- C12N2740/10011—Retroviridae
- C12N2740/16011—Human Immunodeficiency Virus, HIV
- C12N2740/16211—Human Immunodeficiency Virus, HIV concerning HIV gagpol
- C12N2740/16222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
Definitions
- the present invention relates to compositions and methods for inhibiting activity of functional dimeric retroviral proteases. More specifically, the invention relates to defining specific regions critical for dimer formation and production of folded monomers that block functional protease dimerization. The present invention defines regions in the protease critical for dimerization and thereby provides a design or target of retroviral proteases to form folded monomers. The invention also relates to HIV-1 inhibitors targeting the regions critical for dimerization. Additionally, methods for interfering with viral maturation in HIV patients using these folded monomers and their encoding nucleic acids are provided. Also provided are methods for treating HIV in conjunction with other antiviral therapies and medications. Further, the present invention provides assays for measuring dimerization ability of retroviral proteases and for evaluating the viral infection, and methods of screening for agents capable of binding to HIV-1 protease at the areas critical for dimerization.
- the human immunodeficiency virus type I (HIV-1) protease serves as one ofthe primary targets for the treatment of AIDS.
- the drugs that are currently designed for the treatment of patients with HIV-1 infection target the active site of the mature dimeric protease. Although this approach had some success in curtailing the progression ofthe disease and extending the life ofthe patients, lasting therapeutic effect is compromised by the selection process resulting in protease variants that are resistant or less-sensitive to the administered drugs.
- alternative strategies are necessary in the development of novel types of anti-HIV drugs that engender less drug resistance.
- HIV-1 protease Human immunodeficiency virus type-1 (HIV-1) protease is a homodimer composed of two 99 amino acid sequence. This enzyme plays a critical role in the life cycle of retro viruses by processing the precursor proteins Gag and Gag-Pol into the essential mature structural and function proteins (Oroszlan, S., and Lucasig, R. B. (1990) Curr. Top. Microbiol. Immunol. 157, 153-185). Dimerization ofthe protease is indispensable for catalytic activity since the interface ofthe free protease dimer is stabilized through interactions between the two subunits at the active site and at the termini (Weber, I. T. (1990) J. Biol. Chem.
- the two major areas that constitute the dimer interface are 1) the active-site region comprising residues 24-29 that form a hydrogen bond network, called the fireman's grip (Strisovsky, K. et al (2000)) and 2) the four-stranded anti-parallel ⁇ -sheet comprising residues 1-4, and 96-99 (Weber, I. T. (1990)). These two interfaces are adjacent in the three-dimensional structure and form a nearly continuous region.
- Inhibitor or substrate binding to the protease further enhances the stability ofthe dimer (Grant SK, et al (1992) Biochemistry 31, 9491-9501; Todd, M. J. et al (1998)).
- the protease catalyzes its own release from the Gag-Pol polyprotein in addition to the maturation of the virally encoded structural proteins and replication enzymes required for the assembly and production of viable virions (Oroszlan, S., and Heilig, R. B. (1990)).
- the protease serves as one ofthe primary targets for the development of drugs against AIDS.
- mutants modulate structure and interactions within the active site as well as inter- and intra-domain flexibility (Rose, R. B. et al (1998) Biochemistry 37, 2607-2621; Erickson, J. W. et al (1999) AIDS 13, S189-S204; Mahalingam, B. et al (1999) Eur. J. Biochem. 263, 238-245).
- New approaches for inhibiting retroviral infections using retroviral proteases as a target are critical, especially m view of the drug resistance issue.
- the present invention addresses these and related needs.
- compositions and methods are provided that are effective in inhibiting the activity of particular components associated with viral replication, specifically retroviral proteases, such as HIV proteases, and more particularly HIV-1 protease.
- the present invention relates to targets or regions c ⁇ tical for dimenzation and protease activity, which thereby provide the basis of drug or compound development for the treatment of viral infections.
- the present invention provides a method of treating mammalian diseases mediated by viral infection by administering a composition in a dosage sufficient to inhibit the propagation of viral particles.
- One such disease is Human Immunodeficiency Virus (HIV).
- HIV Human Immunodeficiency Virus
- other viral diseases may be treated with the method ofthe present invention.
- compositions include folded monome ⁇ c HIV proteases, inhibitor molecules that mimic the folded monome ⁇ c HIV proteases, functional protease antagonists, and various related compounds.
- this invention provides folded monome ⁇ c retroviral proteases, which prevent the formation of funcfional proteases and thereby inhibit viral replication.
- the folded monome ⁇ c retroviral protease includes various additions, deletions, or substitutions of ammo acids within conserved regions ofthe protease, as commonly understood by one skilled m the art.
- One embodiment is related to structural, biochemical and inhibition studies that target the protease precursor monomer using both the ⁇ p6pol-PR and ⁇ p6pol-PR D25N constructs and similar constructs that target the protease prior to its maturation.
- Another example of these constructs is provided in SEQ ID NO: 14, i.e., TFP-P6pol-PR D2 5N, beaut.
- An additional example is SFNFI-PR as set forth in SEQ ID NO: 15.
- a particular embodiment of the invention relates to specific regions or targets critical for dimerization and proper protein folding, where drugs or compounds may be designed to inhibit or block formation of functional protease dimers.
- Another object of the present invention is to provide a treatment for retroviral infections including, but not limited to HIV -associated conditions and AIDS.
- a HIV-1 protease defective in dimerization which protease having an amino acid sequence whose last four C-terminus residues are deleted.
- a HIV-1 protease defective in dimerization which protease having an amino acid sequence whose first four N-terminus residues are deleted.
- a HIV-1 protease defective in dimerization which protease having an amino acid sequence wherein Arg87 is substituted with another amino acid residue.
- the substituted amino acid residue is Lys.
- a HIV-1 protease defective in dimerization which protease having an amino acid sequence wherein Asp29 is substituted with another amino acid residue.
- the substituted amino acid residue is Asn.
- a HIV-1 protease defective in dimerization which protease having an amino acid sequence wherein one of the residues at positions 1-4 is substituted with Cys and one ofthe residues at positions 95-99 is substituted with Cys.
- a disulfide bond is formed between the Cysteines substituting one ofthe residues at positions 1-4 and one of the residues at positions 95-96.
- Gln2 is substituted with Cys and Leu97 is substituted with Cys.
- Gln2 is substituted with Cys and Asn98 is substituted with Cys.
- Gln2 is substituted with Cys and Thr96 is substituted with Cys.
- Thr4 is substituted with Cys and Asn98 is substituted with Cys.
- Ile3 is substituted with Cys and Leu97 is substituted with Cys.
- a folded monomer ofthe HIV-1 protease having an amino acid sequence set forth in SEQ ID NO: 6 there is provided a folded monomer of the HIV-1 protease having an amino acid sequence set forth in SEQ ID NO: 1 except that Asp29 is substituted with Asn.
- a folded monomer ofthe HIV-1 protease having an amino acid sequence set forth in SEQ ID NO:9 there is provided a folded monomer of the HIV-1 protease having an amino acid sequence set forth in SEQ ID NO: 1 except that Gln2 is substituted with Cys and Leu97 is substituted with Cys.
- a folded monomer of the HTV-l protease having an amino acid sequence set forth in SEQ ID NO: 10.
- the amino acid sequence ofthe folded monomer of the HIV-1 protease has a Cys2 and Cys97, a disulfide bond is formed between them.
- a disulfide bond is formed between the cysteines at positions 2 and 98.
- HIV protease precursor having an amino acid sequence set forth in SEQ ID NO: 12.
- a HIV protease precursor having an amino acid sequence set forth in SEQ ID NO: 13.
- a HIV protease precursor having an amino acid sequence set forth in SEQ ID NO: 14.
- a HIV protease precursor having an amino acid sequence set forth in SEQ ID NO: 15.
- a nucleic acid molecule having a nucleotide sequence encoding the amino acid sequence ofthe folded monomer of the HIV-1 protease or the HIV protease precursor in any of the various embodiments according to this disclosure.
- a pharmaceutical composition comprising the folded monomer of the HIV-1 protease in any ofthe various embodiments according to this disclosure, or fragment or variants thereof, and a suitable pharmaceutical carrier, excipient, or diluent.
- a pharmaceutical composition comprising the HIV protease precursor in any of the various embodiments according to this disclosure, or fragment or variants thereof, and a suitable pharmaceutical carrier, excipient, or diluent.
- a purified antibody capable of reacting specifically with the folded monomer ofthe HIV-1 protease or the HIV protease precursor in any of the various embodiments according to this disclosure, or an antigenic epitope thereof.
- an anti-idiotypic antibody capable of reacting specifically with these purified antibodies.
- a method for inhibiting the activity of a retroviral protease comprises allowing the retroviral protease to interact with the folded monomer of the HIV-1 protease or the HIV protease precursor in any ofthe various embodiments according to this disclosure thereby forming inactive protease dimers and blocking functional dimerization of the retroviral protease.
- the retroviral protease is a HIV protease.
- the HIV protease is the HIV-1 protease.
- a method for interfering with viral maturation in a HIV patient comprises administering an effective amount ofthe pharmaceutical composition according to various embodiments of this disclosure thereby inhibiting the HIV protease activity in the patient.
- the administration is carried out orally, topically, or by intravenous, subcutaneous or intramuscular injection.
- the effective amount of pharmaceutical composition is administered in the form of a lyophilized powder.
- the effective amount of pharmaceutical composition is delivered by liposomes.
- the effective amount is (i) between 0.01 and 75 mg per kilogram body weight ofthe patient per day orally or (ii) between 10 ⁇ g to 1000 mg per kilogram body weight of the patient per day through systemic administration.
- the effective amount is (i) between 2.5 and 20 mg per kilogram of body weight of said patient per day orally or (ii) between 50 ⁇ g to 500 mg per kilogram of body weight of said patient per day through systemic administration.
- a method for treating a HIV patient wherein the patient is subject to one or more anti-HIV medications or therapies, which method comprises interfering with viral maturation in the HTV patient by administering an effective amount ofthe pharmaceutical composition according to various embodiments of this disclosure.
- the administration is carried out orally, topically, or by intravenous, subcutaneous or intramuscular injection.
- the effective amount of pharmaceutical composition is administered in the form of a lyophilized powder.
- the effective amount of pharmaceutical composition is delivered by liposomes.
- the effective amount is (i) between 0.01 and 75 mg per kilogram body weight of the patient per day orally or (ii) between 10 ⁇ g to 1000 mg per kilogram body weight ofthe patient per day through systemic administration. In a still further embodiment, the effective amount is (i) between 2.5 and 20 mg per kilogram of body weight of said patient per day orally or (ii) between 50 ⁇ g to 500 mg per kilogram of body weight of said patient per day through systemic administration.
- a method for producing a folded monomer of a retroviral protease comprises identifying a region on the retroviral protease necessary for dimerization, introducing amino acid additions, deletions, substitutions, or any other structural changes to the retroviral protease or its precursor thereby destructing the dimerization ability and producing the folded monomer.
- the folded monomer of a retroviral protease is a folded monomer of a HIV protease.
- the folded monomer of a HIV protease is a folded monomer of the HIV-1 protease.
- an assay for measuring the dimerization ability of a retroviral protease comprises, in a solution ofthe retroviral protease, applying a predetermined amount of the folded monomer ofthe HIV-1 protease or the HTV protease inhibitor according to any of the various embodiments of this disclosure, and determining the levels of the retroviral protease in the monomer and dimer states, wherein the folded monomer ofthe HFV-1 protease acts as a competitive inhibitor for dimerization.
- the predetermined amount ofthe folded monomer ofthe HTV-1 protease is varied within a range such that the level of competition is varied during the assay.
- the retroviral protease is a HTV protease.
- the HTV protease is a HIV-1 protease.
- a method of screening for an agent capable of binding to a retroviral protease comprises: contacting, in a solution, the HTV-1 protease defective in dimerization or the folded monomer ofthe HIV-1 protease or the HIV-1 protease precursor according to any of the various embodiments, with a candidate agent; and measuring the level of binding between the candidate agent and the HIV-1 protease defective in dimerization or the folded monomer ofthe HIV-1 protease, wherein the HIV-1 protease defective in dimerization or the folded monomer ofthe HIV-1 protease is attached to a solid substrate, wherein a labeled compound capable of binding to the HIV-1 protease defective in dimerization or the folded monomer of the HTV-1 protease is present in the solution at a predetermined amount, wherein the labeled compound is a competitive inhibitor ofthe binding.
- the solid substrate is a plate or a column.
- the labeled compound is fluorescent labeled and the measuring is based on fluorescent signals.
- the labeled compound is radio-labeled and the measuring is based on radioactive signals.
- the labeled compound is an antibody reactive to the HFV-1 protease defective in dimerization or the folded monomer of the HTV-1 protease, or the HIV-1 protease precursor.
- a method for interfering viral maturation in a HTV patient comprises delivering in the infected cells ofthe patient, the nucleic acid molecule encoding the folded monomers ofthe HIV-1 protease or the HIV-1 protease precursor according to any of the various embodiments, thereby allowing the encoded protein ofthe molecule to interact with the HTV protease in the patient and inhibit its activity.
- the delivering is ultrasound or electronically mediated.
- the delivering is carried out using liposomes or cationic lipids.
- the delivering is carried out using viral vectors, wherein the viral vectors are selected from the group consisting of retro viral vectors, adenoviral vectors, AAV, lentiviral vectors, and modified vaccinia ankara (MVA) viral vectors.
- the delivering is carried out using DNA vectors, wherein the DNA vectors are selected from the group consisting of P element transposons and plasmid DNAs.
- HIV-1 protease inhibitor capable of interfering with the interactions between Asp 29 and Arg 87 thereby inhibiting dimerization ofthe HIV-1 protease.
- HIV-1 protease inhibitor capable of interfering with the interactions between the side chains of the HFV-1 protease thereby inhibiting dimerization of the HTV-1 protease.
- Figure 1 shows the amino acid sequences of mature HIV-1 protease constructs.
- the shaded regions indicate the two highly conserved regions, the first of which is the active site (DTG) and the second conserved region comprising a Gly-Arg-Asn/Asp triad, in retroviral proteases. All the constructs bear 5 mutations, 3 mutations Gln7Lys (Q7K), Leu33Ile (L33I), Leu63Ile (L63I) that restrict degradation and 2 mutations Cys65Ala (C65A) and Cys95Ala (C95A) to avoid Cys-thiol oxidation.
- the N- and C-terminal residues are involved in forming the interface ⁇ sheet.
- WT PR The wild type HIV-1 protease
- PR corresponds to SEQ ID NO:2
- PR minimally mutated
- 95 is SEQ ID NO:3, PR5.99 is SEQ ID NO:4, PR 5-9 5 is SEQ ID NO:5, PR R87K is SEQ ID NO:6, PR D 25N is SEQ ID NO:7, PR D29 N is SEQ ID NO:8, PR D 25N/Q2C/ 97C is SEQ ID NO:9, PRQ 2C L97C is SEQ ID NO: 10, PRQ 2 C/N 9 8C is SEQ ID NO: 11 , ⁇ p6pol F48r PR is SEQ ID NO: 12, and ⁇ p6 ⁇ ol-PR D25 N is SEQ ID 13. Additionally, P6pol-PR D25N is SEQ ID NO: 14 and SFNFI-PR D25N is SEQ ID: 15
- Figure 2 A shows ribbon drawing of the polypeptide backbone of the HTV-1 protease (PDB 1A30) with one protease monomer in green and the other in orange.
- the positions of the conserved residues G86R87N88 are colored gray.
- Residues D29 and R87 are represented as a ball- and stick model; the dotted yellow lines indicate hydrogen bonds between the side chains.
- Residues Q2, L97 and N98 that were mutated to cysteine residues are colored yellow.
- Figure 2B shows side chain orientation of residues Q2, L97 and N98 in one of the monomers (depicted in A) in ball-and- stick representation.
- Figures C and D show schematic drawing depicting the four-stranded terminal ⁇ -sheet of the native protease dimer and comparison with possible orientations ofthe terminal strands linked by a single, intra-monomer disulfide bridge. Residues in the second monomer of the dimer are labeled by prime.
- Figure 3 shows the amide ⁇ - 15 N HSQC (heteronuclear single quantum coherence spectroscopy) spectra of freshly prepared (a) PR RS7 K and (b) PR RS7 K in the presence of DMP323 measured at 20°C. Boxes in (a) and (b) delineate the location of peaks that exhibit significant changes due to dimer formation. Peaks of G68 for the dimer and monomer forms of PRR87 are labeled G68 D and G68 M , respectively.
- Figure 4 shows the differences in backbone C ⁇ chemical shifts between PR and PRR 87 K in the (a) absence and (b) presence of DMP323 together with the secondary structure of PR.
- the single ⁇ -helix and the ⁇ -strands are depicted as a coil and boxed arrows, respectively.
- Residue 51 whose C ⁇ carbon was not assigned due to broadening ofthe signal in PR R87K is indicated.
- Figure 5 shows (a) 15 N T 2 , (b) 15 N T,, and (c) ⁇ H ⁇ - 15 N NOE values of backbone amides of PR R87 ⁇ .
- the secondary structure of PR is depicted at the top ofthe figure.
- Figure 6 shows the amide ⁇ - 15 N HSQC spectra of freshly prepared (a) PR 5 . 99 and (b) PR ⁇ - 5 at 20°C. Locations of peaks unique to the dimer are boxed (see legend to Figure 3).
- Figure 7 shows ⁇ - 15 N HSQC spectra of PR D 29N and PR T26A in 20 mM sodium phosphate buffer, pH 5.8 at 20°C.
- A freshly prepared PR D 29N
- B PRT 26A in the absence and
- C presence of DMP323.
- Inset in (A) shows duplicate lanes of PR D29N sample in the absence of inhibitor analyzed by SDS-PAGE under reducing conditions after the NMR experiment.
- Figure 8 shows the decrease in signal intensity ofthe amide resonance G68 (tentative assignment) in the ⁇ - 15 N HSQC spectra of (a) PR D 25N/C 2 -S-S-C97, (b) PR T2 6 A , and (c) PR-(l-95) with time in 20 mM sodium phosphate buffer, pH 5.8, 20 °C.
- the initial intensity was normalized to 1.
- ten other peaks decayed similarly to G68 within the error ofthe measurement (-5%).
- Figure 9 shows ⁇ - 15 N HSQC spectra of (a) oxidized and (b) oxidized and reduced PR- D25N/Q2C / L9 7 C - Signals arising from a small fraction of protease containing the free cysteine sulfhydrals are indicated by arrows in (b).
- Inset shows duplicate lanes of oxidized P D25N Q2C 97C analyzed by SDS-PAGE under non-reducing conditions. No inter-molecularly disulfide linked dimers or multimeric forms of the protein are observed (sensitivity ⁇ 5%).
- Figure 10 shows ⁇ - 15 N HSQC spectra of (a) ⁇ p6pol F48 ⁇ -PR and (b) ⁇ p6pol-PR D25N . Solid and dashed boxes delineate the location of peaks unique for the protease monomer and dimer, respectively.
- the invention identifies regions conserved within a retroviral protease monomer, whose sequence modification results in non-functional retroviral proteases. Additionally, the present invention provides a folded human immunodeficiency virus (HTV) protease monomer containing amino acid modifications in the positions essential for dimerization and protease activity. Further, critical sites of interaction between monomers are identified as residues 1-4 and 96-99. Modifications, deletions or amino acid changes within these regions produce folded, non-functional HIV protease monomers. D29 is also identified as a residue that is involved in pivotal interactions within the monomer and critical for dimerization.
- HTV human immunodeficiency virus
- the invention further relates to HIV proteases having a modification, where Arg87 is substituted with Lys.
- the present invention further relates to methods of using the regions critical for protease folding and dimerization, modified retroviral protease monomer, fragments of the folded protease monomer, inhibitors or antagonists of the functional protease for treating patients having a retroviral infection.
- Regions essential for dimerization and protease function have been identified in the present invention.
- one region where two monomers interact known as the "interface" is critical for dimerization.
- the presence of at least one of the terminal ⁇ -strands (residues 1-4 or 96-99), preferably residues 96-99, and the interaction between the two monomers at their C-terminal ⁇ -strands is pivotal for dimerization.
- the interface contains the C-termini of two monomers, where amino acid residues 96-99 are important for monomer- monomer interaction and dimerization.
- a "folded monomer” refers to a retroviral protease monomer that has been modified or mutated, such that when present in retrovirally-infected cells, substantially inhibits retroviral protease activity and is stable and folded.
- Examples include the PR R87K , PR 1 - 95 and PR5. 99 , PR D29N and most preferably the cysteine-substituted constructs, such as, PR Q2C L97C ) PR D25N Q 2C L 97C. and PRQ2C/N98C- Unlike its wild-type relative, the "folded monomer” is stable and folded in its monomeric form at approximately ImM and does not form a fully functional protease upon dimerization.
- the wild-type protease does not exist in its monomeric form at about lOnM and quickly forms functional dimers.
- the folded monomers ofthe present invention may be used to inhibit the enzymatic activity of a functional protease or a family of related proteases, such as, but not limited to, retroviral proteases, and more preferably HTV proteases.
- a functional protease or a family of related proteases, such as, but not limited to, retroviral proteases, and more preferably HTV proteases.
- the terms “folded monomer,” “stable monomer,” “monomeric protease,” “protease defective in dimerization” are used interchangeably.
- the folded monomer (PR) is an HIV protease that may contain mutations Gln7Lys, Leu33Ile, Leu63Ile, Cys67Ala and Cys95Ala or could be fragments or variants thereof due to genetic polymorpholism or drug resistance. These protease sequences are also applicable in their precursor forms.
- folded monomers ofthe present invention may contain additional mutations, preferably at the interface domains.
- the folded monomer may block the interaction or dimerization between the wild-type monomers.
- "PR ⁇ -95 " is defined herein as the stable monomer, as described previously, having an additional C-terminal deletion of residues 96-99 (SEQ ID NO:3). More specifically, PR 1 -95 lacks the last four amino acid residues (96-99) ofthe C-terminus.
- the folded monomers ofthe present invention are also useful as a reagent in blocking functional protease dimerization.
- PR R87K is another stable monomer having a substitution within a highly conserved Gly86-Arg87-Asn88 amino acid sequence.
- the modification comprising an Arg to Lys substitution at amino acid residue 87 forms a stable monomer (SEQ ID NO:6) with a fold similar to a single subunit of the dimer.
- PR R87 ⁇ also forms a stable dimer in the presence of an inhibitor, such as DMP323, and may be used as a reagent in blocking functional protease dimerization and structure formation.
- a particular embodiment relates to specific regions critical to proper protein folding and dimerization. A hydrogen bond between Arg87 and Asp29 contributes to the stabilization ofthe dimer interface.
- a folded monomer of HIV-1 protease may have an amino acid sequence in which Arg87 or Asp29 is substituted with any other amino acid residue, according to various embodiments of this disclosure.
- An example substitution is D29N in one embodiment; and another example is R87K, in another embodiment.
- Another embodiment of this disclosure relates to inhibitors of HIV proteases that target regions critical for dimerization. For example, the interactions between Asp 29 and Arg 87 and the side chain interaction are critical for monomer and dimer stability of HTV-1 protease. It is also known that the conserved D29 residues is involved in substrate/inhibitor binding (Prabu-Jeyabalan M et al (2000) J Mol Biol 301, 1207-1220; Tozser J. (2001) Ann N Y Acad Sci 946, 145-159). Thus, according to one embodiment of this disclosure, inhibitors may be designed and made to bind to the protease and compete or abolish interactions of the native Asp 29 and Arg 87, and to inhibit dimer formation and catalytic activity.
- substituting one ofthe residues at positions 1-4 and one ofthe residues at positions 95-99 with Cysteine may derive a folded monomer ofthe H ⁇ V-1 protease.
- the disulfide bond formed between the two substituted cysteines helps to reduce aggregation.
- Gln2 is substituted with Cys and Leu97 is substituted with Cys
- Gln2 is substituted with Cys and Asn98 is substituted with Cys
- Gln2 is substituted with Cys and Thr96 is substituted with Cys
- Thr4 is substituted with Cys and Asn98 is substituted with Cys
- Ile3 is substituted with Cys and Leu97 is substituted with Cys.
- Two specific examples include PR D2 5N/Q2C/L97C (SEQ ID NO:9) and PRQ 2 C/L97C (SEQ ID NO: 10).
- a specific embodiment relates to modifications to the terminal ends ofthe monomer in order to create disulfide bonds linking the terminal ends.
- mimetic refers to a molecule, having a structure which is developed from knowledge of the structure of a retroviral protease, or portions thereof, and as such, is able to affect some or all ofthe actions ofthe retroviral protease.
- a mimetic may comprise a synthetic peptide or an organic molecule.
- amino acid sequences may be altered without adversely affecting the function of a particular protein. In fact, some alterations in amino acid sequence may result in a protein with improved characteristics. The determination of which amino acids may be altered without adversely affecting the function of a protein is well within the ordinary skill in the art. Moreover, proteins that include more or fewer amino acids may result in modified HTV proteins, proteins that are functionally equivalent to the stable monomers ofthe invention. The phrase “equivalent proteins” is intended to encompass all of these amino acid sequences. According to this disclosure, the terms “equivalent proteins,” “protein variants,” “variants,” and “fragments” are used interchangeably, all of which maintain the essential function or structural features ofthe protein. Further, in this disclosure, the terms “protein,” “polypeptide,” and “peptide” are used interchangeably. These molecules have their specific amino acid sequences and they may present certain structural features such as ⁇ helices and ⁇ sheets.
- a further embodiment ofthe invention relates to nucleic acids corresponding to amino acids ofthe present invention.
- nucleic acids directed to folded monomers, the active site, the interface, and other amino acid sequences critical for protease folding and dimerization are encompassed by the invention.
- preferred nucleic acid sequences include but are not limited to, those encoding the amino acid of PR R g ⁇ , Gly86-Arg87-Asn88, the interaction between Arg87 and Asp29, and the C-terminal -sheet residues, amino acids 96-99.
- a further embodiment ofthe present invention relates to the use of folded monomers to interfere with viral maturation.
- the stable monomeric proteases ofthe invention result in the formation of inactive, non-functional protease dimers, thereby inhibiting the polyprotein processing events that are essential for viral maturation and infectivity.
- the monomeric protease derived from the retrovirus HIV-1 can interfere with viral maturation.
- the present invention is particularly advantageous in the control of virus infection in that the folded monomers combine inhibition of protease maturation with a competitive inhibitory activity against mature protease. This two-fold activity is a substantial advantage. With the folded monomers ofthe present invention, mature protease production is dramatically reduced, and any available mature or nascent protease is secondarily inhibited by a competitive mechanism.
- a further embodiment is related to structural, biochemical and inhibition studies that target the protease precursor monomer using ⁇ p6pol F 8 ⁇ -PR (SEQ ID NO: 12), ⁇ p6pol-PRD25N (SEQ ID NO: 13), TFP-P6pol-PR D2 SN (SEQ ED NO: 14) or similar constructs which represent different lengths ofthe TFP-p6pol domain targeting the protease prior to its maturation.
- One example ofthe similar construct is SFNFI-PR D2 5N (SEQ ED: NO: 15) which include a five residue precursor.
- the folded monomers ofthe present invention are used to inhibit HTV activity in a population of cells.
- the folded monomer may be used to inhibit virus activity in a retrovirally-infected human.
- One or more stable monomers may be used to treat, for example, an HEV-infected patient.
- the monomeric protease competes to dimerize with wild type retroviral protease.
- the folded HTV protease monomers may therefore be used to control or regulate HTV virus activity in vitro and in vivo. It is recognized that inhibition of the HTV protease has important implications for control of HTV infection in humans.
- Another embodiment relates to any antibody, or antibody-containing composition, which effectively binds the protease at regions critical for dimerization.
- This includes by way of example, polyclonal and monoclonal antibodies, recombinant antibodies, chimeric antibodies, humanized antibodies, bispecific antibodies, single chain antibodies, antibodies from different species (e.g., mouse, goat, rabbit, human, rat, bovine, etc.), anti-idiotypic antibodies, antibodies of different isotype (IgG, IgM, IgE, IgA, etc.), as well as fragments and derivatives thereof (e.g., (Fab) 2 , Fab, Fv, scFv, Fab, 2(Fab), Fab', (Fab') 2 fragments).
- any antibody that interacts with regions critical for monomer folding and dimerization is encompassed by the invention.
- interface antibody antibodies directed to the interface
- these interface antibodies are specifically directed to the Gly86-Arg87-Asn/Asp88 conserved region, which is critical for dimerization.
- anti-idiotypic antibodies that interfere with protease activity may be generated.
- Interface antibodies and any anti-idiotypic antibodies may be used as "intracellular vaccines" in treating virally infected cells. Such intracellular uses involve the use of so-called single chain antibodies, which can be introduced into cells by methods well-known in the art (Huston, J.S., et al. (1988), Proc. Natl. Acad Sci., USA) or may be directly expressed within cells under the appropriate cellular controls.
- interface antibodies are preferably against amino acid residues 96-99, and can be used to inhibit protease activity directly by binding to the interface sequence, thereby blocking dimerization. These preferred antibodies and anti-idiotypic antibodies interfere with dimerization and protease activity.
- Natural peptides to the C-termini residues may be isolated from viral samples. Synthetic peptides may be custom ordered or commercially made based on the amino acid sequences ofthe present invention or chemically synthesized by methods known to one skilled in the art (Merrifield, R.B. (1963), J. Amer. Soc, 85:2149). If the peptide is too short to be antigenic it may be conjugated to a carrier molecule to enhance the antigenicity ofthe peptide.
- carrier molecules include, but are not limited to, human albumin, bovine albumin and keyhole limpet hemo-cyanin ("Basic and Clinical Immunology” (1991) Stites, D.P. and Terr A.I. (eds) Appleton and Lange, Norwalk, Connecticut, San Mateo, California).
- Exemplary antibody molecules for use in the detection methods ofthe present invention are intact immunoglobulin molecules, substantially intact immunoglobulin molecules or those portions of an immunoglobulin molecule that contain the antigen binding site, including those portions of immunoglobulin molecules known in the art as F(ab), F(ab*), F(ab*) 2 and F(v).
- Polyclonal or monoclonal antibodies may be produced by methods known in the art (Kohler and Milstein (1975), Nature 256:495-497; Campbell (1985), Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 13, Burdon, et al. (Eds.), Elsevier Science Publishers, Amsterdam).
- This disclosure also provides screening methods to identify any agent or compound that can bind to a retroviral protease, particularly a HTV protease, or the HTV-1 protease. Such binding may occur specifically to the regions that are critical for dimerization.
- the screening may be carried out using folded monomers ofthe HTV-1 protease in various embodiments. These folded monomers may be attached to a solid phase or solid substrate such as a plate or a column. For example, a 96-well, or 360-well plate may be used. An affinity column may be built that has the folded monomers attached to it.
- a competitive inhibitor that is, a compound or substance that is capable of binding to the folded monomers is used in the screening assay.
- This inhibitor may be an antibody reactive to the folded monomer or any other substance that can bind with a binding constant to the folded monomers. Therefore, the screening assay is essentially a competitive binding reaction where the inhibitor competes with the candidate agent for binding to the folded monomers.
- Such screening system can thus provide the desired sensitivity.
- the competitive inhibitor may be radiolabeled or fluorescently labeled. The binding may be measured based on the labeling signals.
- Varying amounts of test compounds are added to the complex in order to displace the original monomer-peptide complexes.
- Analysis ofthe release of the peptide indicates the relative binding affinity ofthe test sample in the complex and thus is indicative of a new anti-viral compound.
- the new complex may then be assayed for inhibition of protease activity by standard kinetic assays (Ferhst, A. (1977), Enzyme Structure and Mechanisms, W.H. Freeman and Co., San Francisco; Segal, I.H. (1975), Enzyme Kinetics, John Wiley and Sons, New York).
- the test compound may be any peptide or non-peptide composition in a purified or non-purified form. Chemical compounds, synthetic compounds, biological compounds or other specimens may be used from any source, including plant and animal. The test compound may also comprise a complex mixture or "cocktail" of molecules.
- Solid matrices or supports are available to the skilled artisan for screening multiple or a plurality of candidate compounds.
- Solid phases useful as matrices for the present invention include but are not limited to polystyrene, polyethylene, polypropylene, polycarbonate, or any solid plastic material in the shape of test tubes, beads, microparticles, dip-sticks, plates or the like. Additionally matrices include, but are not limited to membranes, 96-well microtiter plates, test tubes and Eppendorf tubes. Solid phases also include glass beads, glass test tubes and any other appropriate shape made of glass. A functionalized solid phase such as plastic or glass, which has been modified so that the surface carries carboxyl, amino, hydrazide, or aldehyde groups, can also be used. In general, such matrices comprise any surface wherein a ligand-binding agent can be attached or a surface which itself provides a ligand attachment site.
- Another embodiment ofthe present invention involves a method of treating an individual with a folded monomer, where the monomer inhibits dimerization and protease activity, or compounds which mimic the folded monomer.
- the folded monomer preferably comprises modification ofthe C-termini, more preferably residues 96-99.
- the folded monomer comprises a substitution at the Gly86-Arg87-Asn/Asp88 consensus region, more preferably an Arg87Lys substitution.
- the folded monomer also comprises a substitution at Asp29 preferably to Asn.
- the folded monomer also comprises active and inactive truncated precursor, ⁇ p6polp 48 ⁇ -PR (SEQ ED NO: 12) and ⁇ p6pol-PR D25 N, respectively.
- stable monomers having cysteine constructs such as, PRQ 2 C L 97 C and PR D2 5N Q 2 C/L97C, or mimetics thereof, are preferred for inhibiting dimerization and protease activity.
- the stable monomer or composition comprising the stable monomer is preferably administered in an amount effective to treat a patient in need of thereof.
- fragments or regions ofthe stable monomer such that the fragments mimic the structure and/or function ofthe monomers.
- Treatment of infected cells with the stable monomer fragments thereof, or protease antagonists to inhibit virus activity may be for a specific period of time or may be continuous.
- Virus activity may be measured by monitoring levels of viral protein, such as P24, or by measuring reverse transcriptase levels, or by monitoring virus protein activity by 35 S-met pulse-chase labeling and immunoprecipitation experiments, or by other methods which are well known by one of skill in the art. (Kayeyama, S., et al. (1994), AIDS Res. and Human Retroviruses, 10:735-745).
- An alternative embodiment of this disclosure relates to target delivery ofthe nucleic acid molecules encoding the folded monomers of HTV-1 protease into the infected cells of a HTV patient.
- the HTV protease activity in the patient may be inhibited as the encoded protease monomers interfere with its effective dimerization.
- the gene deliver techniques are known to those of ordinary skill in the art and may be adopted according to this disclosure.
- the delivery may be ultrasound or electronically mediated; it may be carried out using liposomes or cationic lipids.
- viral vectors may be used as the delivery system, including, e.g., retro viral vectors, adenoviral vectors, AAV, lentiviral vectors, and modified vaccinia ankara (MVA) viral vectors.
- DNA vectors such as P element transposon or plasmid DNAs may also be used.
- compositions suitable for use in a variety of drug delivery systems may be prepared. Suitable formulations for use in the present invention are found in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, PA, 17th ed. (1985).
- the pharmaceutical compositions ofthe present invention comprise a stable monomer, preferably PR5-99, PR 1 - 9 5, and/or PR R8 7 ⁇ , cysteine- containing constructs, such as PRQ 2 C/L97C and PR D2 5N/Q 2 C 97C» mimetics thereof, and polypeptides or fragments that mimic the structure and/or function of stable monomers as defined herein, where the pharmaceutical composition contains the inhibitory monomers or mimics thereof.
- the pharmaceutical composition ofthe present invention may take the form of a lyophilized powder ofthe active substance, to be dissolved immediately before use in a physiological solution for the purpose of injection.
- the stable monomer or fragments thereof of the formula is administered by either intravenous, subcutaneous or intramuscular injection, in compositions with pharmaceutically acceptable vehicles or carriers.
- the pharmaceutical composition according to the invention can also take a form which is suitable for oral administration.
- suitable forms are tablets, food gelatin capsules, dragees, powders and granules.
- the formation of such oral forms is well known to those skilled in the art. Any of the known formulations are useful in preparing the instant oral pharmaceutical compositions.
- Suitable vehicles or carriers for the above noted formulations can be found in standard pharmaceutical texts, e.g. in Remington's Pharmaceutical Sciences (1985).
- liposomes may be used to deliver the stable monomers to the target cell population.
- Targeting of liposomes using a variety of targeting agents e.g., ligands, receptors and monoclonal antibodies
- targeting agents e.g., ligands, receptors and monoclonal antibodies
- the contents ofthe liposomes are delivered to the intracellular space by a number of mechanisms, such as endocytosis, exchange of lipids with the cell membrane, or fusion ofthe liposome with the cell membrane.
- the dosage of the folded monomer will vary with the form of administration, the frequency of administration, the nature and severity of the infection and the particular active agent chosen. Furthermore, it will vary with the particular host under treatment. Generally, treatment is initiated with small dosages substantially less than the optimum dose of the stable monomer. Thereafter, the dosage is increased by small increments until the optimum effect under the circumstances is reached.
- the actual dosage administered will be determined by physiological factors such as age, body weight, severity of condition and/or chemical history ofthe patient. With these considerations in mind, the dosage ofthe stable monomer composition for a particular subject can be readily determined by the physician. In general, the stable monomer is most desirably administered at a concentration level that will generally afford antivirally effective results without causing harmful or deleterious side effects. However, it is noted that in extreme cases, a dosage approaching the toxic level may be an acceptable treatment protocol.
- compositions for parenteral administration which comprise a defective monomer dissolved or suspended in an acceptable carrier, preferably an aqueous carrier, such as but not limited to water, buffered water, saline, glycine, and the like.
- an acceptable carrier preferably an aqueous carrier, such as but not limited to water, buffered water, saline, glycine, and the like.
- These compositions may be sterilized by conventional sterilization techniques, or may be sterile filtered.
- the resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration.
- the stable monomer may be administered in the range of 0.01 to 75 mg per kilogram of body weight per day, with a preferred range of 2.5 to 20 mg per kilogram.
- the stable monomer ofthe formula may be administered at a dosage of 10 ⁇ g to 1000 mg per kilogram of body weight per day, although the aforementioned variations will occur.
- a dosage level that is in the range of from about 50 ⁇ g to 500 mg per kilogram of body weight per day is most desirably employed in order to achieve effective results.
- formulations disclosed herein above are effective and relatively safe medications for treating HTV infections, the possible concurrent administration of these formulations with other antiviral medications or agents to obtain beneficial results is not excluded.
- antiviral medications or agents include soluble CD4, thalidomide, dideoxyinosine, dideoxythymine, zidovudine, dideoxycytidine, gancyclovir, acyclovir, phosphonoformate, amatradine, ribavarin, antiviral interferons (e.g.
- the stable monomer formulations may be used in conjunction with other protease inhibitors or antagonists such as those described in Winslow, D.L. and Otto, M.J. (1995).
- the R87K mutation and a stop codon were introduced into the PR template [which encodes the 5 mutations Q7K, L33I, L63I, C67A and C95A (31)] to generate the constructs PR R87K and PRi- 95 , respectively, using the Quick-Change mutagenesis protocol (Stratagene; La Jolla, CA).
- the construct PR5-99 (Louis, J. M. et al (1999) Nat. Struct. Biol. 6, 868-875) was used to generate the clone PR 5 - 95 using the same mutagenesis protocol and the primers used for creating PR 1 . 95 .
- the protease mutants are listed in Figure 1. PR and its derived mutants were expressed in E.
- Proteins (2-3 mg) at a concentration of ⁇ 0.33 mg/ml in 35% acetonitrile/water containing 0.05% trifluoroacetic acid (TFA) were folded by dialysis into 2 L of 30 mM formic acid, pH 2.8, for 1.5 hr followed by diluting the protein in 5-fold excess of 10 mM acetate buffer, pH 6.0 to shift the pH to 4, either with or without saturating amount of DMP323 [Kj ⁇ lOnM (Lam, P. Y. et al (1996) J. Med. Chem. 39, 3514-3525)], followed by dialysis in 4 L of 20 mM sodium phosphate buffer, pH 5.8, for another 1.5 hr.
- TFA trifluoroacetic acid
- Proteins were concentrated to achieve a final concentration of about 0.4 mM (as a dimer) for NMR analysis and to a concentration of about 0.05 mM for sedimentation equilibrium studies and enzyme kinetics. Concentrations of PR and its mutants were expressed for a dimer, unless otherwise noted. Although the amount of DMP323 added was equivalent to 5M final concentration, the actual concentration was indeterminable due to the poor stability of DMP323 in aqueous buffers.
- Protease assays were initiated by mixing 5 ⁇ l of freshly folded PR 87K (59 ⁇ M) or PR,. 95 (52 ⁇ M), 10 ⁇ l of 2X incubation buffer [(200 mM potassium phosphate buffer at pH 5.6, 0.2 M (buffer A) or 2 M NaCl (buffer B)] and 5 ⁇ l of 0.2 mM substrate. PR 5 . 99 was assayed in buffer B at a final enzyme concentration of 1 ⁇ M. The reaction mixture was incubated at 37 °C for 1 hour and the reaction was terminated by the addition of guanidine-HCl to a final concentration of 6 M.
- #Assays were performed in 250 mM sodium phosphate, pH 5.6, 2M NaCl at 37 °C in a final enzyme concentration of 0.01-0.1 ⁇ M PR and 1 ⁇ M PR 5 - 99 .
- a r A o r exp[HM(r 2 - r 2 0 )] + E, where v is the absorbance ofthe solute at a reference radius, r 0 and A r is the absorbance at a given radial position, r.
- H represents ⁇ 2 /2RT, ⁇ the angular speed in radians per second, R is the gas constant and T is the absolute temperature.
- M represents the experimentally returned value ofthe buoyant molecular mass, M(l-vp).
- E is a small baseline correction determined experimentally at 30,000 rpm.
- NMR experiments were conducted using protein concentrations of 0.4-0.5 mM in 20 mM phosphate buffer in 95% H 2 0/5% D 2 0 with a sample volume of- 280 ⁇ l in a 5 mm Shigemi tube (Shigemi, Inc.; Allison Park, PA). NMR spectra were acquired on a DMX500 spectrometer (Broker Instruments; Billerica, MA). All experiments were conducted at 20 °C unless noted otherwise. Data were processed and analyzed using the software nmrPipe, nmrDraw, and PTPP softwares (Garrett, D.S. et al (1991) J. Magn. Reson. 95, 214-220; Delaglio, F. et al (1995) J. Biomol. NMR 6, 277-293).
- T , 15 N transverse relaxation times (T 2 ), and 15 N- ⁇ H ⁇ NOES for free PR R87 ⁇ were measured in an interleaved manner (Tjandra, N. et al (1996) J. Am. Chem. Soc. 118, 6986-6991) with repetition delays of 2 s for T[ and T 2 , and 3 s for NOE determination.
- Relaxation delays were 0.0016, 0.16, 0.32, 0.48, 0.64, 0.8, and 0.96 s for T, and 6, 12, 24, 42, 60, 84, and 96 ms for T 2 measurements.
- PR R87 was assayed against substrates representing cleavage sites between the major Gag and Gag-Pol domains. No sign of cleavage was observed using PR R87K , except for the MA/CA and p6 pol /PR substrates, for which very low levels of cleavage were observed. Based on the specific activity values, PR R87 was calculated to have 6700 and 1800-fold lower activity than PR m buffer A and B, respectively (Table 3). PR 87 exhibited a 4600-fold lower specific activity as compared to that of PR measured using the spectrophotometnc assay. TABLE 3
- PR 1 - 95 did not show any degradation products (similar to PR R87 ⁇ ) whereas PR 5 - 99 clearly was proteolyzed as evidenced by the appearance of additional resonances in the ⁇ - 15 N HSQC spectrum ( Figure 6A, dotted enclosed area).
- the degradation products of PR 5 - 99 most likely resulted from cleavage at the dipeptide sequences I33-E34 and 163-164 (Mildner, A.M. et al (1994)). Based on these observations, PR 5 . 99 may have formed an active dimeric protein that was capable of autoproteolysis at higher protein concentrations.
- Table 1 The kinetic parameters for PR and PR 5-99 -catalyzed hydrolysis of substrates under identical conditions are summarized in Table 1.
- the catalytic activity of PR was similar to that ofthe WT-PR (Tozser, J. et al (1991) FEBSLet. 281, 77-80).
- the low k cat /K m observed for PR5-99 using 5 different substrates suggested that only a small fraction ofthe protein contributed to the observed activity.
- These current results are consistent with our earlier study in which we observed a - 50-fold lower k cat /K n , for PR 5 . 99 compared to PR assayed using a spectrophotometric substrate (Louis, J. M. et al (1999)).
- PR 1 - 95 did not exhibit detectable cleavage of any ofthe substrates tested.
- PR 5 - 99 exhibited a spectrum typical of a random coil polypeptide after 2 days at a concentration of- 1.2 mM. In addition, weak intensity dispersed signals corresponding to a folded conformation were also observed (Louis, J. M. et al (1999)). Freshly prepared samples of PR 1 - 95 and PR5.9 9 at a concentration of -1 mM were reexamined to investigate the effect of protein concentration on dimerization. The spectrum of PR 1 - 95 essentially remained that of a monomer ( Figure 6B) whereas the spectrum of PR 5 . 99 showed a significant fraction ofthe signals corresponding to a dimer. The propensity of PR 5 . 99 to dimerize with increasing protein concentration was similar to that observed for an analogous deletion construct ofthe RSV protease (Schatz, G.W. et al (2000) J. Virol. 75, 4761-4770).
- protease precursor was mainly in an unfolded form with transient dimer formation leading to intramolecular autocatalytic cleavage first at the N-terminus of the protease (p6 pol -PR site) and stable structure formation (Louis, J. M. et al (1999)). Subsequent cleavage at the C-terminus (PR-RT site) occurred via an intermolecular process ofthe protease (Louis, J. M.
- binding of inhibitor or possibly substrate to the active site promoted dimer formation and thereby compensated for the loss of dimer stability, due to displacement ofthe outer ⁇ -strands (residues 1-4).
- the binding of the N- terminal polypeptide comprising the p6 pol -PR cleavage site to the active site also contributed to the stability of the transient dimer formation of the precursor, leading to the hydrolysis ofthe scissile peptide bond and formation of the stable dimeric structure.
- PRc 2 -s-s-c97 PRD25N/C2-S-S-C97, and PRc2-s-s-c98, respectively.
- Cells were grown at 37 °C either in Luria-Bertani medium or in a modified minimal medium for uniform (>99%) 15 N labeling with 15 NH 4 C1 as the sole nitrogen source and induced with 2 mM TPTG for 4 hr.
- Cells derived from IL of culture were suspended in 20 volumes of buffer A (50 mM Tris-HCl pH 8.2, 10 mM EDTA and 10 mM DTT) and lyzed by sonication at 4°C in the presence of 100 ⁇ g/ml lysozyme.
- buffer A 50 mM Tris-HCl pH 8.2, 10 mM EDTA and 10 mM DTT
- the insoluble fraction was washed by resuspension in buffer A containing 2 M urea and 0.5 % Triton X-100 and subsequently in buffer A. In both cases, the insoluble fraction (inclusion bodies) was pelleted by centrifugation at 20,000 g for 30 min at 4 °C. The final pellet of inclusion bodies was solubilized in 50 mM Tris-HCl, pH 8.0, 7.5 M guanidine-HCl, 5 mM EDTA, 10 mM DTT to yield a protein concentration not exceeding 20 mg/ml.
- PRj26 A and PR D29N were isolated using an established protocol comprising isolation of inclusion bodies followed by fractionation of the protease by size-exclusion chromatography in buffer B (50 mM Tris-HCl, pH 8, 4 M guanidine-HCl, 5 mM EDTA, 2 mM DTT) and reverse-phase high pressure liquid chromatography (see below).
- buffer B 50 mM Tris-HCl, pH 8, 4 M guanidine-HCl, 5 mM EDTA, 2 mM DTT
- reverse-phase high pressure liquid chromatography see below.
- the proteins were folded according to the procedure previously described (Ishima R et al (2001) / Bid Chem 276, 49110-49116).
- Peak fractions corresponding to the monomer were combined and subjected to reverse-phase HPLC on POROS RU resin (Perceptive Biosystems, MA) using a linear gradient of 0 to 60 % acetonitrile/0.05% trifluoroacetic acid. Peak fractions were combined and stored at - 80 °C. Protein (2 mg) was diluted to about 0.33 mg/ml in 35% acetonirrile/water/0.05% TFA or in 0.1 M formic acid and dialyzed (Slide-A-Lyzer, 10K dialysis cassettes, Pierce) against 2 L of 30 mM formic acid, pH 2.8 for 1 to 1.5 hr.
- the sample was drawn out of the dialysis cassette, diluted with 5 volumes of 10 mM sodium acetate, pH 6.0 and dialyzed further in 4 L of 20 mM sodium phosphate, pH 5.8 for 1.5 to 2 hr. Finally it was concentrated to - 8 mg/ml and stored at 4 °C or used for experiments described below.
- proteolytic digests in 20 mM sodium phosphate, pH 5.8, were carried out by injecting protein (50-100 pmol) onto a Zorbax C3 column equilibrated in 5% acetic acid (2.3 x 150 mm, Hewlett Packard, San Jose, CA) fitted to an HP1100 integrated high-pressure liquid chromatography /electrospray mass spectrometer (Hewlett Packard). The solvent was held isocratic for 25 min to allow desalting of the protein and them ramped to 100 % acetonitrile over a period of 25 min at a flow rate of 200 ul/min. Protein peaks that eluted into the mass spectrometer were scanned from m/z 500 to 1700 every 4 s. Spectra were deconvoluted using the Hewlett Packard software to yield the mass ofthe protein.
- Protease Assays were assayed using a spectrophotometric substrate, Lys-Ala-Arg- Val-Nle-(4-nitrophenyl-alanine)-Glu-Ala-Nle-NH 2 , in 100 mM sodium acetate (pH 5.0) at 25 °C at final enzyme concentrations of 29 ⁇ M PRD 2 9N > 22.8 ⁇ M PRc2-s-s-c97 or 1 ⁇ M PRc 2 -s-s-c98 and 460 ⁇ M substrate.
- NMR experiments All NMR experiments were carried out at a protein concentration of 0.6-1.0 mM in monomer (unless noted otherwise) in 20 mM phosphate buffer at pH 5.8, 95% H 2 0/5% D 2 0 at 20°C with a sample volume of -280 ⁇ l in a 5 mm Shigemi tube (Shigemi, Inc., Allison Park, PA).
- NMR spectra were acquired on a DMX500 spectrometer (Bruker Instruments, Billerica, MA). Data were processed and analyzed using the nmrPipe, nmrDraw, and PTPP softwares (Garrett, D.S. et al (1991); Delaglio, F. et al (1995)).
- a time course to estimate the aggregation of the protein ( ⁇ 1 mM) by HSQC spectra was recorded keeping the sample temperature constant, either in the magnet or in an incubator between spectra.
- PR D2 N a construct containing the complementary change to that of PR R 87 ⁇ in the R87/D29 pair was constructed and investigated.
- PR 87 and PR D29N were -4600- and 920-fold less active than PR.
- the ⁇ - 15 N HSQC spectrum of PR D29N recorded on a 0.9 mM sample is displayed in Fig. 7A. Characteristic peaks resulting from the monomeric protein (squares) as well as dimer peaks are apparent. This demonstrated that PR D29N is also a dimerization deficient mutant.
- R8Q mutant of the mature PR does not exhibit any changes in the dimerization constant (Id).
- the kinetic parameters for mature PR R8Q -catalyzed hydrolysis of a peptide substrate and the inhibition constant for the hydrolytic reaction with an inhibitor are comparable to that of PR.
- the dimer interface of the free mature protease is formed by residues contributing to the active-site and those located at the N- and C-termini. Of these, residues 96-99 constitute about 50% of the total interface interactions (Weber, I. T. (1990); Miller M, et al (1989) S ⁇ ence, 246, 1149- 1152).
- the T26A mutation of the active-site interface was also shown to prevent dimer formation (Strisovsky, K. et al (2000)). In order to compare the effect of these two distinct interfaces (active- site residues versus terminal ⁇ -sheet), T26A mutant was investigated further. The T26A change was introduced into our idealized PR construct and the protein was purified and assessed by NMR.
- PR T26A slowly aggregates.
- the decay in signal intensity of selected peaks in the ⁇ - 15 N HSQC spectrum for PR ⁇ OA and PR ⁇ -95 at 0.6 mM protein concentration indicates the loss of monomer species at approximately similar rates.
- the time course for the G68 resonances is plotted for both proteins in Fig. 8.
- a comparison with PR 87 at pH 5.8 and PR 5 _ 99 could not be carried out since the former aggregates considerably faster and the latter experiences substantial autoproteolysis (Louis, J. M. et al (1999); Ishima R etal (2001)).
- the terminal residues of the monomer subunits in the protease dimer form a four-stranded anti-parallel ⁇ -sheet, thereby creating a tight interface. Interfering with the formation of this sheet by deleting either the N- or C-terminal 4 residues disrupts dimerization of the free protease. Except for the conservative substitutions L97V and V3I no other reported drug-resistant mutations of protease terminal residues have been reported. This suggests that hydrophobic packing of the terminal side-chains may be critical for dimer stability.
- PR D25N Q2C L97C was constructed in order to create an intra-chain disulfide bridge between the N- and C-terminal strands without the added complication of autoproteolysis (self- degradation) of PR.
- This construct is devoid of enzymatic activity due to the mutation of the active- site residue (D25N) and was used to optimize the protocol for disulfide bond formation (see Example 7 for details). Oxidation prior to the final size-exclusion column chromatography was chosen since this allows for efficient separation of monomer, inter-molecularly disulfide linked dimer and multimeric forms of the protein.
- the behavior of the oxidized PR D2 SN/ C2 - S -S-/ C 9 7 with respect to aggregation was assessed by ⁇ - I5 N HSQC spectroscopy.
- the relative signal intensity of at least 10 individual peaks was followed over time at 20 °C. This data is illustrated for the G68 peak in Figure 8.
- the decrease in signal intensity is clearly less than observed for the PR ⁇ 26A and PR 1 . 95 monomers. This indicates that the folded monomer stabilized by the intra-chain disulfide bond exhibits superior attributes with respect to biophysical characterization.
- Inhibitor mediated interactions enhance dimer formation by the protease (Grant SK, et al (1992)).
- PR D2 5N/ C2 - S - S - C9 7 is clearly a monomer and the equivalent PRc 2 -s-s-c 97 protein was used to assess whether inhibitor binding promotes dimerization.
- PRc2-s-s-c97 is mainly monomeric with a tertiary fold nearly identical to that of PR D2 5N/C 2 -S-S-C97-
- peaks characteristic of both the monomer and the dimer are observed (see Table 4) indicating that DMP323 binding by PRc 2 -s-s-c 9? facilitates dimer formation.
- PRc 2 -s-s- C 97 (at 22 ⁇ M) is enzymatically active, albeit about 200-fold less than PR, indicating that substrate promotes the active dimeric PRc 2 -s- S-C97 complex.
- the interaction between the two C-terminal strands is indispensable for dimer formation even in the presence of inhibitor.
- the two C-terminal strands of the PRc 2 -s-s- C 97 may also interact upon DMP323 binding.
- the C-terminal strands cross over (99', 99) and are sandwiched on the outside by the N-terminal strands (1, 1 ') to form the 4-stranded anti-parallel ⁇ -sheet (l-99'-99-l ', see Figure 2).
- the disulfide link between the N- and C-terminal strands will prevent this cross over.
- the terminal sheet may contain a 1-99-99'-! ' configuration.
- PRc2-s- s-c 98 was analyzed, in which N98 was substituted by a Cys to form an intra-chain disulfide bridge with the C2 residue. NMR analyses indicated that this construct was also a folded monomer at -0.6 mM concentration.
- PRc2-s-s-C98 displays only a 15 -fold decrease in k ⁇ /K m when compared to PR under identical conditions (Louis, J. M. et al (1999)). For comparison, the kinetic parameters k ⁇ , and K m for PRc 2 .
- S -s-c 98 -catalyzed hydrolysis of the substrate were 0.87 ⁇ 0.07 s "1 and 0.427 ⁇ 0.06 mM, respectively, representing approximately a 6.3- and 2.4-fold decrease in k ⁇ and K ra , respectively, when compared with PR (Id.).
- the specific activity values of PRc 2 -s-s-c 98 is ⁇ 18-times higher than that of PRc 2 -s-s- C 97- hi the free and inhibitor/substrate bound three-dimensional structures of the mature protease dimer, the Q2 and N98 side chains are solvent exposed whereas the L97 side chain points inward into the protein core ( Figures 2A and 2B). Based on the particular side-chain orientations, the intra-chain disulfide link between C2 and C98 residues will probably introduce less strain into the backbone conformation of the C-terminal strand than one between C2 and C97 residues.
- Both disulfide linked proteases, PRc2-s-s-C97 and PRc2-s-s-c98 become dimeric in the presence of substrate or inhibitor.
- the folded monomer of PRc 2 -s-s-c 98 at 1.5 mg/ml in 20 mM sodium phosphate buffer, pH 5.8 is stable for up to 6 months at 4 °C with no loss in catalytic activity.
- the enhanced properties of PRc 2 -s-s-c 98 especially with respect to suppressed autoproteolysis are mainly due to the fact that PRc 2 -s-s-c 98 exists predominantly as a stably folded monomer.
- This mutant is the first HTV-1 protease that exists as a defined monomeric species at a concentration of 0.6 mM, pH 5.8, which upon the addition of substrate becomes the enzymatically active dimer.
- protease precursor TFP-p6pol-PR in the presence of a potent protease inhibitor has the tendency to aggregate at high protein concentrations thus restricting structural studies.
- the protease fused to a minimal sequence ( ⁇ p ⁇ pol) of- 22 amino acids (residues G27 to F48) ofthe native N-terminal p6pol domain also exhibits very low catalytic activity and undergoes time-dependent maturation to release the mature protease.
- the C- terminal p6pol residue (Phe48) was substituted to a He.
- the HSQC spectrum recorded for a 6 mg/ml sample of ⁇ p6polp 8 rPR Figure 10A shows peaks corresponding both to dimer and monomer forms of the protein.
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WO2003017934A3 WO2003017934A3 (en) | 2003-12-24 |
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PCT/US2002/026757 WO2003017934A2 (en) | 2001-08-23 | 2002-08-23 | Folded monomers of the hiv-1 protease and methods of their use |
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AU (1) | AU2002327506A1 (en) |
WO (1) | WO2003017934A2 (en) |
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US6165794A (en) * | 1994-11-10 | 2000-12-26 | The Regents Of The University Of California | Suppression of proteolytic activity by dysfunctional protease formation |
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US6165794A (en) * | 1994-11-10 | 2000-12-26 | The Regents Of The University Of California | Suppression of proteolytic activity by dysfunctional protease formation |
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AU2002327506A1 (en) | 2003-03-10 |
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