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. • Design of Renin Inhibitors


. Fig. 24.1 Catalytic mechanism of aspartic proteases. Awater mol-
ecule, placed at the apex between the two catalytically active aspar­tates, is polarized by the deprotonated carboxylic acid. As aresult, it acts as anucleophile to attack the carbonyl carbon atom of the amide bond to be cleaved. The second, less acidic and protonated aspartate
. Fig. 24.2 Possible transition
state isosteres for the design of aspartic protease inhibitors. Hydroxyl groups are particularly well suited. Statin, anonpro­teinogenic amino acid, is found in many inhibitor structures
where hydrogen bonds are formed to the peptide back­bone of the substrate. Asimilar pattern is found on the upper half of the tunnel, which is not shown in the image because it has been clipped off. The hydrogen-bonding pattern along the tunnel is common to all aspartic pro­teases. Individual binding pockets to the left and right of the cleavage site are responsible for the selective recog­nition of substrates. They accommodate the side chains of the residues of the substrate molecules. It is striking that, in contrast to serine proteases, the pockets are well
forms an H-bond to the carbonyl oxygen of this amide bond. This increases the electrophilicity of the carbonyl carbon(a). With the in­termediate formation of atetrahedral coordinated diol and the simul­taneous cleavage of the former amide bond(b), the original peptide chain decomposes into the cleaved chain products(c)
Hamao Umezawa isolated one of the rst potent
and specic aspartic protease inhibitors, pepstatin, from a culture of Streptomyces sp. This peptide, Iva–Val– Val–Sta–Ala–Sta–OH, 24.1 (. Fig.24.4) is agood- to high-afnity inhibitor of many members of the aspartic protease family. It contains the nonproteinogenic amino acid statin with ahydroxyethyl group. The 3D structure of the pepsin–pepstatin complex shows that statin actu­ally binds as atransition state mimicry to the catalytic
aspartic acids. established on both sides of the cleavage site. This obser­vation is explained by the reaction mechanism. Unlike serine proteases, no intermediate is formed that is co-

24.2 Design of Renin Inhibitors

valently bound to the enzyme. Aspartic proteases often cleave between hydrophobic amino acids (. Table24.1). Since strong and directional interactions cannot form with such residues, recognition and xation of substrate molecules over several positions to the left and right of the cleavage site is important. This explains the distinct character of the pockets on either side. Therefore, to design inhibitors, one must rst nd groups that mimic good interactions with the binding pockets S3, S2, S1 and
,
,
. One of the groups shown in . Fig.24.2, which
is an analogue of the transition state, is placed directly at the cleavage site.
Renin is an aspartic protease that is composed of 340
amino acids. It plays apivotal role in endogenous blood
pressure regulation and in electrolyte and water homeo-
stasis. The enzyme cleaves the peptide angiotensinogen to
form the decapeptide angiotensinI (. Fig.24.5). This is
subsequently cleaved by angiotensin-converting enzyme
(ACE, Sect.25.4), ametalloprotease, to give the octa-
peptide angiotensinII, which increases blood pressure.
Inhibition of the enzyme renin leads to adecrease in the
concentration of angiotensinI and, as aconsequence, of
angiotensinII. Renin inhibition, therefore, has ahypo-
tensive effect. Because of the great therapeutic success of
24
0
3
ab
Chapter  • Aspartic Protease Inhibitors
cde
. Fig. 24.3 Sectional view of the binding pockets of ve aspartic
proteases: aHIV protease, bendothiapepsin, ccathepsinD, dplasme- psin, and erenin. The catalytic center extends as atunnel through the proteases (top left, schematic view from the side into the tunnel). In the gures, the proteins are cut in such away that the clipping plane passes through the center of the tunnels (right part of the schematic drawing, the cut protease has to be rotated by 90°). When looking from the side
ACE inhibitors, many pharmaceutical companies began searching for selective renin inhibitors in the early 1980s. Renin has an unusually high specicity. Angiotensino- gen is the only known natural substrate of this enzyme. Therefore, it should be possible to nd ahighly specic renin inhibitor that does not block other enzymes and does not cause side effects, which is not the case with many other antihypertensive agents.
The starting point for the work was the peptide se­quence of the substrate angiotensinogen. Renin cleaves angiotensinogen between Leu and Val. First, asuitable surrogate for the Leu–Val unit was sought that would allow the retention of the amino acids in the positions
to
P
(. Table24.3). The octapeptide His–Pro–Phe–
5
His–LeuVal–Ile–His is cleaved as arenin substrate. Re­placement of the Leu–Val amide bond that is cleaved by the enzyme with the stable, isosteric groups –CH2NH–
(in the direction of the arrow), only the back side of the tunnels can be seen. The protein surfaces are cut in the upper and lower part and show the course of the polypeptide chain (red ribbons). The blue areas on the backside of the tunnel refer to H-bond donor and acceptor sites beneath the protein surface to which a bound substrate is attached along its peptide backbone
. Fig. 24.4 Pepstatin 24.1 is an inhibitor for alarge number of dif-
ferent aspartic proteases. (Iva isovaleric acid, Sta statin)
or –COCH2– resulted in modestly effective inhibitors. The isostere with the hydroxyethylene group, –CH(OH) CH2–, was better suited as atransition state analogue, and afforded astrong inhibitor (IC50 = 3 nM). The in­corporation of the nonproteinogenic amino acid statin
0
1
. • Design of Renin Inhibitors


. Fig. 24.5 The renin–angiotensin system. The conversion of angio-
tensinogen to angiotensinII (ATII), which increases blood pressure, is accomplished in two steps. Degradation by an Asp–aminopeptidase,
(see . Fig.24.4) produced astrongly binding inhibitor. As adipeptide isostere, statin replaces the P1–
unit in
the Leu–Val segment of the substrate.
The next step was the optimization of the P1 moiety. Different groups were investigated as areplacement for the leucine side chain. The results of such astructural variation of 24.2 are listed in . Table24.4. Replacing the iso-butyl group with alarger cyclohexylmethylene group increased the afnity by afactor of20. An adamantyl­methylene group is obviously too large for the pocket, as the corresponding derivative only weakly inhibits the enzyme. Next, the P2 moiety was investigated. Replac­ing the histidine with another group did not signicantly improve the binding afnity. Nevertheless, the substitu­tion of the basic histidine in the P2 position was amajor
advance in renin research because it allowed the discov­ery that glycols are potent renin inhibitors. Afew com-
pounds from the 24.3 class are listed in . Table24.5. The introduction of asecond hydroxyl group in the correct conguration increased the afnity by afactor of 10–200 depending on the chosen P1 side chain. Accordingly, it was possible to nd tripeptide analogues with binding constants of about 1 nM. Several companies developed renin inhibitors to the point of clinical trials. Examples are A-64662 24.4 (. Fig.24.6) from Abbott and Ro 45­5892 24.5 from Roche.
However, the desired goal had not yet been achieved. The compounds had short half-lives and were not orally available. It turned out that the amide bond between the P3 residue Phe and the P2 residue His was rapidly
angiotensinaseA, leads to angiotensinIII (ATIII), which is still bio­logically active. Different angiotensinases (aminopeptidases, carboxy­peptidases) degrade these two peptides into inactive fragments
. Table 24.3 The replacement of the cleavable amide bond
in Leu–Val (highlighted in bold) by astable isostere leads to potent renin inhibitors. The Leu–Val group is replaced by agroup in the inhibitors that the enzyme cannot cleave
Substrate/Inhibitor IC50
(nM)
His–Pro–Phe–His–Leu–Val–Ile–His 300,000
His–Pro–Phe–His–Leu[COCH2]–Val–Ile–His 500
His–Pro–Phe–His–Leu[CH2NH]–Val–Ile–His 200
His–Pro–Phe–His–Statin–Ile–His 20
His–Pro–Phe–His–Leu[CHOHCH2]–Val–Ile–His
a
Substrate, KM value
a
3
cleaved by the digestive enzyme chymotrypsin. The high molecular weight of the compounds, which led to rapid biliary excretion, was also aproblem. Further work fo­cused on nding asuitable replacement for the P2 and P3 side chains.
Inhibitor stability against chymotrypsin was achieved
by modication of the P3 group, phenylalanine. The sta­bilities for some of these modied renin inhibitors 24.6 are summarized in . Table24.6. One compound that was no longer cleaved by chymotrypsin was obtained by using β,β-dimethylphenylalanine. This is because, in contrast to phenylalanine, the very bulky side chain no longer ts into the specicity pocket of chymotrypsin.
Chapter  • Aspartic Protease Inhibitors
24
. Table 24.4 Optimization of the P1 side chainR. The bind-
ing pocket is lipophilic and obviously has just the right size for acyclohexylmethylene group
R IC50 (nM)
Isobutyl 81
Cyclohexylmethylene 4
Cyclohexyl 150
Adamantylmethylene 2500
Benzyl 15
Boc=tert-butoxycarbonyl protecting group
. Table 24.5 The introduction of asecond hydroxyl group
in the R2 position leads to asignicant increase in the binding afnity
R
1
Isobutyl H 1500
Cyclohexylmethyl H 10
Boc=tert-butoxycarbonyl protecting group
R
2
OH 11
OH 1.5
IC50 (nM)
The extended search for possible replacements of
Phe–His as the P3–P2 moiety led to aplethora of new non­peptidic renin inhibitors with high afnity. The introduc­tion of aterminal basic group was highly effective, even though adequate oral bioavailability was not achieved. Typical examples are 24.8 and 24.9 (. Fig.24.7).
Despite enormous efforts, renin research stagnated
worldwide because no compound could achieve the re­quired oral bioavailability. All compounds contained at least one amide bond and their molecular weights were too high. In addition, the 3D structure of renin did not become available until the late 1980s in the laboratory of Michael James in Edmonton, Alberta, Canada. By then, it had been recognized that renin had acertain, albeit modest, sequence homology of 20–30% with as­partic proteases from fungi, for which 3D structures were known. This was the starting point for homology model-
. Fig. 24.6 Enalkiren 24.4 and remikiren 24.5 were the rst renin
inhibitors to be tested in clinical trials
ing in several laboratories. The rst model was published by Tom Blundell’s group in 1984. They used the crystal structure of endothiapepsin as areference. First, the re­nin sequence was compared with that of other aspartic proteases to nd structurally conserved regions. They then modeled the interior of the protein by replacing residues in endothiapepsin with those in renin. Dele­tions and insertions in the polypeptide chain had to be taken into account. The ap region was of particular importance. It opens to allow the ligand to enter and form hydrogen bonds with the protein. Its structural ar­chitecture is, therefore, important for ligand binding. Un­fortunately, the renin sequence differed from that of the fungal enzymes in the ap region. Acomparison of the renin model with the later determined crystal structure of renin showed good agreement, especially in the lower part of the binding pocket near the two aspartic acids. However, signicant differences were found in the loops of the ap region. In the context of the overall protein architecture, these were less important. In the context of drug design, however, they were critical! Errors in the structural model had to inevitably lead to incorrect sug­gestions for inhibitor design.
The structure of renin complexed with the inhibitor
CGP-38560 24.10 determined by Markus Grütter and John Priestle at Ciba in Basel, Switzerland, is shown in
. Fig.24.8. It was on the basis of this structure that
the researchers at Ciba, now Novartis, made their break­through. Looking at the arrangement in the binding pocket of renin, it is apparent that the S1 and S3 pockets merge into one large hydrophobic cavity. The substitu­ents in the P1 and P3 positions, acyclohexylmethylene and abenzyl group, come spatially close together. In­stead of spanning the molecule with its side chains on apeptidic backbone, the scientists broke the chain at the amide bond. This created anew polar moiety, aterminal charged amino group. In place of the former backbone,
. • Design of Renin Inhibitors
. Table 24.6 By modifying the P3 substituentR, the stability to chymotrypsin is improved


R IC50 (nM) Hydrolysis by chymotrypsin t
0.35 2.2
0.76 727
0.58 Stable
. Fig. 24.7 Structures 24.7–24.9 are afew renin inhibitors
with moderate oral availability. All have in common adiol unit and acyclohexylmethylene side chain that binds in the
pocket
P
1
1/2
(min)
24
0
1
0
2
Chapter  • Aspartic Protease Inhibitors
. Fig. 24.8 Superposition of the crystal structures of renin complex-
es with the inhibitors CGP-38560 24.10 (gray carbon atoms) and ali­skiren 24.12 (light-green carbon atoms). The inhibitors bind with their peptide-like architecture in an extended, pleated-sheet-like conforma­tion. Compound 24.10 orients its benzyl and cyclohexylmethyl groups in the broad S3/S1 pocket. To design aliskiren, the two hydrophobic side chains of 24.10 were chemically linked (pink arrow). The newly
the linkage of the molecule was redirected to the closely adjacent hydrophobic substituents in the large S3/S1 pocket. The result was acompletely new dipeptide-like scaffold (24.11, . Figs.24.8 and24.9). It had an IC50 of 6 nM. Finally, several steps of side chain optimization were performed on the aromatic ring and the amide link­age. The methoxypropoxy side chain occupies aslightly different pocket than the corresponding groups in CGP-
38560. It results in asignicant increase in binding af­nity. The optimized substituent in
has little effect on in vitro afnity, but is critical for duration of action. Ageminal substitution with two methyl groups and ater­minal carboxamide group proved to be optimal for the position. The resulting inhibitor was launched in 2006 as aliskiren (24.12), the rst orally available renin inhibitor. Despite being so well optimized, the compound does not have ideal bioavailability. As aresult, it must be admin­istered at relatively high doses. However, aliskiren shows virtually no binding to other aspartic proteases such as cathepsinD or pepsin.
Roche achieved another success with their work
on renin, which later proved to be stimulating for the
formed bond allowed the peptide chain to be cleaved and anew, polar N-terminus could be formed. (7 https://sn.pub/BGi2k5)
entire eld of research. With remikiren 24.5, the com­pany had apotent inhibitor that unfortunately lacked the desired oral bioavailability. The company, there­fore, initiated anew comprehensive screening program. Chlorophenylmethoxybenzyloxypiperidine 24.13 was discovered (. Fig.24.10) with an IC50 value of 50 μM. This structure was surprising because it did not have the typical group mimicking the transition state. The crys­tal structure of avery similar derivative showed that the protonated nitrogen on the piperidine ring binds between the two catalytic aspartic acids. The lipophilic chlorophe­nyl moiety aligns with the broad S1/S3 pocket normally occupied by the leucine and phenylalanine residues of the angiotensinogen substrate. Since the available space in this pocket was not yet fully occupied, the Roche re­searchers initially focused on structural variations in the para-position of the aromatic ring as asurrogate for the chlorine atom. The introduction of aromatic groups with variable chain lengths yielded derivatives with up to 100­fold improved activity. It appeared to be critical that only hydrophobic groups could be placed in this position. The best results were obtained with apropylenedioxybenzyl
. • Design of Substrate Analogue HIV Protease Inhibitors

. Fig. 24.10 A piperidine derivative 24.13 that was found in
ascreening campaign for renin inhibitors at Roche. Acrystal structure was determined with the optimized compound24.14
family in more conformations than the closed-ap con­formation. The open conformer can also be stabilized by an inhibitor. These exemplary studies on renin provided important information for novel work on the aspartic proteases (Sect.24.6).

. Fig. 24.9 For the further development of 24.10 to aliskiren 24.12
as an orally available renin inhibitor the benzyl and cyclohexylmethyl side chain groups in 24.10 were tethered together to yield 24.11. Then the peptide chain could be cleaved after the nitrogen atom, and anew polar group could be formed that binds to the catalytic center. The analogous molecular parts in both inhibitors are highlighted in red
side chain. This moved the compounds into the subnano­molar inhibition range. Acrystal structure determina­tion was performed on derivative 24.14, which showed acompletely unexpected binding mode (. Fig.24.11). The protonated nitrogen of the piperidine ring is still between the two aspartic acid residues, but the lipophilic naphthyl group is oriented in the broad S1/S3 pocket. The long hydrophobic side chain of the 4-substituted phe­nyl group opens anew pocket in renin. Like all aspartic proteases, renin has aexible ap region that collapses over the binding pocket after substrate binding. In this case, the ap is pushed outwards by the inhibitor. The enzyme adopts ageometry that is more consistent with an open-ap conformation. Ahydrogen bond between Trp39 and Tyr75, which closes the ap, is ruptured. At the same time, the 4-phenyl group of the inhibitor occu­pies aregion where the aromatic ring of Tyr75 would be located if the ap were closed. This structure provided the researchers with two important pieces of informa­tion: (i)anitrogen-containing heterocycle is an interest­ing peptidomimetic that binds to the catalytic aspartic acids, and (ii)inhibitors can bind to the aspartic protease
24.3 Design of Substrate Analogue HIV
Protease Inhibitors
AIDS (Acquired Immune Deciency Syndrome) is an infectious disease caused by the human immunode- ciency virus, HIV, which was isolated and identied in 1983 by the French virologists Luc Antoine Montag­nier and Françoise Barré-Sinoussi. Many years later, in 2008, they were awarded the Nobel Prize for their work. HIV protease, which is required for viral replication, is encoded as alarge proprotein in the viral genome. The function of HIV protease is to cleave the initial poly­peptide chain produced in the life cycle of the virus into smaller functional proteins. Inhibitors of HIV protease should, therefore, be able to suppress HIV replication. The existence of HIV protease was postulated in 1985 and experimentally conrmed in 1988.
In 1989, the rst 3D structure of the enzyme as well as afew enzyme–inhibitor complexes were determined. HIV protease is ahomodimer made up of two identical chains. One catalytic aspartic acid comes from each chain of the homodimer. The dimeric structure of HIV prote­ase with its twofold symmetry is shown in . Fig.24.12.
It was soon discovered that HIV protease is also inhibited by pepstatin. This was the starting point for the search for HIV protease inhibitors. Many compa­nies already active in the renin eld tested compounds generated in these programs for possible HIV protease inhibition. Starting with the nonproteinogenic amino acid statin known from the renin work, anumber of ac­tive HIV protease inhibitors were discovered. As with renin, the hydroxyethylene isostere proved to be apartic- ularly suitable building block. For example, H-261 24.15 (. Fig.24.13) is apotent HIV protease inhibitor with
Ki = 5 nM.
24
0
1
Chapter  • Aspartic Protease Inhibitors
. Fig. 24.11 The crystallographically determined binding mode
of the piperidine lead structure 24.14 with renin. The basic nitrogen of the inhibitor binds between the two aspartic acids of the catalytic dyad. The lipophilic side chain lies in anewly opened binding pocket. It was formed by breaking ahydrogen bond that was originally present between Trp39 and Tyr75 in the uncomplexed protein. Both residues
Heptapeptides have been identied as aminimal sub-
strate for HIV protease. Ser–Leu–Asn–Phe–Pro–Ile–Val is such asubstrate. Cleavage of the amide bond occurs between the amino acids Phe and Pro. Replacement of the cleavable amide bond with ahydrolytically stable hy­droxyethylamino group –CHOH–CH2–NH– led to 24.16 (JG 365, . Fig.24.13), ahigh-afnity HIV protease in­hibitor (Ki = 0.66 nM). This compound was, however, inactive in cell culture assays. It is unable to penetrate the cell membrane to exert its antiviral effects.
Chemists at Roche have demonstrated that the design of an HIV protease substrate analogue can lead to an ef­fective drug. Proline is often found in the
position (e.g.,
24.17, . Fig.24.14). Therefore, isosteres of analogues of the dipeptide Phe–Pro were investigated as HIV protease inhibitors. Replacement of proline by homoproline 24.18 or decahydroisoquinoline 24.19 resulted in asignicant increase in potency. In addition, 24.19 showed marked selectivity towards the other aspartic proteases renin,
adopt anew position with larger distance between one another after binding of 24.14. (7 https://sn.pub/lrGrOq)
pepsin, cathepsinD, and cathepsinE. More importantly, the compound was active in acellular assay. It has the ability to penetrate the cell membrane. In enzyme assays,
24.19 inhibited HIV protease with Ki < 0.12 nM. Viral replication is inhibited in cell culture with EC50 values of 1–10 nM. The activity in cells is, therefore, on the same order of magnitude as the pure enzyme inhibition. Saquinavir 24.19 was the rst HIV protease inhibitor to complete all phases of clinical testing and receive market­ing approval in November 1995. In the years since, other pharmaceutical companies have succeeded in bringing substrate-like HIV protease inhibitors to market. As are­sult, our drug arsenal now includes eight approved drugs (24.1924.27) with peptide-like scaffolds (. Fig.24.15). However, nelnavir 24.24 was withdrawn from the Eu­ropean market in 2007. It was noticed that tablets con­taining this substance had an unusual smell. Subsequent analysis revealed that the drug was contaminated with ethyl mesylate from synthesis. Because saquinavir has
0
1
. • Structure-Based Design of Nonpeptidic HIV Protease Inhibitors


. Fig. 24.12 The 3D Structure of HIV protease complexed with the
peptide substrate Arg–Pro–Gly–Asn–Phe–Leu–Gln–Ser–Arg–Pro. The structure with the substrate could be obtained with acatalytically inactive enzyme variant because both acidic aspartic acids of the cat­alytic dyad had been mutated to asparagines. The protease exists as aC2-symmetric homodimer. The peptide chains are shown in green and red, respectively. (7 https://sn.pub/r7ffVB)
unsatisfactory bioavailability (3–5%), it is administered in combination with ritonavir 24.20, apotent CYP3A4 inhibitor (Ki = 17 nM; Sect. 27.6). This signicantly minimizes the rst pass effect when coadministered with saquinavir. Ritonavir has established itself as abooster for other drugs and is increasingly used in combinations with other drug molecules. For example, it is used in combination with the recently approved COVID-19 in­hibitor nirmatrelvir (Paxlovid®, Sect.23.9). Amprenavir
24.23 was withdrawn in 2004 because it was replaced by the more soluble prodrug fosamprenavir (Lexiva®).
24.4 Structure-Based Design of
Nonpeptidic HIV Protease Inhibitors
The relationship to the parent substrate is clearly seen in the inhibitors introduced in the last section. The com­pounds are still essentially peptides. The crystal struc­tures of the peptidic HIV protease inhibitors complexed with the enzyme all show that the inhibitors form es­sentially the same H-bonding pattern in the immediate
vicinity of the catalytically active aspartic acid residues (. Fig.24.16). One water molecule is of particular in­terest because it is present in all crystal structures. This water molecule forms hydrogen bonds with both the in­hibitor and the enzyme. Inhibitors designed to displace this water molecule were hoped to increase the binding afnity by the entropically favorable release of this wa­ter (Sect.4.6). The release of water molecules is often associated with an entropic gain. Note, however, that at best this gain is not fully compensated by acomparable loss of enthalpy, leaving anet contribution to binding afnity. Moreover, it was expected that such an approach would also increase selectivity, since awater molecule with asimilar function is not known to exist in the other aspartic proteases of similar pharmaceutical relevance.
At Dupont–Merck, a3D database was searched for new scaffolds for HIV protease inhibitors. Apharma­cophore pattern was derived from the crystal structure of the enzyme. The occupancy of the S1 and
pockets was considered essential for binding and interaction with the catalytic aspartates. Two lipophilic groups, separated by 8.5–12 Å and also 3.5–6.5 Å from ahydrogen bond
24
Chapter  • Aspartic Protease Inhibitors
. Fig. 24.13 The peptidic HIV protease inhibitors
H-261 24.15 and JG365 24.16 are potent inhibitors in the enzyme assay. They are inactive in cell culture
. Fig. 24.14 The stepwise optimization of the
substrate analogue inhibitor 24.17 led to the highly potent HIV protease inhibitor Ro 31-8959 24.19 via 24.18. This compound was the rst protease inhibitor to pass clinical trials and is marketed with the name saquinavir
acceptor or donor, were sought (. Fig.24.16, right). In addition, there should be afunctional group between the two lipophilic groups that can displace the structur­ally conserved water molecule from the binding pocket. Asearch in the Cambridge database (Sect.17.11) yielded amolecular scaffold derived from asubstituted phenol (24.28). This led to the idea of using 4-hydroxycyclohexa­none as the scaffold (. Fig.24.16). Modeling studies and intensive discussions with synthetic chemists eventually led to acyclic urea (24.29) as the scaffold for the new
inhibitors 24.3024.33 (. Fig.24.17). The rst result of this development was DMP-323 24.32, asmall-molecule HIV protease inhibitor. The 3D structure of 24.31 com­plexed with the protease is shown in . Fig.24.18. It con­rms the hypothesis that the carbonyl group displaces the structural water molecule and the two hydroxyl groups bind to the catalytic aspartate residues. As promising as the design of the cyclic urea as an HIV protease inhibi­tor seemed, no compound has yet survived all stages of clinical testing to gain regulatory approval.