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A series of P1/P1' substituted cyclic urea analogues were prepared in an attempt to increase the intra-cellular antiviral potency of the nonsymmetrical 3-aminoindazoles DMP 850 and DMP 851. The effect of alkyl substitution of the P1/P1' residues on cellular antiviral potency, protein binding, resistance profile and pharmacokinetics are described.

A series of peptide boronic acids containing extended, hydrophobic P1 residues was prepared to probe the shallow, hydrophobic S1 region of HCV NS3 protease. The p-trifluoromethylphenethyl P1 substituent was identified as optimal with respect to inhibitor potency for NS3 and selectivity against elastase and chymotrypsin.

3-Alkoxymethyl- and 3-aryloxymethyl-2-pyridinones were synthesized and evaluated for activity as non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV-1. It was found that several compounds were potent inhibitors of HIV-1 with the most potent compound 24 exhibiting an IC90=32 nM. Compound 24 also possessed a potent resistance profile as demonstrated by submicromolar IC90s against several clinically meaningful mutant virus strains.

A series of unique 3,3a-dihydropyrano[4,3,2-de]quinazolin-2(1H)-ones and a 2a,5-dihydro-2H-thieno[4,3,2-de]quinazoline-4(3H)-thione were found to be HIV-1 non-nucleoside reverse transcriptase inhibitors. One of these compounds, as the racemate, possessed an IC90=4.6 nM against wild-type virus in a whole cell antiviral assay and had an IC90=76 and 897 nM against the clinically significant K103N and K103N/L100I mutant viruses, respectively.

Two series of benzoxazinones differing in the aromatic substitution pattern were prepared and evaluated as HIV-1 reverse transcriptase inhibitors. The 5-fluoro (5a-d) and 6-nitro (5e-h) substituted compounds displayed activity comparable or better than Efavirenz, the lead structure of the series.

Two series of cyclic ureas modified at the P1/P1′ residue were prepared and evaluated for HIV protease inhibition and whole cell antiviral activity. Compounds 8b, 10 (3- and 4-pyridylmethyl analogs) and 6b (4-methoxy analog) showed significant improvement in antiviral activity relative to lead compounds DMP323 and DMP 450.

Comparison of the high-resolution X-ray structures of the native HIV-1 protease and its complexes with the inhibitors suggested that the enzyme flaps are flexible. The movement at the tip of the flaps could be as large as 7 A. On the basis of this observation, cyclic cyanoguanidines have been designed, synthesized, and evaluated as HIV-1 protease (PR) inhibitors. Cyclic cyanoguanidines were found to be very potent inhibitors of HIV-1 protease. The choice of cyclic cyanoguanidines over cyclic guanidines was based on the reduced basicity of the former. X-ray structure studies of the HIV PR complex with cyclic cyanoguanidine demonstrated that in analogy to cyclic urea, cyclic cyanoguanidines also displace the unique structural water molecule. The structure-activity relationship of the cyclic cyanoguanidines is compared with that of the corresponding cyclic urea analogues. The differences in binding constants of the two series of compounds have been rationalized using high-resolution X-ray structure information.

Cyclic ureas containing 3-aminoindazole P2/P2′ groups are extremely potent inhibitors of HIV protease. The parent 3-aminoindazole 6 showed a K i × 0.01 nM but poor translation of enzyme activity to antiviral activity was observed. A series of 3-alkylaminoindazoles revealed that translation improved with increasing lipophilicity. An X-ray crystal structure of 6 bound to HIV protease was obtained.

A series of analogs of HIV protease inhibitor DMP323 containing functionalized aliphatic P2/P2′ groups was prepared and evaluated for HIV protease inhibition and antiviral activity in a cell-based assay. Asymmetric compounds with a 5-hydroxypentyl substituent at P2 and a benzylic substituent at P2′ showed increased potency over the corresponding symmetrically substituted analogs.

A new era has begun in the chemotherapeutic treatment of AIDS with the marketing of the first generation of peptidomimetic HIV protease inhibitors from Roche, Merck and Abbott. Owing to the potential drug resistance problems associated with HIV mutations, a main emphasis in the search for the next generation of HIVPR drugs is in the area of structurally different cyclic nonpeptides. This article reviews the different approaches that have been undertaken to find or design cyclic nonpeptides that are capable of displacing the structural water molecule usually associated with the peptidomimetic class of inhibitors. The favorable entropic effect from water displacement and preorganization can lead to smaller and more potent inhibitors with improved therapeutic potential.

Several bis- N -alkylated (+)-biotin derivatives were synthesized and evaluated for activities against HIV-1 protease. The most potent inhibitor, 2D , synthesized in two steps from (+)-biotin, has K i of 0.50 μM and antiviral IC 90 of 7 μM. The (+)-biotin analogs in general have good translations from enzymatic K i to antiviral cell assay IC 90 .

Low-molecular-weight peptidyl aldehyde inhibitors of HIV protease that reach in vivo plasma concentrations after oral administration substantiailly in excess of the antiviral IC90 are described. We also report efforts to improve the potency and stability of these compounds that culminated in a series of peptidyl trifluoromethyl ketones with increased potency but decreased bioavailability.

DMP 323 is a potent inhibitor of the protease of human immunodeficiency virus (HIV), with antiviral activity against both HIV type 1 and HIV type 2. This compound is representative of a class of small, novel, nonpeptide cyclic urea inhibitors of HIV protease that were designed on the basis of three-dimensional structural information and three-dimensional database searching. We report here studies of the kinetics of DMP 323 inhibition of the cleavage of peptide and HIV-1 gag polyprotein substrates. DMP 323 acts as a rapidly binding, competitive inhibitor of HIV protease. DMP 323 is as potent against both peptide and viral polyprotein substrates as A-80987, Q8024, and Ro-31-8959, which are among the most potent inhibitors of HIV protease described in the literature to date. Incubation with human plasma or serum did not decrease the effective potency of DMP 323 for HIV protease, suggesting that plasma protein binding is of a low affinity relative to that of HIV protease. DMP 323 was also assessed for its ability to inhibit the mammalian proteases renin, pepsin, cathepsin D, cathepsin G, and chymotrypsin. No inhibition of greater than 12% was observed for any of these enzymes at concentrations of DMP 323 that were 350 to 40,000 times higher than that required to inhibit the viral protease 50%.

Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule. The success of the design in both displacing and mimicking the structural water molecule was confirmed by x-ray crystallographic studies. Highly selective, preorganized inhibitors with relatively low molecular weight and high oral bioavailability were synthesized.

A series of 4,4-disubstituted quinolinones was prepared and evaluated as HIV-1 reverse transcriptase inhibitors. The C-3 substituted compound 9h displayed improved antiviral activity against clinically significant single (K103N) and double (K103N/L100I) mutant viruses.

Several bis- N -alkylated (+)-biotin derivatives were synthesized and evaluated for activities against HIV-1 protease. The most potent inhibitor, 2D , synthesized in two steps from (+)-biotin, has K i of 0.50 μM and antiviral IC 90 of 7 μM. The (+)-biotin analogs in general have good translations from enzymatic K i to antiviral cell assay IC 90 .

A complete chemical synthesis and assembly of genes for the production of human immunodeficiency virus type-I protease (HIV-PR) and its precursors are described. The T7 expression system was used to produce high levels of active HIV-PR and its precursors in Escherichia coli inclusion bodies. The gene encoding the open reading frames of HIV-PR was expressed in E. coli as a 10-kDa protein, while the genes encoding HIV-PR precursors were expressed as larger proteins, which were partially processed in E. coli to the 10-kDa form. These processing events are autoproteolytic, since a single-base mutation, changing the active-site aspartic acid to glycine, completely abolished the conversion. HIV-PR can be released with 8 M urea from washed cellular inclusion bodies, resulting in a preparation with few bacterial host proteins. After refolding, this preparation contains no nonspecific protease or peptidase activities. The recombinant HIV-PR isolated from inclusion bodies cleaves HIV-PR substrates specifically with a specific activity comparable to column-purified HIV-PR.

The backbone of effective highly active antiretroviral therapy regimens for the treatment of HIV infections currently contains at least two nucleosides. Among the features that influence the potency of each component of a regimen and the overall efficacy of the combination are the cellular uptake and bioconversion of nucleoside analogues to their active triphosphate form, and the extent of possible interactions in these steps that might occur when more than one nucleoside is used in a regimen. D-d4FC (Reverset™), a new cytidine analogue with the ability to inhibit many nucleoside-resistant viral variants, was examined for these parameters. In phytohemaglutinin-stimulated human peripheral blood mononuclear cells, D-d4FC was taken up in a rapid (8 h to 50% maximal value), saturable (plateau above 10 μM parent nucleoside concentration) process, resulting in levels of D-d4FC triphosphate that should provide potent antiviral activity against a variety of virus genotypes. Based on measurement of antiviral effects in cell culture, additive and in some cases, synergistic interactions were observed with protease inhibitors, non-nucleoside reverse transcriptase inhibitors or other nucleosides, including cytidine analogues.

A series of 4,1-benzoxazepinone analogues of efavirenz (Sustiva) as potent NNRTIs has been discovered. The cis-3-alkylbenzoxazepinones are more potent then the trans isomers and can be synthesized preferentially by a novel stereoselective cyclization. The best compounds are potent orally bioavailable inhibitors of both wild-type HIV-1 and its clinically relevant K103N mutant virus, but are highly protein-bound in human plasma.

A series of 3,3-disubstituted quinoxalinones was prepared and evaluated as HIV-1 reverse transcriptase inhibitors. The N-allyl (6b and 6f), N-cyclopropylmethyl (6a, 6g, 6h, and 6k) and N-carboalkoxy (6m-6y) substituted compounds displayed activity comparable or better than Efavirenz and GW420867X.

Benzothiadiazine non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV have been synthesized via a novel process to afford active inhibitors, with the most potent compound exhibiting an IC90=180 nM in a whole cell assay. The 2,2-dioxide-1H-2,1,3-benzothiadiazine ring system was constructed in one step from 2-amino-5-chlorobenzonitrile.

Efavirenz (SUSTIVA TM ) is a potent non-nucleoside reverse transcriptase inhibitor. Due to the observation of breakthrough mutations of the reverse transcriptase enzyme during Efavirenz therapy, we sought to develop an optimized second generation series. To that end, SAR of the substituents on the aromatic ring was undertaken and the results are summarized here. The 5,6-difluoro ( 4f ) and the 6-methoxy ( 4m ) substituted benzoxazinones were determined to be equipotent, and as a result such substitution patterns will be incorporated in second generation scaffolds.

Cyclic urea SD146, a potent HIV protease inhibitor bearing a flat resistance profile, possessed poor solubility and bioavailability, which precluded further development of the compound. In an effort to improve upon the pharmacokinetic profile of the compound, several analogs modified at the P1/P1' residues were prepared and evaluated. Several of those compounds displayed significant improvement of physical properties.

Resistance of HIV-1 to protease inhibitors has been associated with changes at residues Val82 and Ile84 of HIV-1 protease (HIV PR). Using both an enzyme assay with a peptide substrate and a cell-based infectivity assay, we examined the correlation between the inhibition constants for enzyme activity (Ki values) and viral replication (IC90 values) for 5 active site mutants and 19 protease inhibitors. Four of the five mutations studied (V82F, V82A, I84V, and V82F/I84V) had been identified as conferring resistance during in vitro selection using a protease inhibitor. The mutant protease genes were expressed in Escherichia coli for preparation of enzyme, and inserted into the HXB2 strain of HIV for test of antiviral activity. The inhibitors included saquinavir, indinavir, nelfinavir, 141W94, ritonavir (all in clinical use), and 14 cyclic ureas with a constant core structure and varying P2, P2' and P3, P3' groups. The single mutations V82F and I84V caused changes with various inhibitors ranging from 0.3- to 86-fold in Ki and from 0.1- to 11-fold in IC90. Much larger changes compared to wild type were observed for the double mutation V82F/I84V both for Ki (10-2000-fold) and for IC90 (0.7-377-fold). However, there were low correlations (r2 = 0.017-0.53) between the mutant/wild-type ratio of Ki values (enzyme resistance) and the mutant/wild-type ratio of viral IC90 values (antiviral resistance) for each of the HIV proteases and the viruses containing the identical enzyme. Assessing enzyme resistance by "vitality values", which adjust the Ki values with the catalytic efficiencies (kcat/Km), caused no significant improvement in the correlation with antiviral resistance. Therefore, our data suggest that measurements of enzyme inhibition with mutant proteases may be poorly predictive of the antiviral effect in resistant viruses even when mutations are restricted to the protease gene.

Using the structural information gathered from the X-ray structures of various cyclic urea/HIVPR complexes, we designed and synthesized many nonsymmetrical P2/P2'-substituted cyclic urea analogues. Our efforts concentrated on using an indazole as one of the P2 substituents since this group imparted enzyme (Ki) potency as well as translation into excellent antiviral (IC90) potency. The second P2 substituent was used to adjust the physical and chemical properties in order to maximize oral bioavailability. Using this approach several very potent (IC90 11 nM) and orally bioavailable (F% 93-100%) compounds were discovered (21, 22). However, the resistance profiles of these compounds were inadequate, especially against the double (I84V/V82F) and ritonavir-selected mutant viruses. Further modification of the second P2 substituent in order to increase H-bonding interactions with the backbone atoms of residues Asp 29, Asp 30, and Gly 48 led to analogues with much better resistance profiles. However, these larger analogues were incompatible with the apparent molecular weight requirements for good oral bioavailability of the cyclic urea class of HIVPR inhibitors (MW610).

A new photoreactive amino acid analog, p-benzoyl-L-phenylalanine, is described. Convenient methods for the preparation of this amino acid and its subsequent incorporation into synthetic peptides by the solid-phase technique are outlined. To illustrate its utility, p-benzoyl-L-phenylalanine was substituted in place of tryptophan in a 17-residue calmodulin-binding peptide. The substitution did not measurably affect the affinity of this peptide for calmodulin. When this peptide was photolyzed at 350 nm in a 1:1 molar ratio with calmodulin in the presence of 500 microM CaCl2, 70% of the calmodulin was derivatized. The specificity of the reaction was investigated by photolysis in the absence of CaCl2 where little binding occurs; under these conditions little or no photolabeling occurred.

A novel photoreactive amino acid has been incorporated synthetically into two model peptides and the calmodulin-binding domain from myosin light chain kinase. Cross-linked photoadducts of each peptide with calmodulin have been prepared and digested by chemical and/or enzymatic methods to determine the site of label attachment. Depending on the position of the photoprobe in the peptide sequence, either Met-144 or Met-71 is photolabeled. These results are discussed in relation to the three-dimensional structure of calmodulin obtained crystallographically and the known solution properties of calmodulin.

A peptide containing 41 amino acid residues has been isolated from trout liver and identified as a member of the beta-thymosin family. Sequence analysis shows it to be 78% homologous to thymosin beta 4, which is the peptide present in the thymus and other tissues of higher vertebrates, including, as reported here, livers of a species of reptile. Thymosin beta 11 appears to replace the more prevalent thymosin beta 4 in at least two species of bony fish, and represents the sixth structurally characterized member of this widely distributed family of peptides.

Two homologous peptides, designated thymosin beta 4 and thymosin beta 10, respectively, have been shown to be widely distributed in mammalian cells and tissues (S. Erickson-Viitanen, S. Ruggieri, P. Natalini, and B.L. Horecker (1983) Arch. Biochem. Biophys. 221, 570-576; S. Erickson-Viitanen, S. Ruggieri, P. Natalini, and B.L. Horecker, (1983) Arch. Biochem. Biophys. 225, 407-413). In the rabbit, thymosin beta 4 is replaced by a variant, thymosin beta ala4, that contains alanine in place of serine at the blocked NH2-terminus. It is reported that in rabbit tissues thymosin beta 10 is also replaced by a variant, designated thymosin beta arg10, that contains an additional amino acid, arginine, inserted following lysine-38. The rabbit tissues analyzed also differ from those of other mammals in the relative quantities of thymosin beta ala4 and beta arg10, which are nearly equal, compared to tissues from other mammals where the quantities of thymosin beta 10 are only one-third to one-tenth those of thymosin beta 4.

Publisher Summary This chapter discusses thymosin β 4 -1ike peptides. Thymosin β 4 is isolated from preparations of calf thymosin fraction 5 by preparative isoelectric focusing followed by high-performance liquid chromatography (HPLC). A simple two-step procedure for the direct isolation from fresh thymus tissue of β 4 -like peptides (thymosin β 9 , β 10 , and β 11 ) and leading also to the separation of thymosin β 4 is illustrated in the chapter. In the first procedure described here endogenous proteinases are inactivated by extracting the frozen tissue with guanidinium chloride and the peptides in the desalted extracts separated by HPLC. The chapter also explains isolation of thymosin β 4 and thymosin β 10 from guanidinium chloride extracts of rat tissues. Calf thymus remains the only known source of thymosin β 4 . In other species of mammals, including man, thymosin β 9 is replaced by another related peptide, thymosin β 10 . For the isolation of thymosin β 10 the most convenient sources are rat thymus or spleen. Rat spleens are removed immediately after sacrifice of the animals, frozen in liquid N2, and stored at -70 °. The procedures employed, including extraction with guanidium chloride, desalting on disposable Sep-Pak cartridges, and separation of peptides by HPLC.

Rabbit liver cathepsin M, a sulfhydryl proteinase similar in catalytic properties to cathepsin B, causes a decrease in the activity of rabbit muscle aldolase assayed with fructose 1,6-bisphosphate but not with fructose 1-phosphate. Proteolytic modification of aldolase by cathepsin M is limited to the removal of small peptides from the COOH-terminus, including the COOH-terminal hexapeptide NH2-Ile-Ser-Asn-His-Ala-TyrOH. Correlation of loss of aldolase activity with COOH-terminal modification indicates that only three of the four subunits of muscle aldolase contribute to the catalytic activity of the tetrameric enzyme.

There are two viewpoints regarding the role of the enzyme creatine Phosphokinase (CPK), which catalyzes the reversible transphosphorylation of creatine and adenine nucleotides in energy transport. The classical viewpoint (Fig. 1) regards CPK as a near equilibrium enzyme buffering cytosolic changes in nucleotide concentration (1,2), with creatine phosphate representing a reservoir of high energy phosphate equivalents (3) and with regulation of energy production relegated to the adenine nucleotides whether in the form of energy charge (4), adenylate phosphate potential (5,6), or ATP/ADP ratio (7). The second viewpoint places CPK and its products, creatine and creatine phosphate, in the central role of energy transport (8–11). The evidence for the latter viewpoint has come about from several diverse lines of reasoning (reviewed in 9). Jacobs et al discovered a distinct isoenzyme of CPK bound to mitochondria in 1964 (12). The significance of this mitochondrial bound form of CPK was studied by Bessman and Fonyo (13) in pigeon breast mitochondria where the possibility of feedback regulation of respiration through production of acceptor creatine was suggested, in accordance with Bessman’s earlier observation on the insulin-like effect of exercise in diabetics (14).

A new analog of thymosin β 4 has been isolated from tissues of several mammalian species. This peptide, designated thymosin β 10 , is composed of 42 amino acid residues and shows 75% sequence homology with thymosin β 4 . It occurs together with thymoxin β 4 in a variety of tissues including spleen, liver, and thymus and also in several cultured cell lines. In the spleen of rat, mouse, cat, and man, the new peptide accounts for approximately 0.02% by weight of the total protein. In the calf it is replaced by another homologous peptide, designated thymosin β 9 , whose structure has been reported.

A basic amphiphilic alpha-helix is a structural feature common to many calmodulin-binding peptides and proteins. A set of fluorescent analogues of a very tight binding inhibitor (dissociation constant of 200 picomolar) of calmodulin has been synthesized. The fluorescent amino acid tryptophan has been systematically moved throughout the sequence of this peptide. The fluorescence properties for the peptides repeat every three to four residues and are consistent with the periodicity observed for an alpha-helix.

Publisher Summary This chapter provides methods for the recognition and analysis of basic, amphiphilic calmodulin-binding regions in peptides and proteins. The first calmodulin-binding peptides were discovered through screening of peptide hormones for calmodulin-binding activity. Calmodulin also contains a hydrophobic patch that becomes more exposed upon calcium binding. Recent evidence has given credence to the premise that amphiphilic α helical peptides are good models for the calmodulin-binding site of target enzymes. A 27-residue peptide has been isolated from a CNBr digest of skeletal muscle myosin light chain kinase (MLCK), which appears to comprise this enzyme's calmodulin-binding domain. The helical wheel is a widely used qualitative method for locating potential calmodulin-binding sites within a protein sequence. A rapid method of quantitating the information presented on a helical wheel involves calculation of the average helical hydrophobic moment (μH), which is defined as the mean vector sum of the hydrophobicities of the residues in the helix. Binding of peptides to calmodulin can be determined in a number of ways that rely on monitoring changes in the physical and spectroscopic properties of calmodulin and/or peptides that accompany complex formation. Fluorescence spectroscopy is an excellent method for evaluating. It is also shown that peptides become more helical when they bind calmodulin and that this increase in helicity is readily measured by far-ultraviolet circular dichroism spectroscopy (CD).